A Fast and Efficient Incremental Approach toward Dynamic Community Detection

Community detection is a discovery tool used by network scientists to analyze the structure of real-world networks. It seeks to identify natural divisions that may exist in the input networks that partition the vertices into coherent modules (or communities). While this problem space is rich with efficient algorithms and software, most of this literature caters to the static use-case where the underlying network does not change. However, many emerging real-world use-cases give rise to a need to incorporate dynamic graphs as inputs. In this paper, we present a fast and efficient incremental approach toward dynamic community detection. The key contribution is a generic technique called $\Delta-screening$, which examines the most recent batch of changes made to an input graph and selects a subset of vertices to reevaluate for potential community (re)assignment. This technique can be incorporated into any of the community detection methods that use modularity as its objective function for clustering. For demonstration purposes, we incorporated the technique into two well-known community detection tools. Our experiments demonstrate that our new incremental approach is able to generate performance speedups without compromising on the output quality (despite its heuristic nature). For instance, on a real-world network with 63M temporal edges (over 12 time steps), our approach was able to complete in 1056 seconds, yielding a 3x speedup over a baseline implementation. In addition to demonstrating the performance benefits, we also show how to use our approach to delineate appropriate intervals of temporal resolutions at which to analyze an input network

Challenges recruiting to a proof-of-concept pharmaceutical trial for a rare disease: The trigeminal neuralgia experience

Background: This study aimed to describe recruitment challenges encountered during a phase IIa study of vixotrigine, a state and use-dependent Nav1.7 channel blocker, in individuals with trigeminal neuralgia. Methods: This was an international, multicenter, placebo-controlled, randomized withdrawal study that included a 7-day run-in period, a 21-day open-label phase, and a 28-day double-blind phase in which patients (planned n = 30) were randomized to vixotrigine or placebo. Before recruitment, all antiepileptic drugs had to be stopped, except for gabapentin or pregabalin. After the trial, patients returned to their original medications. Patient recruitment was expanded beyond the original five planned (core) centers in order to meet target enrollment (total recruiting sites N = 25). Core sites contributed data related to patient identification for study participation (prescreening data). Data related to screening failures and study withdrawal were also analyzed using descriptive statistics. Results: Approximately half (322/636; 50.6%) of the patients who were prescreened at core sites were considered eligible for the study and 56/322 (17.4%) were screened. Of those considered eligible, 26/322 (8.1%) enrolled in the study and 6/322 (1.9%) completed the study. In total, 125 patients were screened across all study sites and 67/125 (53.6%) were enrolled. At prescreening, reasons for noneligibility varied by site and were most commonly diagnosis change (78/314; 24.8%), age > 80 years (75/314; 23.9%), language/distance/mobility (61/314; 19.4%), and noncardiac medical problems (53/314; 16.9%). At screening, frequently cited reasons for noneligibility included failure based on electrocardiogram, insufficient pain, and diagnosis change. Conclusions: Factors contributing to recruitment challenges encountered in this study included diagnosis changes, anxiety over treatment changes, and issues relating to distance, language, and mobility. Wherever possible, future studies should be designed to address these challenges. Trial registration: ClinicalTrials.gov, NCT01540630. EudraCT, 2010-023963-16. 07 Aug 2015

UBR2 of the N-end rule pathway is required for chromosome stability via histone ubiquitylation in spermatocytes and somatic cells

