The scope and scale of biological data are increasing at an exponential rate, as technologies like next-generation sequencing are becoming radically cheaper and more prevalent. Over the last two decades, the cost of sequencing a genome has dropped from $100 million to nearly $100—a factor of over 106—and the amount of data to be analyzed has increased proportionally. Yet, as Moore’s Law continues to slow, computational biologists can no longer rely on computing hardware to compensate for the ever-increasing size of biological datasets. In a field where many researchers are primarily focused on biological analysis over computational optimization, the unfortunate solution to this problem is often to simply buy larger and faster machines. Here, we introduce Seq, the first language tailored specifically to bioinformatics, which marries the ease and productivity of Python with C-like performance. Seq starts with a subset of Python—and is in many cases a drop-in replacement—yet also incorporates novel bioinformatics- and computational genomics-oriented data types, language constructs and optimizations. Seq enables users to write high-level, Pythonic code without having to worry about low-level or domain-specific optimizations, and allows for the seamless expression of the algorithms, idioms and patterns found in many genomics or bioinformatics applications. We evaluated Seq on several standard computational genomics tasks like reverse complementation, k-mer manipulation, sequence pattern matching and large genomic index queries. On equivalent CPython code, Seq attains a performance improvement of up to two orders of magnitude, and a 160× improvement once domain-specific language features and optimizations are used. With parallelism, we demonstrate up to a 650× improvement. Compared to optimized C++ code, which is already difficult for most biologists to produce, Seq frequently attains up to a 2× improvement, and with shorter, cleaner code. Thus, Seq opens the door to an age of democratization of highly-optimized bioinformatics software.

Many users need social media platforms to improve business. The usage of those platforms is usually focused on the marketing and customer targeting. Platforms like Facebook, Instagram or YouTube give their users a large number of reports and analytic tools. Public figures and organizations have a large number of followers who generate a significant number of activities. This paper focuses on the use of Facebook's geography analytic in the process of events planning. The problem is formulated as a combinatorial optimization problem. Data from social media platforms are used as an input to nature-inspired optimization algorithm. A public data set has been created with cities from 20 European countries. An adjusted genetic algorithm (AGA) is proposed. The greedy approach and AGA are compared on real data from several Facebook pages and on the created public dataset. The genetic algorithm shows better results and it gives the same solution as an exhaustive search for smaller instances.

The planning of concert tours can be a challenging process which requires a large amount of data to be analyzed. The greatest profit cannot be obtained only by maximizing the expected number of visitors. However, most of the organizers mainly focus on that part of planning. To achieve the maximum profit possible, organizers must include other data in their analysis. Social media play a powerful role in music industry. Most of the mentioned data can be found online on social media like Facebook, YouTube or Instagram. Such data can be found in analytic sections of fan or event pages. In this paper, algorithms for tour planning have been introduced by using above mentioned data. Proposed algorithms are based on heuristic methods such as simulated annealing and genetic algorithm. A clustering based method is also implemented. Aforementioned algorithms were tested on real-world instances from Facebook fan page analytics and use number of fans and distance between cities.

