Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.

MOTIVATION: Disease module mining methods (DMMMs) extract subgraphs that constitute candidate disease mechanisms from molecular interaction networks such as protein-protein interaction (PPI) networks. Irrespective of the employed models, DMMMs typically include non-robust steps in their workflows, i.e. the computed subnetworks vary when running the DMMMs multiple times on equivalent input. This lack of robustness has a negative effect on the trustworthiness of the obtained subnetworks and is hence detrimental for the widespread adoption of DMMMs in the biomedical sciences. RESULTS: To overcome this problem, we present a new DMMM called ROBUST (robust disease module mining via enumeration of diverse prize-collecting Steiner trees). In a large-scale empirical evaluation, we show that ROBUST outperforms competing methods in terms of robustness, scalability and, in most settings, functional relevance of the produced modules, measured via KEGG (Kyoto Encyclopedia of Genes and Genomes) gene set enrichment scores and overlap with DisGeNET disease genes. AVAILABILITY AND IMPLEMENTATION: A Python 3 implementation and scripts to reproduce the results reported in this article are available on GitHub: https://github.com/bionetslab/robust, https://github.com/bionetslab/robust-eval. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Real-World Rheumatology Registry and Research Consortium: The German RheumaDatenRhePort (RHADAR) Registry.

Real-world data are crucial to continuously improve the management of patients with rheumatic and musculoskeletal diseases (RMDs). The German RheumaDatenRhePort (RHADAR) registry encompasses a network of rheumatologists and researchers in Germany providing pseudonymized real-world patient data and allowing timely and continuous improvement in the care of RMD patients. The RHADAR modules allow automated anamnesis and adaptive coordination of appointments regarding individual urgency levels. Further modules focus on the collection and integration of electronic patient-reported outcomes in between consultations. The digital RHADAR modules ultimately allow a patient-centered adaptive approach to integrated medical care starting as early as possible in the disease course. Such a closed-loop system consisting of various modules along the whole patient pathway enables comprehensive and timely patient management in an unprecedented manner.

Probing the interplay between geometric and electronic-structure features via high-harmonic spectroscopy.

We present molecular-frame measurements of the recombination dipole matrix element (RDME) in CO2, N2O, and carbonyl sulfide (OCS) molecules using high-harmonic spectroscopy. Both the amplitudes and phases of the RDMEs exhibit clear imprints of a two-center interference minimum, which moves in energy with the molecular alignment angle relative to the laser polarization. We find that whereas the angle dependence of this minimum is consistent with the molecular geometry in CO2 and N2O, it behaves very differently in OCS; in particular, the phase shift which accompanies the two-center minimum changes sign for different alignment angles. Our results suggest that two interfering structural features contribute to the OCS RDME, namely, (i) the geometrical two-center minimum and (ii) a Cooper-like, electronic-structure minimum associated with the sulfur end of the molecule. We compare our results to ab initio calculations using time-dependent density functional theory and present an empirical model that captures both the two-center and the Cooper-like interferences. We also show that the yield from unaligned samples of two-center molecules is, in general, reduced at high photon energies compared to aligned samples, due to the destructive interference between molecules with different alignments.

Genetic and phenotypic overlap of specific obsessive-compulsive and attention-deficit/hyperactive subtypes with Tourette syndrome.

BACKGROUND: The unique phenotypic and genetic aspects of obsessive-compulsive (OCD) and attention-deficit/hyperactivity disorder (ADHD) among individuals with Tourette syndrome (TS) are not well characterized. Here, we examine symptom patterns and heritability of OCD and ADHD in TS families. METHOD: OCD and ADHD symptom patterns were examined in TS patients and their family members (N = 3494) using exploratory factor analyses (EFA) for OCD and ADHD symptoms separately, followed by latent class analyses (LCA) of the resulting OCD and ADHD factor sum scores jointly; heritability and clinical relevance of the resulting factors and classes were assessed. RESULTS: EFA yielded a 2-factor model for ADHD and an 8-factor model for OCD. Both ADHD factors (inattentive and hyperactive/impulsive symptoms) were genetically related to TS, ADHD, and OCD. The doubts, contamination, need for sameness, and superstitions factors were genetically related to OCD, but not ADHD or TS; symmetry/exactness and fear-of-harm were associated with TS and OCD while hoarding was associated with ADHD and OCD. In contrast, aggressive urges were genetically associated with TS, OCD, and ADHD. LCA revealed a three-class solution: few OCD/ADHD symptoms (LC1), OCD & ADHD symptoms (LC2), and symmetry/exactness, hoarding, and ADHD symptoms (LC3). LC2 had the highest psychiatric comorbidity rates (⩾50% for all disorders). CONCLUSIONS: Symmetry/exactness, aggressive urges, fear-of-harm, and hoarding show complex genetic relationships with TS, OCD, and ADHD, and, rather than being specific subtypes of OCD, transcend traditional diagnostic boundaries, perhaps representing an underlying vulnerability (e.g. failure of top-down cognitive control) common to all three disorders.

