High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression

Motivation: The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to instable and non convergent methods due to inappropriate computational frameworks. We hereby propose a stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS). Results: We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, which combines iterative optimization of logistic regression and sparse PLS to ensure convergence and stability. Our results are confirmed on synthetic and experimental data. In particular we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method on the prediction of cell-types based on single-cell expression data. Availability: Our approach is implemented in the plsgenomics R-package.Comment: 9 pages, 3 figures, 4 tables + Supplementary Materials 8 pages, 3 figures, 10 table

Aluminium in Brain Tissue in Multiple Sclerosis.

Multiple sclerosis (MS) is a devastating and debilitating neurodegenerative disease of unknown cause. A consensus suggests the involvement of both genetic and environmental factors of which the latter may involve human exposure to aluminium. There are no data on the content and distribution of aluminium in human brain tissue in MS. The aluminium content of brain tissue from 14 donors with a diagnosis of MS was determined by transversely heated graphite furnace atomic absorption spectrometry. The location of aluminium in the brain tissue of two donors was investigated by aluminium-specific fluorescence microscopy. The aluminium content of brain tissue in MS was universally high with many tissues bearing concentrations in excess of 10 μg/g dry wt. (10 ppm) and some exceeding 50 ppm. There were no statistically significant relationships between brain lobes, donor age or donor gender. Aluminium-specific fluorescence successfully identified aluminium in brain tissue in both intracellular and extracellular locations. The association of aluminium with corpora amylacea suggests a role for aluminium in neurodegeneration in MS

Addiction in Europe, 1860s-1960s: Concepts and Responses in Italy, Poland, Austria, and the United Kingdom

Concepts play a central part in the formulation of problems and proposed solutions to the use of substances. This article reports the initial results from a cross European historical study, carried out to a common methodology, of the language of addiction and policy responses in two key periods, 1860–1930 and the 1950s and 1960s. It concludes that the language of addiction was varied and nonstandard in the first period. The Anglo-American model of inebriety did not apply across Europe but there was a common focus on theories of heredity and national degeneration. After World War II, there was a more homogenous language but still distinct national differences in emphasis and national interests and policy responses to different substances. More research will be needed to deepen understanding of the conditions under which these changes took place and the social and policy appeal of disease theories

Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4†

Wybutosine (yW), one of the most complicated modified nucleosides, is found in the anticodon loop of eukaryotic phenylalanine tRNA. This hypermodified nucleoside ensures correct codon recognition by stabilizing codon-anticodon pairings during the decoding process in the ribosome. TYW4 is an S-adenosylmethionine (SAM)-dependent enzyme that catalyzes the final step of yW biosynthesis, methylation and methoxycarbonylation. However, the structural basis for the catalytic mechanism by TYW4, and especially that for the methoxycarbonylation, have remained elusive. Here we report the apo and cofactor-bound crystal structures of yeast TYW4. The structures revealed that the C-terminal domain folds into a β-propeller structure, forming part of the binding pocket for the target nucleoside. A comparison of the apo, SAM-bound, and S-adenosylhomocysteine-bound structures of TYW4 revealed a drastic structural change upon cofactor binding, which may sequester solvent from the catalytic site during the reaction and facilitate product release after the reaction. In conjunction with the functional analysis, our results suggest that TYW4 catalyzes both methylation and methoxycarbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide

What are the most effective interventions to improve physical performance in pre-frail and frail adults? A systematic review of randomised control trials

Background: With life expectancy continuing to rise in the United Kingdom there is an increasing public health focus on the maintenance of physical independence among all older adults. Identifying interventions that improve physical outcomes in pre-frail and frail older adults is imperative. Methods: A systematic review of the literature 2000 to 2017 following PRISMA guidelines and registered with PROSPERO (no. CRD42016045325). Results: Ten RCT trials fulfilled selection criteria and quality appraisal. The study quality was moderate to good. Interventions included physical activity; nutrition, physical activity combined with nutrition. Interventions that incorporated one or more physical activity components significantly improved physical outcomes in pre-frail and/or frail older adults. Conclusions: Physical activity interventions are key to maintaining independence in pre-frail and frail older adults. A lack of consensus regarding the definition of frailty, and an absence of core measures to assess this means any attempt to create an optimal intervention will be impeded. This absence may ultimately impact on the ability of older and frail adults to live well and for longer in the community

