Search

We propose a survey of the research contributions on the field of Educational Timetabling with a specific focus on "standard" formulations and the corresponding benchmark instances. We identify six of such formulations and we discuss their features, pointing out their relevance and usability. Other available formulations and datasets are also reviewed and briefly discussed. Subsequently, we report the main state-of-the-art results on the selected benchmarks, in terms of solution quality (upper and lower bounds), search techniques, running times, statistical distributions, and other side settings.

OBJECTIVE: To assess the reproducibility of peripapillary, optic nerve head (ONH-PP) and macular vessel density (VD) by Spectral Domain optical coherence tomography angiography (SD OCT-A) in glaucoma patients and healthy subjects. METHODS: Cross-sectional study assessing 63 eyes of 63 subjects, including 33 glaucoma patients and 30 healthy subjects. Glaucoma was classified in mild, moderate, or advanced. Two consecutive scans were acquired by Spectralis Module OCT-A (Heidelberg, Germany), and provided images of the superficial vascular complex (SVC), nerve fiber layer vascular plexus (NFLVP), superficial vascular plexus (SVP); deep vascular complex (DVC), intermediate capillary plexus (ICP) and deep capillary plexus (DCP). VD (%) was calculated by AngioTool. Intraclass correlation coefficients (ICCs) and coefficients of variation (CV) were calculated. RESULTS: Among ONH-PP VD, better ICC presented advanced (0.83-0.97) and moderate glaucoma (0.86-0.96) compared with mild glaucoma (0.64-0.86). For the macular VD reproducibility, ICC results for superficial retinal layers were better for mild glaucoma (0.94-0.96) followed by moderated (0.88-0.93) and advanced glaucoma (0.85-0.91), and for deeper retinal layers ICC was better for moderate glaucoma (0.96-0.95) followed by advanced (0.80-0.86) and mild glaucoma (0.74-0.91). CVs ranged from 2.2% to 10.94%. Among healthy subjects, ICCs for the ONH-PP VD measurements (0.91-0.99) and for the macular VD measurements (0.93-0.97) were excellent in all layers, with CVs from 1.65% to 10.33%. CONCLUSIONS: SD OCT-A used to quantify macular and ONH-PP VD showed excellent and good reproducibility in most layers of the retina, both in healthy subjects and in glaucoma patients regardless of the severity of the disease.

Total marrow (lymph node) irradiation (TMI/TMLI) delivery requires more time than standard radiotherapy treatments. The patient’s extremities, through the joints, can experience large movements. The reproducibility of TMI/TMLI patients’ extremities was evaluated to find the best positioning and reduce unwanted movements. Eighty TMI/TMLI patients were selected (2013–2022). During treatment, a cone-beam computed tomography (CBCT) was performed for each isocenter to reposition the patient. CBCT-CT pairs were evaluated considering: (i) online vector shift (OVS) that matched the two series; (ii) residual vector shift (RVS) to reposition the patient’s extremities; (iii) qualitative agreement (range 1–5). Patients were subdivided into (i) arms either leaning on the frame or above the body; (ii) with or without a personal cushion for foot positioning. The Mann-Whitney test was considered (p < 0.05 significant). Six-hundred-twenty-nine CBCTs were analyzed. The median OVS was 4.0 mm, with only 1.6% of cases ranked < 3, and 24% of RVS > 10 mm. Arms leaning on the frame had significantly smaller RVS than above the body (median: 8.0 mm/6.0 mm, p < 0.05). Using a personal cushion for the feet significantly improved the RVS than without cushions (median: 8.5 mm/1.8 mm, p < 0.01). The role and experience of the radiotherapy team are fundamental to optimizing the TMI/TMLI patient setup.

Information on the dimensional changes in maxillary and mandibular dentures made by using computer-aided design and computer-aided manufacturing (CAD-CAM) techniques under uniform testing conditions is lacking.The purpose of this in vitro study was to evaluate the dimensional changes and reproducibility of maxillary and mandibular dentures by using CAD-CAM-milled and 3D-printed techniques.Maxillary and mandibular edentulous models with wax occlusal rims were scanned, and dentures were designed by using a CAD software program and fabricated by using 2 techniques and materials: CAD-CAM-milled (CCM) and 3D-printed (3DP). The 3DP fabrications included 4 subgroups: dentures printed with a 90-degree build angle with UV light polymerization on the reference model (3DP 90M), dentures printed with a 90-degree build angle and light polymerization without the reference model (3DP 90), dentures printed with a 45-degree build angle with light polymerization on the reference model (3DP 45M), and dentures printed with a 45-degree build angle and light polymerization without the reference model (3DP 45). The preprocessing and postprocessing scan files of each denture produced by CCM and 3DP were superimposed by using a surface matching software program. Ten points each on maxillary and mandibular dentures were measured for deviations after processing. Additionally, for each denture, the widths were measured between the canines and molars, the anteroposterior plane from cusp tips between the canines and molars, and the vertical plane from the cusp tip of the canines to the marginal gingiva. They were then compared with those in the denture design CAD cast. The Kruskal-Wallis analysis of variance test was used for statistical analyses (α=.05).According to digital superimposition, CCM had the smallest values of deviation with no statistical difference (P.05), indicating more uniform results from measurement points in both maxillary and mandibular dentures, followed by 3DP 90M, 3DP 90, 3DP 45M, and 3DP 45. Regarding the width measurements, CCM had the smallest values of deviation (P.05). In 3DP, smaller deviation values were observed at the vertical plane from the tip of the canine to the marginal gingiva, and larger values were observed in the intermolar width (P.05).CCM exhibited smaller dimensional changes and better reproducibility among the tested techniques. In 3DP, the build angle and methods of light postprocessing influenced the dimensional stability. The 90-degree build angle with additional light polymerization on the cast improved the dimensional deviations.