Abstract Background BRAF genomic alterations (GA) occur in multiple tumor types and BRAF/MEK targeted therapies are approved in melanoma and NSCLC. Diverse mechanisms of AR to these therapies have been proposed but have not been comprehensively assessed. Methods Hybrid-capture based comprehensive genomic profiling (CGP) was performed on FFPE (n = 228,629) or blood-based cell free DNA (cfDNA, n = 15,069) samples for 222,952 patients (pts). Tumor mutational burden (TMB) was determined on 0.8-1.1 Mbp of sequenced DNA. Samples without evidence of tumor DNA or known to have not received RAF/MEK inhibitors were excluded. Paired samples were collected >60 days apart (median 523, range 71-5571). Results Paired samples with BRAF V600E (64%) or other activating BRAF GA (36%) were available for 154 pts with NSCLC (20%), melanoma (19%), CRC (15%) myeloma (8.4%) glioma (7.1%) or other (30%) cancers. Acquired GA previously described preclinically or clinically including in BRAF, KRAS, NRAS, MEK1, PIK3CA, PTEN, MET, and CCND1 occurred in 34 cases (Table). 56 additional cases had reportable acquired GA in other genes (eg. STK11, NF1). Median TMB was 4.0 vs 5.2 mut/Mb in the first vs second sample (p = 0.23). In 12% of cases (9 tissue, 9 cfDNA) a BRAF GA was not detected in the second sample. Most AR mechanisms (MET amp, KRAS mut, secondary BRAF GA) were tumor agnostic, but PIK3CA and PTEN GA were enriched in brain samples and absent in CRC, and NRAS mut were exclusive to melanoma (Table). Treatment status was available for a subset of cases. Notably V600E CRC, NSCLC and melanoma each had acquired MET amp post-dabrafenib + trametinib, and a V600E myeloma had acquired MEK C121S post-trametinib + vemurafenib. Additional clinical data will be presented. Table: 1878PD . Potential AR mechanism No. cases# AR subtypes Disease Histologies Associated Primary BRAF GA Biopsy location * KRAS mut 7 G12D (2), G12R, G12V, G13D, Q61H, K117N CRC (2), NSCLC (2), cholangiocarcinoma, multiple myeloma, CLL V600E (6), G466A omentum (2), liver NRAS mut 4 G12C, G13R, G13R/Q61H, Q61H/K melanoma (4) V600E (2), V600R, G469A brain (1), lymph node (1), soft tissue (1) NRAS amp 1 amp estimated copies: 41 NSCLC V600E pericardial fluid Secondary BRAF GA 10 N-terminal deletion exons 2-8 (6), duplications exons 10-18, L505H, N581I/D594G, amp estimated copies: 6 NSCLC (4), CRC (2), melanoma (2), multiple myeloma, pancreatic V600E (9), G466A liver (3), lymph node (2), lung, abdominal wall, brain MEK1 mut 1 C121S multiple myeloma V600E NA PIK3CA mut 5 H1047R (2), G1049R, R88Q, S405F glioma (3), NSCLC, thyroid V600E (3), N486_T491>K, R506_K507insVLR brain (4), lung PTEN GA 5 E7fs * , R130 * , G129R, splice site 165-1G>A, loss melanoma (2), glioma, NSCLC, UP neuroendocrine V600E, V600K, R506_K507insVLR, KHDRBS2-BRAF fusion brain (2), abdomen, soft tissue CCND1 amp 2 amp estimated copies: 9, 10 NSCLC, thyroid V600E, G464V brain, pleural fluid MET amp 4 amp estimated copies: 12, 14, 15, 56 NSCLC, CRC, melanoma, UP adenocarcinoma V600E (4) lymph node, colon, brain, liver * Indicated for tissue samples only (NA= not applicable); #5 cases had AR alterations in multiple genes included here; NSCLC: non-small cell lung cancer, CRC: colorectal carcinoma; CLL: chronic lymphocytic leukemia; UP: unknown primary; AR: acquired resistance; mut: mutation; amp: amplification. Conclusions Novel and previously observed potential AR alterations in paired BRAF altered clinical samples were detected using CGP. Most AR mechanisms appeared independent of tumor type and biopsy site. Additional clinical studies to explore effective treatments for these AR subsets are needed. Legal entity responsible for the study The authors. Funding Foundation Medicine. Disclosure F. Pietrantonio: Advisory / Consultancy: Roche; Advisory / Consultancy: Amgen; Advisory / Consultancy: Eli-Lily; Advisory / Consultancy: Bayer; Advisory / Consultancy: Sanofi; Advisory / Consultancy: Servier; Advisory / Consultancy: Merck Serono. J. Lee: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. L. Boussemart: Advisory / Consultancy: Novartis; Advisory / Consultancy: Pierre Fabre. G. Srkalovic: Speaker Bureau / Expert testimony: Foundation Medicine. R. Madison: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. J.S. Ross: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. V.A. Miller: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche; Advisory / Consultancy: Revolution Medicines. B.M. Alexander: Leadership role, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. S.M. Ali: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. A.B. Schrock: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. All other authors have declared no conflicts of interest.

