Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot.

More than any other genome components, Transposable Elements (TEs) have the capacity to move across species barriers through Horizontal Transfer (HT), with substantial evolutionary consequences. Previous large-scale surveys, based on full-genomes comparisons, have revealed the transposition mode as an important predictor of HT rates variation across TE superfamilies. However, host biology could represent another major explanatory factor, one that needs to be investigated through extensive taxonomic sampling. Here we test this hypothesis using a field collection of 460 arthropod species from Tahiti and surrounding islands. Through targeted massive parallel sequencing, we uncover patterns of HT in three widely-distributed TE superfamilies with contrasted modes of transposition. In line with earlier findings, the DNA transposons under study (TC1-Mariner) were found to transfer horizontally at the highest frequency, closely followed by the LTR superfamily (Copia), in contrast with the non-LTR superfamily (Jockey), that mostly diversifies through vertical inheritance and persists longer within genomes. Strikingly, across all superfamilies, we observe a marked excess of HTs in Lepidoptera, an insect order that also commonly hosts baculoviruses, known for their ability to transport host TEs. These results turn the spotlight on baculoviruses as major potential vectors of TEs in arthropods, and further emphasize the importance of non-vertical TE inheritance in genome evolution.

Ecological networks to unravel the routes to horizontal transposon transfers.

Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.

Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model.

Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning.Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.

Core-periphery dynamics in a plant-pollinator network.

Mutualistic networks are highly dynamic, characterized by high temporal turnover of species and interactions. Yet, we have a limited understanding of how the internal structure of these networks and the roles species play in them vary through time. We used 6 years of observation data and a novel statistical method (dynamic stochastic block models) to assess how network structure and species' structural position within the network change throughout subseasons of the flowering season and across years in a quantitative plant-pollinator network from a dryland ecosystem in Argentina. Our analyses revealed a core-periphery structure persistent through subseasons and years. Yet, species structural position as core or peripheral was highly dynamic: virtually all species that were at the core in some subseasons were also peripheral in other subseasons, while many other species always remained peripheral. Our results illuminate our understanding of the dynamics of mutualistic networks and have important implications for ecosystem management and conservation.

Diversity indices for ecological networks: a unifying framework using Hill numbers.

Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to understand and predict ecosystem trajectories. However, it requires having an appropriate framework to measure network diversity locally, regionally and between samples (α-, γ- and ß-diversity). Here, we propose a unifying framework that builds on Hill numbers and accounts both for the probabilistic nature of biotic interactions and the abundances of species or groups. We emphasise the importance of analysing network diversity across different species aggregation levels (e.g. from species to trophic groups) to get a better understanding of network structure. We illustrate our framework with a simulation experiment and an empirical analysis using a global food-web database. We discuss further usages of the framework and show how it responds to recent calls on comparing ecological networks and analysing their variation across environmental gradients and time.

How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience.

Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities' response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species (i.e., "multiplex networks"), as well as their consequences for community dynamics. Using network statistical modeling applied to a comprehensive ecological network, which includes trophic and diverse non-trophic links, we provide a first glimpse at what the full "entangled bank" of species looks like. The community exhibits clear multidimensional structure, which is taxonomically coherent and broadly predictable from species traits. Moreover, dynamic simulations suggest that this non-random patterning of how diverse non-trophic interactions map onto the food web could allow for higher species persistence and higher total biomass than expected by chance and tends to promote a higher robustness to extinctions.

Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies.

