Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal variation in effect sizes in a long-term, split-plot field experiment.

Ecological field experiments initiate successional and evolutionary changes amongst resident species, yet effect sizes are often reported as if they were constants. Few ecological studies have addressed their questions through long-term, experimental approaches, and many questions remain unanswered regarding temporal patterns in ecological effect sizes. We document temporal variation in effect sizes in response to pulse and press manipulations in a long-term factorial field experiment at Nash's Field, England. The experiment comprises seven treatments applied in a split-plot design to test the single and interactive effects of herbivory by insects, molluscs and rabbits, liming, nutrient limitation (applied as press experiments), competition (exclusion of grasses or herbs with specific herbicides), and seed limitation (pulse experiments) on plant community dynamics. The response of all vascular plant species was followed for two decades. High species richness was positively related to the minus-grass herbicide in the first decade and negatively related to both nitrogen addition and the abundance of dominant species in both decades. Many significant effects appeared quickly, but some large effects were not detected until year 15. Press experiments produced some long-lasting effects, but effect sizes changed due to both idiosyncratic 'year effects' and secular trends. For pulse experiments, most effects -including positive and negative responses to herbicide application and the invasion of most of the sown species- disappeared quickly. However, some endured or grew monotonically, such as the invasion of two sown species that benefited from particular combinations of the press treatments. The fastest effects to appear were the responses from established species. Many of these responses were negative, likely resulting from reduced niche dimensionality and competitive exclusion by new dominant species. Contrarily, one of the largest community-level effects took well over a decade to appear: the natural invasion by one species, which responded to a four-way interaction between experimental treatments. The insights gained from individual effects increased with the duration of the lag before their first appearance, drawing attention to the importance of long-term, manipulative field experiments. This experiment also reinforces the point that factorial experiments are the most insightful way to explore ecological interactions.
A genome wide association study of resistance to Puccinia striiformis f. sp. hordei and Puccinia graminis f. sp. tritici in barley and development of resistant germplasm.

Stripe rust (incited by Puccinia striiformis f. sp. hordei) and stem rust (incited by Puccinia graminis f. sp. tritici) are two of the most important diseases affecting barley. Building on prior work involving the introgression of the resistance genes rpg4/Rpg5 into diverse genetic backgrounds and the discovery of additional QTLs for stem rust resistance, we generated an array of germplasm in which we mapped resistance to stripe rust and stem rust. Stem rust races TTKSK and QCCJB were used for resistance mapping at the seedling and adult plant stages, respectively. Resistance to stripe rust, at the adult plant stage, was determined by QTLs on chromosomes 1H, 4H, and 5H that were previously reported in the literature. The rpg4/Rpg5 complex was validated as a source of resistance to stem rust at the seedling stage. Some parental germplasm, selected as potentially resistant to stem rust or susceptible but having other positive attributes, showed resistance at the seedling stage, which appears to be allelic to rpg4/Rpg5. The rpg4/Rpg5 complex, and this new allele, were not sufficient for adult plant resistance to stem rust in one environment. A QTL on 5H, distinct from Rpg5 and a previously reported resistance QTL, was required for resistance at the adult plant stage in all environments. This QTL is coincident with the QTL for stripe rust resistance. Germplasm with mapped genes/QTLs conferring resistance to stripe and stem rust was identified and is available as a resource to the research and breeding communities.
ER-resident sensor PERK is essential for mitochondrial thermogenesis in brown adipose tissue

The endoplasmic reticulum-resident sensor PERK is phosphorylated during brown adipocyte differentiation and is required for mitochondrial inner membrane protein biogenesis and thermogenic function. Mitochondria play a central role in the function of brown adipocytes (BAs). Although mitochondrial biogenesis, which is indispensable for thermogenesis, is regulated by coordination between nuclear DNA transcription and mitochondrial DNA transcription, the molecular mechanisms of mitochondrial development during BA differentiation are largely unknown. Here, we show the importance of the ER-resident sensor PKR-like ER kinase (PERK) in the mitochondrial thermogenesis of brown adipose tissue. During BA differentiation, PERK is physiologically phosphorylated independently of the ER stress. This PERK phosphorylation induces transcriptional activation by GA-binding protein transcription factor α subunit (GABPα), which is required for mitochondrial inner membrane protein biogenesis, and this novel role of PERK is involved in maintaining the body temperatures of mice during cold exposure. Our findings demonstrate that mitochondrial development regulated by the PERK–GABPα axis is indispensable for thermogenesis in brown adipose tissue.
Variation in soil properties under different cropping and other land-use systems in Dura catchment, Northern Ethiopia

