A machine learning pipeline for discriminant pathways identification

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a machine learning solution for molecular profiling with a recent network comparison method. The pipeline can identify changes occurring between specific sub-modules of networks built in a case-control biomarker study, discriminating key groups of genes whose interactions are modified by an underlying condition. The proposal is independent from the classification algorithm used. Three applications on genomewide data are presented regarding children susceptibility to air pollution and two neurodegenerative diseases: Parkinson's and Alzheimer's. Availability: Details about the software used for the experiments discussed in this paper are provided in the Appendix

Quality of life after sleeve gastrectomy and adjustable gastric banding

Abstract Background: With the addition of laparoscopic vertical sleeve gastrectomy (SG) to the bariatric surgery procedural toolkit, patients desiring a restrictive bariatric procedure often choose between adjustable gastric banding (LAGB) and SG. One study compared quality of life after these 2 procedures and found no difference. The purpose of our study was to re-evaluate the postoperative quality of life in LAGB and SG patients at a military teaching hospital in the United States. Methods: A retrospective review of 108 consecutive laparoscopic restrictive bariatric procedures performed within 15 months at a Department of Defense hospital was conducted. Of these 108 patients, 69 had undergone laparoscopic vertical SG and 39 LAGB. A validated quality of life questionnaire (Bariatric Quality of Life) was conducted a mean of 9.3 Ϯ 3.2 months (range 5-16) postoperatively. The weight loss and standard laboratory parameters were measured at 0, 1, 3, 6, and 12 months. Results: The quality of life assessment revealed significantly better scores after SG than after LAGB (66.5 versus 57.9, P ϭ .0002). The excess weight loss and excess body mass index loss at 3, 6, and 12 months postoperatively were significantly greater in the laparoscopic SG group. The patients demonstrated a clear preference over time for SG once it was offered. Conclusion: Early postoperative quality of life was superior after SG than after LAGB. SG also resulted in superior early excess weight loss. In a practice not constrained by reimbursement, these findings were associated with increased patient choice of SG after it began to be offered. (Surg Obes Relat Dis 2012;8:31-40.

THE AFTERCARE SURVEY:Assessment and intervention practices after brain tumour surgery in Europe

Introduction People with gliomas need specialized neurosurgical, neuro-oncological, psycho-oncological, and neuropsychological care. The role of language and cognitive recovery and rehabilitation in patients’ well-being and resumption of work is crucial, but there are no clear guidelines for the ideal timing and character of assessments and interventions. The goal of the present work was to describe representative (neuro)psychological practices implemented after brain surgery in Europe. Methods An online survey was addressed to professionals working with individuals after brain surgery. We inquired about the assessments and interventions and the involvement of caregivers. Additionally, we asked about recommendations for an ideal assessment and intervention plan. Results Thirty-eight European centres completed the survey. Thirty of them offered at least one post-surgical (neuro)psychological assessment, mainly for language and cognition, especially during the early recovery stage and at long-term. Twenty-eight of the participating centres offered post-surgical therapies. Patients who stand the highest chances of being included in evaluation and therapy post-surgically are those who underwent awake brain surgery, harboured a low-grade glioma, or showed poor recovery. Nearly half of the respondents offer support programs to caregivers, and all teams recommend them. Treatments differed between these offered to individuals with low-grade glioma versus those with high-grade glioma. The figure of caregiver is not yet fully recognized in the recovery phase. Conclusion We stress the need for more complete rehabilitation plans, including the emotional and health-related aspects of recovery. In respondents´ opinions, assessment and rehabilitation plans should also be individually tailored and goal-directed (e.g., professional reinsertion)

Evaluation of National Surgical Practice for Lateral Lymph Nodes in Rectal Cancer in an Untrained Setting

