Automated extraction of potential migraine biomarkers using a semantic graph

Problem Biomedical literature and databases contain important clues for the identification of potential disease biomarkers. However, searching these enormous knowledge reservoirs and integrating findings across heterogeneous sources is costly and difficult. Here we demonstrate how semantically integrated knowledge, extracted from biomedical literature and structured databases, can be used to automatically identify potential migraine biomarkers. Method We used a knowledge graph containing more than 3.5 million biomedical concepts and 68.4 million relationships. Biochemical compound concepts were filtered and ranked by their potential as biomarkers based on their connections to a subgraph of migraine-related concepts. The ranked results were evaluated against the results of a systematic literature review that was performed manually by migraine researchers. Weight points were assigned to these reference compounds to indicate their relative importance. Results Ranked results automatically generated by the knowledge graph were highly consistent with results from the manual literature review. Out of 222 reference compounds, 163 (73%) ranked in the top 2000, with 547 out of the 644 (85%) weight points assigned to the reference compounds. For reference compounds that were not in the top of the list, an extensive error analysis has been performed. When evaluating the overall performance, we obtained a ROC-AUC of 0.974. Discussion Semantic knowledge graphs composed of information integrated from multiple and varying sources can assist researchers in identifying potential disease biomarkers

Migraine biomarkers in cerebrospinal fluid: a systematic review and meta-analysis

Analytical BioScience

The effect of needle size on cerebrospinal fluid collection time and post-dural puncture headache: a retrospective cohort study

Objective The main objective of this study was to compare cerebrospinal fluid (CSF) collection time and patient's discomfort between 20G (a)traumatic and 22G atraumatic needles.Background Risk of post-dural puncture headache (PDPH) is decreased using atraumatic needles. Smaller needles may give lower risk but possibly at the cost of increased CSF collection time (due to lower flow), leading to additional patient's discomfort.Methods We performed a retrospective study of lumbar puncture data from a research program on CSF metabolomics and compared traumatic 20G (n = 210) with atraumatic 20G (n = 39) and 22G (n = 105) needles. In this cohort, incidence of PDPH was prospectively registered with other procedure details. Primary outcome was CSF collection time (time to fill the tube). Secondary outcomes were pain and stress scores during procedure, and incidence of PDPH.Results The time to collect 10 mL of CSF was longer for 22G needles (6.1 minutes; 95% CI 5.8-6.5) than for 20G traumatic (2.2 minutes; 95% CI 2.1-2.2) and 20G atraumatic needles (2.9 minutes; 95% CI 2.8-3.1). There were no differences in pain and stress scores. PDPH was lower for 22G atraumatic needles: odds ratio 0.41 (95% CI 0.25-0.66) versus 20G traumatic needles and 0.53 (95% CI 0.40-0.69) versus 20G atraumatic needles. Absolute PDPH rates were 69/210 (32.9%) for 20G traumatic, 13/39 (33.3%) for 20G atraumatic, and 19/105 (18.1%) for 22G atraumatic needles.Conclusions CSF collection time is slightly longer for smaller 22G needles, but this does not lead to more discomfort for the patient.Development and application of statistical models for medical scientific researc

Quantifying Social Asymmetric Structures

Many social phenomena involve a set of dyadic relations among agents whose actions may be dependent. Although individualistic approaches have frequently been applied to analyze social processes, these are not generally concerned with dyadic relations nor do they deal with dependency. This paper describes a mathematical procedure for analyzing dyadic interactions in a social system. The proposed method mainly consists of decomposing asymmetric data into their symmetrical and skew-symmetrical parts. A quantification of skew-symmetry for a social system can be obtained by dividing the norm of the skew-symmetrical matrix by the norm of the asymmetric matrix. This calculation makes available to researchers a quantity related to the amount of dyadic reciprocity. Regarding agents, the procedure enables researchers to identify those whose behavior is asymmetric with respect to all agents. It is also possible to derive symmetric measurements among agents and to use multivariate statistical techniques

