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We report key learning from the public health management of the first two confirmed cases of COVID-19 identified in the UK. The first case imported, and the second associated with probable person-to-person transmission within the UK. Contact tracing was complex and fast-moving. Potential exposures for both cases were reviewed, and 52 contacts were identified. No further confirmed COVID-19 cases have been linked epidemiologically to these two cases. As steps are made to enhance contact tracing across the UK, the lessons learned from earlier contact tracing during the country's containment phase are particularly important and timely.
In clinical and translational research, data science is often and fortuitously integrated with data collection. This contrasts to the typical position of data scientists in other settings, where they are isolated from data collectors. Because of this, effective use of data science techniques to resolve translational questions requires innovation in the organization and management of these data.
We propose an operational framework that respects this important difference in how research teams are organized. To maximize the accuracy and speed of the clinical and translational data science enterprise under this framework, we define a set of eight best practices for data management.
In our own work at the University of Rochester, we have strived to utilize these practices in a customized version of the open source LabKey platform for integrated data management and collaboration. We have applied this platform to cohorts that longitudinally track multidomain data from over 3000 subjects.
We argue that this has made analytical datasets more readily available and lowered the bar to interdisciplinary collaboration, enabling a team-based data science that is unique to the clinical and translational setting.
In contrast to the visual, auditory or olfactory senses, the sense of touch (a form of mechanoreception) has been relatively neglected in primate studies. Over the last few decades, our understanding of the ecology of touch, or how an animal explores and exploits its environment using tactile cues (or tactile information), has improved in both primates and non-primate mammals. Touch can take many forms in mammals, including vibrissal (or whisker) touch, hand touch (especially in glabrous fingertips) and skin touch. Comparative studies exploring the relative sensitivities of touch (e.g. vibrissae/face, hands, feet) in primates and non-primate mammals are often challenging without extensive behavioural training (Bauer et al., 2012; Dehnhardt and Dücker, 1996; Dehnhardt and Kaminski, 1995) or complex anatomical studies (Marshall et al., 2014; Mattson and Marshall, 2016a, 2016b; Peterson et al., 1998). We have had success in using anatomical and skeletal proxies to investigate the ecology and evolution of vibrissal touch. Indeed, there are established ecological correlates between touch sensory-end organs, like number and movement, and skeletal landmarks linked with touch acuity (Muchlinski, 2010a; Muchlinski et al., 2018). It is also possible to connect vibrissa movement to differences in behaviour (Dehnhardt and Kaminski, 1995; Grant et al., 2018; Kemble and Lewis, 1982; Muchlinski, 2010b). We have even modelled the evolution of vibrissae, discussing our findings in the context of touch (Muchlinski et al., 2013, 2018). In this chapter, we examine the ecology of face touch (i.e. vibrissal touch) among the lorisids using the above-mentioned lines of evidence. We suggest that the sensory ecology of the lorisids may be more specialised and novel than we initially thought.
Objectives: Research has shown that analyzing intrusion errors generated on verbal learning and memory measures is helpful for distinguishing between the memory disorders associated with Alzheimer’s disease (AD) and other neurological disorders, including Huntington’s disease (HD). Moreover, preliminary evidence suggests that certain clinical populations may be prone to exhibit different types of intrusion errors. Methods: We examined the prevalence of two new California Verbal Learning Test-3 (CVLT-3) intrusion subtypes – across-trial novel intrusions and across/within trial repeated intrusions – in individuals with AD or HD. We hypothesized that the encoding/storage impairment associated with medial-temporal involvement in AD would result in a greater number of novel intrusions on the delayed recall trials of the CVLT-3, whereas the executive dysfunction associated with subcortical-frontal involvement in HD would result in a greater number of repeated intrusions across trials. Results: The AD group generated significantly more across-trial novel intrusions than across/within trial repeated intrusions on the delayed cued-recall trials, whereas the HD group showed the opposite pattern on the delayed free-recall trials. Conclusions: These new intrusion subtypes, combined with traditional memory analyses (e.g., recall versus recognition performance), promise to enhance our ability to distinguish between the memory disorders associated with primarily medial-temporal versus subcortical-frontal involvement.
Individuals with schizophrenia have deficits in social cognition that are associated with poor functional outcome. Unfortunately, current treatments result in only modest improvement in social cognition. Oxytocin, a neuropeptide with pro-social effects, has significant benefits for social cognition in the general population. However, studies examining the efficacy of oxytocin in schizophrenia have yielded inconsistent results. One reason for inconsistency may be that oxytocin has typically not been combined with psychosocial interventions. It may be necessary for individuals with schizophrenia to receive concurrent psychosocial treatment while taking oxytocin to have the context needed to make gains in social cognitive skills.