There are limited reports about the impacts of long-term cropping and land-use systems (CLUS) on soil properties and nutrient stocks under smallholder farmers’ conditions in developing countries. The objective of this research was to examine variation in soil properties and OC and TN stocks across the different CLUS in Dura sub-catchment, northern Ethiopia. Surveys and discussions on field history were used to identify nine CLUS, namely, tef (Eragrostis tef (Zucc) Trot)) mono-cropping (TM), maize (Zea mays L.) mono-cropping (MM), cauliflower (Brassica oleracea var. botrytis)-maize intercropping (IC1), red beet (Beta Vulgaris)-maize intercropping (IC2), cauliflower-tef-maize rotation (R1), onion (Allium cepa L.)-maize-onion rotation (R2), tr eated gully (TG), untreated gully (UTG), and natural forest system (NF). A total of 27 composite soil samples were randomly collected from the CLUS for soil analysis. Data were subjected to one-way analysis of variance and PCA. The lowest and highest bulk density was determined from NF (1.19 Mg m-3) and UTG (1.77 Mg m-3), respectively. Soil pH, EC and CEC varied significantly among the CLUS. The highest CEC (50.3 cmolc kg-1) was reported under TG followed by NF. The highest soil OC stock (175.3 Mg C ha−1) and TN stock (13.6 Mg C ha−1) were found from NF. The PCA chosen soil properties explained 87% of the soil quality variability among the CLUS. Such soil properties and nutrient stocks variability among the CLUS suggested that introduction of suitable management practices that sustain the soil system of the CLUS with poor soil properties and nutrient stocks are crucial for the study area conditions.
IGF1R regulates retrograde axonal transport of signalling endosomes in motor neurons

Signalling endosomes are essential for trafficking of activated ligand–receptor complexes and their distal signalling, ultimately leading to neuronal survival. Although deficits in signalling endosome transport have been linked to neurodegeneration, our understanding of the mechanisms controlling this process remains incomplete. Here, we describe a new modulator of signalling endosome trafficking, the insulin‐like growth factor 1 receptor (IGF1R). We show that IGF1R inhibition increases the velocity of signalling endosomes in motor neuron axons, both in vitro and in vivo. This effect is specific, since IGF1R inhibition does not alter the axonal transport of mitochondria or lysosomes. Our results suggest that this change in trafficking is linked to the dynein adaptor bicaudal D1 (BICD1), as IGF1R inhibition results in an increase in the de novo synthesis of BICD1 in the axon of motor neurons. Finally, we found that IGF1R inhibition can improve the deficits in signalling endosome transport observed in a mouse model of amyotrophic lateral sclerosis (ALS). Taken together, these findings suggest that IGF1R inhibition may be a new therapeutic target for ALS.
Development of an early intervention programme for adolescents with emotion dysregulation and their families: Actions for the treatment of adolescent personality (ATraPA)

Borderline personality disorder and severe emotion dysregulation in adolescence is a major public health concern. Dialectical Behaviour Therapy is a promising treatment for suicidality in adolescents. The aim of this work is to present an adaptation of this intervention to the Spanish national health system, Actions for the Treatment of Adolescent Personality (ATraPA).
Interventions to optimize spinal cord perfusion in patients with acute traumatic spinal cord injuries: A systematic review.

Interventions to optimize spinal cord perfusion via support of mean arterial pressure (MAP) or spinal cord perfusion pressure (SCPP) are thought to play a critical role in the management of patients with acute traumatic spinal cord injuries, but there is ongoing controversy about efficacy and safety. We aimed to determine the effects of optimizing spinal cord perfusion on neurological recovery and risks for adverse events. We searched multiple databases for published and unpublished reports. Two reviewers independently screened articles, extracted data, and evaluated risk of bias. We synthesized data and evaluated confidence in anticipated treatment effects according to the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) approach. We identified 20 eligible observational studies and 1 eligible randomized controlled trial. According to low or very low quality evidence, the effect of MAP support on neurological recovery after acute traumatic spinal cord injury is uncertain, and the use of vasopressors to support MAP may be associated with increased rates of predominantly cardiac adverse events. Increased SCPP appears likely to be associated with improved neurological recovery, but SCPP monitoring via intradural catheters at the anatomical site of injury may involve increased risks of cerebrospinal fluid leakage requiring revision surgery or pseudomeningocele. No study directly compared the effects of specific MAP goal ranges, SCPP ranges, SCPP monitoring techniques, or durations of treatment. Very low quality evidence suggests that norepinephrine may have less risk of adverse events than dopamine. The current literature is insufficient to make strong recommendations about interventions to support spinal cord perfusion via MAP or SCPP goals in patients with acute traumatic spinal cord injuries. Data are compatible with a variety of treatment decisions, and individualized approaches may be optimal. Further investigation to clarify the risks, benefits, and alternatives to MAP or SCPP support in this population is warranted.
Do organization-level quality management systems influence department-level quality? A cross-sectional study across 32 large hospitals in Australia.

