Miracle-dz/UniFAR-FTUs huggingface dataset:
Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney

Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster.

Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here we investigate the population biology of recently evolved de novo genes expressed in the D. melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.
The reactome pathway knowledgebase 2022

Abstract The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied (‘dark’) proteins from analyzed datasets in the context of Reactome’s manually curated pathways.
Limits on non-canonical heating and turbulence in the intergalactic medium from the low redshift Lyman-alpha forest

We examine the column density distribution function (CDDF) and Doppler parameter distribution from hydrodynamical simulations and Cosmic Origins Spectrograph (COS) observations of the Ly α forest at redshift 0 ≤ z ≤ 0 . 2. Allowing for a factor of two uncertainty in the metagalactic H I photoionisation rate, our hydrodynamical simulations are in good agreement (1–1 . 5 σ ) with the shape and amplitude of the observed CDDF at H I column densities 10 13 . 3 cm − 2 ≤ N HI ≤ 10 14 . 5 cm − 2 . However, the Doppler widths of the simulated lines remain too narrow with respect to the COS data. We argue that invoking AGN feedback does not resolve this discrepancy. We also disfavour enhanced photoheating rates as a potential solution, as this requires an unphysically hard UV background spectrum. If instead appealing to a non-canonical source of heating, an additional speciﬁc heat injection of u (cid:46) 6 . 9eVm − 1 p is required at z (cid:46) 2 . 5 for gas that has N HI (cid:39) 10 13 . 5 cm − 2 by z = 0 . 1. Alternatively, there may be an unresolved line of sight turbulent velocity component of v turb (cid:46) 8 . 5kms − 1 ( N HI / 10 13 . 5 cm − 2 ) 0 . 21 for the coldest gas in the diffuse IGM.
REIMAGINING SCHOOL LIBRARIES: CHILDREN'S PERSPECTIVES AND NEW OPPORTUNITIES

The Federal Government’s recent Building the Education Revolution program resulted in, among other features, the creation of over 600 new school libraries in Queensland alone. This paper reports on a component of a research project carried out with students in six primary schools and one secondary school that benefitted from the program, investigating the influences of these new physical environments on learning and teaching. In particular, this paper discusses one missing voice from the design process - that of the students who would be key users of the newly-created spaces in those schools. While opportunities for real involvement in design were minimal for most potential users of the new spaces, students’ imagined possibilities for school libraries, as submitted to the research project, suggest that students could have contributed different perspectives to enhance learning engagement through imaginative design elements. The findings of the project have relevance for teachers and teacher librarians in reconsidering the ways in which the new learning spaces are used as well as informing school designers in planning engaging school facilities. The findings may be extrapolated to the design and planning of general classrooms and other learning environments. Recently, many classrooms and school libraries have been built or refurbished through the Building the Education Revolution (BER) program (DEEWR, 2011) resulting in the creation of over 600 new school libraries in Queensland alone, contributing much needed facilities and resources to help improve educational offerings to thousands of students and to encourage pedagogical renewal. While it is highly unlikely that schools benefitting from this program would relinquish their new facilities, the Implementation Taskforce Review of the BER process highlighted some shortcomings which were clearly influenced by the urgency in the underlying economic stimulus plan for the Australian economy (Orgill & Chandler, 2011). In particular, the Review found evidence that the tight timeline for completion of facilities inhibited the adequate preparation, direct participation and creative professional influence of school communities (DEEWR, 2011; Orgill & Chandler, 2011). This paper discusses a component of a research program, Reimagining Schools to inform the design and use of learning spaces, carried out on behalf of the Queensland Centre for Social Science Innovation (QCSSI). The research team interviewed teacher librarians, principals, other teaching staff and students in seven schools in various areas of Queensland to better understand the influences on learning and teaching of these new physical environments established through the BER. In particular, this paper focuses on one missing voice from the design process: the study found, while opportunities for real involvement in the design of the new school libraries were minimal for all potential users of
Obstructive sleep apnea therapy for cardiovascular risk reduction—Time for a rethink?

