Miracle-dz/UniFAR-FTUs huggingface dataset:
SuperDARN data simulation, processing, access, and use in analysis of midlatitude convection

The Super Dual Auroral Radar Network (SuperDARN) is a chain of HF radars for monitoring plasma flows in the high and mid latitude E and F regions of the ionosphere. The targets of SuperDARN radars are plasma irregularities which can flow up to several kilometers per second and can be detected out to ranges of several thousand kilometers. We have developed a simulator which is able to model SuperDARN data realistically. The simulation system is composed of four separate parts: model scatterers, model collective properties, a model radar, and post-processing. Importantly, the simulator is designed using the collective scatter approach which accurately captures the expected statistical fluctuations of the radar echoes. The output of the program can represent either receiver voltages or autocorrelation functions (ACFs) in standard SuperDARN file formats. The simulator is useful for testing and implementation of SuperDARN data processing software and for investigation of how radar data and performance change when the nature of the irregularities or radar operation varies. The companion paper demonstrates the application of simulated data to evaluate the performance of different ACF fitting algorithms. The data simulator is applicable to other ionospheric radar systems. AJ Ribeiro Chapter 2. Simulator 23
Deep Surgical Site Infection after Fracture Has a Profound Effect on Functional Outcomes

Background: Fracture-related infection is one of the most challenging complications in orthopaedic trauma surgery. However, the effect of infection on functional and pain-related outcomes has not been well established. The aims of this study were to evaluate functional recovery for patients with fracture and a deep surgical site infection compared with patients with fracture without infection and to evaluate whether pain severity, social support, and preinjury mental health have a moderating effect on the magnitude and direction of the relationship between deep surgical site infection and functional recovery. Methods: This is a secondary retrospective cohort study using prospectively collected data from the VANCO trial (Local Antibiotic Therapy to Reduce Infection After Operative Treatment of Fractures at High Risk of Infection) and the OXYGEN (Supplemental Perioperative Oxygen to Reduce Surgical Site Infection After High Energy Fracture Surgery) trial. In this study, 2,116 patients with tibial plateau, pilon, or calcaneal fractures at high risk for infection were included. Patients were divided into cohorts of patients who experienced a deep surgical site infection and those who did not. The primary outcome measure was the functional outcome using the Veterans RAND 12-Item Health Survey (VR-12). Results: After controlling for covariates, deep surgical site infection was independently associated with functional outcome, with a 3.3-point reduction in the VR-12 Physical Component Score, and pain severity was independently associated with functional outcome, with a 2.5-point reduction in the VR-12 Physical Component Score. Furthermore, the Brief Pain Inventory pain severity demonstrated an important moderating effect on the relationship between infection and functional outcome. In patients with lower pain scores, infection had a large negative impact on functional outcome, whereas, in patients with higher pain scores, infection had no significant impact on functional outcome. Furthermore, the functional outcome in the entire cohort remains at only 61% of baseline. Conclusions: This study documents the negative impact of postoperative infection on functional recovery after injury, as well as the novel finding of pain severity as an important moderating factor. This study emphasizes not only the importance of developing effective interventions designed to reduce postoperative infection, but also the role that factors that moderate pain severity plays in limiting recovery of physical function. Level of evidence: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand

Abstract Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under‐studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome‐wide single nucleotide polymorphisms (SNPs), generating genotyping‐by‐sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.
Self-management of chronic, non-communicable diseases in South Asian settings: A systematic mixed-studies review

