Statistical hypothesis testing and common misinterpretations: should we abandon p-value in forensic science applications?

Many people regard the concept of hypothesis testing as fundamental to inferential statistics. Various schools of thought, in particular frequentist and Bayesian, have promoted radically different solutions for taking a decision about the plausibility of competing hypotheses. Comprehensive philosophical comparisons about their advantages and drawbacks are widely available and continue to span over large debates in the literature. More recently, controversial discussion was initiated by an editorial decision of a scientific journal [1] to refuse any paper submitted for publication containing null hypothesis testing procedures. Since the large majority of papers published in forensic journals propose the evaluation of statistical evidence based on the so called p-values, it is of interest to expose the discussion of this journal's decision within the forensic science community. This paper aims to provide forensic science researchers with a primer on the main concepts and their implications for making informed methodological choices.

Comparing Etest and Broth Microdilution for Antifungal Susceptibility Testing of the Most-Relevant Pathogenic Molds.

Invasive mold infections are life-threatening diseases for which appropriate antifungal therapy is crucial. Their epidemiology is evolving, with the emergence of triazole-resistant Aspergillus spp. and multidrug-resistant non-Aspergillus molds. Despite the lack of interpretive criteria, antifungal susceptibility testing of molds may be useful in guiding antifungal therapy. The standard broth microdilution method (BMD) is demanding and requires expertise. We assessed the performance of a commercialized gradient diffusion method (Etest method) as an alternative to BMD. The MICs or minimal effective concentrations (MECs) of amphotericin B, voriconazole, posaconazole, caspofungin, and micafungin were assessed for 290 clinical isolates of the most representative pathogenic molds (154 Aspergillus and 136 non-Aspergillus isolates) with the BMD and Etest methods. Essential agreements (EAs) within ±2 dilutions of ≥90% between the two methods were considered acceptable. EAs for amphotericin B and voriconazole were >90% for most potentially susceptible species. For posaconazole, the correlation was acceptable for Mucoromycotina but Etest MIC values were consistently lower for Aspergillus spp. (EAs of <90%). Excellent EAs were found for echinocandins with highly susceptible (MECs of <0.015 μg/ml) or intrinsically resistant (MECs of >16 μg/ml) strains. However, MEC determinations lacked consistency between methods for strains exhibiting mid-range MECs for echinocandins. We concluded that the Etest method is an appropriate alternative to BMD for antifungal susceptibility testing of molds under specific circumstances, including testing with amphotericin B or triazoles for non-Aspergillus molds (Mucoromycotina and Fusarium spp.). Additional study of molecularly characterized triazole-resistant Aspergillus isolates is required to confirm the ability of the Etest method to detect voriconazole and posaconazole resistance among Aspergillus spp.

Emergent patterns of social organization in captive Cercocebus torquatus: Testing the GrooFiWorld agent-based model

We empirically applied the GrooFiWorld agent-based model (Puga-González et al. 2009) in a group of captive mangabeys (Cercocebus torquatus). We analysed several measurements related to aggression and affiliative patterns. The group adopted a combination of despotic and egalitarian behaviours resulting from the behavioural flexibility observed in the Cercopithecinae subfamily. Our study also demonstrates that the GrooFiWorld agent-based model can be extended to other members of the Cercopithecinae subfamily generating parsimonious hypotheses related to the social organization.

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

A new alternative method for testing skin irritation using a fresh human skin model

