Classification of time series by shapelet transformation

Time-series classification (TSC) problems present a specific challenge for classification algorithms: how to measure similarity between series. A \emph{shapelet} is a time-series subsequence that allows for TSC based on local, phase-independent similarity in shape. Shapelet-based classification uses the similarity between a shapelet and a series as a discriminatory feature. One benefit of the shapelet approach is that shapelets are comprehensible, and can offer insight into the problem domain. The original shapelet-based classifier embeds the shapelet-discovery algorithm in a decision tree, and uses information gain to assess the quality of candidates, finding a new shapelet at each node of the tree through an enumerative search. Subsequent research has focused mainly on techniques to speed up the search. We examine how best to use the shapelet primitive to construct classifiers. We propose a single-scan shapelet algorithm that finds the best $k$ shapelets, which are used to produce a transformed dataset, where each of the $k$ features represent the distance between a time series and a shapelet. The primary advantages over the embedded approach are that the transformed data can be used in conjunction with any classifier, and that there is no recursive search for shapelets. We demonstrate that the transformed data, in conjunction with more complex classifiers, gives greater accuracy than the embedded shapelet tree. We also evaluate three similarity measures that produce equivalent results to information gain in less time. Finally, we show that by conducting post-transform clustering of shapelets, we can enhance the interpretability of the transformed data. We conduct our experiments on 29 datasets: 17 from the UCR repository, and 12 we provide ourselve

Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser

We present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase–Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins

Preoperative FDG-PET/CT Is an Important Tool in the Management of Patients with Thick (T4) Melanoma

The yield of preoperative PET/CT (PET/CT) for regional and distant metastases for thin/intermediate thickness melanoma is low. Objective of this study is to determine if PET/CT performed for T4 melanomas helps guide management and alter treatment plans. Methods. Retrospective cohort of 216 patients with T4 melanomas treated at two tertiary institutions. Fifty-six patients met our inclusion criteria (T4 lesion, PET/CT and no clinical evidence of metastatic disease). Results. Fifty-six patients (M: 32, F: 24) with median tumor thickness of 6 mm were identified. PET/CT recognized twelve with regional and four patients with metastatic disease. Melanoma-related treatment plan was altered in 11% of the cases based on PET/CT findings. PET/CT was negative 60% of the time, in 35% of the cases; it identified incidental findings that required further evaluation. Conclusion. Patients with T4 lesions, PET/CT changed the treatment plan 18% of the time. Regional findings changed the surgical treatment plan in 11% and the adjuvant plan in 7% of our cases due to the finding of metastatic disease. Additionally 20 patients had incidental findings that required further workup. In this subset of patients, we feel there is a benefit to PET/CT, and further studies should be performed to validate our findings