The current study tested this hypothesis in a 24-week (48 session) double-blind, placebo-controlled trial that combined oxytocin and Cognitive-Behavioral Social Skills Training (CBSST), which included elements from Social Cognition and Interaction Training (SCIT). Participants included 62 outpatients diagnosed with schizophrenia (placebo n = 31; oxytocin n = 31) who received 36 IU BID, with supervised administration 45 min prior to sessions on CBSST group therapy days. Participants completed a battery of measures administered at 0, 12, and 24 weeks that assessed social cognition.
CBSST generally failed to enhance social cognition from baseline to end of study, and there was no additive benefit of oxytocin beyond the effects of CBSST alone.
Findings suggest that combined CBSST and oxytocin had minimal benefit for social cognition, adding to the growing literature indicating null effects of oxytocin in multi-dose trials. Methodological and biological factors may contribute to inconsistent results across studies.
Objectives: The third edition of the California Verbal Learning Test (CVLT-3) includes a new index termed List A versus Novel/Unrelated recognition discriminability (RD) on the Yes/No Recognition trial. Whereas the Total RD index incorporates false positive (FP) errors associated with all distractors (including List B and semantically related items), the new List A versus Novel/Unrelated RD index incorporates only FP errors associated with novel, semantically unrelated distractors. Thus, in minimizing levels of source and semantic interference, the List A versus Novel/Unrelated RD index may yield purer assessments of yes/no recognition memory independent of vulnerability to source memory difficulties or semantic confusion, both of which are often seen in individuals with primarily frontal-system dysfunction (e.g., early Huntington’s disease [HD]). Methods: We compared the performance of individuals with Alzheimer’s disease (AD) and HD in mild and moderate stages of dementia on CVLT-3 indices of Total RD and List A versus Novel/Unrelated RD. Results: Although AD and HD subgroups exhibited deficits on both RD indices relative to healthy comparison groups, those with HD generally outperformed those with AD, and group differences were more robust on List A versus Novel/Unrelated RD than on Total RD. Conclusions: Our findings highlight the clinical utility of the new CVLT-3 List A versus Novel/Unrelated RD index, which (a) maximally assesses yes/no recognition memory independent of source and semantic interference; and (b) provides a greater differentiation between individuals whose memory disorder is primarily at the encoding/storage level (e.g., as in AD) versus at the retrieval level (e.g., as in early HD). (JINS, 2018, 24, 833–841)
We report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.
A 2,000-bed tertiary-care psychiatric hospital.
Active surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)–based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.
The study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1–C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0–5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21–45 and 26–58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.
WGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.
In the context of water use for agricultural production, water footprints (WFs) have become an important sustainability indicator. To understand better the water demand for beef and sheep meat produced on pasture-based systems, a WF of individual farms is required. The main objective of this study was to determine the primary contributors to freshwater consumption up to the farm gate expressed as a volumetric WF and associated impacts for the production of 1 kg of beef and 1 kg of sheep meat from a selection of pasture-based farms for 2 consecutive years, 2014 and 2015. The WF included green water, from the consumption of soil moisture due to evapotranspiration, and blue water, from the consumption of ground and surface waters. The impact of freshwater consumption on global water stress from the production of beef and sheep meat in Ireland was also computed. The average WF of the beef farms was 8391 l/kg carcass weight (CW) of which 8222 l/kg CW was green water and 169 l/kg CW was blue water; water for the production of pasture (including silage and grass) contributed 88% to the WF, concentrate production – 10% and on-farm water use – 1%. The average stress-weighted WF of beef was 91 l H2O eq/kg CW, implying that each kg of beef produced in Ireland contributed to freshwater scarcity equivalent to the consumption of 91 l of freshwater by an average world citizen. The average WF of the sheep farms was 7672 l/kg CW of which 7635 l/kg CW was green water and 37 l/kg CW was blue water; water for the production of pasture contributed 87% to the WF, concentrate production – 12% and on-farm water use – 1%. The average stress-weighted WF was 2 l H2O eq/kg CW for sheep. This study also evaluated the sustainability of recent intensification initiatives in Ireland and found that increases in productivity were supported through an increase in green water use and higher grass yields per hectare on both beef and sheep farms.
