Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Response of the Brain to Cross-Generational Warming in a Coral Reef Fish

Ocean warming is a threat to marine biodiversity, as it can push marine species beyond their physiological limits. Detrimental effects can occur when marine poikilotherms are exposed to conditions beyond their thermal optima. However, acclamatory mechanisms, such as plasticity, may enable compensation of detrimental effects if warming is experienced during development or across generations. Studies evaluating the molecular responses of fishes to warming have mostly focused on liver, muscle, and gonads, and little is known about the effects on other vital organs, including the brain. This study evaluated the transcriptional program of the brain in the coral reef fish Acanthochromis polyacanthus, exposed to two different warming scenarios: +1.5°C and +3.0°C, across successive generations. Fish were exposed to these conditions in both developmental (F1 and F2) and transgenerational settings (F2 only), as well as a treatment with step-wise warming between generations. The largest differences in gene expression were between individuals of the first and second generation, a pattern that was corroborated by pairwise comparisons between Control F1 and Control F2 (7,500 DEGs) fish. This large difference could be associated with parental effects, as parents of the F1 generation were collected from the wild, whereas parents of the F2 generation were reared in captivity. A general response to warming was observed at both temperatures and in developmental and transgenerational treatments included protein folding, oxygen transport (i.e., myoglobin), apoptosis and cell death, modification of cellular structure, mitochondrial activity, immunity and changes in circadian regulation. Treatments at the highest temperature showed a reduction in synaptic activity and neurotransmission, which matches previous behavioral observations in coral reef fishes. The Transgenerational +3.0°C treatment showed significant activation of the gene pls3, which is known for the development of neuro-muscular junctions under heat-stress. F2 samples exposed to step-wise warming showed an intermediate response, with few differentially expressed genes compared to developmental and transgenerational groups (except for Transgenerational +1.5°C). In combination with previous studies on liver gene expression, this study indicates that warming produces a molecular signature of stress response in A. polyacanthus that is influenced both by the intensity of warming as well as the duration of exposure.
DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) Within Unsorted Trap Catches

The spotted wing drosophila (Drosophila suzukii, Matsumara) is a rapidly spreading global pest of soft and stone fruit production. Due to the similarity of many of its life stages to other cosmopolitan drosophilids, surveillance for this pest is currently bottlenecked by the laborious sorting and morphological identification of large mixed trap catches. DNA metabarcoding presents an alternative high-throughput sequencing (HTS) approach for multi-species identification, which may lend itself ideally to rapid and scalable diagnostics of D. suzukii within unsorted trap samples. In this study, we compared the qualitative (identification accuracy) and quantitative (bias toward each species) performance of four metabarcoding primer pairs on D. suzukii and its close relatives. We then determined the sensitivity of a non-destructive metabarcoding assay (i.e., which retains intact specimens) by spiking whole specimens of target species into mock communities of increasing specimen number, as well as 29 field-sampled communities from a cherry and a stone fruit orchard. Metabarcoding successfully detected D. suzukii and its close relatives Drosophila subpulchrella and Drosophila biarmipes in the spiked communities with an accuracy of 96, 100, and 100% respectively, and identified a further 57 non-target arthropods collected as bycatch by D. suzukii surveillance methods in a field scenario. While the non-destructive DNA extraction retained intact voucher specimens, dropouts of single species and entire technical replicates suggests that these protocols behave more similarly to environmental DNA than homogenized tissue metabarcoding and may require increased technical replication to reliably detect low-abundance taxa. Adoption of high-throughput metabarcoding assays for screening bulk trap samples could enable a substantial increase in the geographic scale and intensity of D. suzukii surveillance, and thus likelihood of detecting a new introduction. Trap designs and surveillance protocols will, however, need to be optimized to adequately preserve specimen DNA for molecular identification.
Nurse Adaptability and Post-traumatic Stress Disorder Symptoms During the COVID-19 Pandemic: The Effects of Family and Perceived Organizational Support