Report of the 11th Liaison Meeting

The   11thLiaison   Meeting   between   the   Chairs   of   the   RCMs,   the   ICES   PGCCDBS,   PGMED  and  PGECON,  the  STECF  EWGs  on  the  DCF,  the  Regional  Database  Steering   Committees,  the  ICES  and  GFCM  representatives  and  the  European  Commission  was   held  at  the  DG  Maritime  Affairs  and  Fisheries,  Brussels  from  8th  to  9th  October  2014. The  11th  Liaison  meeting  was  held  in  Brussels  on  8th  and  9th  October  2014  to  address  the   following  terms  of  reference:     TOR  1.  Discussion  on  possible  follow-­‐‑up  to  the  main  outputs/recommendations  of:   • The  2014  RCMs  and  to  the   sp ecific  re commenda tions  a ddr e sse d  to  th e  Liaison   Meeting   • P G ECO N ,  PG CCDBS,  PG Med   –   ou tcome s  an d  r e commendation s  fr om  the ir   2014  meeting     • STECF  EWG  and  STEC F  Plen ary   -­‐‑   ou tcome s  a n d  r e commendation s  fr om  the ir   2014  meeting     • Data  end-­‐‑ users  (IC ES,  G F C M,  RC Ms)   TOR  2.  Compilation  of  recommendations  on  the  DCF   A  compilation  of  DCF  recommendations  will  be  established  by  the  COM  by  end  2014.   LM   needs   to   agree   on   which   recommendations   should   be   included   (i.e.   from   which   bodies)  &  covering  which  years.     TOR  3.  Regional  cooperation   • G r ants  for  str eng thene d  reg ion al  coop eration     • R e g ional  da ta b ases   o O ver view  of  use  of  the  Reg ional  Datab ases  for  R CMs  in  2014,  and  p rob lems   identified   o O ther  deve lop ments  (RDB  training s  in  2014,  RDB  Med&BS  develop ment)   o Chang es  for  the  fu tu re   –  an y  re commen da tions  from  th e  LM?   • R C M  data  calls   –  ove rview  of  h ow  MS  r esp onde d.   TOR  4.  Recommended  meetings/workshops   • P r ep a r e  a  list  of  r ecommen ded  me etin g s  for  2015  as  g u idance  for  MS   TOR  5.  Studies   • O ver view  of  p rocess   • LM  comme nts  and  p r ioritization  of  studies  p r op osed  b y  RC Ms,  PG ECO N ,  ICES,   GFCM   TOR  6.  AOB     1. The  DCF  website  has  been  revamped  by  the  JRC.  Any  comments  on  this?   2. Access  to  the  RCM  SharePoint   3. Derogations  –  List  of  derogations  by  Member  State  has  been  prepared  by  DG   MARE.  Have  any  RCMs  updated  this?     4. ICES  will  provide  an  update  on  their  plans  to  re-­‐‑evaluate  surveys.  Should  this   be  followed  by  STECF  work  on  surveys  to  be  included  in  future  EU  MAP?   5. Annual  reports  –  simplification:  presentation  of  process. 6. Data  transmission:   a. new   platform   for   information   exchanges   between   COM,   MS   and   end-­‐‑ users   b. new   tool   for   reporting   on   how   MS   complied   with   the   DG   MARE/JRC   data  calls     In   addition   to   the   above   Terms   of   Reference,   an   item   was   added   at   the   start   of   the   meeting,  regarding  the  implication  of  the  Landing  Obligation  on  data  collection  and   the  Discard  Plans.

Short reflex expirations (expiration reflexes) induced by mechanical stimulation of the trachea in anesthetized cats

Fifty spontaneously breathing pentobarbital-anesthetized cats were used to determine the incidence rate and parameters of short reflex expirations induced by mechanical stimulation of the tracheal mucosa (ERt). The mechanical stimuli evoked coughs; in addition, 67.6% of the stimulation trials began with ERt. The expiration reflex mechanically induced from the glottis (ERg) was also analyzed (99.5% incidence, p < 0.001 compared to the incidence of ERt). We found that the amplitudes of abdominal, laryngeal abductor posterior cricoarytenoid, and laryngeal adductor thyroarytenoid electromyograms (EMG) were significantly enhanced in ERg relative to ERt. Peak intrathoracic pressure (esophageal or intra-pleural pressure) was higher during ERg than ERt. The interval between the peak in EMG activity of the posterior cricoarytenoid muscle and that of the EMG of abdominal muscles was lower in ERt compared to ERg. The duration of thyroarytenoid EMG activity associated with ERt was shorter than that in ERg. All other temporal features of the pattern of abdominal, posterior cricoarytenoid, and thyroarytenoid muscles EMGs were equivalent in ERt and ERg