The study aimed to evaluate relative validity and reproducibility of seven WHO indicators of dietary practices in children aged 6-23.9 months. Data from probabilistic sample of children who used primary healthcare services in Rio de Janeiro, Brazil were collected using a 24h dietary recall (24HR) and a closed questionnaire (Q1) on feeding in the day before the study. The last one was reapplied (Q2) around 16 days later. Validity was assessed by comparing the prevalence rates estimated by 24HR and Q1 and calculating the positive (PPV) and negative (NPV) predictive values, sensitivity (Se), specificity (Sp), and accuracy index (AI) for the resulting indicators. For reproducibility, estimated prevalence rates based on Q1 and Q2 were compared and the kappa index and prevalence-adjusted bias-adjusted kappa were estimated. Of the seven estimated indicators, the prevalence of two was overestimated (Continued breastfeeding: 50.0% vs 40.0%; Sweet beverage consumption: 65.1% vs 52.7%) and the prevalence of one was underestimated (Zero vegetable or fruit consumption: 6.5% vs 18.1%). For most indicators, Se and PPV were higher than Sp and NPV. The prevalence rates determined with Q1 and Q2 were similar for 6 indicators. More than half showed good, very good or excellent agreement. Resumo O estudo avaliou a validade relativa e a reprodutibilidade de sete indicadores da OMS sobre alimentação de crianças de 6-23,9 meses. Dados de amostra probabilística de usuários de serviços básicos de saúde na cidade do Rio de Janeiro, Brasil, foram coletados por meio de recordatório alimentar de 24 horas (R24h) e questionário fechado (Q1) sobre alimentação no dia anterior ao estudo. Este último foi reaplicado (Q2) em torno de 16 dias depois. A validade foi avaliada comparando-se as prevalências estimadas pelo R24h e Q1 e calculando-se os valores preditivos positivo (VPP) e negativo (VPN), sensibilidade (Se), especificidade (Esp) e índice de acurácia (IA) dos indicadores resultantes. Para reprodutibilidade, as prevalências estimadas com base em Q1 e Q2 foram comparadas e estimados o índice kappa e o kappa ajustado pela prevalência. Dos sete indicadores estimados, houve superestimação da prevalência de dois (aleitamento continuado: 50,0% versus 40,0%; consumo de bebidas adoçadas: 65,1% vs. 52,7%) e subestimação da prevalência de um (não consumo de frutas e hortaliças: 6,5% vs. 18,1%). Para a maioria deles, Se e VPP foram maiores do que Esp e VPN. As prevalências determinadas com Q1 e Q2 foram semelhantes para seis indicadores. Mais da metade dos indicadores apresentaram concordância boa, muito boa ou excelente.

The verification of analytical methods is a requirement of the standard NF EN ISO 15 189. It consists of evaluating the performance of an analytical method according to a well-defined protocol and then comparing it with pre-established analytical objectives. The mastery of this approach must be the concern of any biologist. Through this work we present the results of the protocol of verification of the method of determination of microalbumin by comparing two automats: Alinity ci®and Architect ci-8200®Abbott. Microalbumin monitoring in urine is an important element in the treatment of diabetes mellitus types I and II. It can also be used to predict diabetic nephropathy, which is the leading cause of death in people with insulin-dependent diabetes.

International audience; Molecular biology amplification enables sensitive detection of most respiratory viruses through nasopharyngeal swabbing. We developed an innovative approach to detect viral genomes on used facial tissues. In 2 communities of children, used tissues were collected once weekly for 1 year. Pooled analysis of tissues enabled detection of successive virus circulation in 4 age groups over time and forecasted by several weeks the circulation of influenza in the general population. At the individual level, in a proof-of-concept study of 30 volunteers with influenza-like signs/symptoms, we identified common respiratory viruses. The signals for SARS-CoV-2 obtained in parallel from 15 facial tissues and swab samples were similar and often higher for the tissues (11/15). Individual analysis of tissues offers a noninvasive, sensitive, and affordable alternative to self-sampling without a medical care requirement. Pooled analyses may be used to detect virus spread in specific communities, predict seasonal epidemics, and alert the population to viral infections. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.

Relevant to co-clinical trials, the goal of this work was to assess repeatability, reproducibility, and bias of the apparent diffusion coefficient (ADC) for preclinical MRIs using standardized procedures for comparison to performance of clinical MRIs. A temperature-controlled phantom provided an absolute reference standard to measure spatial uniformity of these performance metrics. Seven institutions participated in the study, wherein diffusion-weighted imaging (DWI) data were acquired over multiple days on 10 preclinical scanners, from 3 vendors, at 6 field strengths. Centralized versus site-based analysis was compared to illustrate incremental variance due to processing workflow. At magnet isocenter, short-term (intra-exam) and long-term (multiday) repeatability were excellent at within-system coefficient of variance, wCV [±CI] = 0.73% [0.54%, 1.12%] and 1.26% [0.94%, 1.89%], respectively. The cross-system reproducibility coefficient, RDC [±CI] = 0.188 [0.129, 0.343] µm2/ms, corresponded to 17% [12%, 31%] relative to the reference standard. Absolute bias at isocenter was low (within 4%) for 8 of 10 systems, whereas two high-bias (>10%) scanners were primary contributors to the relatively high RDC. Significant additional variance (>2%) due to site-specific analysis was observed for 2 of 10 systems. Base-level technical bias, repeatability, reproducibility, and spatial uniformity patterns were consistent with human MRIs (scaled for bore size). Well-calibrated preclinical MRI systems are capable of highly repeatable and reproducible ADC measurements.

