Small Group Research Research Articles

On the standardization of ZooMS nomenclature

Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region. Significance statementWe propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.

The Impact of COVID-19 on the State of Clinical and Laboratory Research Globally in Transplantation in May 2020.

The Impact of COVID-19 on the State of Clinical and Laboratory Research Globally in Transplantation in May 2020.

Revision of Sustainable Road Rating Systems: Selection of the Best Suited System for Hungarian Road Construction Using TOPSIS Method

There are a number of sustainable and environmentally friendly techniques and methods currently available in the construction industry. To promote sustainable development, different rating and certificating systems that evaluate the level of sustainability during the development of infrastructure construction projects have been developed. The aim of the research presented in this paper was to examine the applicability of sustainability rating systems in Hungary and find the most suitable option. After a review of commonly used rating systems, i.e., Greenroads, GreenLITES, I-LAST, Envision, and INVEST, the most suitable existing rating system is selected with the help of the Technique for Order Preference by Similarity to the Ideal Solution (TOPSIS) mathematical decision analysis method. This was achieved by utilizing 12 categories of input data (weights) analyzed through TOPSIS. The input data (weights) of the TOPSIS method were determined by a small research group of industry experts and academic professionals based on Hungarian practices and methodology. As a result of the calculation, the study found that the Envision rating system satisfies the criteria best, closely followed by Greenroads.

Application of thermography in equine veterinary practice

Thermography is a non-invasive diagnostic method that measures the temperature of the body surface. Its operation is based on the recording and visualization of infrared radiation emitted by the surface of the body in the form of temperature distribution. The result is a thermogram, which reveals the physiological state of the horse, reflecting the pattern of blood flow and the speed of metabolic processes in the area of the horse’s body under examination. It also shows the influence of environmental conditions prevailing during the test. Thermography has been widely used in veterinary medicine as a supplementary diagnostic tool for injuries and other pathologies of the locomotory apparatus, as a tool for monitoring the process of tissue regeneration and the effectiveness of anti-inflammatory drugs, and as an auxiliary tool for distinguishing between acute, chronic and subclinical disease states. However, most of the studies on thermography in equine veterinary medicine are based on relatively small research groups, which limits the sensitivity and specificity of this method in scientific research. This review article presents the latest research on the use of thermography in veterinary medicine, including its benefits and limitations.

Hawthorne and Presentism: A Backward Glance

Hawthorne and Presentism: A Backward Glance

All eyes on you: how researcher presence changes the way you walk

Most human movement research takes place within controlled laboratories where researchers observe participant movement. Because a majority of daily activity is performed without observation, we hypothesized movement within a laboratory would vary when there was a small, large or absence of research group. We also hypothesized that personality type would influence movement during observation. Participants completed a personality questionnaire, then walked in a laboratory during three different conditions: no research group (no researchers), small research group (2 researchers), and large research group (6–10 researchers). Results revealed spatiotemporal parameters were altered between conditions, however personality type did not influence changes in movement. As the number of researchers increased, gait speed, cadence, and stride length increased, and step duration decreased. Gait speed increased by .03 m/s from the no research group to the small research group, by .06 m/s from the no research group to the large research group, and by .03 m/s from the small to large research group (all p values < .001). Understanding how researcher observation modifies movement is important and affects the replicability of results, as well as the interpretation of laboratory-based movement studies to activities of daily living in real world settings.

Tailoring education of adults with cognitive impairment in the inpatient hospital setting: A scoping review.