Report of the 12th Liaison Meeting

The 12th Liaison meeting was held in Brussels on 8th and 9th October 2015 to address the following Terms of Reference: TOR 1. Discussion on possible follow-­‐‑up to the main outputs/recommendations of: • The 2015 RCMs -­‐‑ specific recommendations addressed to the Liaison Meeting • PGECON, PGDATA, PGMed – outcomes and recommendations from their 2015 meeting • STECF EWG and STECF Plenary -­‐‑ outcomes and recommendations from their 2015 meetings • Data end users (ICES, STECF, RFMOs – GFCM, IATTC, ICCAT, IOTC, WCPFC, NAFO, SPRFMO, CECAF, WECAFC) TOR2. End user feedback on data transmission and related issues • Discuss feedback received from data end-­‐‑users on data transmission: main issues and possible harmonization of end user feedback to the Commission • JRC data transmission IT platform: experience gained and future steps • Discuss best practices on automatization of data upload by MS: data validation tools used by end users • Discussion on new set-­‐‑up for STECF evaluation of AR2014 & data transmission 2014 used in 2015 – continue like this next year? • Harmonisation and dissemination of DCF metadata: codelists, metiers, nomenclatures, best practices, standards • RCM data calls – overview of how MS responded TOR 3. Regional cooperation • Call for proposals MARE/2014/19 'ʹStrengthening Regional Cooperation in the area of fisheries data collection– state of play'ʹ. Presentation by a representative of the two RCG grants and discussions by LM thereafter. What should be the way forward? • Regional databases • Overview of use of the Regional Databases for RCMs in 2015 and problems identified • Other developments (RDB trainings in 2015, RDB Med&BS development) • Changes for the future – any recommendations from the LM? • Future role of RCMs and DCF-­‐‑related meetings: best practices, coordination, cohesion and common structure in line with emerging needs of DCF TOR 4. EU MAP • Discuss recommendations/ output of RCMs: List of proposed stocks, landing obligation, metiers • Discuss design-­‐‑based sampling in relation to DCF: does it fulfil DCF requirements? TOR 5. Availability of data • Overview of latest developments (DCF Database Feasibility Study and plans for a follow-­‐‑up study to this) TOR 6. AOB • Agree on a list of recommendations relating to DCF (that MS will need to report on in their AR2015) – COM will provide a compilation of proposed recommendations from LM & STECF Plenaries in 2014 as input • Prepare a list of recommended meetings for 2016 as guidance for MS • Review and prioritize DCF-­‐‑related study proposals from RCMs, PGECON, EGs etc • ICES update on workshop on concurrent sampling and plans to re-­‐‑evaluate survey

A Small Molecule that Binds and Inhibits the ETV1 Transcription Factor Oncoprotein

Members of the ETS transcription factor family have been implicated in several cancers, where they are often dysregulated by genomic derangement. ETS variant 1 (ETV1) is an ETS factor gene that undergoes chromosomal translocation in prostate cancers and Ewing\u27s sarcomas, amplification in melanomas, and lineage dysregulation in gastrointestinal stromal tumors. Pharmacologic perturbation of ETV1 would be appealing in these cancers; however, oncogenic transcription factors are often deemed “undruggable” by conventional methods. Here, we used small-molecule microarray (SMM) screens to identify and characterize drug-like compounds that modulate the biological function of ETV1. We identified the 1,3,5-triazine small molecule BRD32048 as a top candidate ETV1 perturbagen. BRD32048 binds ETV1 directly, modulating both ETV1-mediated transcriptional activity and invasion of ETV1-driven cancer cells. Moreover, BRD32048 inhibits p300-dependent acetylation of ETV1, thereby promoting its degradation. These results point to a new avenue for pharmacological ETV1 inhibition and may inform a general means to discover small molecule perturbagens of transcription factor oncoproteins