Objective To examine the effect of family and perceived organizational support on the relationship between nurse adaptability and their experience with COVID-related PTSD (post-traumatic stress disorder) symptoms in frontline nurses working on COVID-19 units. Background Proximity to and survival of life-threatening events contribute to a diagnosis of PTSD, which is characterized by avoidance of reminders of trauma, intrusive thoughts, flashbacks of events, sleep disturbances, and hypervigilance. Using the job-demands and resource model, we examined the effect of adaptability, family support, and perceived organizational support on PTSD symptoms for nurses during the COVID-19 pandemic. Specifically, we tested whether perceptions of environmental supports—i.e., family and organizational support—moderated the relationship between nurse adaptability and COVID-related PTSD symptoms. Methods A sample of frontline nurses working on COVID-19 units during the COVID-19 pandemic in Texas (N = 277) participated in this cross-sectional, observational study. Frontline Nurses reported demographic information and completed surveys designed to measure adaptability, perceived organizational support, family support, and COVID-related PTSD symptoms. Results Adaptability was significantly positively correlated (medium effects) to perceived organizational and family support (r = 0.51 and 0.56, respectively, p < 0.01). Adaptability and perceived organizational support were also negatively correlated with COVID-related PTSD symptoms (medium effects). Adaptability was negatively correlated with COVID-related PTSD symptoms, supporting Hypothesis 1 (r = −0.43, p < 0.01). Perceived organizational support was also significantly negatively correlated with COVID-19-related PTSD symptoms (r = −0.30, p < 0.01). Family support was not significantly correlated with COVID-related PTSD but was positively related to experiencing COVID-related PTSD after other variables were accounted for. Conclusion Findings suggest that individual adaptability and organizational support may reduce PTSD severity in frontline nurses working during a crisis; however, family support may increase PTSD symptoms. We provide suggestions for strengthening individual adaptability and healthcare leadership including remaining highly engaged to show support by providing rapid communication, remaining calm during difficult circumstances, and maintaining a consistent, physical presence during difficult times. Moreover, our results suggest additional support for nurses with families to adapt to crisis.
Thermoelectric Conversion From Interface Thermophoresis and Piezoelectric Effects

Piezoelectric effect has proved itself to be a promising energy conversion mechanism that can convert mechanical energy into electricity. Here, we propose an indirect thermoelectric conversion mechanism based on a combination of the thermophoresis and piezoelectric effects. We first analyze this thermally driven mechanism using a simplified theoretical model and then numerically analyze a molecular dynamics (MD) simulation of a hybrid system constructed of a single-layer MoS2 nanoribbon and a concentric carbon nanotube. We show that the thermophoresis-induced piezoelectric output voltage can reach 3.5 V, and this value can be tuned using a temperature difference. The output voltage obtained using this mechanism is significantly higher than that obtained by heating piezoelectric materials directly. Given the generality of the thermophoresis effect in Van der Waals structures, this mechanism has potential applications in the conversion of thermal energy into electrical energy at the nanoscale level.
Title: Understanding a Low Vitamin D State in the Context of COVID-19

While a low vitamin D state has been associated with an increased risk of infection by SARS-CoV-2 in addition to an increased severity of COVID-19 disease, a causal role is not yet established. Here, we review the evidence relating to i) vitamin D and its role in SARS-CoV-2 infection and COVID-19 disease ii) the vitamin D status in the Irish adult population iii) the use of supplemental vitamin D to treat a deficient status and iv) the application of the Bradford-Hill causation criteria. We conclude that reverse causality probably makes a minimal contribution to the presence of low vitamin D states in the setting of COVID-19. Applying the Bradford-Hill criteria, however, the collective literature supports a causal association between low vitamin D status, SARS-CoV-2 infection, and severe COVID-19 (respiratory failure, requirement for ventilation and mortality). A biologically plausible rationale exists for these findings, given vitamin D’s role in immune regulation. The thresholds which define low, deficient, and replete vitamin D states vary according to the disease studied, underscoring the complexities for determining the goals for supplementation. All are currently unknown in the setting of COVID-19. The design of vitamin D randomised controlled trials is notoriously problematic and these trials commonly fail for a number of behavioural and methodological reasons. In Ireland, as in most other countries, low vitamin D status is common in older adults, adults in institutions, and with obesity, dark skin, low UVB exposure, diabetes and low socio-economic status. Physiological vitamin D levels for optimal immune function are considerably higher than those that can be achieved from food and sunlight exposure alone in Ireland. A window exists in which a significant number of adults could benefit from vitamin D supplementation, not least because of recent data demonstrating an association between vitamin D status and COVID-19. During the COVID pandemic, we believe that supplementation with 20-25ug (800–1000 IU)/day or more may be required for adults with apparently normal immune systems to improve immunity against SARS-CoV-2. We expect that higher monitored doses of 37.5–50 ug (1,500–2,000)/day may be needed for vulnerable groups (e.g., those with obesity, darker skin, diabetes mellitus and older adults). Such doses are within the safe daily intakes cited by international advisory agencies.
Neuroinflammation, Microglia and Implications for Retinal Ganglion Cell Survival and Axon Regeneration in Traumatic Optic Neuropathy