Masting, a breeding strategy common in perennial plants, is defined by seed production that is highly variable over years and synchronized at the population level. Resource budget models (RBMs) proposed that masting relies on two processes: (i) the depletion of plant reserves following high fruiting levels, which leads to marked temporal fluctuations in fruiting; and (ii) outcross pollination that synchronizes seed crops among neighboring trees. We revisited the RBM approach to examine the extent to which masting could be impacted by the degree of pollination efficiency, by taking into account various logistic relationships between pollination success and pollen availability. To link masting to other reproductive traits, we split the reserve depletion coefficient into three biological parameters related to resource allocation strategies for flowering and fruiting. While outcross pollination is considered to be the key mechanism that synchronizes fruiting in RBMs, our model counterintuitively showed that intense masting should arise under low-efficiency pollination. When pollination is very efficient, medium-level masting may occur, provided that the costs of female flowering (relative to pollen production) and of fruiting (maximum fruit set and fruit size) are both very high. Our work highlights the powerful framework of RBMs, which include explicit biological parameters, to link fruiting dynamics to various reproductive traits and to provide new insights into the reproductive strategies of perennial plants.

Treatment of holocord spinal epidural abscess via alternating side unilateral approach for bilateral laminectomy.

To date, this is the first reported case of the surgical management of a holocord epidural abscess done through level-skipping laminectomies. It is also the first reported case of these laminectomies being performed via an alternating side unilateral approach for this condition. A 51-year-old patient presenting with progressive lower extremity weakness secondary to a spinal epidural abscess extending from C4 to S1. A minimally disruptive method of relieving the spinal cord compression via evacuation of the abscess was employed successfully. This report demonstrates the efficacy of level skipping laminectomies via a unilateral approach for holocord epidural abscesses (extending 20 vertebral levels). Performing the laminectomies via a unilateral approach as well as alternating the side of the approach minimized iatrogenic instability risk. Both strategies were designed to minimize incision size, tissue disruption, and the amount of muscular weakness/imbalance postoperatively.

Restoration of sensory feedback from the foot and reduction of phantom limb pain via closed-loop spinal cord stimulation.

Restoring somatosensory feedback in individuals with lower-limb amputations would reduce the risk of falls and alleviate phantom limb pain. Here we show, in three individuals with transtibial amputation (one traumatic and two owing to diabetic peripheral neuropathy), that sensations from the missing foot, with control over their location and intensity, can be evoked via lateral lumbosacral spinal cord stimulation with commercially available electrodes and by modulating the intensity of stimulation in real time on the basis of signals from a wireless pressure-sensitive shoe insole. The restored somatosensation via closed-loop stimulation improved balance control (with a 19-point improvement in the composite score of the Sensory Organization Test in one individual) and gait stability (with a 5-point improvement in the Functional Gait Assessment in one individual). And over the implantation period of the stimulation leads, the three individuals experienced a clinically meaningful decrease in phantom limb pain (with an average reduction of nearly 70% on a visual analogue scale). Our findings support the further clinical assessment of lower-limb neuroprostheses providing somatosensory feedback.

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

MOTIVATION: Proteins can be naturally classified into families of homologous sequences that derive from a common ancestor. The comparison of homologous sequences and the analysis of their phylogenetic relationships provide useful information regarding the function and evolution of genes. One important difficulty of clustering methods is to distinguish highly divergent homologous sequences from sequences that only share partial homology due to evolution by protein domain rearrangements. Existing clustering methods require parameters that have to be set a priori. Given the variability in the evolution pattern among proteins, these parameters cannot be optimal for all gene families. RESULTS: We propose a strategy that aims at clustering sequences homologous over their entire length, and that takes into account the pattern of substitution specific to each gene family. Sequences are first all compared with each other and clustered into pre-families, based on pairwise similarity criteria, with permissive parameters to optimize sensitivity. Pre-families are then divided into homogeneous clusters, based on the topology of the similarity network. Finally, clusters are progressively merged into families, for which we compute multiple alignments, and we use a model selection technique to find the optimal tradeoff between the number of families and multiple alignment likelihood. To evaluate this method, called HiFiX, we analyzed simulated sequences and manually curated datasets. These tests showed that HiFiX is the only method robust to both sequence divergence and domain rearrangements. HiFiX is fast enough to be used on very large datasets. AVAILABILITY AND IMPLEMENTATION: The Python software HiFiX is freely available at http://lbbe.univ-lyon1.fr/hifix.

Ultra-fast sequence clustering from similarity networks with SiLiX.