Report of the Regional Coordination Meeting for the North Atlantic (RCM NA) 2015

The 12th RCM North Atlantic was held in Hamburg (Germany) 14-18 September 2015. The main purpose of the RCM is to coordinate the National Programmes (NP) of the Member States (MS) in the North Atlantic region. National Programmes for 2011-2013 have been rolled over for the period 2014-2016. Therefore, the main focus at this year was to improve regional data collection, analysis and storage and the evolution towards Regional Coordination Groups (RCG).The impact of the introduction of the landing obligation and preparations for its implementation was also discussed taking into account possible changes in scientific sampling schemes. The participation of four National Correspondents make possible to address National administration issues related to the oncoming EU MAP. A data call was launched by the chairs of the RCM NA, RCM Baltic and RCM NS&EA where MS were requested to upload data for 2014 in the regional database (RDB Fishframe) hosted by ICES. All MS except France and Northern Ireland complied with this request on landings and effort data. All MS except France uploaded sample data for 2014. French data were available for the meeting using a web base interface. Evaluation of the data call for submission data to the RDB revealed the numbers of species in landings and sample data and the numbers of metiers in effort data are in general data stable. RCM NA see big improvements in the work MS are doing regarding data calls coming from a situation where some countries didn´t provide any data to a new scenario where everyone is providing data; at the same time the overall quality has significantly improved, which is a large step forward. Regional data collection, analysis, storage and the evolution towards Regional Coordination Groups (RCG). Optimizing and harmonizing fisheries management across MS is dependent on improving regional coordination. The group discussed various needs and aspects relevant for facilitating future work of the RCM. Future tasks for the RCM don’t differ much from the current tasks. The discussion was focused on the structure of the RCGs, funding and short term needs to address tasks in an efficient way in the future. Regional coordination encompasses many different aspects, ranging from regional cooperation, sampling design, quality control procedures, data storage and analysis to the actual coordination, reporting and accountancy. Current task sharing and coordination procedures as well as future mechanisms are partially covered under the current MARE study 2014/19 (FISHPI). The project and its progress were presented to the group. The outcomes of this study will demonstrate future procedures based on case studies. As substantial effort and costs are involved to facilitate the process of regional coordination, the group highlighted the importance to access to budgets to cover these costs. Development of the RDB is also crucial for future work of the RCGs; funds are needed for the development. Additionally, RCM NA identified 4 supra regional topics where work can be done intersesionally in cooperation with the rest of RCMs: (1) Cost sharing of funding surveys; (2) Impact of landing obligation; (3) reviewing the ICES list of data needs ; and (4) review and follow up on RDB upload logs. Due to the importance to moving to a regional catch sampling scheme, an exercise was realised using the distribution of landings by harbour and fleet segment as a proxy of sampling frames that could hypothetically operate in a regional probability based design. The exercise was based on landing weight, for the simple reason that this was the only complete variable that was available for all the various national data sets. A regional sampling design can however be optimized in any number of ways (e.g. by landings value, by métier diversity, by species diversity, by number of fishing trips). The aims and aspirations of the end users need to be defined to ascertain which is most appropriate. It is one of the overriding advantages of a regional sampling design (as opposed to the aggregation of national designs) that the overall coverage can be set out to achieve regional goals. The RCM NA analyzed and discussed the main achievements of WKISCON2. It was clear that concurrent sampling at-sea is a long-established practice in most MS and that, where it was applied, concurrent sampling of fishing trips on-shore resulted in substantial increases in species collected without jeopardizing the main uses of data. Stock assessment and discard estimation and management are the major current uses of concurrent sampling data. Concurrent sampling has also been providing other benefits than its initial reason, such as advice to local, national and international authorities, research on MSFD descriptors, mixed fisheries and gear interactions and on mortality of rare species, data-poor stocks and PETS. It was clear that concurrent sampling being a statistically valid method for species selection which has proven to fulfil different end-users needs, implementation constraints hinder concurrent sampling on-shore. Thus, in order to meet end-users needs and to overcome the constraints that may arise from the implementation of concurrent sampling in some countries, particularly on-shore, RCM NA considers that different statistically sound approaches other than concurrent sampling must be developed to be tested in the field, so they may provide useful alternatives. Introduction of the landing obligation and its impact in the implementation in scientific sampling schemes. In terms of evaluating the impact of the introduction of the Landing Obligation (LO) regulation on data collection, there is only limited experience as the current implementation only covers Pelagic and Industrial fisheries in this region but MS have or are preparing for the implementation where they can. It is currently perceived that this year is a transition period for the pelagic fisheries and that these fisheries and control agencies are not fully implementing the LO (managing but not enforcing). As a result MS did not have a lot of comments on the current year and are in general preparing for next year. During the meeting it was decided to gather further information to address this issue by getting member states who were present to fill in a table on “Monitoring the impact of the landing obligation on data collection in the North Atlantic region” outlining the current state of play. This table could be considered as a live document which should be filled in year by year as the Landing Obligation is phased in. This table will then serve to provide an historical record as countries can document the changes year by year and will also provide guidance and act as a learning tool to all member states on how other countries are implementing the LO. National administrations The group discussed the proposal for task sharing and criteria for joint surveys. RCM NS&EA and RCM NA 2014 discussed a cost model for the present joint MS financed surveys and for future joint surveys. In addition to this model, the RCM NA 2015 highlighted that four categories of surveys should be considered in relation to task sharing and criteria for joint surveys. In the light of cost sharing, the group commented that the current DCF recast proposal refers to ‘exploitation of stocks’ rather than EU TAC or landings. Given the relative stability, EU TAC shares are the preferred basis for sharing costs. The exploitation of stocks shall be interpreted as EU-TAC share as a default. In specific cases, RCGs can in the future agree on different interpretation where needed and feasible. Fully agreement among the group was concerning to the engagement and participation of National Correspondent (NC) in this meeting. The future role of the NCs in the RCG context was discussed, indicating a formal role for the NCs in the RCG process to approve and agree on regional arrangements. However, the current recast of the DCF doesn’t include the formal involvement of the NCs in the coordination procedures and meetings. RCM NA highlights this as potentially problematic for the foreseen formal role of the NCs. Other items on the agenda were the consideration of the follow up of relevant recommendations made last years by Liaison Meeting and presentations and relevant development from ICES, EC and SC-RDB