Traumatic optic neuropathy (TON) refers to a pathological condition caused by a direct or indirect insult to the optic nerves, which often leads to a partial or permanent vision deficit due to the massive loss of retinal ganglion cells (RGCs) and their axonal fibers. Retinal microglia are immune-competent cells residing in the retina. In rodent models of optic nerve crush (ONC) injury, resident retinal microglia gradually become activated, form end-to-end alignments in the vicinity of degenerating RGC axons, and actively internalized them. Some activated microglia adopt an amoeboid morphology that engulf dying RGCs after ONC. In the injured optic nerve, the activated microglia contribute to the myelin debris clearance at the lesion site. However, phagocytic capacity of resident retinal microglia is extremely poor and therefore the clearance of cellular and myelin debris is largely ineffective. The presence of growth-inhibitory myelin debris and glial scar formed by reactive astrocytes inhibit the regeneration of RGC axons, which accounts for the poor visual function recovery in patients with TON. In this Review, we summarize the current understanding of resident retinal microglia in RGC survival and axon regeneration after ONC. Resident retinal microglia play a key role in facilitating Wallerian degeneration and the subsequent axon regeneration after ONC. However, they are also responsible for producing pro-inflammatory cytokines, chemokines, and reactive oxygen species that possess neurotoxic effects on RGCs. Intraocular inflammation triggers a massive influx of blood-borne myeloid cells which produce oncomodulin to promote RGC survival and axon regeneration. However, intraocular inflammation induces chronic neuroinflammation which exacerbates secondary tissue damages and limits visual function recovery after ONC. Activated retinal microglia is required for the proliferation of oligodendrocyte precursor cells (OPCs); however, sustained activation of retinal microglia suppress the differentiation of OPCs into mature oligodendrocytes for remyelination after injury. Collectively, controlled activation of retinal microglia and infiltrating myeloid cells facilitate axon regeneration and nerve repair. Recent advance in single-cell RNA-sequencing and identification of microglia-specific markers could improve our understanding on microglial biology and to facilitate the development of novel therapeutic strategies aiming to switch resident retinal microglia’s phenotype to foster neuroprotection.
The Role of Weather and Long-Term Prey Dynamics as Drivers of Wolf Population Dynamics in a Multi-Prey System

As climate change accelerates in northern latitudes, there is an increasing need to understand the role of climate in influencing predator-prey systems. We investigated wolf population dynamics and numerical response in Denali National Park and Preserve in Alaska, United States from 1986 to 2016 under a long-term range of varying climatic conditions and in the context of prey vulnerability, abundance, and population structure using an integrated population modeling approach. We found that wolf natality, or the number of wolves added to packs, increased with higher caribou population size, calf:cow ratio, and hare numbers, responding to a 1-year lag. Apparent survival increased in years with higher calf:cow ratios and cumulative snowfall in the prior winter, indicators of a vulnerable prey base. Thus, indices of prey abundance and vulnerability led to responses in wolf demographics, but we did not find that the wolf population responded numerically. During recent caribou and moose population increases wolf natality increased yet wolf population size declined. The decline in wolf population size is attributed to fewer packs in recent years with a few very large packs as opposed to several packs of comparable size. Our results suggest that territoriality can play a vital role in our study area on regulating population growth. These results provide a baseline comparison of wolf responses to climatic and prey variability in an area with relatively low levels of human disturbance, a rare feature in wolf habitat worldwide.
Benchmarking Whole‐Body Controllers on the TALOS Humanoid Robot