Benefit-risk of Patients' Online Access to their Medical Records: Consensus Exercise of an International Expert Group

BACKGROUND:  Patients' access to their computerised medical records (CMRs) is a legal right in many countries. However, little is reported about the benefit-risk associated with patients' online access to their CMRs. OBJECTIVE:  To conduct a consensus exercise to assess the impact of patients' online access to their CMRs on the quality of care as defined in six domains by the Institute of Medicine (IoM), now the National Academy of Medicine (NAM). METHOD:  A five-round Delphi study was conducted. Round One explored experts' (n = 37) viewpoints on providing patients with access to their CMRs. Round Two rated the appropriateness of statements arising from Round One (n = 16). The third round was an online panel discussion of findings (n = 13) with the members of both the International Medical Informatics Association and the European Federation of Medical Informatics Primary Health Care Informatics Working Groups. Two additional rounds, a survey of the revised consensus statements and an online workshop, were carried out to further refine consensus statements. RESULTS:  Thirty-seven responses from Round One were used as a basis to initially develop 15 statements which were categorised using IoM's domains of care quality. The experts agreed that providing patients online access to their CMRs for bookings, results, and prescriptions increased efficiency and improved the quality of medical records. Experts also anticipated that patients would proactively use their online access to share data with different health care providers, including emergencies. However, experts differed on whether access to limited or summary data was more useful to patients than accessing their complete records. They thought online access would change recording practice, but they were unclear about the benefit-risk of high and onerous levels of security. The 5-round process, finally, produced 16 consensus statements. CONCLUSION:  Patients' online access to their CMRs should be part of all CMR systems. It improves the process of health care, but further evidence is required about outcomes. Online access improves efficiency of bookings and other services. However, there is scope to improve many of the processes of care it purports to support, particularly the provision of a more effective interface and the protection of the vulnerable

Electronic Consultation in Primary Care Between Providers and Patients: Systematic Review

Background: Governments and health care providers are keen to find innovative ways to deliver care more efficiently. Interest in electronic consultation (e-consultation) has grown, but the evidence of benefit is uncertain. Objective: This study aimed to assess the evidence of delivering e-consultation using secure email and messaging or video links in primary care. Methods: A systematic review was conducted on the use and application of e-consultations in primary care. We searched 7 international databases (MEDLINE, EMBASE, CINAHL, Cochrane Library, PsycINFO, EconLit, and Web of Science; 1999-2017), identifying 52 relevant studies. Papers were screened against a detailed inclusion and exclusion criteria. Independent dual data extraction was conducted and assessed for quality. The resulting evidence was synthesized using thematic analysis. Results: This review included 57 studies from a range of countries, mainly the United States (n=30) and the United Kingdom (n=13). There were disparities in uptake and utilization toward more use by younger, employed adults. Patient responses to e-consultation were mixed. Patients reported satisfaction with services and improved self-care, communication, and engagement with clinicians. Evidence for the acceptability and ease of use was strong, especially for those with long-term conditions and patients located in remote regions. However, patients were concerned about the privacy and security of their data. For primary health care staff, e-consultation delivers challenges around time management, having the correct technological infrastructure, whether it offers a comparable standard of clinical quality, and whether it improves health outcomes. Conclusions: E-consultations may improve aspects of care delivery, but the small scale of many of the studies and low adoption rates leave unanswered questions about usage, quality, cost, and sustainability. We need to improve e-consultation implementation, demonstrate how e-consultations will not increase disparities in access, provide better reassurance to patients about privacy, and incorporate e-consultation as part of a manageable clinical workflow