The N-end rule pathway is a proteolytic system in which its recognition components (N-recognins) recognize destabilizing N-terminal residues of short-lived proteins as an essential element of specific degrons, called N-degrons. The RING E3 ligases UBR2 and UBR1 are major N-recognins that share size (200 kDa), conserved domains and substrate specificities to N-degrons. Despite the known function of the N-end rule pathway in degradation of cytosolic proteins, the major phenotype of UBR2-deficient male mice is infertility caused by arrest of spermatocytes at meiotic prophase I. UBR2-deficient spermatocytes are impaired in transcriptional silencing of sex chromosome-linked genes and ubiquitylation of histone H2A. In this study we show that the recruitment of UBR2 to meiotic chromosomes spatiotemporally correlates to the induction of chromatin-associated ubiquitylation, which is significantly impaired in UBR2-deficient spermatocytes. UBR2 functions as a scaffold E3 that promotes HR6B/UbcH2-dependent ubiquitylation of H2A and H2B but not H3 and H4, through a mechanism distinct from typical polyubiquitylation. The E3 activity of UBR2 in histone ubiquitylation is allosterically activated by dipeptides bearing destabilizing N-terminal residues. Insufficient monoubiquitylation and polyubiquitylation on UBR2-deficient meiotic chromosomes correlate to defects in double strand break (DSB) repair and other meiotic processes, resulting in pachytene arrest at stage IV and apoptosis. Some of these functions of UBR2 are observed in somatic cells, in which UBR2 is a chromatin-binding protein involved in chromatin-associated ubiquitylation upon DNA damage. UBR2-deficient somatic cells show an array of chromosomal abnormalities, including hyperproliferation, chromosome instability, and hypersensitivity to DNA damage-inducing reagents. UBR2-deficient mice enriched in C57 background die upon birth with defects in lung expansion and neural development. Thus, UBR2, known as the recognition component of a major cellular proteolytic system, is associated with chromatin and controls chromatin dynamics and gene expression in both germ cells and somatic cells. © 2012 Kwon et al

Assembly of Helicobacter pylori initiation complex is determined by sequence-specific and topology-sensitive DnaA-oriC interactions

In bacteria, chromosome replication is initiated by binding of the DnaA initiator protein to DnaA boxes located in the origin of chromosomal replication (oriC). This leads to DNA helix opening within the DNA-unwinding element. Helicobacter pylori oriC, the first bipartite origin identified in Gram-negative bacteria, contains two subregions, oriC1 and oriC2, flanking the dnaA gene. The DNA-unwinding element region is localized in the oriC2 subregion downstream of dnaA. Surprisingly, oriC2–DnaA interactions were shown to depend on DNA topology, which is unusual in bacteria but is similar to initiator–origin interactions observed in higher organisms. In this work, we identified three DnaA boxes in the oriC2 subregion, two of which were bound only as supercoiled DNA. We found that all three DnaA boxes play important roles in orisome assembly and subsequent DNA unwinding, but different functions can be assigned to individual boxes. This suggests that the H. pylori oriC may be functionally divided, similar to what was described recently for Escherichia coli oriC. On the basis of these results, we propose a model of initiation complex formation in H. pylori

The Ecological and Ethical Consumption Development Prospects in Poland Compared with the Western European Countries

An overview of the Western European literature shows that one of the most distinct trends in consumption that has been noted in the recent years is globally increasing environmental and social awareness. The issue of consumers' behaviours and attitudes towards "socially responsible products" has been gaining importance in Polish economy as well. This article evaluates the development prospects of ethical and ecological consumption in Poland vis-à-vis Western European countries. The comparative analysis being part of the article utilizes primary sources of information, i.e. interviews with a representative sample of Polish adults, as well as secondary sources of information. A factor analysis or, more precisely, a principal component analysis, allowed dividing Polish consumers into groups that were typologically homogeneous in respect of their sensitivity to various aspects of business ethics and ecology.Przegląd literatury zachodnio-europejskiej pozwala stwierdzić, że jednym z najbardziej zauważalnych trendów w sferze konsumpcji w ostatnich latach jest coraz większa świadomość ekologiczna i społeczna w wymiarze globalnym. Problematyka zachowań i postaw konsumentów wobec produktów "społecznie odpowiedzialnych" nabiera coraz większego znaczenia także w polskiej gospodarce. Celem artykułu jest ocena perspektyw rozwoju etyczneji ekologicznej konsumpcji w Polsce na tle krajów zachodnio-europejskich. Analizę porównawczą prowadzono bazując na źródłach wtórych jak i badaniach pierwotnych realizowanych na reprezentatywnej próbie losowej dorosłych mieszkańców Polski. W oparciu o analizę czynnikową, a dokładniej metodę analizy głównych składowych, dokonano także podziału polskich konsumentów na jednorodne grupy typologiczne pod względem ich wrażliwości na różne aspekty związane z ekologią i etyką