La dermatite irritative est décrite comme une réaction réversible, non immunologique caractérisée par des lésions d'aspect très variable, allant de la simple rougeur jusqu'à la formation de bulles voire d'une nécrose, accompagnée de prurit ou d'une sensation de brûlure suite à I' application d'une substance chimique. Le teste de prédiction d'irritation cutanée est traditionnellement depuis les années 1940 le Test de Draize. Ce test consiste en l'application d'une substance chimique sur une peau rasée de lapin pendant 4h et de regarder à 24h si des signes cliniques d'irritations sont présents. Cette méthode critiquable autant d'un point de vue éthique que qualitative reste actuellement le teste le plus utilisé. Depuis le début des années 2000 de nouvelles méthodes in vitro se sont développées tel que le model d'épiderme humain recombiné (RHE). Il s agit d'une multicouche de kératinocyte bien différencié obtenu depuis une culture de don d'ovocyte. Cependant cette méthode en plus d'être très couteuse n'obtient au mieux que 76% de résultat similaire comparé au test in vivo humain. Il existe donc la nécessité de développer une nouvelle méthode in vitro qui simulerait encore mieux la réalité anatomique et physiologique retrouvée in vivo. Notre objectif a été de développer cette nouvelle méthode in vitro. Pour cela nous avons travaillé avec de la peau humaine directement prélevée après une abdominoplastie. Celle ci après préparation avec un dermatome, un couteau dont la lame est réglable pour découper l'épaisseur souhaitée de peau, est montée dans un système de diffusion cellulaire. La couche cornée est alors exposée de manière optimale à 1 ml de la substance chimique testée pendant 4h. L'échantillon de peau est alors fixé dans du formaldéhyde pour permettre la préparation de lames standards d'hématoxyline et éosine. L'irritation est alors investiguée selon des critères histopathologiques de spongioses, de nécroses et de vacuolisations cellulaires. Les résultats de ce.tte première batterie de testes sont plus que prometteurs. En effet, comparé au résultat in vivo, nous obtenons 100% de concordance pour les 4 même substances testes irritantes ou non irritantes, ce qui est supérieur au model d épiderme humain recombiné (76%). De plus le coefficient de variation entre les 3 différentes séries est inférieur à 0.1 ce qui montre une bonne reproductibilité dans un même laboratoire. Dans le futur cette méthode va devoir être testée avec un plus grand nombre de substances chimiques et sa reproductibilité évaluée dans différents laboratoires. Mais cette première evaluation, très encourageante, ouvre des pistes précieuses pour l'avenir des tests irritatifs.

Preparation of a blood culture pellet for rapid bacterial identification and antibiotic susceptibility testing.

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

Aquaculture production in areas with high seasonal temperature variations: Development of planning tools

Postprint (published version)

Student Journalism 2.0 : Testing Models for Participatory Learning in the Digital Age

Many educators and educational institutions have yet to integrate web-based practices into their classrooms and curricula. As a result, it can be difficult to prototype and evaluate approaches to transforming classrooms from static endpoints to dynamic, content-creating nodes in the online information ecosystem. But many scholastic journalism programs have already embraced the capabilities of the Internet for virtual collaboration, dissemination, and reader participation. Because of this, scholastic journalism can act as a test-bed for integrating web-based sharing and collaboration practices into classrooms. Student Journalism 2.0 was a research project to integrate open copyright licenses into two scholastic journalism programs, to document outcomes, and to identify recommendations and remaining challenges for similar integrations. Video and audio recordings of two participating high school journalism programs informed the research. In describing the steps of our integration process, we note some important legal, technical, and social challenges. Legal worries such as uncertainty over copyright ownership could lead districts and administrators to disallow open licensing of student work. Publication platforms among journalism classrooms are far from standardized, making any integration of new technologies and practices difficult to achieve at scale. And teachers and students face challenges re-conceptualizing the role their class work can play online.

Lastuttavuuskokeiden kartoitus ja suunnitelma m-terästen laadun testaamiseen soveltuvasta uudesta lastuttavuuspikakokeesta

Teräksen hyvällä lastuttavuudella tarkoitetaan useita eri tekijöitä, joita ovat esimerkiksi terän pitkä kestoikä, prosessin kannalta edullinen lastun muoto sekä lastuttavan kappaleen hyvä mittatarkkuus ja pinnan laatu. Materiaalin lastuttavuuden mittaamisella teräksen valmistaja pyrkii varmistumaan siitä, että asiakkaan teräkselle asettamat lastuttavuusvaatimukset täyttyisivät mahdollisimman hyvin. Tämä diplomityö on tehty Ovako Bar Oy Ab:lle Imatran terästehtaalle. Diplomityön tavoitteena oli kartoittaa olemassa olevat lastuttavuuskokeet ja laatia suunnitelma M-teräksen laadun testaamiseen soveltuvasta uudesta lastuttavuuskokeesta Ovakon yli 20 vuotta vanhan lastuttavuuskokeen eli Mq-kokeen tilalle. Mq-kokeen toimivuus on erittäin riippuvainen käytettävästä teräpalasta. Kyseisten teräpalojen valmistus on lopetettu eikä vastaavaa teräpalaa ole saatavilla. Tämän vuoksi oli tarve selvittää mahdollisuuksia korvata Mq-koe. Uuden lastuttavuuskokeen suunnittelua ohjaavat lastuttavuuskokeelle asetettavat vaatimukset, joita ovat luotettavuus, nopeus, helppokäyttöisyys ja pieni koemateriaalimäärän tarve. Tämän työn kirjallisuusosuudessa esitetyistä poraamalla, sorvaamalla ja jyrsimällä tehtävistä lastuttavuuskokeista ei löydy suoraa ratkaisua M-teräksen testaamiseen. Työn soveltavassa osuudessa esitetään kolme koevariaatiota uudeksi lastuttavuuskokeeksi. Ensimmäinen on Mq-koe täydennettynä sitä tukevilla lastuttavuuskokeilla ja siihen liittyvien ongelmien poistaminen. Toinen koevariaatio on pistosorvauskoe, ja kolmantena koekappaleen ja teräpalan väliseen resistanssiin perustuva koe. Kokeiden toimivuudesta M-teräksen testaukseen ei tarkalleen tiedetä, joten työssä on laadittu koejärjestely kokeiden toimivuuden testaamiseksi. Työn keskeisimpiä havaintoja on, että M-teräksen ja normaalin teräksen välinen ero terän kestoiässä mitattuna on kaventunut nykyaikaisten pinnoitettujen teräpalojen vuoksi. Tämä asettaa suuren haasteen uuden kokeen laadinnalle. Lyhyessä kokeellisessa osuudessa testattu pistosorvauskoe kuitenkin antoi myönteisiä tuloksia sen kehityspotentiaalista toimia M-teräksen lastuttavuuskokeena. Diplomityö antaa Ovakolle näkemyksiä erilaisista lastuttavuuskoe vaihtoehdoista ja niiden mahdollisista hyödyistä, haitoista ja mahdollisuuksista. Työssä esitettyjen vaihtoehtojen pohjalta pystytään laatimaan uusi lastuttavuuspikakoe.