OBJECTIVE Little is known about the influence that hospital quality systems have on quality at department level, in Australia and elsewhere. This study assessed the relationships between organizational-level quality management systems, and the extent to which hospital-level quality management systems and department-level quality management strategies are related. DESIGN A multi-level, cross-sectional, mixed-method study. SETTING AND PARTICIPANTS As part of the Deepening our Understanding of Quality in Australia (DUQuA) project, we invited all large hospitals in Australia (~200 or more beds) which provided acute myocardial infarction (AMI), hip fracture and stroke care. The quality managers of these hospitals were the respondents for one of seven measures of hospital quality management systems and strategies. Data across the six remaining measures were collected through site visits by external surveyors assessing the participating hospitals. MAIN OUTCOME MEASURES Relationships were assessed between three organization-level quality management system measures: a self-report measure assessing organization-level quality activities (quality management systems index, QMSI); externally assessed organization-level compliance to procedures used to plan, monitor and improve quality of care (quality management compliance index, QMCI); and externally assessed implementation of quality systems (clinical quality implementation index, CQII). Associations were also assessed between organization-level quality management systems and department-level quality management strategies: how clinical responsibilities are assigned for a particular condition; whether department organization processes are organized to facilitate evidence-based care recommendations; compliance with selected recommendations of international agencies; and whether clinical reviews are performed systematically. RESULTS Of 78 invited hospitals, 32 participated in the study. QMSI was positively associated with QMCI and CQII, but after controlling for QMSI, no relationship was found between QMCI and CQII. There appears to be a cluster of relationships between QMSI and department-level measures, but this was not consistent across all departments. CONCLUSION This is the first national study undertaken in Australia to assess relationships within and between organization-level and department-level quality management systems. These quality management system tools align with many components of accreditation standards and may be useful for hospitals in continuously monitoring and driving improvement.
Exploring the Scope of Macrocyclic “Shoe-last” Templates in the Mechanochemical Synthesis of RHO Topology Zeolitic Imidazolate Frameworks (ZIFs)

The macrocyclic cavitand MeMeCH2 is used as a template for the mechanochemical synthesis of 0.2MeMeCH2@RHO-Zn16(Cl2Im)32 (0.2MeMeCH2@ZIF-71) and RHO-ZnBIm2 (ZIF-11) zeolitic imidazolate frameworks (ZIFs). It is shown that MeMeCH2 significantly accelerates the mechanochemical synthesis, providing high porosity products (BET surface areas of 1140 m2/g and 869 m2/g, respectively). Templation of RHO-topology ZIF frameworks constructed of linkers larger than benzimidazole (HBIm) was unsuccessful. It is also shown that cavitands other than MeMeCH2—namely MeHCH2, MeiBuCH2, HPhCH2, MePhCH2, BrPhCH2, BrC5CH2—can serve as effective templates for the synthesis of x(cavitand)@RHO-ZnIm2 products. The limitations on cavitand size and shape are explored in terms of their effectiveness as templates.
Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid Zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.
Discovery of a Gatekeeper Residue in the C-Terminal Tail of the Extracellular Signal-Regulated Protein Kinase 5 (ERK5)

The extracellular signal-regulated protein kinase 5 (ERK5) is a non-redundant mitogen-activated protein kinase (MAPK) that exhibits a unique C-terminal extension which comprises distinct structural and functional properties. Here, we sought to elucidate the significance of phosphoacceptor sites in the C-terminal transactivation domain of ERK5. We have found that Thr732 acted as a functional gatekeeper residue controlling C-terminal-mediated nuclear translocation and transcriptional enhancement. Consistently, using a non-bias quantitative mass spectrometry approach, we demonstrated that phosphorylation at Thr732 conferred selectivity for binding interactions of ERK5 with proteins related to chromatin and RNA biology, whereas a number of metabolic regulators were associated with full-length wild type ERK5. Additionally, our proteomic analysis revealed that phosphorylation of the Ser730-Glu-Thr732-Pro motif could occur independently of dual phosphorylation at Thr218-Glu-Tyr220 in the activation loop. Collectively, our results firmly establish the significance of C-terminal phosphorylation in regulating ERK5 function. The post-translational modification of ERK5 on its C-terminal tail might be of particular relevance in cancer cells where ERK5 has be found to be hyperphosphoryated.
Comparative Transcriptome Analyses of Drug‐sensitive and Drug‐resistant Strains of Eimeria tenella by RNA‐sequencing