BACKGROUND: The number of gene sequences that are available for comparative genomics approaches is increasing extremely quickly. A current challenge is to be able to handle this huge amount of sequences in order to build families of homologous sequences in a reasonable time. RESULTS: We present the software package SiLiX that implements a novel method which reconsiders single linkage clustering with a graph theoretical approach. A parallel version of the algorithms is also presented. As a demonstration of the ability of our software, we clustered more than 3 millions sequences from about 2 billion BLAST hits in 7 minutes, with a high clustering quality, both in terms of sensitivity and specificity. CONCLUSIONS: Comparing state-of-the-art software, SiLiX presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. SiLiX is freely available at http://lbbe.univ-lyon1.fr/SiLiX.

Evaluation of free-hand screw placement in cervical, thoracic, and lumbar spine by neurosurgical residents.

BACKGROUND: Knowledge of free-hand screw technique remains critical to adequately train neurosurgical residents. The purpose of this study was to evaluate the accuracy of screw placement via the free-hand technique in lumbar, thoracic, and cervical spine by neurosurgical residents completing an enfolded spine fellowship. METHODS: Medical records of all patients who underwent free-hand screw placement at all spinal levels over a 6-month period by senior neurosurgical residents enrolled in an in-folded spine fellowship were retrospectively reviewed. Postoperative CT images were assessed for presence and direction of cortical breach. RESULTS: Twenty-six patients underwent 162 free-hand screw placements. The most commonly placed screws were cervical lateral mass screws (n = 69), thoracic (n = 41), and lumbar pedicle screws (n = 41). The most common indication for surgery was deformity (n = 22), followed by infection (n = 2) and trauma (n = 2). Fifty-five breaches were identified in 44 (27 %) screws placed in 21 patients (81 %). Anterior breach was identified in 22 cases (40.0 %), lateral in 12 (23.6 %), superior in 7 (12.7 %), and inferior in 7 (12.7 %), and medial in 6 (10.9 %). The most common level of breach was observed in cervical lateral mass screws (n = 19, 43 %) and least common in C2 pars screws (n = 1, 2%). With an average length of follow up of 12.1 ± 7.7 months of follow-up, no clinical sequalae of screw breach was observed. CONCLUSIONS: Despite the high prevalence of screw breach using the free-hand technique by neurosurgical residents, the absence of clinical sequelae implies safety and emphasizes the importance of early exposure to this technique during neurosurgical residency training.

Impact of Coronavirus Disease 2019 Shutdown on Neurotrauma Volume in Pennsylvania.

OBJECTIVE: The 2020 coronavirus disease 2019 (COVID-19) pandemic resulted in state-specific quarantine protocols and introduced the concept of social distancing into modern parlance. We assess the impact of the COVID-19 pandemic on neurotrauma presentations in the first 3 months after shutdown throughout Pennsylvania. METHODS: The Pennsylvania Trauma Systems Foundation was queried for registry data from the Pennsylvania Trauma Outcomes Study between March 12 and June 5 in each year from 2017 to 2020. RESULTS: After the COVID-19 shutdown, there was a 27% reduction in neurotrauma volume, from 2680 cases in 2017 to 2018 cases in 2020, and a 28.8% reduction in traumatic brain injury volume. There was no significant difference in neurotrauma phenotype incurred relative to total cases. Injury mechanism was less likely to be motor vehicle collision and more likely caused by falls, gunshot wound, and recreational vehicle accidents (P < 0.05). Location of injury was less likely on roads and public locations and more likely at indoor private locations (P < 0.05). The proportion of patients with neurotrauma with blood alcohol concentration >0.08 g/dL was reduced in 2020 (11.4% vs. 9.0%; P < 0.05). Mortality was higher during 2020 compared with pre-COVID years (7.7% vs. 6.4%; P < 0.05). CONCLUSIONS: During statewide shutdown, neurotrauma volume and alcohol-related trauma decreased and low-impact traumas and gunshot wounds increased, with a shift toward injuries occurring in private, indoor locations. These changes increased mortality. However, there was not a change in the types of injuries sustained.

