Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved

The Educational Adjustment Program Profile: A Queensland Initiative in the identification and Monitoring of Students with a Disability

The effective identification and monitoring of students with a disability is a complex and important aspect of educational service delivery for students with a disability in Queensland. Building on previous initiatives in this domain Education Queensland has piloted the development of the Educational Adjustment Program (EAP) profile. Based on the data from the initial survey sample of more than 1500 school age students with a disability across Queensland, this paper highlights: the design of the Education Adjustment Program Adjustment Profile (EAP); some of its psychometric properties; gender and Indigenous student dimensions within the data; and how the EAP instrument compares with the 1 to 6 ascertainment rating scale

Adducts of functionalized Graphene layers with Ag nanoparticles for Antimicrobial applications

Health and environmental impacts of multi-drug resistance (MDR) pathogens are becoming more and more relevant nowadays, thus increasing the need of developing new, safe and effective antimicrobials. This research was focused on the synthesis, the characterization and the evaluation of the antimicrobial and cytotoxic activity of hybrid nanomaterials made up through a simple and sustainable functionalization of three carbon substrates, namely Graphite, Carbon black and Carbon nanotubes, with a pyrrole moiety (SP) and silver nanoparticles (Ag-NP) [1, 2]. The adducts were analyzed by means of thermogravimetric analyses (TGA), transmission electron microscopy (HRTEM) and X-ray diffraction analyses (WAXD), which confirmed the successful functionalization of raw materials. UV-vis spectroscopy and dynamic/electrophoretic light scattering (DLS/ELS) provided information regarding carbon suspensions stability, particles sizes and surface charge. Results from microbiological tests revealed an outstanding enhancement of the antimicrobial activity promoted by the functionalization with Ag nanoparticles, maintaining unaltered the cytotoxic levels exerted by not-functionalized materials. In the light of these results, a possible bactericidal mechanism based on the synergy between mechanical and oxidative stresses at the bacterial membrane level is proposed

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved

Performance of HPGe Detectors in High Magnetic Fields

A new generation of high-resolution hypernuclear gamma$-spectroscopy experiments with high-purity germanium detectors (HPGe) are presently designed at the FINUDA spectrometer at DAPhiNE, the Frascati phi-factory, and at PANDA, the antiproton proton hadron spectrometer at the future FAIR facility. Both, the FINUDA and PANDA spectrometers are built around the target region covering a large solid angle. To maximise the detection efficiency the HPGe detectors have to be located near the target, and therefore they have to be operated in strong magnetic fields B ~ 1 T. The performance of HPGe detectors in such an environment has not been well investigated so far. In the present work VEGA and EUROBALL Cluster HPGe detectors were tested in the field provided by the ALADiN magnet at GSI. No significant degradation of the energy resolution was found, and a change in the rise time distribution of the pulses from preamplifiers was observed. A correlation between rise time and pulse height was observed and is used to correct the measured energy, recovering the energy resolution almost completely. Moreover, no problems in the electronics due to the magnetic field were observed.Comment: submitted to Nucl. Instrum. Meth. Phys. Res. A, LaTeX, 19 pages, 9 figure

New detectors for the kaon and hypernuclear experiments with KaoS at MAMI and with PANDA at GSI

The KaoS spectrometer at the Mainz Microtron MAMI, Germany, is perceived as the ideal candidate for a dedicated spectrometer in kaon and hypernuclei electroproduction. KaoS will be equipped with new read-out electronics, a completely new focal plane detector package consisting of scintillating fibres, and a new trigger system. First prototypes of the fibre detectors and the associated new front-end electronics are shown in this contribution. The Mainz hypernuclei research program will complement the hypernuclear experiments at the planned FAIR facility at GSI, Germany. At the proposed antiproton storage ring the spectroscopy of double Lambda hypernuclei is one of the four main topics which will be addressed by the PANDA Collaboration. The experiments require the operation of high purity germanium (HPGe) detectors in high magnetic fields (B= 1T) in the presence of a large hadronic background. The performance of high resolution Ge detectors in such an environment has been investigated.Comment: Presentation at International Symposium on the Development of Detectors for Particle, Astroparticle and Synchrotron Radiation Experiments, Stanford, Ca (SNIC06), 6 pages, LaTeX, 11 eps figure

Pion radii in nonlocal chiral quark model

The electromagnetic radius of the charged pion and the transition radius of the neutral pion are calculated in the framework of the nonlocal chiral quark model. It is shown in this model that the contributions of vector mesons to the pion radii are noticeably suppressed in comparison with a similar contribution in the local Nambu--Jona-Lasinio model. The form-factor for the process gamma*pi+pi- is calculated for the -1 GeV^2<q^2<1.6 GeV^2. Our results are in satisfactory agreement with experimental data.Comment: 7 pages, 7 figure

Multiplicity correlations of intermediate-mass fragments with pions and fast protons in 12C + 197Au

Low-energy pi+ (E < 35 MeV) from 12C+197Au collisions at incident energies from 300 to 1800 MeV per nucleon were detected with the Si-Si(Li)-CsI(Tl) calibration telescopes of the INDRA multidetector. The inclusive angular distributions are approximately isotropic, consistent with multiple rescattering in the target spectator. The multiplicity correlations of the low-energy pions and of energetic protons (E > 150 MeV) with intermediate-mass fragments were determined from the measured coincidence data. The deduced correlation functions 1 + R \approx 1.3 for inclusive event samples reflect the strong correlations evident from the common impact-parameter dependence of the considered multiplicities. For narrow impact-parameter bins (based on charged-particle multiplicity), the correlation functions are close to unity and do not indicate strong additional correlations. Only for pions at high particle multiplicities (central collisions) a weak anticorrelation is observed, probably due to a limited competition between these emissions. Overall, the results are consistent with the equilibrium assumption made in statistical multifragmentation scenarios. Predictions obtained with intranuclear cascade models coupled to the Statistical Multifragmentation Model are in good agreement with the experimental data.Comment: 9 pages, 11 figures, subm. to EPJ

WormBase: a modern Model Organism Information Resource

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources

Surgical stress and metabolic response after totally laparoscopic right colectomy

No clear consensus on the need to perform an intracorporeal anastomosis (IA) after laparoscopic right colectomy is currently available. One of the potential benefits of intracorporeal anastomosis may be a reduction in surgical stress. Herein, we evaluated the surgical stress response and the metabolic response in patients who underwent right colonic resection for colon cancer. Fifty-nine patients who underwent laparoscopic resection for right colon cancer were randomized to receive an intracorporeal or an extracorporeal anastomosis (EA). Data including demographics (age, sex, BMI and ASA score), pathological (AJCC tumour stage and tumour localization) and surgical results were recorded. Moreover, to determine the levels of the inflammatory response, mediators, such as C-reactive protein (CRP), tumour necrosis factor (TNF), interleukin 1β (IL-1β), IL-6, IL-10, and IL-13, were evaluated. Similarly, cortisol and insulin levels were evaluated as hormonal responses to surgical stress. We found that the proinflammatory mediator IL-6, CRP, TNF and IL-1β levels, were significantly reduced in IA compared to EA. Concurrently, an improved profile of the anti-inflammatory cytokines IL-10 and IL-13 was observed in the IA group. Relative to the hormone response to surgical stress, cortisol was increased in patients who underwent EA, while insulin was reduced in the EA group. Based on these results, surgical stress and metabolic response to IA justify advocating the adoption of a totally laparoscopic approach when performing a right colectomy for cancer. This trial is registered on ClinicalTrials.gov (ID: NCT03422588)