Miracle-dz/UniFAR-FTUs huggingface dataset:
Microsatellite‐based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China

Abstract The oriental armyworm, Mythimna separata, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < F ST < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear‐cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large‐scale and long‐distance migration of M. separata has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of M. separata outbreaks in China.
Red oak seedlings as indicators of deer browse pressure: Gauging the outcome of different white‐tailed deer management approaches

Abstract After decades of high deer populations, North American forests have lost much of their previous biodiversity. Any landscape‐level recovery requires substantial reductions in deer herds, but modern societies and wildlife management agencies appear unable to devise appropriate solutions to this chronic ecological and human health crisis. We evaluated the effectiveness of fertility control and hunting in reducing deer impacts at Cornell University. We estimated spring deer populations and planted Quercus rubra seedlings to assess deer browse pressure, rodent attack, and other factors compromising seedling performance. Oak seedlings protected in cages grew well, but deer annually browsed ≥60% of unprotected seedlings. Despite female sterilization rates of >90%, the deer population remained stable. Neither sterilization nor recreational hunting reduced deer browse rates and neither appears able to achieve reductions in deer populations or their impacts. We eliminated deer sterilization and recreational hunting in a core management area in favor of allowing volunteer archers to shoot deer over bait, including at night. This resulted in a substantial reduction in the deer population and a linear decline in browse rates as a function of spring deer abundance. Public trust stewardship of North American landscapes will require a fundamental overhaul in deer management to provide for a brighter future, and oak seedlings may be a promising metric to assess success. These changes will require intense public debate and may require new approaches such as regulated commercial hunting, natural dispersal, or intentional release of important deer predators (e.g., wolves and mountain lions). Such drastic changes in deer management will be highly controversial, and at present, likely difficult to implement in North America. However, the future of our forest ecosystems and their associated biodiversity will depend on evidence to guide change in landscape management and stewardship.
Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava

Abstract Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (Manihot esculenta Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, MeTLPs, and further analysed structure, duplication, chromosome localization and collinearity, cis-acting elements in the promoter regions and expression patterns of MeTLPs, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a MeTLP family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of MeTLPs that show the duplication which took place between 10.11 and 126.69 million years ago. Two MeTLPs 6 and 9 likely originate from one gene in an ancestral species, may be common ancestors for other MeTLPs and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. MeTLPs feature differences in the number from TLPs in wheat, apple, Arabidopsis, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato StTLPs. MeTLPs are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among MeTLPs are predictable partly because of their differential expression profiles, which are coupled with various cis‑acting elements existing in the promoter regions depending on genes.
Phylogenetic structure and formation mechanism of shrub communities in arid and semiarid areas of the Mongolian Plateau

Abstract The mechanisms of species coexistence within a community have always been the focus in ecological research. Community phylogenetic structure reflects the relationship of historical processes, regional environments, and interactions between species, and studying it is imperative to understand the formation and maintenance mechanisms of community composition and biodiversity. We studied the phylogenetic structure of the shrub communities in arid and semiarid areas of the Mongolian Plateau. First, the phylogenetic signals of four plant traits (height, canopy, leaf length, and leaf width) of shrubs and subshrubs were measured to determine the phylogenetic conservation of these traits. Then, the net relatedness index (NRI) of shrub communities was calculated to characterize their phylogenetic structure. Finally, the relationship between the NRI and current climate and paleoclimate (since the Last Glacial Maximum, LGM) factors was analyzed to understand the formation and maintenance mechanisms of these plant communities. We found that desert shrub communities showed a trend toward phylogenetic overdispersion; that is, limiting similarity was predominant in arid and semiarid areas of the Mongolian Plateau despite the phylogenetic structure and formation mechanisms differing across habitats. The typical desert and sandy shrub communities showed a significant phylogenetic overdispersion, while the steppified desert shrub communities showed a weak phylogenetic clustering. It was found that mean winter temperature (i.e., in the driest quarter) was the major factor limiting steppified desert shrub phylogeny distribution. Both cold and drought (despite having opposite consequences) differentiated the typical desert to steppified desert shrub communities. The increase in temperature since the LGM is conducive to the invasion of shrub plants into steppe grassland, and this process may be intensified by global warming.
Self‐Supply of O2 and H2O2 by a Nanocatalytic Medicine to Enhance Combined Chemo/Chemodynamic Therapy