The prenatal environment may program health and disease susceptibility via epigenetic mechanisms. We evaluated associations of maternal trimester-specific intake of micronutrients with global DNA methylation (%5mC) and 5-hydroxymethylation (%5hmC) at birth in cord blood and tested for persistence into childhood. We quantified global %5mC and %5hmC in cord blood cells (n= 434) and in leukocytes collected in early (n= 108) and mid-childhood (n= 390) from children in Project Viva, a pre-birth cohort from Boston, MA. Validated food frequency questionnaires estimated maternal first- and second-trimester intakes of vitamin B2, vitamin B6, vitamin B12, folate, betaine, choline, methionine, iron, and zinc. Mean (SD) cord blood %5mC and %5hmC was 5.62% (2.04) and 0.25% (0.15), respectively. Each μg increase in first-trimester B12intake was associated with 0.002 lower %5hmC in cord blood (95% CI: −0.005, −0.0003), and this association persisted in early childhood (β= −0.007; 95% CI: −0.01, −0.001) but not mid-childhood. Second-trimester iron (mg) was associated with 0.01 lower %5mC (95% CI: −0.02, −0.002) and 0.001 lower %5hmC (95% CI: −0.01, −0.00001) in cord blood only. Increased second-trimester zinc (mg) intake was associated with 0.003 greater %5hmC in early childhood (β= 0.003; 95% CI: 0.0004, 0.006). Second-trimester folate was positively associated with %5hmC in early childhood only (β= 0.08, 95% CI: 0.003, 0.16). Associations did not survive multiple testing adjustment; future replication is needed. Trimester-specific nutrients may impact various sensitive windows of epigenetic programming some with lasting effects in childhood. Further research is needed to understand the role of gene-specific epigenetic changes and how global DNA methylation measures relate to child health.

Background: Concerns over scientific reproducibility have grown in recent years, leading the National Institutes of Health (NIH) to require researchers to address these issues in research grant applications. Starting in 2020, training grants were required to provide a plan for educating trainees in rigor and reproducibility. Academic medical centers have responded with different solutions to fill this educational need. As experienced instructors with expertise in topics relating to reproducibility, librarians can play a prominent role in providing trainings, classes, and events to educate investigators and trainees, and bolstering reproducibility in their communities. Case Presentations: This special report summarizes efforts at five institutions to provide education in reproducibility to biomedical and life sciences researchers. Our goal is to expand awareness of the range of approaches in providing reproducibility services in libraries. Conclusions: Reproducibility education by medical librarians can take many forms. These specific programs in reproducibility education build upon libraries’ existing collaborations, with funder mandates providing a major impetus. Collaborator needs shaped the exact type of educational or other reproducibility support and combined with each library’s strengths to yield a diversity of offerings based on capacity and interest. As demand for and complexity of reproducibility education increases due to new institutional and funder mandates, reproducibility education will merit special attention.

© The Author(s) 2022 The sports statistics community is rapidly evolving. R is an open-source software in constant development that has gained a lot of popularity within statistical communities and sports analytics. This work presents a systematic review of the available R CRAN sport packages following PRISMA guidelines. We consider all packages active as of 18 February 2021. A total of 81 sport R packages created since 2006 were detected. Of these, 35.9% were authored by an American national, 69.1% include a dataset, 43.2% provide vignettes, and 65.4% have been updated at least once. The sport with the highest representation is basketball (n¿=¿14, 17.3%), followed by soccer (n¿=¿12, 14.8%) and packages related to physical activity (n¿=¿11, 13.6%). There are no sports packages directed solely for the female gender, while 59.3% of packages are focused on professional athletes. Fifty packages (61.7%) are related to the sports performance analysis category, and web scraping (n¿=¿43, 53.1%) was the main functionality in the collected packages. The creation of new R packages in the area of sports could help solve questions and tasks that still remain a challenge in this field, while continuing to help to improve the level of statistical education and computational thinking skills. The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research was funded by the Ministerio de Ciencia e Innovación (Spain) (PID2019-104830RB-I00) and the Departament d’Economia i Coneixement de la Generalitat de Catalunya (Spain) (2017 SGR 622 (GRBIO)).

In the last decade, industry’s demand for deep learning (DL) has increased due to its high performance in complex scenarios. Due to the DL method’s complexity, experts and non-experts rely on blackbox software packages such as Tensorflow and Pytorch. The frameworks are constantly improving, and new versions are released frequently. As a natural process in software development, the released versions contain improvements/changes in the methods and their implementation. Moreover, versions may be bug-polluted, leading to the model performance decreasing or stopping the model from working. The aforementioned changes in implementation can lead to variance in obtained results. This work investigates the effect of implementation changes in different major releases of these frameworks on the model performance. We perform our study using a variety of standard datasets. Our study shows that users should consider that changing the framework version can affect the model performance. Moreover, they should consider the possibility of a bug-polluted version before starting to debug source code that had an excellent performance before a version change. This also shows the importance of using virtual environments, such as Docker, when delivering a software product to clients.

Biomedical science is rapidly developing in terms of more transparency, openness and reproducibility of scientific publications. This is even more important for all studies that are based on results from basic semen examination. Recently two concordant documents have been published: the 6th edition of the WHO Laboratory Manual for the Examination and Processing of Human Semen, and the International Standard ISO 23162:2021. With these tools, we propose that authors should be instructed to follow these laboratory methods in order to publish studies in peer-reviewed journals, preferable by using a checklist as suggested in an Appendix to this article.

Using a database of open data policies for 199 journals in ecology and evolution, we found no detectable link between data sharing requirements and article retractions or corrections. Despite the potential for open data to facilitate error detection, poorly archived datasets, the absence of open code and the stigma associated with correcting or retracting articles probably stymie error correction. Requiring code alongside data and destigmatizing error correction among authors and journal editors could increase the effectiveness of open data policies at helping science self-correct.

This study aimed to assess the validity and reliability of the Turkish version of the Women’s Perception of Respectful Maternity Care Scale. This methodological, cross-sectional study was conducted between December 2020 and July 2021. The sample of the study consisted of 259 women who had vaginal birth and gave birth to a healthy baby with normal birth weight. Data analysis and evaluation were performed using factor analysis, Cronbach’s alpha, split-half, item-total score correlation, Hotelling T2, Tukey’s test and ceiling and floor effect of the scale. The scale consists of 19 items and three sub-dimensions. The scales explained 76.04 percent of the total variance. In both exploratory and confirmatory factor tests, the overall factor loading was greater than 0.30. In the confirmatory factor analysis, all the goodness-of-fit indexes were greater than 0.90, and the root mean square error of approximation was less than 0.08. The Cronbach’s alpha coefficient of the scale was 0.96, with Cronbach’s alpha values ranging between 0.88 and 0.95 for the subscales. In conclusion, this scale can be used by nurses, midwives and other health professionals as a valid and reliable measurement tool to evaluate women’s perception of respectful maternity care. © 2022 Taylor & Francis Group, LLC.

