The complex interplay between perception, cognition, and action: a commentary on Bach et al. 2022.

Bach (Psychological Research 2022, https://doi.org/10.1007/s00426-022-01773-w ) offer a re-conceptualisation of motor imagery, influenced by older ideas of ideomotor action and formulated in terms of action effects rather than motor output. We share the view of an essential role of action effect in action planning and motor imagery processes, but we challenge the claim that motor imagery is non-motoric in nature. In the present article, we critically review some of Bach et al.'s proposed ideas and pose questions of whether effect and motor processes are functionally separable, and if not, what mechanisms underlie motor imagery and what terminology best captures its function.

Amplicon-Based High-Throughput Sequencing Method for Genotypic Characterization of Norovirus in Oysters.

Norovirus is a highly diverse RNA virus often implicated in foodborne outbreaks, particularly those associated with shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbor various pathogens, including human-pathogenic viruses. The application of Sanger or amplicon-based high-throughput sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges: (i) distinguishing multiple genotypes/variants in a single sample and (ii) low concentrations of norovirus RNA. Here, we assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerases and reverse transcriptases (RTs) were compared, and performance was evaluated based on (i) the number of reads passing quality filters per sample, (ii) the number of correct genotypes identified, and (iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterize norovirus populations in naturally contaminated oysters. IMPORTANCE While foodborne outbreaks account for approximately 14% of norovirus cases (L. Verhoef, J. Hewitt, L. Barclay, S. Ahmed, R. Lake, A. J. Hall, B. Lopman, A. Kroneman, H. Vennema, J. Vinjé, and M. Koopmans, Emerg Infect Dis 21:592-599, 2015), we do not have standardized high-throughput sequencing methods for genotypic characterization in foodstuffs. Here, we present an optimized amplicon high-throughput sequencing method for the genotypic characterization of norovirus in oysters. This method can accurately detect and characterize norovirus at concentrations found in oysters grown in production areas impacted by human wastewater discharges. It will permit the investigation of norovirus genetic diversity in complex matrices and contribute to ongoing surveillance of norovirus in the environment.

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus.

In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. IMPORTANCE In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

Mapping relational links between motor imagery, action observation, action-related language, and action execution.

Actions can be physically executed, observed, imagined, or simply thought about. Unifying mental processes, such as simulation, emulation, or predictive processing, are thought to underlie different action types, whether they are mental states, as in the case of motor imagery and action observation, or involve physical execution. While overlapping brain activity is typically observed across different actions which indicates commonalities, research interest is also concerned with investigating the distinct functional components of these action types. Unfortunately, untangling subtleties associated with the neurocognitive bases of different action types is a complex endeavour due to the high dimensional nature of their neural substrate (e.g., any action process is likely to activate multiple brain regions thereby having multiple dimensions to consider when comparing across them). This has impeded progress in action-related theorising and application. The present study addresses this challenge by using the novel approach of multidimensional modeling to reduce the high-dimensional neural substrate of four action-related behaviours (motor imagery, action observation, action-related language, and action execution), find the least number of dimensions that distinguish or relate these action types, and characterise their neurocognitive relational links. Data for the model comprised brain activations for action types from whole-brain analyses reported in 53 published articles. Eighty-two dimensions (i.e., 82 brain regions) for the action types were reduced to a three-dimensional model, that mapped action types in ordination space where the greater the distance between the action types, the more dissimilar they are. A series of one-way ANOVAs and post-hoc comparisons performed on the mean coordinates for each action type in the model showed that across all action types, action execution and concurrent action observation (AO)-motor imagery (MI) were most neurocognitively similar, while action execution and AO were most dissimilar. Most action types were similar on at least one neurocognitive dimension, the exception to this being action-related language. The import of the findings are discussed in terms of future research and implications for application.

High Throughput Sequencing for the Detection and Characterization of RNA Viruses.

This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

A review of the neurobiomechanical processes underlying secure gripping in object manipulation.