Combined chemo/chemodynamic therapy is a promising strategy to achieve an improved anticancer effect. However, the hypoxic microenvironment and limited amount of H2O2 in most solid tumors severely restrict the efficacy of this treatment. Herein, the construction of a nanocatalytic medicine, CaO2@DOX@ZIF‐67, via a bottom‐up approach is described. CaO2@DOX@ZIF‐67 simultaneously supplies O2 and H2O2 to achieve improved chemo/chemodynamic therapy. In the weakly acidic environment within tumors, CaO2@DOX@ZIF‐67 is broken down to rapidly release the Fenton‐like catalyst Co2+ and the chemotherapy drug doxorubicin (DOX). The unprotected CaO2 reacts with H2O to generate both O2 and H2O2. The generated O2 relieves the hypoxia in the tumor and further improve the efficacy of DOX. Meanwhile, the generated H2O2 reacts with Co2+ ions to produce highly toxic •OH through a Fenton‐like reaction, resulting in improved chemodynamic therapy.
Repeated Endovascular Thrombectomy in Patients With Acute Ischemic Stroke

Supplemental Digital Content is available in the text. Background and Purpose— Patients with acute ischemic stroke treated with endovascular thrombectomy may be treated with repeat endovascular thrombectomy (rEVT) in case of recurrent large vessel occlusion. Data on safety and efficacy of these interventions is scarce. Our aim is to report on frequency, timing, and outcome of rEVT in a large nation-wide multicenter registry. Methods— In the Netherlands, all patients with endovascular thrombectomy have been registered since 2002 (MR CLEAN Pretrial registry, MR CLEAN Trial [Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands], and MR CLEAN Registry). We retrospectively reviewed these databases for anterior circulation rEVT cases. Patient characteristics, procedural data, and functional outcome (modified Rankin Scale at 90 days) were analyzed. Results— Of 3928 patients treated between 2002 and 2017, 27 (0.7%) underwent rEVT. Median time between first and second procedure was 78 (1–1122) days; 11/27 patients were re-treated within 30 days. Cardioembolism was the most common etiology (18 patients [67%]). In 19 patients (70%), recurrent occlusion occurred ipsilateral to previous occlusion. At 90 days after rEVT procedure, 44% of the patients had achieved functional independence (modified Rankin Scale score of 0–2), and 33% had died. Adverse events were 2/27 (7.4%) intracranial hemorrhage, 1/27 (3.7%) stroke progression, and 1/27 (3.7%) pneumonia. Conclusions— In this large nationwide cohort of patients with acute ischemic stroke treated with endovascular thrombectomy, rEVT was rare. Stroke cause was mainly cardio-embolic, and most recurrent large vessel occlusions in which rEVT was performed occurred ipsilateral. Although there probably is a selection bias on repeated treatment in case of recurrent large vessel occlusion, rEVT appears safe, with similar outcome as in single-treated cases.
JAK inhibition in the treatment of alopecia areata – a promising new dawn?

ABSTRACT Introduction: Alopecia areata (AA) is a T-cell-mediated disease which produces circular patches of non-scarring hair loss and nail dystrophy. Current treatment options for AA are limited and often yield unsatisfactory results. Pharmacologic inhibition of the Janus kinase (JAK) enzyme family is regrowing hair and reversing nail dystrophy in a number of patients with hitherto refractory AA. The six JAK inhibitors which have been successful in treating AA are tofacitinib, ruxolitinib, baricitinib, CTP-543, PF-06651600 and PF-06700841. Areas covered: This review reports randomized-controlled trials, open-label trials, case series and case reports published in the literature to date and describes the epidemiology and pathophysiology of AA, the mechanism of action of JAK inhibitors and the adverse effects identified. Electronic searches were performed using Medline Ovid, PubMed, Embase, Cochrane Library and Evidence-Based Medicine Reviews. Expert opinion: The discovery of JAK inhibition represents a major breakthrough in the treatment of AA. Positive results in early phase 1 and phase 2 clinical trials have enabled the commencement of phase 3 clinical trials and there is now a growing sense of optimism among patients with long-standing, treatment-refractory AA. Further work is required to determine the optimal dose and treatment duration and whether maintenance therapy is universally required.
On-call simulation for adult gerontology acute care nurse practitioner students: A comparative descriptive study