Sport-Related Structural Brain Injury and Return to Play: Systematic Review and Expert Insight.

BACKGROUND: Sport-related structural brain injury (SRSBI) is intracranial pathology incurred during sport. Management mirrors that of non-sport-related brain injury. An empirical vacuum exists regarding return to play (RTP) following SRSBI. OBJECTIVE: To provide key insight for operative management and RTP following SRSBI using a (1) focused systematic review and (2) survey of expert opinions. METHODS: A systematic literature review of SRSBI from 2012 to present in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and a cross-sectional survey of RTP in SRSBI by 31 international neurosurgeons was conducted. RESULTS: Of 27 included articles out of 241 systematically reviewed, 9 (33.0%) case reports provided RTP information for 12 athletes. To assess expert opinion, 31 of 32 neurosurgeons (96.9%) provided survey responses. For acute, asymptomatic SRSBI, 12 (38.7%) would not operate. Of the 19 (61.3%) who would operate, midline shift (63.2%) and hemorrhage size > 10 mm (52.6%) were the most common indications. Following SRSBI with resolved hemorrhage, with or without burr holes, the majority of experts (>75%) allowed RTP to high-contact/collision sports at 6 to 12 mo. Approximately 80% of experts did not endorse RTP to high-contact/collision sports for athletes with persistent hemorrhage. Following craniotomy for SRSBI, 40% to 50% of experts considered RTP at 6 to 12 mo. Linear regression revealed that experts allowed earlier RTP at higher levels of play (ß = -0.58, 95% CI -0.111, -0.005, P = .033). CONCLUSION: RTP decisions following structural brain injury in athletes are markedly heterogeneous. While individualized RTP decisions are critical, aggregated expert opinions from 31 international sports neurosurgeons provide key insight. Level of play was found to be an important consideration in RTP determinations.

DNA physical properties determine nucleosome occupancy from yeast to fly.

Nucleosome positioning plays an essential role in cellular processes by modulating accessibility of DNA to proteins. Here, using only sequence-dependent DNA flexibility and intrinsic curvature, we predict the nucleosome occupancy along the genomes of Saccharomyces cerevisiae and Drosophila melanogaster and demonstrate the predictive power and universality of our model through its correlation with experimentally determined nucleosome occupancy data. In yeast promoter regions, the computed average nucleosome occupancy closely superimposes with experimental data, exhibiting a <200 bp region unfavourable for nucleosome formation bordered by regions that facilitate nucleosome formation. In the fly, our model faithfully predicts promoter strength as encoded in distinct chromatin architectures characteristic of strongly and weakly expressed genes. We also predict that nucleosomes are repositioned by active mechanisms at the majority of fly promoters. Our model uses only basic physical properties to describe the wrapping of DNA around the histone core, yet it captures a substantial part of chromatin's structural complexity, thus leading to a much better prediction of nucleosome occupancy than methods based merely on periodic curved DNA motifs. Our results indicate that the physical properties of the DNA chain, and not just the regulatory factors and chromatin-modifying enzymes, play key roles in eukaryotic transcription.

Measuring Blunt Force Head Impacts in Athletes.

INTRODUCTION: Although concussion continues to be a major source of acute and chronic injuries, concussion injury mechanisms and risk functions are ill-defined. This lack of definition has hindered efforts to develop standardized concussion monitoring, safety testing, and protective countermeasures. To overcome this knowledge gap, we have developed, tested, and deployed a head impact monitoring mouthguard (IMM) system. MATERIALS AND METHODS: The IMM system was first calibrated in 731 laboratory tests. Versus reference, Laboratory IMM data fit a linear model, with results close to the ideal linear model of form y = x + 0, R2 = 1. Next, during on-field play involving n = 54 amateur American athletes in football and boxing, there were tens of thousands of events collected by the IMM. A total of 890 true-positive head impacts were confirmed using a combination of signal processing and National Institute of Neurological Disorders and Stroke/National Institutes of Health Common Data Elements methods. RESULTS: The median and 99th percentile of peak scalar linear acceleration and peak angular acceleration were 20 and 50 g and 1,700 and 4,600 rad/s2, respectively. No athletes were diagnosed with concussion. CONCLUSIONS: While these data are useful for preliminary human tolerance limits, a larger population must be used to quantify real-world dose response as a function of impact magnitude, direction, location, and accumulation. This work is ongoing.