International audience; Data sharing is gradually becoming a requirement across all fields of science, owing to its key benefits in verifying the reproducibility of findings and reusing existent data for new purposes. Although meta-research studies are complex, time-consuming and hinge on the availability of data produced and curated by others, there has been little focus on how they make their own data available. This is in stark contrast with the heightened attention data sharing has received in clinical research. Yet, as secondary data users par excellence, meta-researchers are ethically bound to both improving and evaluating data sharing practices, as well as correctly sharing their own data. We contrast particularities of data sharing in meta-research and clinical research, such as benefits, barriers, inadequate and potentially pervasive sharing practices. We conclude with an array of concrete and tailored recommendations for improvement.

A crucial asset in the management of invasive species is the open-access sharing of data on the range of invaders and the progression of their spread. Such data should be current, comprehensive, consistent, and standardized, to support reproducible and comparable forecasting efforts among multiple researchers and managers. Here, we present thelydemaprR package containing spatiotemporal data and mapping functions to visualize the current spread of the spotted lanternfly (Lycorma delicatula, White 1841) in the Western Hemisphere. The spotted lanternfly is a forest and agricultural pest in the eastern Mid-Atlantic region of the U.S., where it was first discovered in 2014. As of 2022, it has been found in 12 states according to state and federal departments of agriculture. However, the lack of easily accessible, fine-scale data on its spread hampers research and management efforts. We obtained multiple memoranda-of-understanding from several agencies and citizen-science projects, gaining access to their internal data on spotted lanternfly point observations. We then cleaned, harmonized, anonymized, and combined the individual data sources into a single comprehensive dataset. The resulting dataset contains spatial data gridded at the 1 km2resolution, with yearly information on the presence/absence of spotted lanternflies, establishment status, and population density across 658,392 observations. Thelydemaprpackage will aid researchers, managers, and the public in their understanding, modeling, and managing of the spread of this invasive pest.

Across the past decade, open science has increased in momentum, making research more openly available and reproducible. Educational data mining, as a subfield of education technology, has been expanding in scope as well, developing and providing better understanding of large amount of data within education. However, open science and educational data mining do not often intersect, causing a bit of difficulty when trying to reuse methodologies, datasets, analyses for replication, reproduction, or an entirely separate end goal. In this tutorial, we will provide an overview of open science principles and their benefits and mitigation within research. In the second part of this tutorial, we will provide an example on using the Open Science Framework to make, collaborate, and share projects. The final part of this tutorial will go over some mitigation strategies when releasing datasets and materials such that other researchers may easily reproduce them. Participants in this tutorial will gain a better understanding of open science, how it is used, and how to apply it themselves.

Despite increased efforts to assess the adoption rates of open science and robustness of reproducibility in sub-disciplines of education technology, there is a lack of understanding of why some research is not reproducible. Prior work has taken the first step toward assessing reproducibility of research, but has assumed certain constraints which hinder its discovery. Thus, the purpose of this study was to replicate previous work on papers within the proceedings of the International Conference on Educational Data Mining to accurately report on which papers are reproducible and why. Specifically, we examined 208 papers, attempted to reproduce them, documented reasons for reproducibility failures, and asked authors to provide additional information needed to reproduce their study. Our results showed that out of 12 papers that were potentially reproducible, only one successfully reproduced all analyses, and another two reproduced most of the analyses. The most common failure for reproducibility was failure to mention libraries needed, followed by non-seeded randomness.

The key scientific output of the EATRIS-Plus project is to develop a Multi-omic Toolbox available for researchers in order to have a better understanding of the molecular profiles in personalised medicine. Within work packages 1, 2, and 3, we implement practices based on the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles to ensure reproducibility of our work and to make the multi-omics cohort data reusable for future translational research. The aim of this deliverable (D2.2) is to describe methods developed and applied to the Czech multi-omics cohort 1 that can improve comparability of data when integrating omics data from different sources. Integration of omics data from different sources can be challenging when data and data processing steps are not sufficiently annotated, or sources of biological and technical variation are unknown. The Czech multi-omics demonstrator cohort serves as a demonstrator for the development and application of computational workflows for omics preprocessing and integrative analyses. &nbsp

Presentation highlighting Open Science principles and how can we adapt them in quantitative/wet lab research projects and using existing resources. Mainly based on materials from The Turing Way

The keynote presentation from the 1st ACM conference on reproducibility and replicability (ACM REP'23) Please don't hesitate to provide your feedback via the public Discord serverfrom the MLCommons Task Force on Automation and Reproducibility and GitHub issues. [ GitHub project] [ Public Collective Knowledge repository ] [ Related reproducibility initiatives ] [ cTuning.org ] [ cKnowledge.org ] During the past 10 years, we have considerably improved the reproducibility of experimental results from published papers by introducing the artifact evaluation process with a unified artifact appendix and reproducibility checklists, Jupyter notebooks, containers, and Git repositories. On the other hand, our experience reproducing more than 200 papers shows that it can take weeks and months of painful and repetitive interactions between teams to reproduce artifacts. This effort includes decrypting numerous README files, examining ad-hoc artifacts and containers, and figuring out how to reproduce computational results. Furthermore, snapshot containers pose a challenge to optimize algorithms’ performance, accuracy, power consumption and operational costs across diverse and rapidly evolving software, hardware, and data used in the real world. In this talk, Iexplain how our practical artifact evaluation experience and the feedback from researchers and evaluators motivated us to develop a simple, intuitive, technology agnostic, and English-like scripting language called Collective Mind (CM). It helps to automatically adapt any given experiment to any software, hardware, and data while automatically generating unified README files and synthesizing modular containers with a unified API. It is being developed by MLCommons to facilitate reproducible AI/ML Systems research and minimizing manual and repetitive benchmarking and optimization efforts, reduce time and costs for reproducible research, and simplify technology transfer to production. I also present several recent use cases of how CM helps MLCommons, the Student Cluster Competition, and artifact evaluation at ACM/IEEE conferences. I conclude with our development plans, new challenges, possible solutions, and upcoming reproducibility and optimization challenges powered by the MLCommons Collective Knowledge platform and CM:access.cKnowledge.org.