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

Objective To identify a plasma metabolomic biomarker signature for migraine. Methods Plasma samples from 8 Dutch cohorts (n = 10,153: 2,800 migraine patients and 7,353 controls) were profiled on a 1H-NMR-based metabolomics platform, to quantify 146 individual metabolites (e.g., lipids, fatty acids, and lipoproteins) and 79 metabolite ratios. Metabolite measures associated with migraine were obtained after single-metabolite logistic regression combined with a random-effects meta-analysis performed in a nonstratified and sex-stratified manner. Next, a global test analysis was performed to identify sets of related metabolites associated with migraine. The Holm procedure was applied to control the family-wise error rate at 5% in single-metabolite and global test analyses. Results Decreases in the level of apolipoprotein A1 (β −0.10; 95% confidence interval [CI] −0.16, −0.05; adjusted p = 0.029) and free cholesterol to total lipid ratio present in small high-density lipoprotein subspecies (HDL) (β −0.10; 95% CI −0.15, −0.05; adjusted p = 0.029) were associated with migraine status. In addition, only in male participants, a decreased level of omega-3 fatty acids (β −0.24; 95% CI −0.36, −0.12; adjusted p = 0.033) was associated with migraine. Global test analysis further supported that HDL traits (but not other lipoproteins) were associated with migr

Biochemical profiling of the brain and cerebrospinal fluid in migraine syndromes

Het doel van dit proefschrift was daarom de onderliggende biochemische processen gerelateerd aan migraine te onderzoeken. Het eerste gedeelte (Hoofdstukken 2 en 3) beschrijft twee onderzoeken waarin gekeken is naar de biochemische constitutie van de hersenen van migraine patiënten door middel van proton magnetische resonantie spectroscopie (1H-MRS) en diffusie gewogen spectroscopie (DWS). In het tweede gedeelte (Hoofdstukken 4 en 5) wordt een systematische review met meta-analyse beschreven om een overzicht te geven van eerdere inspanningen om in verschillende lichaamsvloeistoffen biochemische verschillen te detecteren die relevant zijn voor migraine. Daarnaast wordt er een studie beschreven waarin is gekeken naar biochemische verschillen in liquor van migraine patiënten en gezonde controles. In het derde gedeelte worden twee methodologische studies beschreven waarin (Hoofdstukken 6 en 7) de biochemische stabiliteit van liquor en het effect van vervuiling met ethanol werden onderzocht.</p

Biochemical profiling of the brain and cerebrospinal fluid in migraine syndromes

Het doel van dit proefschrift was daarom de onderliggende biochemische processen gerelateerd aan migraine te onderzoeken. Het eerste gedeelte (Hoofdstukken 2 en 3) beschrijft twee onderzoeken waarin gekeken is naar de biochemische constitutie van de hersenen van migraine patiënten door middel van proton magnetische resonantie spectroscopie (1H-MRS) en diffusie gewogen spectroscopie (DWS). In het tweede gedeelte (Hoofdstukken 4 en 5) wordt een systematische review met meta-analyse beschreven om een overzicht te geven van eerdere inspanningen om in verschillende lichaamsvloeistoffen biochemische verschillen te detecteren die relevant zijn voor migraine. Daarnaast wordt er een studie beschreven waarin is gekeken naar biochemische verschillen in liquor van migraine patiënten en gezonde controles. In het derde gedeelte worden twee methodologische studies beschreven waarin (Hoofdstukken 6 en 7) de biochemische stabiliteit van liquor en het effect van vervuiling met ethanol werden onderzocht.This work is funded by grants of the Netherlands Organization for Scientific Research (NWO) (MDF: 903-52-291, Vici 918.56.602; GMT: 907-00-217, Vidi 917-11-319), the European Community (EC) (EUROHEADPAIN) from the European Union’s Seventh Framework (2007-2013) under grant agreement no. 602633, and by a grant from the Centre for Medical Systems Biology (CMSB) established by the Netherlands Genomic Initiative / Netherlands Organisation for Scientific Research (NGI/NWO).LUMC / Geneeskund

Plangebied Lummerwetering, gemeente Oldebroek : archeologisch vooronderzoek: een aanvullend bureauonderzoek en inventariserend veldonderzoek

Lit.opg., bijl

RAAP-rapport 2129

Tijdens het veldonderzoek is door middel van boringen in een grid van 20 bij 30 m een nieuwe archeologische vindplaats gelokaliseerd ter hoogte van locatie 1. Hier zijn in twee boringen archeologische indicatoren aangetroffen. Vermoedelijk gaat het om een nederzettingsterrein uit de Late Middeleeuwen. Voorts werd ter plaatse van locatie 4 archeologisch materiaal gevonden dat samenhangt met een reeds bekende en archeologische vindplaats uit de Late Middeleeuwen (monumentnr. 3401)