Association of the KCNJ5 gene with Tourette Syndrome and Attention-Deficit/Hyperactivity Disorder.

Linkage and association of Tourette Syndrome (TS) and Attention-Deficit/Hyperactivity Disorder (ADHD) have previously been reported in the 11q24 chromosomal region. To identify the risk gene within the region we studied the potassium inwardly-rectifying channel J5 (KCNJ5) gene in a sample of 170 nuclear families with TS. We genotyped eight markers across the gene and observed biased transmission of haplotypes from parents to probands in this sample. We then tested these markers in an independent sample of 242 nuclear families with ADHD and found the same haplotype was significantly over transmitted to ADHD probands. Screening of the coding region of KCNJ5 in 48 probands with TS did not identify any variation that could explain the association of the haplotype. We also genotyped two microsatellite markers, one in the promoter and the other in the 3' region and found no evidence for association for either marker for TS, however, we found significant evidence for association with the 3' repeat and ADHD. A small gene (c11orf45) of unknown function lies within the first intron of KCNJ5 that is transcribed in the opposite orientation and this gene may regulate the expression of KCNJ5. We studied the correlation of the expression of KCNJ5 and the antisense transcript in brain tissues from control individuals and found that the antisense transcript and the short KCNJ5 isoform are co-expressed in three brain regions. The results of this study indicate that KCNJ5 is associated with TS and ADHD in our samples, however, the functional variant(s) remain to be identified.

Genome-wide association study of Tourette's syndrome.

Tourette's syndrome (TS) is a developmental disorder that has one of the highest familial recurrence rates among neuropsychiatric diseases with complex inheritance. However, the identification of definitive TS susceptibility genes remains elusive. Here, we report the first genome-wide association study (GWAS) of TS in 1285 cases and 4964 ancestry-matched controls of European ancestry, including two European-derived population isolates, Ashkenazi Jews from North America and Israel and French Canadians from Quebec, Canada. In a primary meta-analysis of GWAS data from these European ancestry samples, no markers achieved a genome-wide threshold of significance (P<5 × 10(-8)); the top signal was found in rs7868992 on chromosome 9q32 within COL27A1 (P=1.85 × 10(-6)). A secondary analysis including an additional 211 cases and 285 controls from two closely related Latin American population isolates from the Central Valley of Costa Rica and Antioquia, Colombia also identified rs7868992 as the top signal (P=3.6 × 10(-7) for the combined sample of 1496 cases and 5249 controls following imputation with 1000 Genomes data). This study lays the groundwork for the eventual identification of common TS susceptibility variants in larger cohorts and helps to provide a more complete understanding of the full genetic architecture of this disorder.

[Therapy and care of patients with chronic migraine: expert recommendations of the German Migraine and Headache Society/German Society for Neurology as well as the Austrian Headache Society/Swiss Headache Society]. / Therapie und Versorgung bei chronischer Migräne : Expertenempfehlung der Deutschen Migräne- und Kopfschmerzgesellschaft/Deutsche Gesellschaft für Neurologie sowie der Österreichischen Kopfschmerzgesellschaft/Schweizerischen Kopfwehgesellschaft.

Chronic migraine (CM) was first defined in the second edition of the International Headache Society (IHS) classification in 2004. The definition currently used (IHS 2006) requires the patient to have headache on more than 15 days/month for longer than 3 months and a migraine headache on at least 8 of these monthly headache days and that there is no medication overuse. In daily practice the majority of the patients with CM also report medication overuse but it is difficult to determine whether the use is the cause or the consequence of CM. Most the patients also have other comorbidities, such as depression, anxiety and chronic pain at other locations. Therapy has to take this complexity into consideration and is generally multimodal with behavioral therapy, aerobic training and pharmacotherapy. The use of analgesics should be limited to fewer than 15 days per month and use of triptans to fewer than 10 days per month. Drug treatment should be started with topiramate, the drug with the best scientific evidence. If there is no benefit, onabotulinum toxin A (155-195 Units) should be used. There is also some limited evidence that valproic acid and amitriptyline might be beneficial. Neuromodulation by stimulation of the greater occipital nerve or vagal nerve is being tested in studies and is so far an experimental procedure only.

An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.

The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270-277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.

Long-term efficacy of sodium oxybate in 4 patients with chronic cluster headache.

BACKGROUND: Cluster headache (CH) manifests with periodic attacks of severe unilateral pain and autonomic symptoms. Nocturnal attacks may cause severe sleep disruption. In about 10%of cases, patients present with a chronic form (CCH), which is often medically intractable. Few attempts have been made to improve headache via pharmacologic modulation of sleep. METHODS: In an open-label study, 4 patients with CCH and disturbed sleep received increasing dosages of sodium oxybate (SO), a compound known to consolidate sleep and to increase slow-wave sleep. Response to SO was monitored by serial polysomnography, and actimetry, along with pain and sleep diaries. RESULTS: SO was effective in all 4 patients as shown by an immediate reduction in frequency (up to 90%) and intensity (>50%) of nocturnal pain attacks and improved sleep quality. These effects were long-lasting in 3 patients (mean 19 months, range 12-29 months) and transient (for 8 months) in one patient. Long-lasting improvement of daytime headaches was achieved with a latency of weeks in 2 patients. SO was safe, with mild to moderate adverse effects (dizziness, vomiting, amnesia, weight loss). CONCLUSION: SO may represent a new treatment option to reduce nocturnal and diurnal pain attacks and improve sleep quality in CCH. These data also suggest the interest of treating primary headache syndromes by sleep-manipulating substances. CLASSIFICATION OF EVIDENCE: This study provides Class IV evidence that oral SO at night improves sleep and reduces the intensity and frequency of headaches in patients with CCH.