Recent years have seen exciting progress across human embryo research, including new methods for culturing embryos, transcriptional profiling of embryogenesis and gastrulation, mapping lineage trajectories, and experimenting on stem cell-based embryo models. These advances are beginning to define the dynamical principles of development across stages, tissues and organs, enabling a better understanding of human development before birth in health and disease, and potentially leading to improved treatments for infertility and developmental disorders. However, there are still significant roadblocks en route to this goal. Here, we highlight technical challenges to studying early human development and propose ways and means to overcome some of these constraints.

Thursday 1 June, 12:30 – 13:30: The Turing Way – A Collaborative Guide to Data Science and Research With Anne Steele, Community Manager The Turing Way is an open-source, community-led, and collaboratively-developed book for data science and open research. This Lunch and Learn will discuss the evolution of the open source community, and introduce the project’s five guides on reproducibility, project design, collaboration, communication and ethics in research. This Lunch and Learn will be hybrid, with an option to attend in person. Please click here to register.

Thursday 1 June, 12:30 – 13:30: The Turing Way – A Collaborative Guide to Data Science and Research With Anne Steele, Community Manager The Turing Way is an open-source, community-led, and collaboratively-developed book for data science and open research. This Lunch and Learn will discuss the evolution of the open source community, and introduce the project’s five guides on reproducibility, project design, collaboration, communication and ethics in research. This Lunch and Learn will be hybrid, with an option to attend in person. Please click here to register.

Surface-enhanced Raman scattering (SERS) spectroscopy has been employed as a rapid analysis technology for food security inspection recently. Nowadays, it is still a great challenge to rapidly quantify multiple trace antibiotics potentially abused in aquaculture industry. In this work, a magnetic Ti3C2Tx/Fe3O4/Ag substrate was prepared for the development of a reliable rapid SERS quantification method for multiple trace sulfonamides in aquatic products. This magnetic substrate had good uniformity, reproducibility, stability and SERS activity. Moreover, this substrate could integrate the magnetic separation-enrichment and matrix clean-up without cross contamination, which endowed it with good selectivity and anti-interference capability during real sample analysis. The electromagnetic enhancement and chemical enhancement mechanism of this magnetic substrate were studied in detail to reveal its good separation-enrichment performance and SERS activity. Finally, a rapid SERS quantification method was established and practically applied for trace phthalic sulfathiazole (PST) and silver sulfadiazine (SSD) in aquatic products by using Ti3C2Tx/Fe3O4/Ag magnetic substrates. Trace PST and SSD could be actually detected and quantified as 55.9 μg/kg and 64.0 μg/kg in aquatic products respectively. Good recoveries of 83.9%-116% with relative standard deviations (RSDs) of 0.5%-3.2% for PST and 80.2%-102% with RSDs of 1.3%-5.8% for SSD were obtained. This work proposed an efficient and reliable method for rapid quantification of trace multiple sulfonamides in complex aquatic samples during food security inspection.

© 2021, The Author(s), under exclusive licence to United States & Canadian Academy of Pathology.The advancing edge profile is a powerful determinant of tumor behavior in many organs. In this study, a grading system assessing the tumor-host interface was developed and tested in 181 pancreatic neuroendocrine tumors (PanNETs), 63 of which were

Objective: To evaluate the role of hand-wrist radiographs (HWRs) in the assessment of growth and development based on the cervical vertebral maturation (CVM) method and to determine whether clinical experience levels would affect the decision-making process. Materials and Methods: The lateral cephalometric radiographs and HWRs of 48 patients aged 11 to 16 years were assessed in this study. The clinicians first determined the growth stage by the CVM method based on lateral cephalometric images (T1). Then, the clinicians filled out the same questionnaire with HWRs on each question (T2). Subsequently, the clinicians were divided into groups according to their experience levels. Intraclass correlation coefficients were calculated to evaluate intraobserver agreements. The data were analyzed with chi-square or Fisher-Freeman-Halton Exact tests for intergroup comparisons. Results: For all evaluators, the percentage of agreement changed minimally after T2. The most experienced clinicians demonstrated the most consistent decisions for overall CVM stages at both evaluations. Concerning each stage, the percentages of changed decisions showed no significant differences between the groups except for stages CS4 and CS5. There were significant differences between the rates of agreement for CS3 in each group from T1 to T2 (p

In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters PJ23100, PrhaBAD, and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD, and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly German Research Foundation 390713860, 239748522 European Union 760994 Ministerio de Ciencia e Innovación PID2020-112645GB-I00 UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/S020128/1

In recent years, the scientific community has called for improvements in the credibility, robustness, and reproducibility of research, characterized by increased interest and promotion of open and transparent research practices. While progress has been positive, there is a lack of consideration about how this approach can be embedded into undergraduate and postgraduate research training. Specifically, a critical overview of the literature which investigates how integrating open and reproducible science may influence student outcomes is needed. In this paper, we provide the first critical review of literature surrounding the integration of open and reproducible scholarship into teaching and learning and its associated outcomes in students. Our review highlighted how embedding open and reproducible scholarship appears to be associated with (1) students’ scientific literacies (i.e., students’ understanding of open research, consumption of science, and the development of transferable skills); (2) student engagement (i.e., motivation and engagement with learning, collaboration, and engagement in open research), and (3) students’ attitudes towards science (i.e., trust in science and confidence in research findings). However, our review also identified a need for more robust and rigorous methods within pedagogical research, including more interventional and experimental evaluations of teaching practice. We discuss implications for teaching and learning scholarship.