Self-management is crucial in mitigating the impacts of a growing non-communicable disease (NCD) burden, particularly in Low and Middle-Income countries. What influences self-management in these settings, however, is poorly understood. We aimed to identify the determinants of self-management in the high NCD region of South Asia and explore how they influence self-management. A systematic mixed-studies review was conducted. Key electronic databases [MEDLINE (1946+), Embase (1974+), PsycInfo (1967+) and CINAHL (EBSCOhost)] in March 2022 (and updated in April 2023) were searched for studies on the self-management of four high-burden NCD groups: cardiovascular diseases, type 2 diabetes, chronic respiratory diseases and depression. Study characteristics and quantitative data were extracted using a structured template, and qualitative information was extracted using NVivo. Quality appraisal was done using the Mixed Methods Assessment Tool (MMAT). Quantitative findings were organised using the Commission on Social Determinants of Health (CSDH) framework and synthesised narratively, supported by effect direction plots. Qualitative findings were thematically synthesised. Both were integrated in a mixed synthesis. Forty-four studies (26 quantitative, 16 qualitative and 2 mixed-methods studies) were included, the majority of which were conducted in urban settings and among individuals with diabetes and cardiovascular diseases. Higher age, education, and income (structural determinants), health-related knowledge, social support and self-efficacy (psychosocial determinants), longer illness duration and physical comorbidity (biologic determinants), and the affordability of medicine (health-system determinants) were key determinants of self-management. Qualitative themes highlighted the role of financial adversity and the social and physical environment in shaping self-management.A complex interplay of structural and intermediary social determinants shapes self-management in South Asian settings. Multi-component, whole-systems approaches could boost self-management in these settings. Key areas include empowerment and education of patients and wider community, design and delivery of bespoke behavioural interventions and a stronger emphasis on supporting self-management in healthcare settings.
Hypothetical 22-Year Intervention With the Dietary Approaches to Stop Hypertension and Risk of Heart Failure in a General Population

Abstract We used design principles of target trial methodology to emulate the effect of sustained adherence to the Dietary Approaches to Stop Hypertension (DASH) diet on the 22-year risk of heart failure. Women and men aged 45–83 years without previous heart failure, who answered questionnaires in 1997 from the Swedish Mammography Cohort and the Cohort of Swedish Men, were eligible. Follow-up questionnaires were sent in 2008–2009. Incidence of heart failure was ascertained using the Swedish Patient Register, updated until December 31, 2019. The parametric g-formula was used to estimate the 22-year risk of heart failure under sustained adherence to a population-adapted DASH diet compared with no intervention. Intakes before 1997 for before-baseline adjustment was available only for women. In total, 31,238 women and 34,939 men were eligible. The 22-year risk of heart failure was 14.5% with long-term adherence to the DASH diet compared with 15.2% with no intervention (risk difference = −0.7%, 95% confidence interval: 1.6, 0.0%) in women and correspondingly in men 15.3% vs. 16.2% (risk difference = −0.9%, 95% confidence interval: −1.6, −0.2%). Our hypothetical intervention suggests that sustained adherence to the population-adapted DASH diet may reduce risk of heart failure in middle-aged and elderly Swedish women and men.
Reply to comment by Kil et al. on “The night when the auroral and equatorial ionospheres converged”

One of the goals of the Martinis et al. (2015) (M15) paper was to stimulate interest in the topic of “severe events during moderate geomagnetic storms”—and we succeeded. We welcome the Comment by Kil et al. (2016) (K16) who identified weak signatures related to medium‐scale traveling ionospheric disturbances (MSTIDs) and tried to argue that airglow depletion signatures of equatorial spread F (ESF) were not present. We agree with K16 in that MSTIDs were present to the north of the all‐sky imager, but only during the early observations. They are easily distinguished from the ESF‐related dark structures observed at the same time to the south of the imager. We stress some observational facts that K16 overlooked or erroneously used to support their case. M15 offered evidence and discussion evidence and discussion of a dynamical pattern—both in space and time domains—and the counter arguments by K16 should have dealt with the same places and same times. We also point out that the GPS data shown by K16 do not provide any information below ~30° geographic latitude in the longitude sector covered by the all‐sky imager. This is the region where the ESF structures appeared first and grew to reach higher latitudes. We believe that the issues addressed by K16 do not provide conclusive evidence to rule out the interpretation given by M15 on the nature of the airglow depletions observed at McDonald Observatory.
Spatial partitioning by mule deer and elk in relation to traffic.

Elk (Cervus elaphus) and mule deer (Odocoileus hemionus) have overlapping ranges on millions of acres of forests and rangelands in western North America. Accurate prediction of their spatial distributions within these ranges is essential to effective land-use planning, stocking allocation and population management (Wisdom and Thomas 1 996). Many habitat variables influence the distributions of the two ungulates, making predictions a challenging and sometimes daunting task for resource managers (Johnson et al. 1996, Ager et al. 2004).
Seizure-induced LIN28A disrupts pattern separation via aberrant hippocampal neurogenesis