O'SHEA, H. and S. J. Redmond. A review of the neurobiomechanical processes underlying secure gripping in object manipulation. NEUROSCI BIOBEHAV REV 286-300, 2021. Humans display skilful control over the objects they manipulate, so much so that biomimetic systems have yet to emulate this remarkable behaviour. Two key control processes are assumed to facilitate such dexterity: predictive cognitive-motor processes that guide manipulation procedures by anticipating action outcomes; and reactive sensorimotor processes that provide important error-based information for movement adaptation. Notwithstanding increased interdisciplinary research interest in object manipulation behaviour, the complexity of the perceptual-sensorimotor-cognitive processes involved and the theoretical divide regarding the fundamentality of control mean that the essential mechanisms underlying manipulative action remain undetermined. In this paper, following a detailed discussion of the theoretical and empirical bases for understanding human dexterous movement, we emphasise the role of tactile-related sensory events in secure object handling, and consider the contribution of certain biophysical and biomechanical phenomena. We aim to provide an integrated account of the current state-of-art in skilled human-object interaction that bridges the literature in neuroscience, cognitive psychology, and biophysics. We also propose novel directions for future research exploration in this area.

Associations between animal and herd management factors, serological response to three respiratory pathogens and pluck lesions in finisher pigs on a farrow-to-finish farm.

BACKGROUND: Serological screening is a common method to monitor antibody response to pathogen exposure, but results could vary due to several factors. This study aimed to quantify animal and management related factors associated with variation in antibody levels in finisher pigs at slaughter, in an Irish farrow-to-finish farm endemically infected with Actinobacillus pleuropneumonia (App), Mycoplasma hyopneumoniae (Mhyo) and swine influenza virus (SIV). A second objective was to estimate differences in antibody levels in pigs presenting pluck lesions. This was an observational study whereby pigs were managed as per routine farm practice. Data on sow parity, number of born alive (NBA) pigs per litter, cross-fostering status, birth and weaning body weight were recorded from 1016 pigs born from one farrowing batch. At slaughter, blood samples were collected for serological analysis and pigs were inspected for presence of enzootic pneumonia (EP)-like lesions, pleurisy, pericarditis and heart condemnations. Pigs were retrospectively classified into three production flows, depending on time spent in each production stage: flow 1 (F1; pigs followed the normal production flow); flow 2 (F2; pigs which were delayed by 1 week from advancing forward); and flow 3 (F3; pigs delayed by > 1 week from advancing forward). A nested case-control design was applied by matching pigs from each flow by sow parity, birth weight and NBA. RESULTS: Pigs born from primiparous sows had higher antibody levels for App than those born to parity ≥5 sows (P < 0.05) and there was no association between any of the pathogens investigated and other early life indicators (P > 0.05). Pigs in F1 had lower antibody levels for App but higher antibody levels for SIV than F2 and F3 pigs (P < 0.05). There was no association between pluck lesions and respiratory pathogens (P > 0.05), except for increased antibody levels for Mhyo when EP-like lesions were present (P = 0.006). CONCLUSION: Results indicate that offspring from primiparous sows develop higher antibody levels for App IV toxin when exposed to this disease and that enforcement of a strict all-in/all-out production system would reduce on-farm disease circulation. A high percentage of pigs were affected with EP-like lesions which were associated with higher antibody levels for Mhyo.

A cross-sectional survey on respiratory disease in a cohort of Irish pig farms.

BACKGROUND: Respiratory disease is one of the most important factors impacting pig production worldwide. There is no available information on the prevalence of key pathogens implicated in Irish pig production. The objective of this study was to describe the prevalence of pleurisy, pneumonia, lung abscesses, pericarditis and liver milk spots in finisher pigs of a cohort of Irish pig farms, and to describe the seroprevalence of: influenza A virus (IAV), porcine reproductive and respiratory syndrome virus (PRRSv), Mycoplasma hyopneumoniae (Mhyo) and Actinobacillus pleuropneumoniae (APP). RESULTS: In brief, 56 farrow-to-finish farms (29% of the Irish breeding herd) were enrolled in the study in 2017. Data on lungs, heart, and liver lesions were assessed for each farm at slaughter. An average of 417 (range 129-1154) plucks per farm were assessed for pleurisy, pneumonia, lung abscesses, pericarditis, and liver milk spots. Blood samples from 32 finisher pigs were collected at slaughter for each farm. The observed prevalence of pleurisy and pneumonia was one of the lowest reported in similar studies in Europe (13 and 11% estimated average within farm, respectively). Pleurisy lesions were mostly moderate and severe. Pneumonia lesions affected a low level of lung surface (5.8%). Prevalence of pericarditis was mid-high (8%) and the prevalence of liver milk spots was high, with an average of 29% of the livers affected. For serology, 78.6% of the farms were positive for IAV, 50% were positive for PRRSv, 71.4% were positive for Mhyo, and 98.2% were positive for APP. Influenza virus was the main pathogen associated with pleurisy (P < 0.001) and Mhyo was the main pathogen associated with pneumonia (P < 0.001) and pericarditis (P = 0.024). CONCLUSIONS: Farms affected with pleurisy had moderate to severe lesions. Farms affected with pneumonia had mild lesions, which could be the effect of the generalised use of Mhyo vaccination in piglets. The seroprevalence of IAV, PRRSv, Mhyo and APP in the present study sample is similar to or lower than in other European countries. Further research on the PRRSv and APP strains circulating in Ireland is necessary to support the design of national or regional control plans.

