Adaptations of Lumbar Biomechanics after Four Weeks of Running Training with Minimalist Footwear and Technique guidance: Implications for Running-Related Lower Back Pain

Objectives To investigate the changes in lumbar kinematic and paraspinal muscle activation before, during, and after a 4-week minimalist running training. Design Prospective cohort study. Setting University research laboratory. Participants Seventeen habitually shod recreational runners who run 10–50 km per week. Main outcome measures During stance phases of running, sagittal lumbar kinematics was recorded using an electrogoniometer, and activities of the lumbar paraspinal muscles were assessed by electromyography. Runners were asked to run at a prescribed speed (3.1 m/s) and a self-selected speed. Results For the 3.1 m/s running speed, significant differences were found in the calculated mean lumbar posture (p = 0.001) during the stance phase, including a more extended lumbar posture after minimalist running training. A significant reduction in the contralateral lumbar paraspinal muscle activation was also observed (p = 0.039). For the preferred running speed, similar findings of a more extended lumbar posture (p = 0.002) and a reduction in contralateral lumbar paraspinal muscle activation (p = 0.047) were observed. Conclusion A 4-week minimalist running training program produced significant changes in lumbar biomechanics during running. Specifically, runners adopted a more extended lumbar posture and reduced lumbar paraspinal muscle activation. These findings may have clinical implications for treating individuals with running-related lower back pain

Classification of lapses in smokers attempting to stop: A supervised machine learning approach using data from a popular smoking cessation smartphone app

Introduction Smoking lapses after the quit date often lead to full relapse. To inform the development of real-time, tailored lapse prevention support, we used observational data from a popular smoking cessation app to develop supervised machine learning algorithms to distinguish lapse from non-lapse reports. Methods We used data from app users with ≥20 unprompted data entries, which included information about craving severity, mood, activity, social context, and lapse incidence. A series of group-level supervised machine learning algorithms (e.g., Random Forest, XGBoost) were trained and tested. Their ability to classify lapses for out-of-sample i) observations and ii) individuals were evaluated. Next, a series of individual-level and hybrid algorithms were trained and tested. Results Participants (N=791) provided 37,002 data entries (7.6% lapses). The best-performing group-level algorithm had an area under the receiver operating characteristic curve (AUC) of 0.969 (95% CI= 0.961-0.978). Its ability to classify lapses for out-of-sample individuals ranged from poor to excellent (AUC=0.482-1.000). Individual-level algorithms could be constructed for 39/791 participants with sufficient data, with a median AUC of 0.938 (range: 0.518-1.000). Hybrid algorithms could be constructed for 184/791 participants and had a median AUC of 0.825 (range: 0.375-1.000). Discussion Using unprompted app data appeared feasible for constructing a high-performing group-level lapse classification algorithm but its performance was variable when applied to unseen individuals. Algorithms trained on each individual’s dataset, in addition to hybrid algorithms trained on the group plus a proportion of each individual’s data, had improved performance but could only be constructed for a minority of participants. Implications This study used routinely collected data from a popular smartphone app to train and test a series of supervised machine learning algorithms to distinguish lapse from non-lapse events. Although a high-performing group-level algorithm was developed, it had variable performance when applied to new, unseen individuals. Individual-level and hybrid algorithms had somewhat greater performance but could not be constructed for all participants due to lack of variability in the outcome measure. Triangulation of results with those from a prompted study design is recommended prior to intervention development, with real-world lapse prediction likely requiring a balance between unprompted and prompted app data

Worse Postoperative Outcomes and Higher Reoperation in Smokers Compared to Nonsmokers for Arthroscopic Rotator Cuff Repair

Introduction: Smoking impairs healing potential and is a significant risk factor for complications following orthopaedic surgeries. The purpose of this study was to determine if a cohort of former or current smokers at time of surgery met the minimally clinical important difference (MCID) for Patient-Reported Outcomes Measurement Information System Upper Extremity (PROMIS-UE), Depression (PROMIS-D), and Pain Interference (PROMIS-PI) scores in comparison to nonsmokers. Methods: A retrospective review of patients who underwent rotator cuff repair was performed. Patients who completed preoperative and 6-month postoperative PROMIS scores were included. The MCID was calculated using a distribution technique with a threshold of 0.5 standard deviations above the mean. A cohort of nonsmokers was compared to current/former smokers in terms of clinical outcomes and PROMIS scores. Results: A total of 182 patients, 80 current/former smokers and 102 nonsmokers, were included. Smokers had significantly more massive-sized tears and more reoperations (16.3% vs 5.9%,P=0.02). No differences were found in change in PROMIS scores, proportion meeting MCID for PROMIS scores, and retear rate. In the sub-analysis, 74 current/former smokers were matched to 74 nonsmokers. Smokers had lower change in PROMIS-UE (8.6±9.8 vs 12.3±10.0,P=0.007) and PROMIS-PI (-9.1±8.5 vs -12.8±10.1,P=0.03) postoperatively. Fewer met MCID for PROMIS UE postoperatively (60.3% vs 82.4%,P=0.003) and more had reoperations (16.2% vs 4.1%,P=0.02). Conclusion: Smokers or former smokers demonstrated smaller improvements in function, pain scores, and were less likely to meet MCID for PROMIS-UE when compared to nonsmokers after arthroscopic rotator cuff repair. Smokers were more likely to undergo reoperations within 6 months

Phylogeographical Structure and Evolutionary History of Two Buggy Creek Virus Lineages in the Western Great Plains of North America