Abstract We studied numerically the heat transfer in flow over a rotationally oscillating cylinder at a subcritical Reynolds number ( R e = 1.4 × 10 5 ) that is an order of magnitude higher than previously reported in the literature. This paper is a follow-up of the earlier study of hydrodynamics and drag force in a range of forcing frequencies and amplitudes (Palkin et al., 2018). This time we focus on heat transfer and its correlation with the observed flow field and vortical patterns. Four forcing frequencies f = f e / f 0 = 0 , 1 , 2.5 , 4 for two forcing amplitudes Ω = Ω e D / 2 U ∞ = 1 and 2 are considered, where f0 is the natural vortex-shedding frequency, U∞ the free-stream velocity and D the cylinder diameter. The parametric study was performed by solving three-dimensional unsteady Reynolds-averaged Navier–Stokes (URANS) equations closed by a wall-integrated second-moment (Re-stress) model, verified earlier by Large-eddy simulations and experiments in several reference cases including flows over a stagnant, as well as rotary oscillating cylinders at the same Re number. The thermal field, treated as a passive scalar, was obtained from the simultaneous solution of the energy equation, closed by the standard (GGDH) anisotropic eddy-diffusivity model. The computations showed that for the unforced cylinder heat transfer is characterized by very high local rates due to a strong thinning of the thermal boundary layer as a result of the impact and interactions of large coherent structures with the wall. The overall average Nusselt number does not change much for the forced cylinder but its time-averaged, phase-averaged and instantaneous circumferential profiles show some profound differences compared to the stationary cylinder. The distribution of Nu on the back surface becomes more uniform with less frequent occurrence of high values, especially for the higher frequencies f = 2.5 and f = 4 . This is attributed to diminishing of the mean-recirculation zone as well as to the overall suppression of turbulent fluctuations. The rotary oscillation of the cylinder appears potentially efficient in achieving a more uniform circumferential distribution of Nu and avoiding local overheats and hot spots.

In this work we will show a novel method for improving the performance of content-based image retrieval using a deep neural network. The main focus of the method is training the distance function using the deep neural network and transfer learning. An existing pretrained network for image classification is used as a basis. One of the method's benefits is the fact that the existing network is not retrained and features for the distance function are the neural network's layers which were trained and stored before. The method is tested with the publicly available VGG19 deep neural network. Obtained results are comparable or in some cases better than the state of the art methods with a similar approach.

Background Mirror aneurysms represent 2 adjacent arterial protrusions. Although the size is considered a major risk factor in terms of rupture, sometimes it is the smaller aneurysm that ruptures. Here, we present the contemporary management of mirror distal anterior cerebral artery (DACA) aneurysms associated with multiple aneurysms. Computational fluid dynamic (CFD) analysis was performed when assessing multiple aneurysms using Hemoscope, version 2015. Case Description Among multiple aneurysms, a mirror A2/A3 DACA aneurysm was found in a single patient. Surgical treatment was provided for all aneurysms through a single-stage procedure. The left ruptured A2/A3 aneurysm was smaller compared with the right (7.5 × 3.5 mm/10.8 × 3.2 mm). CFD showed greater wall pressure (WP) in the left ruptured A2/A3 aneurysm (left A2/A3 WP 84,000–84,402 Inst. mm Hg/right A2/3 WP 84,224–84,315). WP in the left middle cerebral artery and anterior communicating artery aneurysms showed lesser values compared with the ruptured aneurysm (WP upper values 84,361 and 84,367, respectively). Wall shear stress showed low values for all aneurysms with the lowest flow rate values in the left A2/A3 aneurysm. Conclusions In cases of ruptured mirror aneurysms followed by the presence of intracerebral hematoma, surgery is considered the primary option with the best results. A one-stage dual craniotomy procedure was found safe in the associated treatment of other multiple aneurysms. At present, the size of the aneurysm, the hemodynamic influence, and the local configuration are all considerations during the preoperative assessment of multiple aneurysm cases. According to our knowledge, this article presents the first CFD analysis of mirror DACA aneurysms associated with aneurysm multiplicity.