Background: Involved lateral lymph nodes (LLNs) have been associated with increased local recurrence (LR) and ipsi-lateral LR (LLR) rates. However, consensus regarding the indication and type of surgical treatment for suspicious LLNs is lacking. This study evaluated the surgical treatment of LLNs in an untrained setting at a national level. Methods: Patients who underwent additional LLN surgery were selected from a national cross-sectional cohort study regarding patients undergoing rectal cancer surgery in 69 Dutch hospitals in 2016. LLN surgery consisted of either ‘node-picking’ (the removal of an individual LLN) or ‘partial regional node dissection’ (PRND; an incomplete resection of the LLN area). For all patients with primarily enlarged (≥7 mm) LLNs, those undergoing rectal surgery with an additional LLN procedure were compared to those undergoing only rectal resection. Results: Out of 3057 patients, 64 underwent additional LLN surgery, with 4-year LR and LLR rates of 26% and 15%, respectively. Forty-eight patients (75%) had enlarged LLNs, with corresponding recurrence rates of 26% and 19%, respectively. Node-picking (n = 40) resulted in a 20% 4-year LLR, and a 14% LLR after PRND (n = 8; p = 0.677). Multivariable analysis of 158 patients with enlarged LLNs undergoing additional LLN surgery (n = 48) or rectal resection alone (n = 110) showed no significant association of LLN surgery with 4-year LR or LLR, but suggested higher recurrence risks after LLN surgery (LR: hazard ratio [HR] 1.5, 95% confidence interval [CI] 0.7–3.2, p = 0.264; LLR: HR 1.9, 95% CI 0.2–2.5, p = 0.874). Conclusion: Evaluation of Dutch practice in 2016 revealed that approximately one-third of patients with primarily enlarged LLNs underwent surgical treatment, mostly consisting of node-picking. Recurrence rates were not significantly affected by LLN surgery, but did suggest worse outcomes. Outcomes of LLN surgery after adequate training requires further research.</p

25 Years of Self-organized Criticality: Concepts and Controversies

Introduced by the late Per Bak and his colleagues, self-organized criticality (SOC) has been one of the most stimulating concepts to come out of statistical mechanics and condensed matter theory in the last few decades, and has played a significant role in the development of complexity science. SOC, and more generally fractals and power laws, have attracted much comment, ranging from the very positive to the polemical. The other papers (Aschwanden et al. in Space Sci. Rev., 2014, this issue; McAteer et al. in Space Sci. Rev., 2015, this issue; Sharma et al. in Space Sci. Rev. 2015, in preparation) in this special issue showcase the considerable body of observations in solar, magnetospheric and fusion plasma inspired by the SOC idea, and expose the fertile role the new paradigm has played in approaches to modeling and understanding multiscale plasma instabilities. This very broad impact, and the necessary process of adapting a scientific hypothesis to the conditions of a given physical system, has meant that SOC as studied in these fields has sometimes differed significantly from the definition originally given by its creators. In Bak’s own field of theoretical physics there are significant observational and theoretical open questions, even 25 years on (Pruessner 2012). One aim of the present review is to address the dichotomy between the great reception SOC has received in some areas, and its shortcomings, as they became manifest in the controversies it triggered. Our article tries to clear up what we think are misunderstandings of SOC in fields more remote from its origins in statistical mechanics, condensed matter and dynamical systems by revisiting Bak, Tang and Wiesenfeld’s original papers

Growing Biochemical Networks: Identifying the Intrinsic Properties

SCOPUS: cp.kinfo:eu-repo/semantics/publishe

The Aftercare Survey: Assessment and intervention practices after brain tumor surgery in Europe

Background People with gliomas need specialized neurosurgical, neuro-oncological, psycho-oncological, and neuropsychological care. The role of language and cognitive recovery and rehabilitation in patients' well-being and resumption of work is crucial, but there are no clear guidelines for the ideal timing and character of assessments and interventions. The goal of the present work was to describe representative (neuro)psychological practices implemented after brain surgery in Europe. Methods An online survey was addressed to professionals working with individuals after brain surgery. We inquired about the assessments and interventions and the involvement of caregivers. Additionally, we asked about recommendations for an ideal assessment and intervention plan. Results Thirty-eight European centers completed the survey. Thirty of them offered at least one postsurgical (neuro)psychological assessment, mainly for language and cognition, especially during the early recovery stage and at long term. Twenty-eight of the participating centers offered postsurgical therapies. Patients who stand the highest chances of being included in evaluation and therapy postsurgically are those who underwent awake brain surgery, harbored a low-grade glioma, or showed poor recovery. Nearly half of the respondents offer support programs to caregivers, and all teams recommend them. Treatments differed between those offered to individuals with low-grade glioma vs those with high-grade glioma. The figure of caregiver is not yet fully recognized in the recovery phase. Conclusion We stress the need for more complete rehabilitation plans, including the emotional and health-related aspects of recovery. In respondents' opinions, assessment and rehabilitation plans should also be individually tailored and goal-directed (eg, professional reinsertion)