This is talk presented in the IAA-CSIC Severo Ochoa SKA Open Science School held in Granada on 8th-10th May 2023. It is focused on the reproducibility of computational research analysis. It contains practical tips on how to make an analysis or a publication reproducible. It shows some examples on how to organize information to make a paper reproducible using tools like Github and the workflow management system snakemake. A practical example shown in during the presentation can be found here

These slides were presented for an early career panel on open science and reproducibility at the 2023 edition of GISRUK (https://gisruk.org/gisruk-2023). The Pdf file includes the slides and notes pages.

Reporting of intervention research has been inadequate for many years. The development and promotion of freely available checklists aims to address this problem by providing researchers with a list of items that require reporting to enable study interpretation and replication. In this commentary, we present evidence from a recent systematic review of 51 randomised controlled trials published 2015–2020 that inadequate intervention reporting remains a widespread issue and that checklists are not being used to describe all intervention components. In 2022, we assessed the submission guidelines of 33 journals that published articles included in our review and found that just one at the time encouraged the use of reporting checklists for all intervention components. To drive progress, we contacted the editors of the other 32 journals and requested that they update their submission guidelines in response. We conclude by highlighting the waste associated with current practices and encourage journals from all fields to urgently review their submission guidelines. Only through collective action can we build an evidence base that is fit for purpose.

This archive contains the slides for a talk entitled "Towards computational reproducibility when working with very large datasets", part of the special session " 10 years of reproducibility in biomedical research: How can we achieve generalizability and fairness?" at the ISBI 2023 . &nbsp

Conducting experiments in virtual reality (VR) requires a complex setup of hardware, software, experiment design and implementation, and data collection which is supported by frameworks that provide pre-determined features for scientists to implement their experiment in VR. These VR frameworks have proliferated exponentially since the start of the millennia, and unfortunately, they both only differ slightly from one another and often miss one or more of the key features required by the researcher. Therefore, it has become less clear to researchers which framework to choose for what task and to what benefit. I introduce the design, experiment, analyse, and reproduce (DEAR) principle to develop a new perspective on VR frameworks through a holistic approach to experimentation (i.e., the process of conducting an experiment). The DEAR principle lays out the core components that future frameworks should entail. Most previous VR frameworks have focussed on the design phase and sometimes on the experiment phase to help researchers create and conduct experiments. However, being able to create an experiment with a framework is not sufficient for wide adoption. Ultimately, I argue that it is important to take reproducibility seriously to overcome the limitations of current frameworks. Once experiments are fully reproducible through automation, the adaptation of new experiments becomes easier. Hopefully, researchers can find ways to converge in the use of frameworks or else frameworks may become a hindrance instead of a help., Frontiers in Virtual Reality, 4

Resting-state functional connectivity (RSFC) is a powerful tool for characterizing brain changes, but it has yet to reliably predict higher-order cognition. This may be attributed to small effect sizes of such brain-behavior relationships, which can lead to underpowered, variable results when utilizing typical sample sizes (N∼25). Inspired by techniques in genomics, we implement the polyneuro risk score (PNRS) framework - the application of multivariate techniques to RSFC data and validation in an independent sample. Utilizing the Adolescent Brain Cognitive Development® cohort split into two datasets, we explore the framework's ability to reliably capture brain-behavior relationships across 3 cognitive scores - general ability, executive function, learning & memory. The weight and significance of each connection is assessed in the first dataset, and a PNRS is calculated for each participant in the second. Results support the PNRS framework as a suitable methodology to inspect the distribution of connections contributing towards behavior, with explained variance ranging from 1.0 % to 21.4 %. For the outcomes assessed, the framework reveals globally distributed, rather than localized, patterns of predictive connections. Larger samples are likely necessary to systematically identify the specific connections contributing towards complex outcomes. The PNRS framework could be applied translationally to identify neurologically distinct subtypes of neurodevelopmental disorders.

In recent years, various initiatives from within and outside the HCI field have encouraged researchers to improve research ethics, openness, and transparency in their empirical research. We quantify how the CHI literature might have changed in these three aspects by analyzing samples of 118 CHI 2017 and 127 CHI 2022 papers---randomly drawn and stratified across conference sessions. We operationalized research ethics, openness, and transparency into 45 criteria and manually annotated the sampled papers. The results show that the CHI 2022 sample was better in 18 criteria, but in the rest of the criteria, it has no improvement. The most noticeable improvements were related to research transparency (10 out of 17 criteria). We also explored the possibility of assisting the verification process by developing a proof-of-concept screening system. We tested this tool with eight criteria. Six of them achieved high accuracy and F1 score. We discuss the implications for future research practices and education. This paper and all supplementary materials are freely available at https://doi.org/10.17605/osf.io/n25d6.

Presented at Newcastle University's conference from 6-7 March 2023: "Data Science Perspectives - Multidisciplinary PhD Conference". Originally given as a workshop September 2022 with Malvika Sharan: https://zenodo.org/record/7050678#.ZAdeiOzP2qU Was accompanied by interactive HackMD: https://hackmd.io/@turingway/02-2023-newcastle

Presented at Newcastle University's conference from 6-7 March 2023: "Data Science Perspectives - Multidisciplinary PhD Conference". Originally given as a workshop September 2022 with Malvika Sharan: https://zenodo.org/record/7050678#.ZAdeiOzP2qU Was accompanied by interactive HackMD: https://hackmd.io/@turingway/02-2023-newcastle &nbsp

Peer reviewed: True, Tumour-infiltrating lymphocytes (TILs) reflect antitumour immunity. Their evaluation of histopathology specimens is influenced by several factors and is subject to issues of reproducibility. ONEST (Observers Needed to Evaluate Subjective Tests) helps in determining the number of observers that would be sufficient for the reliable estimation of inter-observer agreement of TIL categorisation. This has not been explored previously in relation to TILs. ONEST analyses, using an open-source software developed by the first author, were performed on TIL quantification in breast cancers taken from two previous studies. These were one reproducibility study involving 49 breast cancers, 23 in the first circulation and 14 pathologists in the second circulation, and one study involving 100 cases and 9 pathologists. In addition to the estimates of the number of observers required, other factors influencing the results of ONEST were examined. The analyses reveal that between six and nine observers (range 2-11) are most commonly needed to give a robust estimate of reproducibility. In addition, the number and experience of observers, the distribution of values around or away from the extremes, and outliers in the classification also influence the results. Due to the simplicity and the potentially relevant information it may give, we propose ONEST to be a part of new reproducibility analyses.

