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.

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.

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.

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.

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.

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.

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.

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.

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.

Laboratory and On-field Data Collected by a Head Impact Monitoring Mouthguard.

Although concussion continues to be a major source of acute and chronic injury in automotive, athletic and military arenas, 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. Recent research has provided evidence of the role of repetitive head impact exposure as a predisposing factor for the onset of concussion using developed instrumented helmets and mouthguards.To overcome this knowledge gap, we have developed, tested and deployed a head impact monitoring mouthguard (IMM) system. In this study, we deployed the IMM system to gather high quality estimates of athlete head impacts in situ. And with enough longer-term data collection, potential concussive events or mild traumatic brain injuries (mTBIs) will be gathered and ideally will provide actionable risk-based threshold.

Revealing the hidden structure of dynamic ecological networks.

In ecology, recent technological advances and long-term data studies now provide longitudinal interaction data (e.g. between individuals or species). Most often, time is the parameter along which interactions evolve but any other one-dimensional gradient (temperature, altitude, depth, humidity, etc.) can be considered. These data can be modelled through a sequence of different snapshots of an evolving ecological network, i.e. a dynamic network. Here, we present how the dynamic stochastic block model approach developed by Matias & Miele (Matias & Miele In press J. R. Stat. Soc. B (doi:10.1111/rssb.12200)) can capture the complexity and dynamics of these networks. First, we analyse a dynamic contact network of ants and we observe a clear high-level assembly with some variations in time at the individual level. Second, we explore the structure of a food web evolving during a year and we detect a stable predator-prey organization but also seasonal differences in the prey assemblage. Our approach, based on a rigorous statistical method implemented in the R package dynsbm, can pave the way for exploration of evolving ecological networks.

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

BACKGROUND: The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this problem has been underestimated so far. Even though we have fewer and shorter repeated sequences in transcriptomics, they do create ambiguities and confuse assemblers if not addressed properly. Most transcriptome assemblers of short reads are based on de Bruijn graphs (DBG) and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. RESULTS: The results of this work are threefold. First, we introduce a formal model for representing high copy-number and low-divergence repeats in RNA-seq data and exploit its properties to infer a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying such subgraphs in a DBG is NP-complete. Second, we show that in the specific case of local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs, and we present an efficient algorithm to enumerate AS events that are not included in repeats. Using simulated data, we show that this strategy is significantly more sensitive and precise than the previous version of KisSplice (Sacomoto et al. in WABI, pp 99-111, 1), Trinity (Grabherr et al. in Nat Biotechnol 29(7):644-652, 2), and Oases (Schulz et al. in Bioinformatics 28(8):1086-1092, 3), for the specific task of calling AS events. Third, we turn our focus to full-length transcriptome assembly, and we show that exploring the topology of DBGs can improve de novo transcriptome evaluation methods. Based on the observation that repeats create complicated regions in a DBG, and when assemblers try to traverse these regions, they can infer erroneous transcripts, we propose a measure to flag transcripts traversing such troublesome regions, thereby giving a confidence level for each transcript. The originality of our work when compared to other transcriptome evaluation methods is that we use only the topology of the DBG, and not read nor coverage information. We show that our simple method gives better results than Rsem-Eval (Li et al. in Genome Biol 15(12):553, 4) and TransRate (Smith-Unna et al. in Genome Res 26(8):1134-1144, 5) on both real and simulated datasets for detecting chimeras, and therefore is able to capture assembly errors missed by these methods.

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.

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.

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

BACKGROUND: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. FINDINGS: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. CONCLUSIONS: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.