Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain white matter damage and its association with neuronal synchrony during sleep

The restorative function of sleep partly relies on its ability to deeply synchronize cerebral networks to create large slow oscillations observable with EEG. However, whether a brain can properly synchronize and produce a restorative sleep when it undergoes massive and widespread white matter damage is unknown. Here, we answer this question by testing 23 patients with various levels of white matter damage secondary to moderate to severe traumatic brain injuries (ages 18-56; 17 males, six females, 11-39 months post-injury) and compared them to 27 healthy subjects of similar age and sex. We used MRI and diffusion tensor imaging metrics (e.g. fractional anisotropy as well as mean, axial and radial diffusivities) to characterize voxel-wise white matter damage. We measured the following slow wave characteristics for all slow waves detected in N2 and N3 sleep stages: peak-to-peak amplitude, negative-to-positive slope, negative and positive phase durations, oscillation frequency, and slow wave density. Correlation analyses were performed in traumatic brain injury and control participants separately, with age as a covariate. Contrary to our hypotheses, we found that greater white matter damage mainly over the frontal and temporal brain regions was strongly correlated with a pattern of higher neuronal synchrony characterized by slow waves of larger amplitudes and steeper negative-to-positive slopes during non-rapid eye movement sleep. The same pattern of associations with white matter damage was also observed with markers of high homeostatic sleep pressure. More specifically, higher white matter damage was associated with higher slow-wave activity power, as well as with more severe complaints of cognitive fatigue. These associations between white matter damage and sleep were found only in our traumatic brain injured participants, with no such correlation in controls. Our results suggest that, contrary to previous observations in healthy controls, white matter damage does not prevent the expected high cerebral synchrony during sleep. Moreover, our observations challenge the current line of hypotheses that white matter microstructure deterioration reduces cerebral synchrony during sleep. Our results showed that the relationship between white matter and the brain's ability to synchronize during sleep is neither linear nor simple.
Early Cardiac Mitochondrial Molecular and Functional Responses to Acute Anthracycline Treatment in Wistar Rats.

Doxorubicin (DOX) is an anticancer drug widely used to treat human and nonhuman tumors but the late and persistent cardio-toxicity reduces the therapeutic utility of the drug. The full mechanism(s) of DOX-induced acute, subchronic and delayed toxicity, which has a preponderant mitochondrial component, remains unclear; therefore, it is clinically relevant to identify early markers to identify patients who are predisposed to DOX-related cardiovascular toxicity. To address this, Wistar rats (16 weeks old) were treated with a single DOX dose (20 mg/kg, i.p.); then, mRNA, protein levels and functional analysis of mitochondrial endpoints were assessed 24 h later in the heart, liver, and kidney. Using an exploratory data analysis, we observed cardiac-specific alterations after DOX treatment for mitochondrial complexes III, IV, and preferentially for complex I. Conversely, the same analysis revealed complex II alterations are associated with DOX response in the liver and kidney. Interestingly, H2O2 production by the mitochondrial respiratory chain as well as loss of calcium-loading capacity, markers of subchronic toxicity, were not reliable indicators of acute DOX cardiotoxicity in this animal model. By using sequential principal component analysis and feature correlation analysis, we demonstrated for the first time alterations in sets of transcripts and proteins, but not functional measurements, that might serve as potential early acute markers of cardiac-specific mitochondrial toxicity, contributing to explain the trajectory of DOX cardiac toxicity and to develop novel interventions to minimize DOX cardiac liabilities.
Inhibition of microRNA‐92a increases blood vessels and satellite cells in skeletal muscle but does not improve duchenne muscular dystrophy–related phenotype in mdx mice

Introduction: The vasculature and blood flow in muscle are perturbed in Duchenne muscular dystrophy (DMD) and its mdx mouse model. MicroRNA‐92a (miR‐92a) is enriched in endothelial cells, especially during ischemic injury. Methods: Because antagonizing miR‐92a was shown to result in increased proliferation and migration of endothelial cells and recovery from ischemia, we assessed the effects of Antagomir‐92a in vitro in muscle stem cell culture and in vivo in mdx mice. Results: miR‐92a was found to be highly expressed in muscle endothelial cells and satellite cells. Treatment with Antagomir‐92a increased capillary density and tissue perfusion, which was accompanied by an increase in satellite cells. However, Antagomir‐92a–treated mdx mice showed no histological improvement and had worse muscle function. Antagomir‐92a suppressed myogenic differentiation in satellite cell culture. Discussion: AntagomiR‐92a improves the vasculature but not the muscle in mdx mice, possibly due to its side effects on satellite cell differentiation. Muscle Nerve 59:594–594, 2019
Randomized controlled trial of Web‐based weight‐loss intervention with human support for male workers under 40