Background: Amide proton transfer (APT) imaging is a chemical exchange saturation transfer (CEST) technique offering potential clinical applications such as diagnosis, characterization, and treatment planning and monitoring in glioma patients. While APT-CEST has demonstrated high potential, reproducibility remains underexplored. Purpose: To investigate whether cerebral APT-CEST with clinically feasible scan time is reproducible in healthy tissue and glioma for clinical use at 3 T. Study Type: Prospective, longitudinal. Subjects: Twenty-one healthy volunteers (11 females; mean age ± SD: 39 ± 11 years) and 6 glioma patients (3 females; 50 ± 17 years: 4 glioblastomas, 1 oligodendroglioma, 1 radiologically suspected low-grade glioma). Field Strength/Sequence: 3 T, Turbo Spin Echo - ampling perfection with application optimized contrasts using different flip angle evolution - chemical exchange saturation transfer (TSE SPACE-CEST). Assessment: APT-CEST measurement reproducibility was assessed within-session (glioma patients, scan session 1; healthy volunteers scan sessions 1, 2, and 3), between-sessions (healthy volunteers scan sessions 1 and 2), and between-days (healthy volunteers, scan sessions 1 and 3). The mean APT CEST values and standard deviation of the within-subject difference (SD diff) were calculated in whole tumor enclosed by regions of interest (ROIs) in patients, and eight ROIs in healthy volunteers—whole-brain, cortical gray matter, putamen, thalami, orbitofrontal gyri, occipital lobes, central brain—and compared. Statistical Tests: Brown-Forsythe tests and variance component analysis (VCA) were used to assess the reproducibility of ROIs for the three time intervals. Significance was set at P < 0.003 after Bonferroni correction. Results: Intratumoral mean APT CEST was significantly higher than APT CEST in healthy-appearing tissue in patients (0.5 ± 0.46%). The average within-session, between-sessions, and between-days SD diff of healthy control brains was 0.2% and did not differ significantly with each other (0.76 > P > 0.22). The within-session SD diff of whole-brain was 0.2% in both healthy volunteers and patients, and 0.21% in the segmented tumor. VCA showed that within-session factors were the most important (60%) for scanning variance. Data Conclusion: Cerebral APT-CEST imaging may show good scan–rescan reproducibility in healthy tissue and tumors with clinically feasible scan times at 3 T. Short-term measurement effects may be the dominant components for reproducibility. Level of Evidence: 2. Technical Efficacy: Stage 2.

Abstract Objective To determine the inter-rater reliability of identifying differences and types of differences in lumbar degenerative findings comparing supine and upright MRI. Materials and methods Fifty-nine participants, low back pain patients (LBP) with or without leg pain and no-LBP individuals were consecutively enrolled to receive supine and upright MRI of the lumbar spine. Three raters independently evaluated the MRIs for degenerative spinal pathologies and compared for differences. Presence/absence of degenerative findings were recorded for all supine and upright images, and then differences from the supine to the upright positions were classified into no-change, appeared, disappeared, worsened, or improved at each individual disc level. Reliability and agreement were calculated using Gwet’s agreement coefficients (AC1 or AC2) and absolute agreement. Results Inter-rater reliability of evaluating differences in eight degenerative lumbar findings comparing the supine and upright MRI position, ranged from 0.929 to 0.996 according to Gwet’s agreement coefficients (AC2). The total number of positive MRI findings in the supine position ranged from 270 to 453, with an average of 366 per rater. Observed differences from supine to upright MRI ranged from 18 to 80, with an average of 56 per rater. Conclusion Inter-rater reliability was found overall acceptable for classification of differences in eight types of degenerative pathology observed with supine and upright MRI of the lumbar spine. Results were primarily driven by high numbers and high reliability of rating negative findings, whereas agreement regarding positive findings and positive positional differences was lower.

Statistical tests are a powerful set of tools when applied correctly, but unfortunately the extended misuse of them has caused great concern. Among many other applications, they are used in the detection of biomarkers so as to use the resulting p-values as a reference with which the candidate biomarkers are ranked. Although statistical tests can be used to rank, they have not been designed for that use. Moreover, there is no need to compute any p-value to build a ranking of candidate biomarkers. Those two facts raise the question of whether or not alternative methods which are not based on the computation of statistical tests that match or improve their performances can be proposed. In this paper, we propose two alternative methods to statistical tests. In addition, we propose an evaluation framework to assess both statistical tests and alternative methods in terms of both the performance and the reproducibility. The results indicate that there are alternative methods that can match or surpass methods based on statistical tests in terms of the reproducibility when processing real data, while maintaining a similar performance when dealing with synthetic data. The main conclusion is that there is room for the proposal of such alternative methods. This work is partially supported by the Basque Government (IT1244-19, Elkartek BID3A and Elkartek project 3KIA, KK2020/00049) and the Spanish Ministry of Economy and Competitiveness MINECO (PID2019-104966GB-I00) and a University-Society Project 15/19 (Basque Government and University of the Basque Country UPV/EHU). Ari Urkullu has been supported by the Basque Government through a predoctoral grant (PRE_2013_1_1313, PRE_2014_2_87, PRE_2015_2_0280 and PRE_2016_2_0314). Aritz Perez has been supported by the Basque Government through the BERC 2022-2025 and Elkartek programs and by the Ministry of Science, Innovation and Universities: BCAM Severo Ochoa accreditation SEV-2017-0718. Borja Calvo has been partially supported by the IT1244-19 project and the ELKARTEK program from Basque Government, and the project PID2019-104966GB-I00 from the Spanish Ministry of Economy and Competitiveness.