Avian coccidiosis is a widespread and economically significant disease in poultry. At present, treatment of coccidiosis mainly relies on drugs. Anticoccidial drugs can be divided into two categories: ionophorous compounds and synthetic drugs. However, the emergence of drug‐resistant strains has become a challenge for coccidiosis control with anticoccidial drugs. To gain insights into the molecular mechanism governing the drug resistance of Eimeria tenella, two drug‐resistant strains of E. tenella, one maduramicin‐resistant (MRR) strain and one diclazuril‐resistant (DZR) strain, were generated. We carried out comparative transcriptome analyses of a drug‐sensitive strain (DS) and two drug‐resistant MRR and DZR strains of E. tenella using RNA‐sequencing. A total of 1,070 differentially expressed genes (DEGs), 672 upregulated and 398 downregulated, were identified in MRR vs. DS, and 379 DEGs, 330 upregulated and 49 downregulated, were detected in DZR vs. DS. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to better understand the functions of these DEGs. In the comparison of DZR vs. DS, some DEGs were involved in peroxisome, biosynthesis of unsaturated fatty acids, and fatty acid metabolism. In the comparison of MRR vs. DS, some DEGs were involved in glycolysis/gluconeogenesis, regulation of actin cytoskeleton, and DNA replication. In addition, some DEGs coded for surface antigens that were downregulated in two drug‐resistant strains involved invasion, pathogenesis, and host–parasite interactions. These results provided suggestions for further research toward unraveling the molecular mechanisms of drug resistance in Eimeria species and contribute to developing rapid molecular methods to detect resistance to these drugs in Eimeria species in poultry.
Applicability of the masseter muscle as a nutritional biomarker

Abstract Nutritional assessment is feasible with computed tomography anthropometry. The abdominal muscle at the L3 vertebra is a well-known nutritional biomarker for predicting the prognosis of various diseases, especially sarcopenia. However, studies on nutritional assessment of the brain using computed tomography are still scarce. This study aimed to investigate the applicability of the masseter muscle as a nutritional biomarker. Patients who underwent simultaneous brain and abdominopelvic computed tomography in the emergency department was retrospectively analyzed. We assessed their masseter muscle 2 cm below the zygomatic arch and abdominal muscle at L3 via computed tomography anthropometry. The skeletal muscle index, prognostic nutritional index, and other nutritional biomarkers were assessed for sarcopenia using the receiver operating characteristic curve analysis. A total of 314 patients (240 men and 72 women) were analyzed (mean age, 50.24 years; mean areas of the masseter and abdominal muscles, 1039.6 and 13478.3 mm2, respectively). Masseter muscle areas significantly differed in sarcopenic, obese, and geriatric patients (P < .001). The areas under the curve of the masseter muscle in sarcopenic, geriatric, and obese patients were 0.663, 0.686, and 0.602, respectively. Multivariable linear regression analysis showed a correlation with the abdominal muscle area, weight, and age. The masseter muscle, analyzed via computed tomography anthropometry, showed a statistically significant association with systemic nutritional biomarkers, and its use as a nutritional biomarker would be feasible.
Acclimation to Water Restriction Implies Different Paces for Behavioral and Physiological Responses in a Lizard Species

Chronic changes in climate conditions may select for acclimation responses in terrestrial animals living in fluctuating environments, and beneficial acclimation responses may be key to the resilience of these species to global changes. Despite evidence that climate warming induces changes in water availability, acclimation responses to water restriction are understudied compared with thermal acclimation. In addition, acclimation responses may involve different modes, paces, and trade-offs between physiological and behavioral traits. Here, we tested the dynamical acclimation responses of a dry-skinned terrestrial ectotherm to chronic water restriction. Yearling common lizards (Zootoca vivipara) were exposed to sublethal water restriction during 2 mo of the summer season in laboratory conditions, then released in outdoor conditions for 10 additional months. Candidate behavioral (exploration, basking, and thermal preferences) and physiological (metabolism at rest and standard water loss rate) traits potentially involved in the acclimation response were measured repeatedly during and after water restriction. We observed a sequential acclimation response in water-restricted animals (yearlings spent less time basking during the first weeks of water deprivation) that was followed by delayed sex-specific physiological consequences of the water restriction during the following months (thermal depression in males and lower standard evaporative water loss rates in females). Despite short-term negative effects of water restriction on body growth, annual growth, survival, and reproduction were not significantly different between water-restricted and control yearlings. This demonstrates that beneficial acclimation responses to water restriction involve both short-term flexible behavioral responses and delayed changes in thermal and water biology traits.