ABSTRACT Background: It is now commonplace for acute care nurse practitioners (ACNPs) to work in positions that include an on-call component or management of emergent concerns through telephone. There are no published reports on the inclusion of an on-call component in ACNP clinical preparation of students; novice ACNPs feel unprepared to competently and confidently manage emergent patient situations and on-call responsibilities. Purpose: To examine ACNP student perception of stress, necessary skills, confidence, and benefit of participating in a simulated on-call experience. Methods: Using simulated faculty callers as nurses, ACNP students participated in a simulated on-call experience that included receiving two calls, eliciting key information from the nurse, diagnosing and managing the patient, and submitting documentation of the encounter. Students completed preparticipation and postparticipation perception surveys, and they were evaluated by the simulated nurse (faculty) using standardized evaluation tools. Results: Acute care nurse practitioner students rated the simulated on-call experience as educationally valuable. High levels of anxiety before participation were notably improved after participation. Students identified critical thinking, clear communication, and knowledge with the specific disease as the most important skills needed to manage nurse calls successfully. Students reported marked improvement in their confidence and were receptive to accepting an nurse practitioner position with call/triage responsibilities after their on-call experience. Implications for practice: Inclusion of a simulated on-call experience in the final semester of an ACNP program is both feasible and relevant to ACNP student development. On-call exposure within the clinical practicum is inconsistent and, therefore, should be added through simulation.
Development and psychometric evaluation of the Group Home Culture Scale

Abstract Background Organizational culture in group homes for people with intellectual disabilities has been identified as influencing staff behaviour and residents’ quality of life (QOL). Despite this influence, culture has been under‐researched, with no published and validated instrument to measure its dimensions in group homes. The aim was to develop such a measure. Method The Group Home Culture Scale (GHCS) was developed using a theory‐driven approach. Items were generated from the research literature, which were reviewed by experts and tested in cognitive interviews. Data from 343 front‐line staff were used for exploratory factor analysis. Results The content and face validity of the GHCS were found to be acceptable. Exploratory factor analysis indicated that the GHCS measured seven dimensions of group home culture. Cronbach's alpha for the dimensions ranged from 0.81 to 0.92. Conclusions The GHCS has potential use in research to determine whether dimensions of group home culture predict the quality of staff support and residents’ QOL.
Deep learning for mining protein data

The recent emergence of deep learning to characterize complex patterns of protein big data reveals its potential to address the classic challenges in the field of protein data mining. Much research has revealed the promise of deep learning as a powerful tool to transform protein big data into valuable knowledge, leading to scientific discoveries and practical solutions. In this review, we summarize recent publications on deep learning predictive approaches in the field of mining protein data. The application architectures of these methods include multilayer perceptrons, stacked autoencoders, deep belief networks, two- or three-dimensional convolutional neural networks, recurrent neural networks, graph neural networks, and complex neural networks and are described from five perspectives: residue-level prediction, sequence-level prediction, three-dimensional structural analysis, interaction prediction, and mass spectrometry data mining. The advantages and deficiencies of these architectures are presented in relation to various tasks in protein data mining. Additionally, some practical issues and their future directions are discussed, such as robust deep learning for protein noisy data, architecture optimization for specific tasks, efficient deep learning for limited protein data, multimodal deep learning for heterogeneous protein data, and interpretable deep learning for protein understanding. This review provides comprehensive perspectives on general deep learning techniques for protein data analysis.
Switches in histone modifications epigenetically control vitamin D3‐dependent transcriptional upregulation of the CYP24A1 gene in osteoblastic cells

In bone cells vitamin D dependent regulation of gene expression principally occurs through modulation of gene transcription. Binding of the active vitamin D metabolite, 1,25‐dihydroxy vitamin D3 (1,25(OH)2D3) to the vitamin D receptor (VDR) induces conformational changes in its C‐terminal domain enabling competency for interaction with physiologically relevant coactivators, including SRC‐1. Consequently, regulatory complexes can be assembled that support intrinsic enzymatic activities with competency to posttranslationally modify chromatin histones at target genomic sequences to epigenetically alter transcription. Here we examine specific transitions in representation and/or enrichment of epigenetic histone marks during 1,25(OH)2D3 mediated upregulation of CYP24A1 gene expression in osteoblastic cells. This gene encodes the 24‐hydroxylase enzyme, essential for biological control of vitamin D levels. We demonstrate that as the CYP24A1 gene promoter remains transcriptionally silent, there is enrichment of H4R3me2s together with its “writing” enzyme PRMT5 and decreased abundance of the istone H3 and H4 acetylation, H3R17me2a, and H4R3me2a marks as well as of their corresponding “writers. ” Exposure of osteoblastic cells to 1,25(OH)2D3 stimulates the recruitment of a VDR/SRC‐1 containing complex to the CYP24A1 promoter to mediate increased H3/H4 acetylation. VDR/SRC‐1 binding occurs concomitant with the release of PRMT5 and the recruitment of the arginine methyltransferases CARM1 and PRMT1 to catalyze the deposition of the H3R17me2a and H4R3me2a marks, respectively. Our results indicate that these dynamic transitions of histone marks at the CYP24A1 promoter, provide a “chromatin context” that is transcriptionally competent for activation of the CYP24A1 gene in osteoblastic cells in response to 1,25(OH)2D3.
Sensing of nutrients by CPT1C regulates late endosome/lysosome anterograde transport and axon growth