Obstructive sleep apnea (OSA) is a highly prevalent and underdiagnosed medical condition, which is associated with various cardiovascular and metabolic diseases. The current mainstay of therapy is continuous positive airway pressure (CPAP); however, CPAP is known to be poorly accepted and tolerated by patients. In randomized controlled trials evaluating CPAP in cardiovascular outcomes, the average usage was less than 3.5 hours, which is below the 4 hours per night recommended to achieve a clinical benefit. This low adherence may have resulted in poor effectiveness and failure to show cardiovascular risk reduction. The mandibular advancement device (MAD) is an intraoral device designed to advance the mandible during sleep. It functions primarily through alteration of the jaw and/or tongue position, which results in improved upper airway patency and reduced upper airway collapsibility. The MAD is an approved alternative therapy that has been consistently shown to be the preferred option by patients who are affected by OSA. Although the MAD is less efficacious than CPAP in abolishing apnea and hypopnea events in some patients, its greater usage results in comparable improvements in quality‐of‐life and cardiovascular measures, including blood pressure reduction. This review summarizes the impact of OSA on cardiovascular health, the limitations of CPAP, and the potential of OSA treatment using MADs in cardiovascular risk reduction.
Analysis of the coaxial helical-groove slow-wave structure

A coaxial helical-groove structure is presented and analyzed in this paper. The dispersion equation and coupling impedance of the structure are given. Numerical calculations of the dispersion relation and coupling impedance with different structure dimensions are carried out. Calculated results indicate that the cold bandwidth of this structure can reach 60%, while the coupling impedance is more than 16 /spl Omega/. It is shown that the coaxial helical groove is a wide-band slow-wave structure with high-power capacity.
Effectiveness of task-specific training using assistive devices and task-specific usual care on upper limb performance after stroke: a systematic review and meta-analysis

Abstract Purpose Task-specific rehabilitation is a key indicator for successful rehabilitation to improve the upper limb performance after stroke. Assistive robotic and non-robotic devices are emerging to provide rehabilitation therapy; however, the effectiveness of task-specific training programs using assistive training devices compared with task-specific usual care training has not been summarized yet. Therefore, the effectiveness of task-specific training using assistive arm devices (TST-AAD) compared with task-specific usual care (TSUC) on the upper limb performance of patients with a stroke was investigated. To assess task specificity, a set of criteria was proposed: participation, program, relevant, repeated, randomized, reconstruction and reinforced. Materials and methods Out of 855 articles, 17 fulfilled the selection criteria. A meta-analysis was performed on the Fugl-Meyer Assessment scores in the subacute and chronic stages after stroke and during follow-up. Results and conclusion Both TST-AAD and TSUC improved the upper limb performance after stroke. In the sub-acute phase after stroke, TST-AAD was more effective than TSUC in reducing the upper limb impairment, although findings were based on only three studies. In the chronic phase, TST-AAD and TSUC showed similar effectiveness. No differences between the two types of training were found at the follow-up measurements. Future studies should describe training, device usage and criteria of task specificity in a standardized way to ease comparison. Implications for rehabilitation Arm or hand function is often undertreated in stroke patients, assistive training devices may be able to improve the upper limb performance. Task-specific training using assistive devices is effective in improving the upper limb performance after stroke. Task-specific training using assistive devices seems to be more effective in reducing impairment compared with task specific usual care in the subacute phase after stroke, but they are equally effective in the chronic phase of stroke.
Rurality as a Risk Factor for Attempted Suicide and Death by Suicide in Ontario, Canada

Objective This study aims to examine rural and urban differences in attempted suicide and death by suicide in Ontario, Canada. Method This is a population-based nested case-control study. Data were obtained from administrative databases held at ICES, which capture all hospital and emergency department visits across Ontario between 2007 and 2017. All adults living in Ontario who attempted suicide or died by suicide are included in the study, and controls were matched by sex and age. Suicides were captured using vital statistics. Suicide attempts were determined using emergency department service codes. Results Rurality is a risk factor for attempted suicide and death by suicide. Rural males are more likely to die by suicide compared with urban males (adjusted odds ratio(AOR) = 1.70, 95% confidence interval (CI), 1.49 to 1.95), and the odds of death by suicide increase with increasing levels of rurality. Rural males and females have an increased risk of attempted suicide compared with their urban counterparts (males: AOR = 1.37, 95% CI, 1.24 to 1.50) (females: AOR = 1.26, 95% CI, 1.14 to 1.39), with a pattern of increasing risk of suicide attempts with increasing rurality. Rural females are not at increased risk of suicide compared with urban females (AOR = 1.08, 95% CI, 0.80 to 1.45). Sensitivity analyses corroborated the results. Conclusions Rural males are almost two times more likely to die by suicide compared with urban males, and both rural males and females have an elevated risk of suicide attempts compared with urban residents. Future research should examine potential mediators of the relationship between rurality and suicide.
During development of rheumatoid arthritis, intermetatarsal bursitis may occur before clinical joint swelling: a large imaging study in patients with clinically suspect arthralgia