High Energy Side and Rear American Football Head Impacts Cause Obvious Performance Decrement on Video.

The objective of this study was to compare head impact data acquired with an impact monitoring mouthguard (IMM) to the video-observed behavior of athletes' post-collision relative to their pre-collision behaviors. A total of n = 83 college and high school American football players wore the IMM and were video-recorded over 260 athlete-exposures. Ex-athletes and clinicians reviewed the video in a two-step process and categorized abnormal post-collision behaviors according to previously published Obvious Performance Decrement (OPD) definitions. Engineers qualitatively reviewed datasets to check head impact and non-head impact signal frequency and magnitude. The ex-athlete reviewers identified 2305 head impacts and 16 potential OPD impacts, 13 of which were separately categorized as Likely-OPD impacts by the clinical reviewers. All 13 Likely-OPD impacts were in the top 1% of impacts measured by the IMM (ranges 40-100 g, 3.3-7.0 m/s and 35-118 J) and 12 of the 13 impacts (92%) were to the side or rear of the head. These findings require confirmation in a larger data set before proposing any type of OPD impact magnitude or direction threshold exists. However, OPD cases in this study compare favorably with previously published impact monitoring studies in high school and college American football players that looked for OPD signs, impact magnitude and direction. Our OPD findings also compare well with NFL reconstruction studies for ranges of concussion and sub-concussive impact magnitudes in side/rear collisions, as well as prior theory, analytical models and empirical research that suggest a directional sensitivity to brain injury exists for single high-energy impacts.

Deciphering the connectivity structure of biological networks using MixNet.

BACKGROUND: As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of the network's topology into a small number of relevant classes. Different strategies are possible for clustering, and in this article we focus on a model-based strategy that aims at clustering nodes based on their connectivity profiles. RESULTS: We present MixNet, the first publicly available computer software that analyzes biological networks using mixture models. We apply this method to various networks such as the E. coli transcriptional regulatory network, the macaque cortex network, a foodweb network and the Buchnera aphidicola metabolic network. This method is also compared with other approaches such as module identification or hierarchical clustering. CONCLUSION: We show how MixNet can be used to extract meaningful biological information, and to give a summary of the networks topology that highlights important biological features. This approach is powerful as MixNet is adaptive to the network under study, and finds structural information without any a priori on the structure that is investigated. This makes MixNet a very powerful tool to summarize and decipher the connectivity structure of biological networks.

Long term delay in onset of prevertebral hematoma following anterior cervical discectomy and fusion: A case report.

Post-operative hematoma following anterior cervical discectomy and fusion (ACDF) is an uncommon but feared complication. Typically, these complications present in the immediate post-operative period. We present a case of a 51 year-old woman who underwent a C4-5 ACDF for left sided radicular pain. Her immediate post-operative course was uncomplicated, but she presented 6 weeks subsequently to the emergency department with neck swelling, difficulty swallowing, cough, and shortness of breath. She was found to have a 4.5 cm anterior neck hematoma with settling of the instrumentation and a new C4 vertebral fragment protruding anteriorly. She underwent evacuation of hematoma without clear evidence of a bleeding source. After several days of observation, she was discharged home and ultimately had resolution of her presenting symptoms. Most hematomas resulting in airway compromise appear in the immediate post-operative period, but a high index of suspicion must remain high in any patient with a prior anterior cervical surgery presenting with symptoms of pre-vertebral compression or respiratory compromise.