Anterograde transport of late endosomes or lysosomes (LE/Lys) is crucial for proper axon growth. However, the role of energetic nutrients has been poorly explored. Malonyl-CoA is a precursor of fatty acids, and its intracellular levels highly fluctuate depending on glucose availability or the energy sensor AMP-activated protein kinase (AMPK). We demonstrate in HeLa cells that carnitine palmitoyltransferase 1C (CPT1C) senses malonyl-CoA and enhances LE/Lys anterograde transport by interacting with the endoplasmic reticulum protein protrudin and facilitating the transfer of Kinesin-1 from protrudin to LE/Lys. In cultured mouse cortical neurons, glucose deprivation, pharmacological activation of AMPK or inhibition of malonyl-CoA synthesis decreases LE/Lys abundance at the axon terminal, and shortens axon length in a CPT1C-dependent manner. These results identify CPT1C as a new regulator of anterograde LE/Lys transport in response to malonyl-CoA changes, and give insight into how axon growth is controlled by nutrients.
Marrow aspiration in aged mice: intramedullary osteogenesis, reduced mechano-adaptation, increased marrow fat

ABSTRACT Introduction: With age, the number of adipocytes and osteoclasts increases, the number of osteoblasts decreases, and mechano-adaptation is impaired. Objectives: Using marrow aspiration, which has a known osteogenic effect in young mice, we sought to recruit osteoblast progenitors to mediate the mechano-adaptive response to in vivo tibial loading. Methods: First, we assessed bone formation and marrow adiposity in the tibiae of old mice (>20 months) sacrificed 1, 2, and 4 weeks after unilateral marrow aspiration. Then, we examined the effects of marrow aspiration on mechano-adaptation in aged mice using tibial loading. Results: Two weeks after aspiration, aspirated tibiae had more bone than contralateral tibiae due to the formation of bone in the medullary canal. Two weeks and four weeks after marrow aspiration, the volume of marrow adipose tissue was higher in the aspirated tibiae, compared to contralateral tibiae. Histomorphometry indicated that aspiration increased non-periosteal (endosteal, intracortical, intramedullary) bone formation, compared to the contralateral tibia. Mice with marrow aspiration had reduced periosteal bone formation in the contralateral tibia, compared to mice that had loading alone. Loading-induced periosteal bone formation was higher in mice that had loading alone, compared to mice that had aspiration + loading, indicating that aspiration further reduced the mechano-adaptive response. Conclusion: These data demonstrate that, in old mice, bone forms in the medullary canal following aspiration. Adiposity is increased following marrow aspiration, and periosteal mechano-adaptation is reduced.
Relaxation of synaptic inhibitory events as a compensatory mechanism in fetal SOD spinal motor networks

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting motor neurons (MNs) during late adulthood. Here, with the aim of identifying early changes underpinning ALS neurodegeneration, we analyzed the GABAergic/glycinergic inputs to E17.5 fetal MNs from SOD1G93A (SOD) mice in parallel with chloride homeostasis. Our results show that IPSCs are less frequent in SOD animals in accordance with a reduction of synaptic VIAAT-positive terminals. SOD MNs exhibited an EGABAAR 10 mV more depolarized than in WT MNs associated with a KCC2 reduction. Interestingly, SOD GABAergic/glycinergic IPSCs and evoked GABAAR-currents exhibited a slower decay correlated to elevated [Cl-]i. Computer simulations revealed that a slower relaxation of synaptic inhibitory events acts as compensatory mechanism to strengthen GABA/glycine inhibition when EGABAAR is more depolarized. How such mechanisms evolve during pathophysiological processes remain to be determined, but our data indicate that at least SOD1 familial ALS may be considered as a neurodevelopmental disease.