Porcine reproductive and respiratory syndrome virus: phylogenetic analysis of circulating strains in the Republic of Ireland from 2016 to 2017.

In order to investigate the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) strains currently circulating in the Republic of Ireland (ROI), the ORF5 gene from 17 field strains originating from four vaccinating commercial herds was sequenced and phylogenetically analysed. High genetic variability was observed between farms at the nucleotide (86.3-95.2%) and amino acid (85.5-96%) levels. Phylogenetic analysis confirmed that all field strains belonged to the European species (type 1) and clustered into three separate groups within the subtype 1 subgroup. This variation may pose challenges for diagnosis and prophylactic control of PRRSV through vaccination in the ROI.

Autoimmune encephalomyelitis in NOD mice is not initially a progressive multiple sclerosis model.

OBJECTIVE: Despite progress in treating relapsing multiple sclerosis (MS), effective inhibition of nonrelapsing progressive MS is an urgent, unmet, clinical need. Animal models of MS, such as experimental autoimmune encephalomyelitis (EAE), provide valuable tools to examine the mechanisms contributing to disease and may be important for developing rational therapeutic approaches for treatment of progressive MS. It has been suggested that myelin oligodendrocyte glycoprotein (MOG) peptide residues 35-55 (MOG35-55 )-induced EAE in nonobese diabetic (NOD) mice resembles secondary progressive MS. The objective was to determine whether the published data merits such claims. METHODS: Induction and monitoring of EAE in NOD mice and literature review. RESULTS: It is evident that the NOD mouse model lacks validity as a progressive MS model as the individual course seems to be an asynchronous, relapsing-remitting neurodegenerative disease, characterized by increasingly poor recovery from relapse. The seemingly progressive course seen in group means of clinical score is an artifact of data handling and interpretation. INTERPRETATION: Although MOG35-55 -induced EAE in NOD mice may provide some clues about approaches to block neurodegeneration associated with the inflammatory penumbra as lesions form, it should not be used to justify trials in people with nonactive, progressive MS. This adds further support to the view that drug studies in animals should universally adopt transparent raw data deposition as part of the publication process, such that claims can adequately be interrogated. This transparency is important if animal-based science is to remain a credible part of translational research in MS.

Are Fast Complex Movements Unimaginable? Pupillometric Studies of Motor Imagery in Expert Piano Playing.

Motor imagery (MI; mental simulation of actions) shares certain mental representations and processes with executed movement (ME). This neurocognitive overlap between MI and ME may explain why the systematic use of MI improves skilled performance in numerous domains. Unfortunately, the attentional mechanisms underlying MI remain unresolved. Therefore, the present studies investigated the role of attentional effort (as measured by pupil dilation) in MI. We evaluated the effects of movement complexity and speed on expert pianists' pupil dilation as they physically executed and used MI to perform easy/complex and slow/fast music phrases. Results revealed that easy movements required similar levels of attentional effort during MI and ME. However, during complex movements performed at a fast speed, the correspondence between execution and imagery of movement was disrupted.

Does Motor Simulation Theory Explain the Cognitive Mechanisms Underlying Motor Imagery? A Critical Review.

Motor simulation theory (MST; Jeannerod, 2001) purports to explain how various action-related cognitive states relate to actual motor execution. Specifically, it proposes that motor imagery (MI; imagining an action without executing the movements involved) shares certain mental representations and mechanisms with action execution, and hence, activates similar neural pathways to those elicited during the latter process. Furthermore, MST postulates that MI works by rehearsing neural motor systems off-line via a hypothetical simulation process. In this paper, we review evidence cited in support of MST and evaluate its efficacy in understanding the cognitive mechanisms underlying MI. In doing so, we delineate the precise postulates of simulation theory and clarify relevant terminology. Based on our cognitive-level analysis, we argue firstly that the psychological mechanisms underlying MI are poorly understood and require additional conceptual and empirical analysis. In addition, we identify a number of potentially fruitful lines of inquiry for future investigators of MST and MI.