This article presents a comparison of three control schemes applied on the commercially available TALOS humanoid robot. The aim is to highlight the advantages and drawbacks of each model applied on three locomotion problems: walking on flat and non-flat terrain and climbing stairs. The different models are based on position control (first and second models) or torque control (third model). The first one uses a hierarchical quadratic program at velocity level. The second one uses a weighted quadratic program named Task Space Inverse Dynamic (TSID) at acceleration level. Finally, the last one also uses TSID but at torque level. The controller performances are compared in simulation, using Gazebo, on the accuracy of their tracking, their energy consumption, and their computational time execution.
Space and Habitat Utilization of the Red King Crab (Paralithodes camtschaticus) in a Newly Invaded Fjord in Northern Norway

The red king crab (RKC, Paralithodes camtschaticus) was introduced to the southern Barents Sea in the 1960s with the aim to develop a new, commercially attractive stock of the species. In the subsequent decades, the stock has indeed become abundant and widespread, but the species’ presence also implies intense predation on benthic biota and thereby severe degradation of benthic ecosystems. Our capacity to monitor and harvest the species efficiently is therefore imperative. Yet, fishermen report highly variable catches despite little variation in the timing and location of fishing, possibly induced by the species’ migratory behavior, which makes the search for crab aggregations time consuming and expensive. Previous studies have shown that the RKC is capable of conducting long-distance migrations, and suggest that the species conduct seasonal migrations between shallow (winter- and springtime) and deep waters (summer and autumn). Here, we applied telemetry to investigate the migratory behavior and habitat utilization of 37 adult individuals of the RKC in a relatively shallow fjord in northern Norway from late May until early November. Approximately half of the crabs (n = 16) left the study area early during the study period, but some individuals (n = 3) were recaptured between 53 and 147 km away from the study area, confirming that the RKC may conduct long-distance migrations. In contrast to expectations, most of the remaining individuals of RKC (n = 16) stayed for a prolonged summer and autumn period and used a limited portion of the fjord. These crabs responded quickly to changes in ambient water temperature, seeking deeper and colder waters masses when the temperature in shallower waters increased. Several individuals showed nearly identical spatio-temporal distributions, which supports earlier observations of crab aggregations. Our data indicates that the area utilization of the RKC is affected by trade-offs between biotic and abiotic factors, in which sub-optimal water temperatures may be tolerated provided appropriate access to food. Thus, our findings suggest that the current knowledge of RKC seasonal migration patterns may need to be revised, which in turn will have implications for managers and the fishing industry. This study demonstrates the high potential of telemetry studies to yield new, high-resolution data and knowledge of species’ ecology.
Novel Highlight in Malarial Drug Discovery: Aspartate Transcarbamoylase

Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 – a potent, yet unselective, antimalarial – is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.
3D Tissue-Engineered Vascular Drug Screening Platforms: Promise and Considerations

Despite the efforts devoted to drug discovery and development, the number of new drug approvals have been decreasing. Specifically, cardiovascular developments have been showing amongst the lowest levels of approvals. In addition, concerns over the adverse effects of drugs to the cardiovascular system have been increasing and resulting in failure at the preclinical level as well as withdrawal of drugs post-marketing. Besides factors such as the increased cost of clinical trials and increases in the requirements and the complexity of the regulatory processes, there is also a gap between the currently existing pre-clinical screening methods and the clinical studies in humans. This gap is mainly caused by the lack of complexity in the currently used 2D cell culture-based screening systems, which do not accurately reflect human physiological conditions. Cell-based drug screening is widely accepted and extensively used and can provide an initial indication of the drugs' therapeutic efficacy and potential cytotoxicity. However, in vitro cell-based evaluation could in many instances provide contradictory findings to the in vivo testing in animal models and clinical trials. This drawback is related to the failure of these 2D cell culture systems to recapitulate the human physiological microenvironment in which the cells reside. In the body, cells reside within a complex physiological setting, where they interact with and respond to neighboring cells, extracellular matrix, mechanical stress, blood shear stress, and many other factors. These factors in sum affect the cellular response and the specific pathways that regulate variable vital functions such as proliferation, apoptosis, and differentiation. Although pre-clinical in vivo animal models provide this level of complexity, cross species differences can also cause contradictory results from that seen when the drug enters clinical trials. Thus, there is a need to better mimic human physiological conditions in pre-clinical studies to improve the efficiency of drug screening. A novel approach is to develop 3D tissue engineered miniaturized constructs in vitro that are based on human cells. In this review, we discuss the factors that should be considered to produce a successful vascular construct that is derived from human cells and is both reliable and reproducible.