Human support can boost weight reduction in Internet‐based weight‐loss intervention. However, the most effective way to combine human support and the Internet for weight loss is unclear. This study aimed to examine the effects of two weight‐loss programs for male workers aged 18‐39 that combined different intensities of human support with website support compared to a delayed‐intervention group (control group; CG), in a randomized controlled trial.
A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

Abstract Background Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage Pacific Biosciences long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes, which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
An efficient method for extracting next‐generation sequencing quality RNA from liver tissue of recalcitrant animal species

The next‐generation RNA sequencing technologies expedite the discovery of a large number of novel transcripts and genes associated with various pathophysiological conditions. These technologies involve poly(A) enrichment, which in turn requires micrograms of high‐quality total RNA. Unfortunately, the available RNA isolation approaches produce poor quality total RNA from difficult‐to‐isolate animal tissues, such as the liver with high glycogen content. Moreover, the extraction efficiencies of these approaches vary significantly depending on the animal species. To address this challenge, we optimized a three‐step protocol for the extraction of high‐yield and high‐quality total RNA from the liver tissue (LT). The procedure effectively resolved the problem of glycogen coprecipitation by its stepwise removal. No signs of RNA degradation on gel electrophoresis analysis and RNA integrity number values ≥8.5 indicated that the extracted RNA is suitable for downstream processing, such as poly(A) enrichment and transcriptome profiling. To demonstrate the robustness of the novel protocol, a comparison was made with other currently available RNA extraction approaches from diverse resources. Whereas other protocols yielded partially degraded bands with either decreased or reversed ribosomal RNA (rRNA) ratio, our protocol yielded intact rRNA with a ratio of 2.0 ± 0.1. This optimized protocol was also successfully followed for other animal tissues, such as the bone and muscles. In conclusion, the study has described a highly efficient method for the next‐generation sequencing quality RNA isolation from LT across a broad range of animal species, with extended applicability to other difficult‐to‐isolate tissues.
Perceptions of Visualizing Physical Activity as a 3D-Printed Object: Formative Study

Background The UK government recommends that children engage in moderate-to-vigorous physical activity for at least 60 min every day. Despite associated physiological and psychosocial benefits of physical activity, many youth fail to meet these guidelines partly due to sedentary screen-based pursuits displacing active behaviors. However, technological advances such as 3D printing have enabled innovative methods of visualizing and conceptualizing physical activity as a tangible output. Objective The aim of this study was to elicit children’s, adolescents’, parents’, and teachers’ perceptions and understanding of 3D physical activity objects to inform the design of future 3D models of physical activity. Methods A total of 28 primary school children (aged 8.4 [SD 0.3] years; 15 boys) and 42 secondary school adolescents (aged 14.4 [SD 0.3] years; 22 boys) participated in semistructured focus groups, with individual interviews conducted with 8 teachers (2 male) and 7 parents (2 male). Questions addressed understanding of the physical activity guidelines, 3D model design, and both motivation for and potential engagement with a 3D physical activity model intervention. Pupils were asked to use Play-Doh to create and describe a model that could represent their physical activity levels (PAL). Data were transcribed verbatim and thematically analyzed, and key emergent themes were represented using pen profiles. Results Pupils understood the concept of visualizing physical activity as a 3D object, although adolescents were able to better analyze and critique differences between low and high PAL. Both youths and adults preferred a 3D model representing a week of physical activity data when compared with other temporal representations. Furthermore, all participants highlighted that 3D models could act as a motivational tool to enhance youths’ physical activity. From the Play-Doh designs, 2 key themes were identified by pupils, with preferences indicated for models of abstract representations of physical activity or bar charts depicting physical activity, respectively. Conclusions These novel findings highlight the potential utility of 3D objects of physical activity as a mechanism to enhance children’s and adolescents’ understanding of, and motivation to increase, their PAL. This study suggests that 3D printing may offer a unique strategy for promoting physical activity in these groups.
MACPET: model-based analysis for ChIA-PET

We present Model-based Analysis for ChIA-PET (MACPET) which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared to MACS in terms of motif occurrence, spatial resolution and false discovery rate. Significant binding sites discovered by MACPET are involved in a higher number of significant 3D interactions than those discovered by MACS. MACPET is freely available on Bioconductor.
Brain atlas of the African mole‐rat Fukomys anselli

African mole‐rats are subterranean rodents that spend their whole life in underground burrow systems. They show a range of morphological and physiological adaptations to their ecotope, for instance severely reduced eyes and specialized somatosensory, olfactory, and auditory systems. These adaptations are also reflected in the accessory sensory pathways in the brain that process the input coming from the sensory organs. So far, a brain atlas was available only for the naked mole‐rat (Heterocephalus glaber). The Ansell's mole‐rat (Fukomys anselli) has been the subject of many investigations in various disciplines (ethology, sensory physiology, and anatomy) including magnetic orientation. It is therefore surprising that an atlas of the brain of this species was not available so far. Here, we present a comprehensive atlas of the Ansell's mole‐rat brain based on Nissl and Klüver‐Barrera stained sections. We identify and label 375 brain regions and discuss selected differences from the brain of the closely related naked mole‐rat as well as from epigeic mammals (rat), with a particular focus on the auditory brainstem. This atlas can serve as a reference for future neuroanatomical investigations of subterranean mammals.
Antibiotic prescribing for residents in long-term-care facilities across the UK