A Blueprint to Evaluate One Health.

One Health (OH) positions health professionals as agents for change and provides a platform to manage determinants of health that are often not comprehensively captured in medicine or public health alone. However, due to the organization of societies and disciplines, and the sectoral allocation of resources, the development of transdisciplinary approaches requires effort and perseverance. Therefore, there is a need to provide evidence on the added value of OH for governments, researchers, funding bodies, and stakeholders. This paper outlines a conceptual framework of what OH approaches can encompass and the added values they can provide. The framework was developed during a workshop conducted by the "Network for Evaluation of One Health," an Action funded by the European Cooperation in Science and Technology. By systematically describing the various aspects of OH, we provide the basis for measuring and monitoring the integration of disciplines, sectors, and stakeholders in health initiatives. The framework identifies the social, economic, and environmental drivers leading to integrated approaches to health and illustrates how these evoke characteristic OH operations, i.e., thinking, planning, and working, and require supporting infrastructures to allow learning, sharing, and systemic organization. It also describes the OH outcomes (i.e., sustainability, health and welfare, interspecies equity and stewardship, effectiveness, and efficiency), which are not possible to obtain through sectoral approaches alone, and their alignment with aspects of sustainable development based on society, environment, and economy.

Molecular detection of kobuviruses in livestock in Northern Ireland and the Republic of Ireland.

Kobuviruses have been detected in a wide range of mammals including cats, dogs, pigs, cattle, goats, sheep and bats. Kobuviruses have been detected in symptomatic and asymptomatic animals; however, the clinical significance of infection in animals is still unclear. To date, there is no information regarding kobuvirus prevalence in livestock in Ireland. This study reports the first detection of kobuviruses in pigs, bovines and ovines using quantitative PCR. In this study, mesenteric lymph node was collected from cattle (n = 57), pigs (n = 53) and sheep (n = 50) from farms in Northern Ireland and the Republic of Ireland, from animals which had been submitted by private veterinary practitioners from 2009 to 2011 for routine post mortem and clinico-pathological examination. Kobuviruses were detected in 14 cows (24.5%), 5 pigs (9.4%) and 1 sheep (2%). Phylogenetic analysis of Irish kobuviruses from cattle and pigs revealed that the isolates clustered according to their host species. Interestingly, the sheep kobuvirus clustered with bovine kobuviruses detected in this study and other published kobuvirus strains. The data presented in this study contributes to the understanding of the epidemiology of these viruses in animals and to the genetic diversity that these viruses possess.

Positioning Animal Welfare in the One Health Concept through Evaluation of an Animal Welfare Center in Skopje, Macedonia.

The Animal Welfare Center (AWC) in Macedonia was established in 2009. The objectives of the center are animal welfare (AW) education, research, raising public awareness of AW, and increasing cooperation between the stakeholders. One Health (OH) was not the major focus of the AWC work initially, but, rather, a focus that evolved recently. The objective of this study was to evaluate the AWC from the OH perspective as an example case for positioning the AW within the overall OH concept. Three types of evaluation were performed: (1) assessment of OH-ness, by quantitative measurement of the operational and infrastructural aspects of the AWC; (2) impact evaluation, by conducting quantitative surveys on stakeholders and students; and (3) transdisciplinary evaluation, using semi-quantitative evaluation of the links of cooperation between the AWC and the stakeholders in society by the custom designed CACA (Cooperation, Activities, Communication, and Agreement) scoring system. Results for the OH-ness of the AWC showed relatively high scores for OH thinking, planning and working and middle scores for OH learning and sharing dimensions, i.e., dominance of the operational over infrastructural aspects of the AWC. The impact evaluation of the AWC shows that familiarity with the OH concept among stakeholders was low (44% of the respondents). However, there was a commonality among stakeholder's interest about AW and OH. According to the stakeholders' and students' opinions, the influence of AW on Animal, Environmental, and Human Health is relatively high (in the upper third of the 1-10 scale). The transdisciplinary evaluation of the AWC indicated the presence of transdisciplinarity work by the AWC, with a higher focus on the Universities and Research Institutions and some governmental institutions, and less linked with the Non-Governmental Organizations and Professional Associations (Chambers), e.g., the Veterinary Chamber in Macedonia. The evaluations conducted indicated that the AWC's work is closely dedicated to improving animal, environmental, and human health and has a considerable OH role among the stakeholders in the society. This study describes the significant role and importance that AW has in OH.