The FaceUOC Project : An Open Social Learning experience by the Open University of Catalonia

The possibilities and expansion of the use of Web 2.0 has opened up a world of possibilities in online learning. In spite of the integration of these tools in education major changes are required in the educational design of instructional processes.This paper presents an educational experience conducted by the Open University of Catalonia using the social network Facebook for the purpose of testing a learning model that uses a participation and collaboration methodology among users based on the use of open educational resources.- The aim of the experience is to test an Open Social Learning (OSL) model, understood to be a virtual learning environment open to the Internet community, based on the use of open resources and on a methodology focused on the participation and collaboration of users in the construction of knowledge.- The topic chosen for this experience in Facebook was 2.0 Journeys: online tools and resources. The objective of this 5 weeks course was to provide students with resources for managing the various textual, photographic, audiovisual and multimedia materials resulting from a journey.- The most important changes in the design and development of a course based on OSL are the role of the teacher, the role of the student, the type of content and the methodology:- The teacher mixes with the participants, guiding them and offering the benefit of his/her experience and knowledge.- Students learn through their participation and collaboration with a mixed group of users.- The content is open and editable under different types of license that specify the level of accessibility.- The methodology of the course was based on the creation of a learning community able to self-manage its learning process. For this a facilitator was needed and also a central activity was established for people to participate and contribute in the community.- We used an ethnographic methodology and also questionnaires to students in order to acquire results regarding the quality of this type of learning experience.- Some of the data obtained raised questions to consider for future designs of educational situations based on OSL:- Difficulties in breaking the facilitator-centred structure- Change in the time required to adapt to the system and to achieve the objectives- Lack of commitment with free courses- The trend to return to traditional ways of learning- Accreditation- This experience has taught all of us that education can happen any time and in any place but not in any way.

Tailored Jeffamine molecular tools for ordering mesoporous Silica

Herein, we report the formation of organized mesoporous silica materials prepared from a novel nonionic gemini surfactant, myristoyl-end capped Jeffamine, synthesized from a polyoxyalkyleneamine (ED900). The behavior of the modified Jeffamine in water was first investigated. A direct micellar phase (L1) and a hexagonal (H1) liquid crystal were found. The structure of the micelles was investigated from the SAXS and the analysis by Generalized Indirect Fourier Transformation (GIFT), which show that the particles are globular of coreshell type. The myristoyl chains, located at the ends of the amphiphile molecule are assembled to form the core of the micelles and, as a consequence, the molecules are folded over on themselves. Mesoporous materials were then synthesized from the self-assembly mechanism. The recovered materials were characterized by SAXS measurements, nitrogen adsorptiondesorption analysis, transmission and scanning electron microscopy. The results clearly evidence that by modifying the synthesis parameters, such as the surfactant/silica precursor molar ratio and the hydrothermal conditions, one can control the size and the nanostructuring of the resulting material. It was observed that, the lower the temperature of the hydrothermal treatment, the better the mesopore ordering.