Education seeks to empower clients to attain and maintain knowledge and skills, and in the context of occupational therapy, to enable occupational participation. While education is routinely provided in the inpatient hospital setting, little is known about how education is best adapted to meet the needs of clients with cognitive impairment. The purpose of this scoping review was to determine what is currently known about approaches to educating adults with cognitive impairment in the inpatient hospital setting. Five databases were systematically searched to find studies that reported on the use of education in the inpatient hospital setting with adults with cognitive impairment. Ten articles were retrieved from the search with duplication of authors across the articles, indicating a small group of research and researchers. Cognitive impairment was not well assessed across all the studies and none included participants with severe cognitive impairment. A number of barriers to education were identified, including time constraints, uncertainty around who should be providing education, a shortage of resources, and client-related barriers such as cognitive deficits. From the retrieved studies it was found that education should occur at multiple time points, be individually tailored, and utilise mixed modal approaches such as verbal and written methods. There was also a preference for less use of jargon, and engagement with carers and clients where possible. This scoping review highlights factors impacting the provision of education tailored to the needs of clients with cognitive impairment in the inpatient setting. The findings also call to attention the need for better assessment of cognition to guide provision of tailored education, as well as future studies exploring how to best educate clients with not only mild/moderate cognitive impairment but also more severe impairments.

Annotation and curation of human genomic variations: an ELIXIR Implementation Study

Background: ELIXIR is an intergovernmental organization, primarily based around European countries, established to host life science resources, including databases, software tools, training material and cloud storage for the scientific community under a single infrastructure. Methods: In 2018, ELIXIR commissioned an international survey on the usage of databases and tools for annotating and curating human genomic variants with the aim of improving ELIXIR resources. The 27-question survey was made available on-line between September and December 2018 to rank the importance and explore the usage and limitations of a wide range of databases and tools for annotating and curating human genomic variants, including resources specific for next generation sequencing, research into mitochondria and protein structure. Results: Eighteen countries participated in the survey and a total of 92 questionnaires were collected and analysed. Most respondents (89%, n=82) were from academia or a research environment. 51% (n=47) of respondents gave answers on behalf of a small research group (&lt;10 people), 33% (n=30) in relation to individual work and 16% (n=15) on behalf of a large group (&gt;10 people). The survey showed that the scientific community considers several resources supported by ELIXIR crucial or very important. Moreover, it showed that the work done by ELIXIR is greatly valued. In particular, most respondents acknowledged the importance of key features and benefits promoted by ELIXIR, such as the verified scientific quality and maintenance of ELIXIR-approved resources. Conclusions ELIXIR is a “one-stop-shop” that helps researchers identify the most suitable, robust and well-maintained bioinformatics resources for delivering their research tasks.

On the impact of selected modern deep-learning techniques to the performance and celerity of classification models in an experimental high-energy physics use case

Beginning from a basic neural-network architecture, we test the potential benefits offered by a range of advanced techniques for machine learning, in particular deep learning, in the context of a typical classification problem encountered in the domain of high-energy physics, using a well-studied dataset: the 2014 Higgs ML Kaggle dataset. The advantages are evaluated in terms of both performance metrics and the time required to train and apply the resulting models. Techniques examined include domain-specific data-augmentation, learning rate and momentum scheduling, (advanced) ensembling in both model-space and weight-space, and alternative architectures and connection methods.Following the investigation, we arrive at a model which achieves equal performance to the winning solution of the original Kaggle challenge, whilst being significantly quicker to train and apply, and being suitable for use with both GPU and CPU hardware setups. These reductions in timing and hardware requirements potentially allow the use of more powerful algorithms in HEP analyses, where models must be retrained frequently, sometimes at short notice, by small groups of researchers with limited hardware resources. Additionally, a new wrapper library for PYTORCH called LUMIN is presented, which incorporates all of the techniques studied.

Evolution of the entrepreneurship and innovation research in Ibero-America between 1986 and 2015

ABSTRACT Ibero-American researchers show an increasing number of studies on entrepreneurship and innovation research. This article analyzes the journals and universities that published research on the discipline developed by Ibero-American authors between 1986 and 2015. The work uses the Web of Science database and provides several bibliometric indicators. The results show that the most outstanding researchers of the region come mainly from Spain and Portugal. In particular, Spanish researchers are the most productive and influential authors in the region. A small group of researchers from Chile, Argentina, and Mexico are also very influential. Latin American researchers must deepen their international academic networks.