Prolonged seizures can disrupt stem cell behavior in the adult hippocampus, an important brain structure for spatial memory. Here, using a mouse model of pilocarpine-induced status epilepticus (SE), we characterized spatiotemporal expression of Lin28a mRNA and proteins after SE. Unlike Lin28a transcripts, induction of LIN28A protein after SE was detected mainly in the subgranular zone, where immunoreactivity was found in progenitors, neuroblasts, and immature and mature granule neurons. To investigate roles of LIN28A in epilepsy, we generated Nestin-Cre:Lin28aloxP/loxP (conditional KO [cKO]) and Nestin-Cre:Lin28a+/+ (WT) mice to block LIN28A upregulation in all neuronal lineages after acute seizure. Adult-generated neuron- and hippocampus-associated cognitive impairments were absent in epileptic LIN28A-cKO mice, as evaluated by pattern separation and contextual fear conditioning tests, respectively, while sham-manipulated WT and cKO animals showed comparable memory function. Moreover, numbers of hilar PROX1-expressing ectopic granule cells (EGCs), together with PROX1+/NEUN+ mature EGCs, were significantly reduced in epileptic cKO mice. Transcriptomics analysis and IHC validation at 3 days after pilocarpine administration provided potential LIN28A downstream targets such as serotonin receptor 4. Collectively, our findings indicate that LIN28A is a potentially novel target for regulation of newborn neuron-associated memory dysfunction in epilepsy by modulating seizure-induced aberrant neurogenesis.
Increased mutations in lipopolysaccharide biosynthetic genes cause time-dependent development of phage resistance in Salmonella

ABSTRACT Understanding how bacteria evolve resistance to phages has implications for phage-based therapies and microbial evolution. In this study, the susceptibility of 335 Salmonella isolates to the wide host range Salmonella phage BPSELC-1 was tested. Potentially significant gene sets that could confer resistance were identified using bioinformatics approaches based on phage susceptibility phenotypes; more than 90 potential antiphage defense gene sets, including those involved in lipopolysaccharide (LPS) biosynthesis, DNA replication, secretion systems, and respiratory chain, were found. The evolutionary dynamics of Salmonella resistance to phage were assessed through laboratory evolution experiments, which showed that phage-resistant mutants rapidly developed and exhibited genetic heterogeneity. Most representative Salmonella hosts (58.1% of 62) rapidly developed phage resistance within 24 h. All phage-resistant mutant clones exhibited genetic heterogeneity and observed mutations in LPS-related genes (rfaJ and rfaK) as well as other genes such as cellular respiration, transport, and cell replication-related genes. The study also identified potential trade-offs, indicating that bacteria tend to escape fitness trade-offs through multi-site mutations, all tested mutants increased sensitivity to polymyxin B, but this does not always affect their relative fitness or biofilm-forming capacity. Furthermore, complementing the rfaJ mutant gene could partially restore the phage sensitivity of phage-resistant mutants. These results provide insight into the phage resistance mechanisms of Salmonella and the complexity of bacterial evolution resulting from phage predation, which can inform future strategies for phage-based therapies and microbial evolution.
Testing for Helicobacter pylori in an era of antimicrobial resistance

ABSTRACT Antimicrobial resistance in Helicobacter pylori has reached alarming levels and is compromising traditional empiric treatment of H. pylori. Antimicrobial susceptibility testing is routinely performed for infectious diseases when there is a risk of resistance and is now recommended to guide therapy for H. pylori. This mini-review overviews the current diagnostics for H. pylori with a focus on tests that enable susceptibility-guided treatment, including molecular tests performed directly on stool and endoscopically collected specimens.
Optimising land use in Central Kalimantan Province, Indonesia : modelling ecosystem benefits and land use dynamics

The rising global population has increased the demand for food, renewable energy and other materials. Yet at the same time to meet this demand requires land and the amount of available land is finite. Considering the importance of land and ecosystems in providing benefits for human, I conducted four independent research on the socio-economic and biophysical aspects of ecosystem service, in Central Kalimantan Province, Indonesia. The first three independent studies were used to understand ecosystem management under decentralised forest governance in Indonesia and its influence on ecosystems, ESs and the benefits that different beneficiaries receive. The fourth study combines the outcomes from the previous three studies to assess and select the most appropriate areas for conservation and community development. As the results, I show the applicability of the ecosystem services concept and land-use modelling in optimising land-use under certain decentralised forest governance systems. My thesis’ results were obtained through the application of methods and steps that integrated a comprehensive set of qualitative and quantitative analyses to support land-use optimisation in the Kapuas Protected Forest Management Unit. My results can inform decision makers on the options of land-use optimisation and the consequences of their management decisions regarding land-use intensification, nature conservation and local economic conditions. I show how land-use optimisation provides an important step in preventing further land degradation and ecosystem loss.
The impact of physical rebound effects on the heat losses in a retrofitted dwelling