[The value of "migraine surgery". Overview of the pathophysiological concept and current evidence]. / Stellenwert der "Migränechirurgie". Ubersicht über das pathophysiologische Konzept und die aktuelle Datenlage.

Often without sufficient scientific evidence, unconventional methods for migraine treatment are being put forward. Recently a trial using "migraine surgery" has been published. Its design is based on a concept of migraine pathogenesis without any scientific background and includes several severe methodological flaws. In spite of the above, the study is frequently cited in the lay press. The surgical procedure as well as the study are critically discussed.

EFNS guideline on the drug treatment of migraine--revised report of an EFNS task force.

BACKGROUND: Migraine is one of the most frequent disabling neurological conditions with a major impact on the patients' quality of life. OBJECTIVES: To give evidence-based or expert recommendations for the different drug treatment procedures in the particular migraine syndromes based on a literature search and the consensus of an expert panel. METHODS: All available medical reference systems were screened for the range of clinical studies on migraine with and without aura and on migraine-like syndromes. The findings in these studies were evaluated according to the recommendations of the European Federation of Neurological Societies (EFNS) resulting in level A, B, or C recommendations and good practice points. RECOMMENDATIONS: For the acute treatment of migraine attacks, oral non-steroidal antiinflammatory drug (NSAID) and triptans are recommended. The administration should follow the concept of stratified treatment. Before intake of NSAID and triptans, oral metoclopramide or domperidone is recommended. In very severe attacks, intravenous acetylsalicylic acid or subcutaneous sumatriptan are drugs of first choice. Status migrainosus can be treated by cortoicosteroids, although this is not universally held to be helpful, or dihydroergotamine. For the prophylaxis of migraine, betablockers (propranolol and metoprolol) flunarizine, valproic acid, and topiramate are drugs of first choice. Drugs of second choice for migraine prophylaxis include amitriptyline, naproxen, petasites, and bisoprolol.

[Spontaneous pneumothorax--management, therapy]. / Spontáinní pneumotorax--management, terapie.

OBJECTIVE: Spontaneous pneumothorax (SPNO) is a surgical disease, which belongs to surgical emergencies. It is divided into a primary, secundary, katamenial and neonatal. A young and healthy men are affected by primary SPNO, usually on the right side of the thorax, recurrence is common. A secondary SPNO typically occurs in patients between the 5th and 7th decenium. These patients usually suffer from some lung disease. A major complications are more common in this type of pneumothorax. METHODS: At Department of surgery, University Hospital Brno, 73 patients were treated for spontaneous pneumothorax from the January, 2006 till August, 2008. We divided patients in two groups. The first one with primary SPNO, and the second one with secondary SPNO. Hospital stay, age distribution, type of operation, duration of drainage, postoperative complication, histological findings and laterality were followed up retrospectively. RESULTS: In group of primary SPNO, 24 patients were operated without major complication. The most frequent cause was bullate emphysema, hospital stay was 8 days, duration of drainage 6 days. The second group with secondary SPNO, five patients were operated, hospital stay was 16.5 days, duration of drainage 10 days. Haemothorax as a postoperative complication occured in one case. In both groups we proved the bullate emphysema as the most frequent cause, as well as a right - sided involvement. CONCLUSION: Spontaneous pneumothorax is a surgical disease. It's treatment has to be provided by surgeon, if possible by a thoracic specialist. The first occurrence of spontaneous pneumothorax is treated by drainage, the recurrence by operation. The principal is to combine an atypical resection of affected lung with a mechanical pleurodesis. Postoperative complications are not frequent.

[Therapy of primary chronic headache: chronic migraine, chronic tension type headache and other forms of daily chronic headache]. / Therapie primärer chronischer Kopfschmerzen: Chronische Migräne, chronischer Kopfschmerz vom Spannungstyp und andere chronische tägliche Kopfschmerzen.

The criteria of the International Headache Society (IHS) define four different primary headache syndromes with daily chronic headaches: chronic migraine, episodic and chronic tension type headache, hemicrania continua, new daily persisting headache. A further important differential diagnosis is medication overuse headache (previously known as analgesia headache). The German, Austrian, and Swiss headache societies now present the first joint guidelines for therapy of these headache syndromes. The current literature was reviewed and a summary is presented. The therapy recommendations do not only include the scientific evidence but also the practical relevance.