Host responses to a strontium releasing high boron glass using a rabbit bilateral femoral defect model.

Borate glasses have shown promising potential as bioactive materials. With recent research demonstrating that glass properties may be modulated by appropriate compositional design. This may provide for indication specific material characteristics and controlled release of therapeutic inorganic ions (i.e., strontium); controlling such release is critical in order to harness the therapeutic potential. Within this sub-chronic pilot study, a rabbit long-bone model was utilized to explore the safety and efficacy of a high borate glass (LB102: 70B2 O3 -20SrO-6Na2 O-4La2 O3 ) particulate (90 - 710 µm) for bone regeneration. Six bilateral full-thickness defects (Ø = 3.5 mm; L = 8 mm) were created in three white New Zealand rabbits. Longitudinal non-decalcified sections of each defect site were produced and stained with Goldner's Trichrome. Histopathological examination revealed that LB102 demonstrated osteoconductive and osseointegrative properties with greater new bone being formed within and surrounding LB102 particles, when compared to the sham control. The inflammatory cell infiltration was observed to be slightly higher in the control when compared to LB102 defect sites, while no significant difference in fibrosis and neovascularization was determined, indicating that healing was occurring in a normal fashion. These data further suggest the possible utility of high borate glasses with appropriate compositional design for medical applications, such as bone augmentation. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1818-1827, 2017.

Child maltreatment and adult psychopathology in an Irish context.

One-hundred-ninety-nine adult mental health service users were interviewed with a protocol that included the Childhood Trauma Questionnaire, the Structured Clinical Interviews for Axis I and II DSM-IV disorders, the Global Assessment of Functioning scale, the SCORE family assessment measure, the Camberwell Assessment of Need Short Appraisal Schedule, and the Readiness for Psychotherapy Index. Compared to a U.S. normative sample, Irish clinical cases had higher levels of maltreatment. Cases with comorbid axis I and II disorders reported more child maltreatment than those with axis I disorders only. There was no association between types of CM and types of psychopathology. Current family adjustment and service needs (but not global functioning and motivation for psychotherapy) were correlated with a CM history. It was concluded that child maltreatment may contribute to the development of adult psychopathology, and higher levels of trauma are associated with co-morbid personality disorder, greater service needs and poorer family adjustment. A history of child maltreatment should routinely be determined when assessing adult mental health service users, especially those with personality disorders and where appropriate evidence-based psychotherapy which addresses childhood trauma should be offered.

Detection and characterisation of novel bocavirus (genus Bocaparvovirus) and gastroenteritis viruses from asymptomatic pigs in Ireland.

BACKGROUND: Livestock animals have been the assumed source of several human epidemics in recent years, for example, influenza H1N1, rotavirus G8/G9, and MERS-CoV. Surveillance of novel viruses in animals is essential to evaluate the risk to human and animal health and to determine any economic impact, for example, failure to thrive. There is a paucity of data regarding detection and characterisation of gastroenteritis viruses, particularly novel viruses, in porcines in Ireland. Recently, a number of small novel porcine DNA viruses have emerged globally, for example, torque teno sus virus, porcine bocavirus, and parvoviruses 2 & 4, and little is known about the biology and potential pathogenicity of these viruses. Bocaparvovirus is a genetically distinct group of viruses which has been recently detected in humans and animals. METHODS: In this study, the presence of gastroenteritis viruses (rotavirus A, porcine circovirus, adenovirus, and porcine bocavirus) was investigated in a selection of archived faecal samples from asymptomatic piglets from a commercial farm in Ireland. A total of 104 specimens were pooled and screened using conventional molecular techniques (PCR and RT-PCR), a subset of specimens (n=44) were then examined individually. Viral diversity was then investigated using statistical and phylogenetic techniques. RESULTS: Initial screening showed a high prevalence of PBoV in this farm, with the formation of three distinct groups in phylogenetic analysis. Other viruses were also investigated in this study with the first report of PCV, PAdV and lineage I G5 RVA in Ireland. Some specimens contained >1 virus, with statistical analysis indicating a strong correlation for mixed infections of PBoV and PAdV on this farm. CONCLUSION: Investigating the diversity of circulating enteric viruses on Irish porcine farms is important to improve the prophylactic tools available and to facilitate the early detection of changes in circulating viruses.