In Flanders, as in many European regions, a calculation method has been developed in the framework of the EPBD-directive to evaluate the energy performance of newly erected dwellings. Although not intended to, this method is now more and more used to predict energy savings when retrofitting existing, badly insulated dwellings. In this calculation method the dwelling is considered as a single zone at a fixed indoor temperature of 18 °C. This paper investigates whether these assumptions are appropriate when calculating energy savings. On the one hand, although this indoor temperature gives a fairly good estimation for new dwellings, it cannot reflect the indoor climate in old, badly insulated dwellings where dwelling mean indoor temperatures can be considerably lower than 18 °C. Energy consumptions before retrofit are thus easily overestimated. On the other hand plays the physical rebound effect. When insulating the building envelope of a poorly insulated dwelling, the indoor temperature will rise, even if the heating pattern of the inhabitants remains unchanged. Using a fixed temperature for all insulation levels cannot incorporate this physical rebound, leading to inaccurate predictions of energy savings. In this paper the impact of a fixed indoor temperature of 18 °C on the net energy demand is analysed by simulations on an existing terraced house with different insulation levels. The comparison is made with a more realistic heating pattern where only part of the dwelling is heated intermittently. The simulations reveal a physical rebound and the need for a correlation between indoor temperature and insulation level.
Digital rhythm training improves reading fluency in children.

Musical instrument training has been linked to improved academic and cognitive abilities in children, but it remains unclear why this occurs. Moreover, access to instrument training is not always feasible, thereby leaving less fortunate children without opportunity to benefit from such training. Although music-based video games may be more accessible to a broader population, research is lacking regarding their benefits on academic and cognitive performance. To address this gap, we assessed a custom-designed, digital rhythm training game as a proxy for instrument training to evaluate its ability to engender benefits in math and reading abilities. Furthermore, we tested for changes in core cognitive functions related to math and reading to inform how rhythm training may facilitate improved academic abilities. Classrooms of 8-9 year old children were randomized to receive either 6 weeks of rhythm training (N = 32) or classroom instruction as usual (control; N = 21). Compared to the control group, results showed that rhythm training improved reading, but not math, fluency. Assessments of cognition showed that rhythm training also led to improved rhythmic timing and language-based executive function (Stroop task), but not sustained attention, inhibitory control, or working memory. Interestingly, only the improvements in rhythmic timing correlated with improvements in reading ability. Together, these results provide novel evidence that a digital platform may serve as a proxy for musical instrument training to facilitate reading fluency in children, and that such reading improvements are related to enhanced rhythmic timing ability and not other cognitive functions associated with reading performance. RESEARCH HIGHLIGHTS: Digital rhythm training in the classroom can improve reading fluency in 8-9 year old children Improvements in reading fluency were positively correlated with enhanced rhythmic timing ability Alterations in reading fluency were not predicted by changes in other executive functions that support reading A digital platform may be a convenient and cost-effective means to provide musical rhythm training, which in turn, can facilitate academic skills.
Effective Stress Analyses of Port Structures

ABSTRACT Effective stress analyses are performed on the seismic response of port structures during the 1995 Hyogoken-Nambu earthquake. The structures analyzed include: caisson type quay walls which moved up to 5 m maximum toward the sea; pneumatic caisson type bridge foundations which moved toward the sea, reducing the distance between the bridge foundations across a sea channel by a total of 0.8 m; and composite breakwaters which settled 2 m. Although these structures were all a rigid concrete type and shaken by the same earthquake, the mode and extent of deformation/failure were different depending on the backfill and embedment conditions of the structures. The constitutive model of soil used for the seismic analyses is a multiple mechanism model defined in strain space. The model can take the effect of principal stress axis rotation into account, which is known to play an important role in the cyclic behavior of sand under anisotropic stress conditions. The model parameters are calibrated based on in-situ and laboratory investigations, including in-situ freeze sampling. The results of the effective stress analyses are consistent with those measured, including the mode and extent of deformation/failure, suggesting that the cyclic behavior of soil, idealized through the effective stress model, can explain the variety of seismic response of the port structures in a unified manner.