Abstract The aim of the paper is to reveal that humour processing is an exertion which requires both, mental and emotional capacities. To prove the point, two theories for humour processing were employed: the conceptual integration theory and the benign violation theory. The paper shows that theories, though different, possess certain common elements and represent useful tools in humour processing. The conceptual integration theory, with its input spaces, blending processes and generic space, together with the benign violation theory and its detection of humorous elements within tragic situations, could be valuable assets in understanding how people find humour in intimidating and life-threatening situations. The paper also sheds some light on how different age groups perceive black humour showing that age and life experience facilitate understanding of black humour.

Teleoperation of multi-robot systems, e.g. dual manipulators, in cooperative manipulation tasks requires haptic feedback of multi-contact interaction forces. Classical haptic devices restrict the workspace of the human operator and provide only one contact point. An alternative solution is to enable the operator to command the robot system via free-hand motions which extends the workspace of the human. In such a setting, a multi-contact haptic feedback may be provided to the human through multiple wearable haptic devices, e.g. fingertip devices that display forces on the human fingertips. In this paper we evaluate the benefit of using wearable haptic fingertip devices to interact with a bimanual robot setup in a pick-and-place manipulation task. We show that haptic feedback through wearable devices improves task performance compared to the base condition of no haptic feedback. Therefore, wearable haptic devices are a promising interface for guidance of multi-robot manipulation systems.

Group recommender systems generate recommendations for a group by aggregating individual members’ preferences and finding items that are liked by most of the members. In this paper we introduce a new approach to preference aggregation and group choice prediction that is based on a new form of weighting individuals’ preferences. The approach is based on network science, and, in particular, it relies on the computation of node centrality scores in preferences similarity networks of groups. We also motivate and introduce a non-linear (exponential) remapping of the individuals’ preferences. Based on offline experiments we demonstrate: 1) non-linear remapping of preferences is useful to better predict group choices and generate recommendations; and 2) our weighted approach predicts the actual group choices more accurately than current state-of-the-art methods for group recommendations.CCS CONCEPTS• Information systems → Recommender systems; • Humancentered computing → User studies; User models; Social network analysis.

Smart Ecosystem reflects in the control decisions of entities of different nature, especially of its software components. Particularly, the malicious behavior requires a more accurate attention. This paper discusses the challenges related to the evaluation of software smart agents and proposes a first solution leveraging the monitoring facilities for a) assuring conformity between the software agent and its digital twin in a real-time evaluation and b) validating decisions of the digital twins during runtime in a predictive simulation.

Introduction: Neurophysiological tests allow accurate assessment of the function of the peripheral nervous system. Detection of neurophysiological changes allows us to understand the neurological clinical symptoms and signs of patients with type 1 and type 2 diabetes and the possibility for their symptomatic treatment. Aim: Evaluate the effect of diabetes mellitus on the “cutaneous silent period” in detecting diabetic polyneuropathy. Material and Methods: The study included 150 subjects, 90 suffering from diabetes, divided into three groups of 30, depending on the disease duration, and a control group of 60 respondents not suffering from diabetes or other polyneuropathies. The control group are referred for EMG analysis on another basis (cervical radiculopathy, brachialgia, etc.). Group 1 consisted of 30 subjects with diabetes mellitus type 2 and duration of illness up to 5 years. Group 2 consisted of 30 subjects with type 2 diabetes mellitus 2 and illness duration from 5 to 10 years. Group 3 consisted of 30 patients with type 1 diabetes mellitus. The study groups consisted of patients referred for EMNG analysis to the EMG office of the Clinical Center of Sarajevo University, Neurology Clinic and the Neurophysiology Laboratory in Ljubljana, from July 1, 2011 to May 1, 2016. All patients were examined neurologically and electroneurographic analysis was performed. Results: A statistically significant difference was found in the incidence of pathologic CSP with respect to the study groups, χ2 = 26.153; p=0.001. Pathologic CSP was more common in group 1 and group 2 of subjects (56.17%) compared to group 3 and control subjects, where it occurred in 13.3% of the cases. Conclusion: The pathological cutaneous period of silence was more frequent in subjects of group 1 and group 2, that is, in subjects with DM type 2, compared to subjects with DM type 1.