Introduction The current technique of angulating for a skyline knee projection relies heavily on the radiographer's estimation of the patella tilt, rendering it subjective and prone to errors. This study therefore aims to (i) examine the correlation between angle ABC measured on the lateral X-ray image and skyline angulation (measured in degrees) and (ii) determine the inter-rater reliability of angle ABC measurements. Methods 145 sets of lateral and skyline X-ray images from patients aged 40–70 years old were retrospectively analysed. Angle ABC was measured using prominent landmarks such as the trochlear sulcus, tibial tuberosity and the anterior border of the patella on the lateral knee radiograph. It was then retrospectively compared with the skyline tube angulations to identify any correlation between the two. An inter-rater reliability test was also conducted using the intraclass correlation coefficient (ICC) to determine the reproducibility of the measurement method. Results A weak correlation was found between angle ABC and skyline angulation (r = 0.1, p = 0.25). The proposed method of measurement shows good inter-rater reliability (ICC = 0.81, 95% CI: 0.77 to 0.84). Conclusion There is insufficient evidence to indicate a correlation between angle ABC and skyline angulation. However, angle ABC can be reliably measured, implying the replicability of the measurement method for other purposes. Implications for practice The proposed measurement method of angle ABC on the lateral view could have future applications in other areas such as in the measurement of patellofemoral alignment and trochlear morphology.

This article describes and justifies a reporting standard to improve data use documentation in Agent-Based Modelling. Following the development of reporting standards for models themselves, empirical modelling has now developed to the point where these standards need to take equally effective account of data use (which previously has tended to be an afterthought to model description). It is particularly important that a standard should allow the reporting of the different uses to which data may be put (specification, calibration and validation), but also that it should be compatible with the integration of different kinds of data (for example, survey, ethnographic and experimental) sometimes known as mixed methods research. The article motivates the need for standards generally, and positions the distinctive contribution of the RAT-RS reporting standard. It describes how the standard was developed to ensure its usability, presents and explains it, and describes possibilities for future development.

Cigarette smoking contributes to poor oral health and dental discoloration. Therefore, stopping smoking may translate into measurable amelioration of dental shade indices. We compared dental shade parameters by digital spectrophotometry among current, former, and never smokers and verified their repeatability at 7 and 30 days. Dental shade parameters (CIE L*a*b* and corresponding whiteness index for dentistry-WID) were measured in current, former, and never smokers with a digital spectrophotometer (Vita Easyshade V) on three separate study visits: at baseline (day 0), at day 7, and day 30. Dental shade parameters were analyzed in 18 current, 18 former, and 20 never smokers. The repeatability of shade parameters was consistent in current, former, and never smokers. L*, a*, b*, and WID show significant short and long-term repeatability (p p = 0.001). No significant differences were observed between current and former smokers and between former smokers and former smokers. Dental shade measurements by digital spectrophotometry were highly reproducible and showed that teeth whiteness of current smokers is substantially inferior compared to never smokers. Objective discrimination of dental shade can be a valuable regulatory science endpoint for investigating oral hygiene and dental aesthetics of consumer care products, smoking cessation medications, and tar-free tobacco products (e-cigarettes, heated tobacco products, oral nicotine products) for cigarette substitution.Clinical trial registration: the study was not registered in ClinicalTrials.gov considering that it is a pilot study, parts of a larger project with ID: NCT04649645

To compare the performance of CT and MRI radiomics for predicting the malignant potential of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas, and to investigate their value compared to the revised 2017 international consensus Fukuoka guidelines.Sixty patients with surgically confirmed IPMNs (37 malignant and 23 benign) were included. Radiomics features were extracted from arterial and venous phase images of CT and T2-weighted images of MRI, respectively. Intraclass correlation coefficients for the radiomics features were calculated to assess the interobserver reproducibility. The least absolute shrinkage and selection operator algorithm was used for feature selection. Radiomics models were constructed based on selected features with logistic regression (LR) and support vector machine (SVM). A clinical and imaging model was constructed based on independent predictors of the revised 2017 Fukuoka guidelines determined in multivariate logistic regression with forward elimination.The reproducibility of MRI radiomics features was higher than that of CT radiomics features, regardless of arterial or venous phase features (all p0.001). MRI radiomics models achieved improved AUCs (0.879 with LR and 0.940 with SVM, respectively), than that of CT radiomics models (0.811 with LR and 0.864 with SVM, respectively). All radiomics models provided better predictive performance than the clinical and imaging model (AUC = 0.764).The MRI radiomics models with higher reproducibility radiomics features performed better than CT radiomics models for predicting the malignant potential of IPMNs. The performance of radiomics models was superior to the clinical and imaging model based on Fukuoka guidelines.

Context: The elastic tubes have been used for clinical rehabilitation programs in which exercises are performed with submaximal intensities due to the difficulty in the measure the applied force. The authors aimed to quantify the elastic constant of elastic tubes used in neuromuscular rehabilitation programs predicting the force related to elastic tube elongation. A force test was performed by stretching the elastic tubes to determine the relationship between force and elongation. Eight elastic tubes with progressive levels of resistance represented by colors (yellow, red, blue, gray, black, grape, purple, and gold—low to higher resistance) were used. Design: Experimental. Methods: The test and retest were compared using the paired t test. The agreement and reliability between the test versus retest of pooled means colors were analyzed by plotting the Bland–Altman graph and intraclass correlation coefficient and the coefficient of variation. Pearson correlation was used to verify the validity between measurements. Results: The force values generated from the elastic tube elongation increase according to the color and thickness of elastic tubes with a strong and significant association between them (P P Conclusions: The force could be quantified according to elastic tube length variation by the linear regression equation with reproducibility. It gives greater measurement precision and better training load control when using elastic tubes in strength training programs.