Introduction / Innovation Concept: Insertion of an internal jugular (IJ) central venous catheter (CVC) under ultrasound guidance (USG) is a complex skill that requires considerable practice in order to achieve technical proficiency. Simulation allows novices to engage in structured and high volume repetitive practice of USG IJ CVC insertion and to work through a predictable pattern of errors prior to real patient encounters. Based on earlier work on learning curves for CVC insertion, this curriculum uses a model of simulation-based high volume deliberate practice of the fundamental skills of USG CVC insertion, and was designed with careful consideration of the conditions associated with optimal learning and improvement of performance. Methods: Eight residents (post graduate year 2) from the Departments of Emergency Medicine and Anesthesiology engaged in deliberate practice of USG CVC insertion during three two-hour sessions, at 2-week intervals. Progress of the residents was monitored with direct observation and regular hand motion analysis (HMA), which was compared to performance metrics set by a local expert. Curriculum, Tool, or Material: Students reviewed online introductory ultrasound video and articles outlining internal jugular (IJ) and femoral CVC insertion prior to the first session. Session 1 focused on ultrasound skills including knobology, transducer movement, and needle tracking. This was followed by 60 minutes of deliberate practice of the skills of USG CVC insertion on both femoral and IJ models. During sessions 2/3, students practiced complete gowning and draping using sterile technique. This was followed again by deliberate practice of the skills of USG CVC insertion on both femoral and IJ models. Students received coaching and feedback throughout all sessions, with HMA assessment of USG IJ CVC insertion at the beginning and end of each session. After three training sessions, consisting of 85 total attempts, 5/8 residents surpassed the expert benchmark for probe hand motion, 6/8 for needle hand motion, and 1/8 for total procedure time, with the remaining residents approaching the expert benchmark for each metric. Conclusion: We have successfully developed a simulation-based curriculum for USG IJ CVC placement. Residents demonstrated continuous improvement in each session, approaching or exceeding the expert benchmarks by the end of the third session.
Thirteen intact cynipine galls (Cynipidae) are identified from the significant late Pleistocene locality of Rancho La Brea, mostly within the range of approximately 30,000 to 48,000 14C yr BP. Late Cenozoic cynipids have a poor fossil record; it is thus of great interest that the provisional dates for this fossil gall collection establish that these insects and their hosts were an important part of the late Pleistocene ecosystem in and around Rancho La Brea. Cynipine host specificity both verifies, as well as augments, the proportionally low record of plants recovered at Rancho La Brea in comparison to records of mammals, birds, and other fauna. Because galler and hosts represent extant species, their climate and habitat restrictions offer a good basis for making paleoecological inferences. In particular, they imply that many of the diverse habitats found in California today, or, at least plant associations with similar environmental restrictions, some presently a distance from the Rancho La Brea Tar Pits, existed in the vicinity of this locality during the late Pleistocene. This material also includes previously undescribed species, several of which are morphologically similar to extant comparative material that exhibits a “jumping” behavior, previously believed to be unique to Neuroterus saltatorius Edwards.
There is little empirical evidence to indicate that dairy cow live weight affects the extent of soil damage at the hoof-soil interface during grazing on poorly drained permanent grassland. In the present study the impact of Holstein-Friesian (HF) dairy cows with a mean (±standard deviation) live weight of 570 (±61) kg were compared with Jersey × Holstein-Friesian (JX) with a mean live weight of 499 (±52) kg each at two stocking densities: mean 2·42 ± (0·062) and 2·66 (±0·079) cows/ha. Soil physical properties (bulk density, macroporosity, gravimetric water content, air-filled porosity, penetration resistance and shear strength), poaching damage (post-grazing soil surface deformation and hoof-print depth), herbage yield and milk production were measured throughout 2011 and 2012. Soil physical properties, post-grazing soil surface deformation and herbage production were not affected by dairy cow breed or by interactions between breed and stocking density. Hoof-print depth was higher in the HF treatments (39 v. 37 mm, s.e. 0·5 mm). Loading pressure imposed at the soil surface was the same for both breeds due to a direct correlation between live weight and hoof size. Poaching damage was greater at higher stocking density. Using the lighter JX cow offered little advantage in terms of lowering the negative impact of treading on soil physical properties or reducing poaching damage and no advantage in terms of herbage or milk production compared with the heavier HF cow.