Buggy Creek virus (BCRV) is an unusual arbovirus within the western equine encephalitis complex of alphaviruses. Associated with cimicid swallow bugs (Oeciacus vicarius) as its vector and the cliff swallow (Petrochelidon pyrrhonota) and house sparrow (Passer domesticus) as its amplifying hosts, this virus is found primarily in the western Great Plains of North America at spatially discrete swallow nesting colonies. For 342 isolates collected in Oklahoma, Nebraska, Colorado, and North Dakota, from 1974 to 2007, we sequenced a 2076 bp region of the 26S subgenomic RNA structural glycoprotein coding region, and analyzed phylogenetic relationships, rates of evolution, demographical histories and temporal genetic structure of the two BCRV lineages found in the Great Plains. The two lineages showed distinct phylogeographical structure: one lineage was found in the southern Great Plains and the other in the northern Great Plains, and both occurred in Nebraska and Colorado. Within each lineage, there was additional latitudinal division into three distinct sublineages. One lineage is showing a long-term population decline. In comparing sequences taken from the same sites 8–30 years apart, in one case one lineage had been replaced by the other, and in the other cases there was little evidence of the same haplotypes persisting over time. The evolutionary rate of BCRV is in the order of 1.6–3.6 × 10–4 substitutions per site per year, similar to that estimated for other temperate-latitude alphaviruses. The phylogeography and evolution of BCRV could be better understood once we determine the nature of the ecological differences between the lineages

Phylogeographical Structure and Evolutionary History of Two Buggy Creek Virus Lineages in the Western Great Plains of North America

Buggy Creek virus (BCRV) is an unusual arbovirus within the western equine encephalitis complex of alphaviruses. Associated with cimicid swallow bugs (Oeciacus vicarius) as its vector and the cliff swallow (Petrochelidon pyrrhonota) and house sparrow (Passer domesticus) as its amplifying hosts, this virus is found primarily in the western Great Plains of North America at spatially discrete swallow nesting colonies. For 342 isolates collected in Oklahoma, Nebraska, Colorado, and North Dakota, from 1974 to 2007, we sequenced a 2076 bp region of the 26S subgenomic RNA structural glycoprotein coding region, and analyzed phylogenetic relationships, rates of evolution, demographical histories and temporal genetic structure of the two BCRV lineages found in the Great Plains. The two lineages showed distinct phylogeographical structure: one lineage was found in the southern Great Plains and the other in the northern Great Plains, and both occurred in Nebraska and Colorado. Within each lineage, there was additional latitudinal division into three distinct sublineages. One lineage is showing a long-term population decline. In comparing sequences taken from the same sites 8–30 years apart, in one case one lineage had been replaced by the other, and in the other cases there was little evidence of the same haplotypes persisting over time. The evolutionary rate of BCRV is in the order of 1.6–3.6 × 10–4 substitutions per site per year, similar to that estimated for other temperate-latitude alphaviruses. The phylogeography and evolution of BCRV could be better understood once we determine the nature of the ecological differences between the lineages

Genetic control of root architectural plasticity in maize

© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-quality reference genomes for single nucleotide polymorphism (SNP) discovery using the critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform reference genomes as proof of concept. We compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) based on kakī SNPs discovered from genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome. Congeneric and confamilial references provide higher correlations and more similar measures of nucleotide diversity, individual heterozygosity, and relatedness. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species

Ion-channel function and cross-species determinants in viral assembly of nonprimate hepacivirus p7

Nonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to date, has recently been discovered in horses. Even though the two viruses share a similar genomic organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for the production of infectious particles. In this study, we analyzed the structural and functional features of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models for NPHV p7 using various nuclear magnetic resonance spectroscopy (NMR) structures were generated, highlighting the conserved residues important for ion channel function. By applying a liposome permeability assay, we observed that NPHV p7 exhibited liposome permeability features similar to those of HCV p7, indicative of similar ion channel activity. Next, we characterized the viral protein using a p7-based trans-complementation approach. A similar subcellular localization pattern at the ER membrane was observed, although production of infectious particles was likely hindered by genetic incompatibilities with HCV proteins. To further characterize these cross-species constraints, chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. The N terminus and transmembrane domains were nonexchangeable and therefore constitute a cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious trans-complemented viral particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins, including liposome permeability, and broadly acting determinants that modulate hepaciviral virion assembly and contribute to the host-species barrier were identified

Infiltration efficiency and subsurface water processes of a sustainable drainage system and consequences to flood management

With increased intensity rainfall events globally and urban expansion decreasing permeable surfaces, there is an increasing problem of urban flooding. This study aims to better understand rainfall infiltration into a Sustainable Drainage System (SuDS) permeable pavement, compared with an adjacent Green Area of made ground, in relationship to groundwater levels below both areas. Both areas were instrumented with soil water content and matric potential sensors and four shallow boreholes were instrumented with groundwater level sensors. Surface infiltration rates were measured using a double‐ring infiltrometer. Results showed that average infiltration rates of the SuDS (1,925 mm/hr) were significantly higher than the Green Area (56 mm/hr). The SuDS was well designed to transfer rainfall rapidly to the aquifer below, where groundwater levels rapidly rose within 1 hr of a 1 in 30 year event (32.8 mm/hr). In comparison, soil compaction of the made ground Green Area decreased infiltration rates, but still enabled the majority of rainfall events to infiltrate. The aquifer below the Green Area responded more slowly, as lower matrix potentials facilitated water retention in the soil profile, slowing water draining to the aquifer. This work reiterates the importance of ensuring a 1 m separation depth between the base of the SuDS infiltration zone and aquifer depth