Abstract Background Antimicrobial resistance (AMR) is a major public health problem. Elderly residents in long-term-care facilities (LTCFs) are frequently prescribed antibiotics, particularly for urinary tract infections. Optimizing appropriate antibiotic use in this vulnerable population requires close collaboration between NHS healthcare providers and LTCF providers. Objectives Our aim was to identify and quantify antibiotic prescribing in elderly residents in UK LTCFs. This is part of a wider programme of work to understand opportunities for pharmacy teams in the community to support residents and carers. Methods This was a retrospective longitudinal cohort study. Data were extracted from a national pharmacy chain database of prescriptions dispensed for elderly residents in UK LTCFs over 12 months (November 2016–October 2017). Results Data were analysed for 341536 residents in LTCFs across the four UK nations, from which a total of 544796 antibiotic prescriptions were dispensed for 167002 residents. The proportion of residents prescribed at least one antibiotic over the 12 month period varied by LTCF, by month and by country. Conclusions Whilst national data sets on antibiotic prescribing are available for hospitals and primary care, this is the first report on antibiotic prescribing for LTCF residents across all four UK nations, and the largest reported data set in this setting. Half of LTCF residents were prescribed at least one antibiotic over the 12 months, suggesting that there is an opportunity to optimize antibiotic use in this vulnerable population to minimize the risk of AMR and treatment failure. Pharmacy teams are well placed to support prudent antibiotic prescribing and improved antimicrobial stewardship in this population.
Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience

Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment, we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 µg/L) or intermediate (100 µg/L) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 µg/L tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 µg/L tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a second disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control.
Septic Arthritis Following Radiofrequency Ablation of the Genicular Nerves.

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The Relationship between Workplace Incivility and Helping Behavior: Roles of Job Dissatisfaction and Political Skill

Abstract This article investigates the mediating role of job dissatisfaction in the relationship between employees’ perceptions of workplace incivility and their helping behavior, as well as the buffering role of political skill in this process. Three-wave, time-lagged data collected from employees and their supervisors revealed that employees’ exposure to workplace incivility diminished their helping behavior through their sense of job dissatisfaction. This mediating role of job dissatisfaction was less salient, however, to the extent that employees were equipped with political skill. For organizations, this study accordingly pinpoints a key mechanism—namely, unhappiness about their job situation—through which rude coworker treatment links to lower voluntary workplace behaviors among employees, and it reveals how this mechanism can be better contained in the presence of political skill.
Impact of ACA-related Insurance Expansion Policies on Mortality and Access to Post-Discharge Care for Trauma Patients: An Analysis of the National Trauma Data Bank.

BACKGROUND Uninsured trauma patients have worse outcomes and worse access to post-discharge care that is critically important for recovery after injury. Little is known regarding the impact of the insurance coverage expansion policies of the Affordable Care Act (ACA), most notably state-level Medicaid expansion, on trauma patients. In this study, we examine the national impact of these policies on payer-mix, inpatient mortality, and access to post-acute care for trauma patients. METHODS We used the 2011-2016 National Trauma Data Bank to evaluate for changes in insurance coverage among 18-64 year-old trauma patients. Our pre-/post-expansion models defined 2011-2013 as the pre-policy period, 2015-2016 as the post-policy period, and 2014 as a washout year. To evaluate for policy-associated changes in inpatient mortality and discharge disposition among the policy-eligible sample, we leveraged multivariable linear regression techniques to adjust for year-to-year variation in patient demographics, injury characteristics, and facility traits. We then examined the relationship between the magnitude of facility-level reductions in uninsured patients and access to post-acute care following policy implementation. RESULTS We identified 1,656,469 patients meeting inclusion criteria between 2011-2016. The pre-policy uninsured rate of 23.4% fell by 5.9 percentage-points after coverage expansion (p<0.001), with a corresponding 7.5 percentage-point increase in Medicaid coverage (p<0.001). Following policy implementation, there were no significant changes in inpatient mortality. However, there was a >30% relative increase in discharge to a post-acute care facility and a similar increase in discharge with home health services (p<0.001 for both). The greatest gains in access to post-acute services were seen among facilities with the greatest reductions in their uninsured rate (p=0.003). CONCLUSION ACA-related coverage expansion policies, most notably Medicaid expansion, were associated with a >25% reduction in the uninsured rate among nonelderly adult trauma patients. Although no immediate impact on inpatient mortality was seen, insurance coverage expansion was associated with a higher proportion of patients receiving critically important post-discharge care. LEVEL OF EVIDENCE Level III, Epidemiological.