SQMtools: automated processing and visual analysis of \u2019omics data with R and anvi\u2019o

BackgroundThe dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.ResultsHere we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi’o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.ConclusionsAltogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.

Open Badges for Promoting Open Practices in the Institutional Repository: A Pilot Project

INTRODUCTION This paper describes a pilot project conducted at a mid-sized research university to integrate an Open Badge into the institutional repository (IR) alongside research articles. The Open Badge was intended to indicate that the research article in question complies with a national funders’ open access (OA) policy. METHODS This study employed a two-step process to investigate the value of badges: first, researchers were surveyed to ask their opinions about using badges in the IR; second, user testing was done with a small group of researchers to assess whether badges are easy to apply during the process of depositing an article to the IR. RESULTS A minority of respondents to the survey indicated that they saw value in an open badge. Participants in the testing component revealed several areas where the overall interface to the IR submission process could be improved. DISCUSSION It was clear that there are opportunities to promote open practices relating to national funders’ open access policy in our sample. However, any incentive represented by an open badge may be overshadowed if the infrastructure in which it is presented is not sufficiently streamlined. CONCLUSION Scholars are not willing to spend much, if any, additional time to indicate compliance with an open access policy. Adding an open badge was neither an incentive nor a disincentive for promoting open practices.

Mapping 50 Years of Small Group Research ThroughSmall Group Research

At its 50-year milestone, we assess the Small Group Research ( SGR) corpus to reflect on the development of group research over the past half century. To do this, we examine the evolution of the corpus’s context and content. We examine its context by assessing its impact, which journals it communicates with, and the internationality of its authors. We examine its content—the topics discussed in its articles—using keyword clustering and co-occurrence network analysis. We identify 10 research communities and track their relationships over the four editorial periods associated with the SGR corpus (lagged 2 years for influence): 1970–1981, 1982–1991, 1992–2010, and 2011–2019. Our analyses indicate that the global and local study of group dynamics has fluctuated over time and that phenomenologically based topics connect theoretical topics and stimulate theoretical development. We also provide three criteria to identify communities and topics of group research most likely to benefit from future integration.