Silver staining of proteins in polyacrylamide gels

Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. It is compatible with downstream processing, such as mass spectrometry analysis after protein digestion. The sequential phases of silver staining are protein fixation, then sensitization, then silver impregnation and finally image development. Several variants of silver staining are described here, which can be completed in a time range from 2 h to 1 d after the end of the electrophoretic separation. Once completed, the stain is stable for several weeks

Uncovering treatment burden as a key concept for stroke care: a systematic review of qualitative research

<b>Background</b> Patients with chronic disease may experience complicated management plans requiring significant personal investment. This has been termed ‘treatment burden’ and has been associated with unfavourable outcomes. The aim of this systematic review is to examine the qualitative literature on treatment burden in stroke from the patient perspective.<p></p> <b>Methods and findings</b> The search strategy centred on: stroke, treatment burden, patient experience, and qualitative methods. We searched: Scopus, CINAHL, Embase, Medline, and PsycINFO. We tracked references, footnotes, and citations. Restrictions included: English language, date of publication January 2000 until February 2013. Two reviewers independently carried out the following: paper screening, data extraction, and data analysis. Data were analysed using framework synthesis, as informed by Normalization Process Theory. Sixty-nine papers were included. Treatment burden includes: (1) making sense of stroke management and planning care, (2) interacting with others, (3) enacting management strategies, and (4) reflecting on management. Health care is fragmented, with poor communication between patient and health care providers. Patients report inadequate information provision. Inpatient care is unsatisfactory, with a perceived lack of empathy from professionals and a shortage of stimulating activities on the ward. Discharge services are poorly coordinated, and accessing health and social care in the community is difficult. The study has potential limitations because it was restricted to studies published in English only and data from low-income countries were scarce.<p></p> <b>Conclusions</b> Stroke management is extremely demanding for patients, and treatment burden is influenced by micro and macro organisation of health services. Knowledge deficits mean patients are ill equipped to organise their care and develop coping strategies, making adherence less likely. There is a need to transform the approach to care provision so that services are configured to prioritise patient needs rather than those of health care systems

Aluminum induces inflammatory and proteolytic alterations in human monocytic cell line

none4noThe increasing exposure to aluminum has been linked with the development of different human pathologies (e.g., breast cancer, myofasciitis, neurodegenerative diseases), probably due to the consistent presence of aluminum salts in widely diffused cosmetic products and vaccines. However, the mechanisms underlying immunologic and proliferative alterations still remain unknown. In the present study we investigated the ability of different aluminum compounds (i.e., aluminum chloride vs Imject® Alum, a mixture of aluminum and magnesium hydroxide) to trigger both inflammatory and proteolytic responses in U-937 human monocytic cell line. We demonstrated, by multiplex immunoassay analyses, that monocytic cells treated with both Imject Alum and aluminum chloride showed different and peculiar expression profiles of 27 inflammatory mediators and 5 matrix metalloproteinases, with respect to untreated control cells. In particular, we found dose-dependent significantly increased levels of pro-inflammatory cytokines, growth factors, and chemoattractant chemokines; whereas among metalloproteinases, only collagenolytic protease showed a significant dose-dependent increase in Imject-treated cells with respect to controls and Al-chloride treated cells. Noteworthy, we found only in Imject Alum-treated cells the significant positive correlations among collagenolytic metalloproteinase and increased expression of pro-inflammatory chemokines, suggesting a possible involvement of aluminum in regulating the acute inflammatory responses. In agreement to emerging evidences, for the first time we demonstrated that the treatment of monocyte cells with aluminum-based adjuvant is able to induce an inflammatory status and a proteolytic cascade activation. In fact, the cell treatment with Imject Alum induced increased levels of several cytokines and proteinases, suggesting these monocyte mediators as possible biomarkers for aluminum-linked diseases. The identification of the biochemical pathways involved in Al-induced cell injury pave the way for improving the knowledge on the potential impact of aluminum in human physio-pathology.openLigi, D; Santi, M; Croce, L; Mannello, FLigi, Daniela; Santi, Martina; Croce, L; Mannello, Ferdinand