Abstract Objectives Intermetatarsal bursitis (IMB) represents juxta-articular synovial inflammation of the intermetatarsal bursae. Recent MRI studies identified IMB as feature of early RA, but whether IMB already occurs in the pre-arthritic phase is unknown. We performed a large MRI study in clinically suspect arthralgia (CSA) to assess the occurrence and prognostic value of IMB. Methods A total of 577 consecutive CSA patients underwent contrast-enhanced MRI of the forefoot, metacarpophalangeal joints and wrist. MRIs were evaluated for subclinical synovitis/tenosynovitis/osteitis in line with the RA MRI scoring system (summed as RAMRIS inflammation) and for IMB. IMB was considered present if uncommon in the general population at the same location (i.e. size scored above the 95th percentile in age-matched symptom-free controls). The relation of IMB with other MRI-detected subclinical inflammation (synovitis/tenosynovitis/osteitis) was studied. Cox-regression assessed the association with clinical arthritis development during median 25 months follow-up. ACPA stratification was performed. Results At presentation with CSA, 23% had IMB. IMB was more frequent in ACPA-positive than ACPA-negative CSA (47% vs 19%, P < 0.001). Patients with IMB were more likely to also have subclinical synovitis [OR 3.4 (95% CI 1.8, 6.5)] and tenosynovitis [5.9(2.8, 12.6)]. IMB conferred higher risk of developing arthritis [HR 1.6(1.0–2.7) adjusted for other subclinical inflammation]. IMB-presence predicted arthritis development in ACPA-positive CSA [adjusted HR 2.2(1.0–4.7)], but not in ACPA-negative CSA-patients [0.8(0.4–1.7)]. Conclusion Approximately a quarter of CSA patients have IMB, which is frequently accompanied by subclinical synovitis and tenosynovitis. IMB precedes development of clinical arthritis, particularly in ACPA-positive CSA. These results reinforce the notion that juxta-articular synovial inflammation is involved in the earliest phases of RA development.
Comparison of player-dependent and independent high-speed running thresholds to model injury risk in football

ABSTRACT High-speed running (HSR) loads have been linked with non-contact injury risks in team-sports. This study investigated whether player-specific speed zones, reflecting individual fitness characteristics, impact the associations between non-contact injury and acute and chronic HSR loads. Semi-professional soccer players from two clubs (n = 47) were tracked over two seasons using 10 Hz GPS (5552 observations). HSR distances were calculated arbitrarily (≥5.5 m·s−1), and in an individualised fashion based on the final speed of the 30–15 intermittent fitness test. Cumulative running loads were represented by exponentially weighted moving averages with 7-(acute) and 28-day (chronic) decay parameters. Physiotherapists collected non-contact, lower-limb, time-loss injury data (n = 101). Injury models using session type (training vs matches), coach, as well as arbitrary or individualised running loads were constructed via mixed-effect logistic regression. Session type had the largest effect on injury (training vs match OR = 0.28; 95%CI:0.17–0.44). Variations in individualised or arbitrary acute and chronic HSR loads within the mid-range of the observed data had negligible effects on predicted injury risk. However, the uncertainty of estimated effects at extreme values of acute and chronic HSR loads prevented any conclusive findings. Therefore, the efficacy of using customised speed thresholds in quantifying load for injury risk mitigation purposes remains unclear.
Serratia marcescens‐S3 inhibits Potato virus Y by activating ubiquitination of molecular chaperone proteins NbHsc70‐2 in Nicotiana benthamiana