A Small Molecule That Binds and Inhibits the ETV1 Transcription Factor Oncoprotein

Members of the ETS transcription factor family have been implicated in several cancers, where they are often dysregulated by genomic derangement. ETS variant 1 (ETV1) is an ETS factor gene that undergoes chromosomal translocation in prostate cancers and Ewing sarcomas, amplification in melanomas, and lineage dysregulation in gastrointestinal stromal tumors. Pharmacologic perturbation of ETV1 would be appealing in these cancers; however, oncogenic transcription factors are often deemed “undruggable” by conventional methods. Here, we used small-molecule microarray screens to identify and characterize drug-like compounds that modulate the biologic function of ETV1. We identified the 1,3,5-triazine small molecule BRD32048 as a top candidate ETV1 perturbagen. BRD32048 binds ETV1 directly, modulating both ETV1-mediated transcriptional activity and invasion of ETV1-driven cancer cells. Moreover, BRD32048 inhibits p300-dependent acetylation of ETV1, thereby promoting its degradation. These results point to a new avenue for pharmacologic ETV1 inhibition and may inform a general means to discover small molecule perturbagens of transcription factor oncoproteins.National Cancer Institute (U.S.) (Initiative for Chemical Genetics Contract N01-CO-12400)National Cancer Institute (U.S.) (Cancer Target Discovery and Development Network RC2 CA148399

A realtime observatory for laboratory simulation of planetary flows

Motivated by the large-scale circulation of the atmosphere and ocean, we develop a system that uses observations from a laboratory analog to constrain, in real time, a numerical simulation of the laboratory flow. This system provides a tool to rapidly prototype new methods for state and parameter estimation, and facilitates the study of prediction, predictability, and transport of geophysical fluids where observations or numerical simulations would not independently suffice. A computer vision system is used to extract measurements of the physical simulation. Observations are used to constrain the model-state of the MIT General Circulation Model in a probabilistic, ensemble based assimilation approach. Using a combination of parallelism, domain decomposition and an efficient scheme to select ensembles of model-states, we show that estimates that effectively track the fluid state can be produced. To the best of our knowledge this is the first such observatory for laboratory analogs of planetary circulation that functions in real time.National Science Foundation (U.S.) (CNS-0540259)National Science Foundation (U.S.) (grant CNS-0540248