Referrals to a facial pain service

AIM: To assess the quality of referral letters to a facial pain service and highlight the key requirements of such letters. METHOD: The source of all referral letters to the service for five years was established. For one year the information provided in 94 referrals was assessed. Using a predetermined checklist of essential information the referral letters were compared to these set criteria. RESULTS: The service received 7,001 referrals and, on average, general dental practitioners (GDPs) referred 303 more patients per year than general medical practitioners (GMPs). Seventy-one percent of all referrals were from primary care practitioners, the rest were from specialists. Over 70% of GMP and 52% of GDP letters included a past medical history, with GMPs more likely to suggest a possible diagnosis and include previous secondary care referrals. The mean score for GMP referrals compared to the standard proforma (maximum of 12) was 5.6 and for GDP referrals 5.0. A relevant drug history was included by 75.6% GMP compared to 38.7% of GDPs. GMPs were more likely to include any relevant mental health history. CONCLUSIONS: The overall quality of referral letters is low which makes it difficult for the specialists to provide robust treatment plans

Chronic central neuropeptide Y infusion in normal rats: status of the hypothalamo-pituitary-adrenal axis, and vagal mediation of hyperinsulinaemia

Summary: Neuropeptide Y in the hypothalamus is a potent physiological stimulator of feeding, and may contribute to the characteristic metabolic defects of obesity when hypothalamic levels remain chronically elevated. Since corticosterone and insulin are important regulators of fuel metabolism, the longitudinal effects of chronic (6 days) intracerebroventricular infusion of neuropeptide Y in normal rats on the hypothalamo-pituitary-adrenal axis and on insulin secretion were studied. Neuropeptide Y-infused rats were either allowed to eat ad libitum, or were pair-fed with normophagic control rats. Neuropeptide Y increased the basal plasma concentrations of adrenocorticotropic hormone and corticosterone during the first 2 days of its intracerebroventricular infusion and increased cold stress-induced plasma adrenocorticotropic hormone concentrations. After 4-6 days of central neuropeptide Y infusion, however, basal plasma adrenocorticotropic hormone and corticosterone concentrations were no different from control values (except in ad libitum-fed rats in which corticosteronaemia remained elevated), they were unaffected by the stress of cold exposure, and the hypothalamic content of corticotropin-releasing factor immunoreactivity was significantly decreased. A state of hyperinsulinaemia was present throughout the 6 days of intracerebroventricular neuropeptide Y infusion, being more marked in the ad libitum-fed than in the pair-fed group. The proportions of insulin, proinsulin, and conversion intermediates in plasma and pancreas were unchanged. Hyperinsulinaemia of the pair-fed neuropeptide Y-infused rats was accompanied by muscle insulin resistance and white adipose tissue insulin hyperresponsiveness, as assessed by the in vivo uptake of 2-deoxyglucose. Finally, bilateral subdiaphragmatic vagotomy prevented both the basal and the marked glucose-induced hyperinsulinaemia of animals chronically infused with neuropeptide Y, demonstrating that central neuropeptide Y-induced hyperinsulinaemia is mediated by the parasympathetic nervous syste

Endothelial glycocalyx integrity is preserved in young, healthy men during a single bout of strenuous physical exercise

In the present study we aimed to evaluate whether oxidative stress and inflammation induced by strenuous exercise affect glycocalyx integrity and endothelial function. Twenty one young, untrained healthy men performed a maximal incremental cycling exercise - until exhaustion. Markers of glycocalyx shedding (syndecan-1, heparan sulfate and hyaluronic acid), endothelial status (nitric oxide and prostacyclin metabolites - nitrate, nitrite, 6-keto-prostaglandin F1a), oxidative stress (8-oxo-2'- deoxyguanosine) and antioxidant capacity (uric acid, nonenzymatic antioxidant capacity) as well as markers of inflammation (sVCAM-1 and sICAM-1) were analyzed in venous blood samples taken at rest and at the end of exercise. The applied strenuous exercise caused a 5-fold increase in plasma lactate and hypoxanthine concentrations (p<0.001), a fall in plasma uric acid concentration and non-enzymatic antioxidant capacity (p<10-4), accompanied by an increase (p=0.003) in sVCAM-1 concentration. Plasma 6-keto-prostaglandin F1a concentration increased (p=0.006) at exhaustion, while nitrate and nitrite concentrations were not affected. Surprisingly, no significant changes in serum syndecan-1 and heparan sulfate concentrations were observed. We have concluded, that a single bout of severe-intensity exercise is well accommodated by endothelium in young, healthy men as it neither results in evident glycocalyx disruption nor in the impairment of nitric oxide and prostacyclin production