The potato virus Y (PVY) is a plant virus that causes massive crop losses globally, especially in Solanaceae crops. A strain of the plant growth‐promoting rhizobacterium (PGPR), Serratia marcescens‐S3 was found to inhibit PVY replication in Nicotiana benthamiana. However, there have been no in‐depth studies demonstrating the underlying mechanism. In the current study, we found that ubiquitination of NbHsc70‐2 is an important way for Serratia marcescens‐S3 to trigger induced systemic resistance (ISR). After the treatment with S. marcescens‐S3, the protein level of NbHsc70‐2 reduced significantly. Inhibiting of ubiquitination increased the accumulation of NbHsc70‐2 in plants and reduced S. marcescens‐S3‐mediated resistance to PVY. Furthermore, transgenic engineered Nicotiana benthamiana NbHsc70‐2KO and NbHsc70‐2USM were constructed using CRISPR‐Cas9‐mediated NbHsc70‐2 knock‐out and ubiquitination respectively. S. marcescens‐S3 significantly reduced the inhibition of NbHsc70‐2 protein accumulation in NbHsc70‐2KO and NbHsc70‐2USM. The virulence of PVY was stronger in NbHsc70‐2USM than the wild‐type plants. These results showed that S. marcescens‐S3 increases the ubiquitination of NbHsc70‐2 to inhibit the recruitment of molecular chaperone NbHsc70‐2 to reduce its replication and infection of PVY.
Data Resource Profile: The Education and Child Health Insights from Linked Data (ECHILD) Database

Data Resource Profile: The Education and Child Health Insights from Linked Data (ECHILD) Database Louise Mc Grath-Lone ,* Nicolás Libuy, Katie Harron , Matthew A Jay , Linda Wijlaars, David Etoori, Matthew Lilliman, Ruth Gilbert, and Ruth Blackburn University College London, Institute of Health Informatics, London, UK, Centre for Longitudinal Studies, University College London, Institute of Education, London, UK and University College London, Great Ormond Street Institute of Child Health, London, UK
SARS-CoV-2 seroprevalence in high-risk health care workers in a Belgian general hospital: evolution from the first wave to the second

ABSTRACT Health care workers (HCWs) are at the frontline for combatting the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To describe recent or past infections, the novel development of serological assays enabled the assessment of the immune response developed in coronavirus disease (COVID-19). Here, we investigate SARS-CoV-2 seroprevalence in high-risk HCWs in a Belgian general hospital after both the first and the second waves. Three different immunoassays were used to determine immune response to SARS-CoV-2 in volunteer HCWs who worked in at least one COVID-19-dedicated ward [emergency department, intensive care unit (ICU) and internal medicine department] in our institution from 8 May 2020 to 19 May 2020 (n = 267) and from 18 January 2021 to 8 February 2021 (n = 189). Risk factors for seropositivity were also assessed using a questionnaire filled out by all participants. We report a steep increase in seroprevalence after the second wave and report a higher seropositivity in HCWs than in the general population. Furthermore, we show that ICU personnel and especially nurses exhibit a proportionally lower SARS-CoV-2 seroprevalence. This study documents the rapid increase in SARS-CoV-2 seroprevalence in highly exposed HCWs in a context of high viral circulation prior to vaccination campaigns. Most importantly, it suggests a lower occupational risk in ICU and illustrates the role of diagnostic labeling and use of personal protective equipment during the COVID-19 pandemic.
Regulation of excitation‐contraction coupling at the Drosophila neuromuscular junction

The Drosophila neuromuscular system is widely used to characterize synaptic development and function. However, little is known about how specific synaptic alterations effect neuromuscular transduction and muscle contractility, which ultimately dictate behavioural output. Here we develop and use a force transducer system to characterize excitation‐contraction coupling at Drosophila larval neuromuscular junctions (NMJs), examining how specific neuronal and muscle manipulations disrupt muscle contractility. Muscle contraction force increased with motoneuron stimulation frequency and duration, showing considerable plasticity between 5 and 40 Hz and saturating above 50 Hz. Endogenous recordings of fictive contractions revealed average motoneuron burst frequencies of 20–30 Hz, consistent with the system operating within this plastic range of contractility. Temperature was also a key factor in muscle contractility, as force was enhanced at lower temperatures and dramatically reduced with increasing temperatures. Pharmacological and genetic manipulations of critical components of Ca2+ regulation in both pre‐ and postsynaptic compartments affected the strength and time course of muscle contractions. A screen for modulators of muscle contractility led to identification and characterization of the molecular and cellular pathway by which the FMRFa peptide, TPAEDFMRFa, increases muscle performance. These findings indicate Drosophila NMJs provide a robust system to correlate synaptic dysfunction, regulation and modulation to alterations in excitation‐contraction coupling.