Prospective memory (PM) is dependent on executive processes known to be impaired in Huntington's disease (HD); however, no study to the authors’ knowledge has investigated PM in this group. We examined performance-based, semi-naturalistic, and self-reported PM in 20 individuals diagnosed with mild–moderate HD and 20 demographically similar controls. Relative to controls, HD participants demonstrated significantly lower scores in time-based PM, event-based PM (at a trend level), and the semi-naturalistic PM trial, all of which were marked by omission errors. HD participants demonstrated comparable recognition memory for the PM intentions relative to controls. HD and control participants also showed comparable scores in self-reported PM complaints. The results suggest that HD is associated with deficits in the strategic aspects of PM. HD-associated PM deficits also are evident in real-world situations, which may relate to an apparent meta-memory deficit for PM functioning as indicated by HD participants’ overestimation of their PM performance on self-report. (JINS, 2014, 20, 1–8)
Agricultural specialists, particularly animal scientists, tend to use process-based life-cycle assessments (LCA), which describe the production system as a series of processes, to study the environmental impact of milk production based on their experimental data. Another approach called input–output (I–O) based LCA, which uses the economic transaction tables and national environmental accounts to determine the environmental impact triggered by final demand of milk production, is often less used due to data scarcity and higher uncertainty. In the current paper, process-based and I–O-based LCA models were developed to evaluate the greenhouse gas (GHG) and acidifying emissions from pasture-based milk production in Ireland. Process-based LCA found 1338·3 kg CO2 eq and 14·4 kg SO2 eq/t energy-corrected milk (ECM), and revealed details related to the farm management. The I–O based LCA found 1003·1 kg CO2 eq and 12·7 kg SO2 eq/tonne ECM and suggested that the agriculture, forestry and fishery (AFF) sector itself was largely responsible for the environmental impact of AFF products, rather than economic interaction with other sectors. The process-based LCA was found to be suitable for developing farm-scale sustainability strategies if variation of tactics across farms is provided, while the I–O based LCA offered potential sustainability guidance at the national scale. Further work is required to incorporate foreign production into the I–O table to account fully for imported goods and services. A detailed disaggregation within the AFF sector is also needed to gain a better understanding of the environmental sustainability of agricultural commodities. The present paper thus provides interesting results for the dairy industry, dairy researchers and LCA practitioners on further understanding of the environmental impact of milk production.
Free-form deformation (FFD) is a method first introduced within the graphics industry to enable flexible deformation of geometric models. FFD uses an R3 to R3 mapping of a deformable space to the global Cartesian space to produce the geometry deformation. This method has been extensively used within the design optimisation field as a shape parameterisation technique. Typically it has been used to parameterise analysis meshes, where new design geometries are produced by deforming the original mesh. This method allows a concise set of design variables to be used while maintaining a flexible shape representation. However, if a computer aided design (CAD) model of the resulting geometry is required, reverse engineering techniques would need to be utilised to recreate the model from the deformed mesh. This paper extends the use of FFD within an optimisation routine by using FFD to directly parameterise a CAD geometry. Two methods of linking the FFD methods with the CATIA V5 CAD package are presented. Each CAD integration technique is then critiqued with respect to shape optimisation. Finally the set-up and initialisation of a case study is illustrated. The case study chosen is the aerodynamic optimisation of the wing-fuselage junction of a typical passenger aircraft.
Brizolis asked for which primes p greater than 3 there exists a pair (g,h) such that h is a fixed point of the discrete exponential map with base g, or equivalently h is a fixed point of the discrete logarithm with base g. Various authors have contributed to the understanding of this problem. In this paper, we use p-adic methods, primarily Hensel’s lemma and p-adic interpolation, to count fixed points, two-cycles, collisions, and solutions to related equations modulo powers of a prime p.
Detailed descriptions of cardiac
geometry and architecture are necessary for examining and
understanding structural changes to the myocardium that are the
result of pathologies, for interpreting the results of
experimental studies of propagation, and for use as a
three-dimensional orthotropically anisotropic model for the
computational reconstruction of propagation during arrhythmias.
Diffusion tensor imaging (DTI) provides a means to reconstruct
fibre and sheet orientation throughout the ventricles. We
reconstruct and quantify canine cardiac architecture in selected
regions of the left and right ventricular free walls and the
inter-ventricular septum. Fibre inclination angle rotates smoothly
through the wall in all regions, from positive in the endocardium
to negative in the epicardium. However, fibre transverse and sheet
angles show large variability in basal regions. Additionally,
regions where two populations (positive and negative) of sheet
structure merge are identified. From these data, we conclude that
a single DTI-derived atlas model of ventricular architecture
should be applicable to modelling propagation in wedges from the
equatorial and apical left ventricle, and allow comparisons to
experimental studies carried out in wedge preparations. However,
due to inter-individual variability in basal regions, individual
(rather than atlas) DTI models of basal wedges or of the whole
ventricles will be required.
Previous applications of genetic programming (GP) have been restricted
to searching for algebraic approximations mapping the design parameters
(e.g., geometrical parameters) to a single design objective (e.g.,
weight). In addition, these algebraic expressions tend to be highly
complex. By adding a simple extension to the GP technique, a powerful
design data analysis tool is developed. This paper significantly extends
the analysis capabilities of GP by searching for multiple simple models
within a single population by splitting the population into multiple
islands according to the design variables used by individual members.
Where members from different islands “cooperate,” simple
design models can be extracted from this cooperation. This relatively
simple extension to GP is shown to have powerful implications to
extracting design models that can be readily interpreted and exploited by
human designers. The full analysis method, GP heuristics extraction
method, is described and illustrated by means of a design case study.