Introduction to Volume 12, Issue 3 of topiCS

For our July 2020 issue (Volume 12, Issue 3), we publish three topics. The first is a one-paper reply from Rafael Núñez and colleagues entitled, "For the Sciences They are A-Changin’: A Response to Commentaries on Núñez et al.'s (2019) 'What Happened to Cognitive Science?' " The history of this topic is unusual. It began life as a Nature Human Behavior paper (Núñez et al., 2019) which “accused” the field of Cognitive Science of being multidisciplinary rather than interdisciplinary. As this paper evoked strong feelings among many cognitive scientists, we invited 10 contributions to the topic, which we published in October 2019 (Volume 11, Issue 4). The current paper is the Núñez response to these 10 papers. Note that the response was reviewed by two distinguished members of our community and I acted as the Action Editor. Also, please note that we will not be publishing replies to the replies. However, if a group is interested in publishing a full paper on this topic, we have procedures for that, and you are invited to follow those procedures to submit a proposal for a topic on this matter. The second topic in this issue was organized and edited by Carel ten Cate (Leiden Institute for Brain and Cognition, Leiden University) and his extensive team of co-editors: Judit Gervain (Integrative Neuroscience and Cognition Center, CNRS), Clara C. Levelt (Leiden Institute for Brain and Cognition), Christopher Petkov (Newcastle University Medical School), and William Zuidema (University of Amsterdam). Their fascinating and important topic is well summarized by the title of the Editors’ Review and Introduction: Learning Grammatical Structures: Developmental, Cross-Species, and Computational Approaches. Please note that all Editors’ Reviews and Introductions written for any topic are available as free downloads courtesy of our publisher. If you are a student, new to the field, or if you are a colleague, in another area of cognitive science, interested in catching up on what your colleagues in our multidisciplinary field are doing, then these papers are what you are looking for. Our third topic in this issue is our annual Best of the International Conference on Cognitive Modeling (ICCM) edited this year by Terrance C. Stewart (Associate Research Officer at the National Research Council Canada) and Christopher W. Myers (U. S. Air Force Research Laboratory). ICCM is a small group of researchers which has been holding meetings and publishing proceeding for about 30 years. As a small group, it has evolved rapidly over time with the one constant (maybe) being its focus on models of human behavior. The group’s original focus on computational models has been augmented lately by mathematical and statistical modeling. Interestingly, as Stewart points out in his introduction, this year none of their “best-ofs” are modeling the mythical average human; rather all of their best papers have something to do with modeling the performance and cognition of individual humans. The ICCM best-ofs has always been a solid and sometimes exciting collection of papers. For those of us interested in understanding “individuals,” it has just become more exciting. To our readers, keep searching and reading topiCS for our high-quality, curated collections of papers on timely topics of interest to the broad cognitive science community. topiCS encourages letters and commentaries on all topics, and proposals for new topics. Letters are typically 400–1,000 words (maximum of two published pages) and will be published without an abstract or references (possibly 1–2 but usually none). Commentaries are often solicited by Topic Editors prior to the publication of their topic. However, commentaries after publication are also considered and should range between 1,000 and 2,000 words. Most commentaries would not have an abstract and would not include many references. The Executive Editor and the Senior Editorial Board (SEB) members are constantly searching for new and exciting topics for topiCS. Feel free to open communications with a short note to the Executive Editor (mail to: grayw@rpi.edu) or an SEB member (SEB members are listed under the Editorial Board heading on the publisher’s homepage for topiCS [http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1756-8765/homepage/EditorialBoard.html]).

Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course.

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

An automated aquatic rack system for rearing marine invertebrates

BackgroundOne hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift towards work on a smaller number of so-called model systems. Those animals are typically non-marine organisms with advantages afforded by short life cycles, high fecundity, and relative ease in laboratory culture. However, a full understanding of biodiversity, evolution, and anthropogenic effects on biological systems requires a broader survey of development in the animal kingdom. To this day, marine organisms remain relatively understudied, particularly the members of the Lophotrochozoa (Spiralia), which include well over one third of the metazoan phyla (such as the annelids, mollusks, flatworms) and exhibit a tremendous diversity of body plans and developmental modes. To facilitate studies of this group, we have previously described the development and culture of one lophotrochozoan representative, the slipper snail Crepidula atrasolea, which is easy to rear in recirculating marine aquaria. Lab-based culture and rearing of larger populations of animals remain a general challenge for many marine organisms, particularly for inland laboratories.ResultsHere, we describe the development of an automated marine aquatic rack system for the high-density culture of marine species, which is particularly well suited for rearing filter-feeding animals. Based on existing freshwater recirculating aquatic rack systems, our system is specific to the needs of marine organisms and incorporates robust filtration measures to eliminate wastes, reducing the need for regular water changes. In addition, this system incorporates sensors and associated equipment for automated assessment and adjustment of water quality. An automated feeding system permits precise delivery of liquid food (e.g., phytoplankton) throughout the day, mimicking real-life feeding conditions that contribute to increased growth rates and fecundity.ConclusionThis automated system makes laboratory culture of marine animals feasible for both large and small research groups, significantly reducing the time, labor, and overall costs needed to rear these organisms.

A half-century of Accounting and Business Research: the impact on the study of international financial reporting

This paper celebrates the contribution of this journal, over its first 50 years, to research on international financial reporting, defined as comprising writings on comparative or harmonisation topics. The paper examines the journal’s output in that field and how it contributed to the field’s development. Even though the journal was sympathetic to international financial reporting, less than 1% of output in its first decade (the 1970s) related to it. In its first 35 years, a large proportion of the journal’s limited output in the field was produced by two small groups of researchers. However, during its fourth decade, the field gradually became dominant as the accounting world changed. By then, the journal had already published the seminal papers on several central topics in international financial reporting, including measuring harmonisation, using reconciliations to measure international accounting differences, assessing international differences in the influence of tax on financial reporting, and measuring international difference in the application of international standards. These topics were later taken up by many researchers in several other journals.

Segmentation of roots in soil with U-Net

BackgroundPlant root research can provide a way to attain stress-tolerant crops that produce greater yield in a diverse array of conditions. Phenotyping roots in soil is often challenging due to the roots being difficult to access and the use of time consuming manual methods. Rhizotrons allow visual inspection of root growth through transparent surfaces. Agronomists currently manually label photographs of roots obtained from rhizotrons using a line-intersect method to obtain root length density and rooting depth measurements which are essential for their experiments. We investigate the effectiveness of an automated image segmentation method based on the U-Net Convolutional Neural Network (CNN) architecture to enable such measurements. We design a data-set of 50 annotated chicory (Cichorium intybus L.) root images which we use to train, validate and test the system and compare against a baseline built using the Frangi vesselness filter. We obtain metrics using manual annotations and line-intersect counts.ResultsOur results on the held out data show our proposed automated segmentation system to be a viable solution for detecting and quantifying roots. We evaluate our system using 867 images for which we have obtained line-intersect counts, attaining a Spearman rank correlation of 0.9748 and an r^2 of 0.9217. We also achieve an F_1 of 0.7 when comparing the automated segmentation to the manual annotations, with our automated segmentation system producing segmentations with higher quality than the manual annotations for large portions of the image.ConclusionWe have demonstrated the feasibility of a U-Net based CNN system for segmenting images of roots in soil and for replacing the manual line-intersect method. The success of our approach is also a demonstration of the feasibility of deep learning in practice for small research groups needing to create their own custom labelled dataset from scratch.

A Badging System for Reproducibility and Replicability in Remote Sensing Research

Remote Sensing is both an active research area and the source of valuable information for decision-making. Many actors play a fundamental role in Remote Sensing, from industry (public or private) to large or small research groups. From that intensive activity, methods, algorithms, and techniques are continuously published or broadcasted through papers, conference presentations, repositories, patents, standards, and other means. The consumers of that information need it to be readily available and dependable. Reproducible research can handle those needs. In this article, we discuss two concepts: reproducibility and replicability in the context of Remote Sensing research. We propose a badging system suited to the specifics of the Remote Sensing community. Such a system aims at both recognizing the level of the reproducibility of the research, and to help increase its visibility. We show examples of reproducible research and provide clues to make easier the transition to the inevitable new times that embrace contemporary science and technology.

Historical Cultures Under Conditions of Deindustrialization Working Group Report

Crumbling smokestacks, shuttered furnaces, and abandoned quarries are all striking representations of deindustrialization. These and other images construct a discourse whose ideological undertones, far from confining them to the realm of symbolic nostalgia, have profound effects on contemporary societies. In 2015, within the European Labor History Network (ELHN), a working group on historical cultures of labor under conditions of deindustrialization (working group) began to critically study and reflect on this nascent theme. It grew from a small group of researchers to a network of academics across Europe and beyond. Though the study of deindustrialization is not new, contemporary work offers insights into the continuing struggle over the meaning of classical industrial work and its loss, revealing unresolved social, cultural, and political tensions. Yet, existing representations of deindustrialization have been criticized as “smokestack nostalgia.” In order to chart how we understand contemporary industrial decay in our political, cultural, and economic climate, the working group explores representations and more-than representations of loss and regeneration in deindustrialized regions, primarily in Europe but widening to include a growing global network.