Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System

Tillage and fertilization are common practices used to enhance soil fertility and increase yield. Changes in soil edaphic properties associated with different tillage and fertility regimes have been widely examined, yet, the microbially mediated pathways and ecological niches involved in enhancing soil fertility are poorly understood. The effects of long-term conventional tillage and no-till in parallel with three fertility treatments (No fertilization, N-only, and NPK) on soil microbial communities were investigated in a long-term field study that was established in the 1970’s. Here, we used high-throughput sequencing of bacterial, fungal and oomycetes markers, followed by community-level functional and ecological assembly to discern principles governing tillage and fertility practices’ influence on associated soil microbiomes. Both tillage and fertilizer significantly altered microbial community structure, but the tillage effect was more prominent than the fertilizer effect. Tillage significantly affected bacteria, fungi, fusaria, and oomycete beta-diversity, whereas fertilizer only affected bacteria and fungi beta-diversity. In our study different tillage and fertilizer regimes favored specific networks of metabolic pathways and distinct ecological guilds. No-till selected for beneficial microbes that translocate nutrients and resources and protect the host against pathogens. Notably, ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and nematophagous fungi were favored in no-till soils, while fungal saprotrophs and plant pathogens dominated in tilled soils. Conventional till and fertilizer management shifted the communities toward fast growing competitors. Copiotrophic bacteria and fusarium species were favored under conventional tillage and in the presence of fertilizers. The analysis of the metagenomes revealed a higher abundance of predicted pathways associated with energy metabolism, translation, metabolism of cofactors and vitamins, glycan biosynthesis and nucleotide metabolism in no-till. Furthermore, no specific pathways were found to be enriched under the investigated fertilization regimes. Understanding how tillage and fertilizer management shift microbial diversity, structure and ecological niches, such as presented here, can assist with designing farming systems that can maintain high crop yield, while reducing soil erosion and nutrient losses.
Stair Gait in Older Adults Worsens With Smaller Step Treads and When Transitioning Between Level and Stair Walking

Older people have an increased risk of falling during locomotion, with falls on stairs being particularly common and dangerous. Step going (i.e., the horizontal distance between two consecutive step edges) defines the base of support available for foot placement on stairs, as with smaller going, the user's ability to balance on the steps may become problematic. Here we quantified how stair negotiation in older participants changes between four goings (175, 225, 275, and 325 mm) and compared stair negotiation with and without a walking approach. Twenty-one younger (29 ± 6 years) and 20 older (74 ± 4 years) participants negotiated a 7-step experimental stair. Motion capture and step-embedded force platform data were collected. Handrail use was also monitored. From the motion capture data, body velocity, trunk orientation, foot clearance and foot overhang were quantified. For all participants, as stair going decreased, gait velocity (ascent pA = 0.033, descent pD = 0.003) and horizontal step clearance decreased (pA = 0.001), while trunk rotation (pD = 0.002) and foot overhang increased (pA,D < 0.001). Compared to the younger group, older participants used the handrail more, were slower across all conditions (pA < 0.001, pD = 0.001) and their foot clearance tended to be smaller. With a walking approach, the older group (Group x Start interaction) showed a larger trunk rotation (pA = 0.011, pD = 0.015), and smaller lead foot horizontal (pA = 0.046) and vertical clearances (pD = 0.039) compared to the younger group. A regression analysis to determine the predictors of foot clearance and amount of overhang showed that physical activity was a common predictor for both age groups. In addition, for the older group, medications and fear of falling were found to predict stair performance for most goings, while sway during single-legged standing was the most common predictor for the younger group. Older participants adapted to smaller goings by using the handrails and reducing gait velocity. The predictors of performance suggest that motor and fall risk assessment is complex and multifactorial. The results shown here are consistent with the recommendation that larger going and pausing before negotiating stairs may improve stair safety, especially for older users.
Role of Epithelial-Mesenchymal Transition in Retinal Pigment Epithelium Dysfunction

Retinal pigment epithelial (RPE) cells maintain the health and functional integrity of both photoreceptors and the choroidal vasculature. Loss of RPE differentiation has long been known to play a critical role in numerous retinal diseases, including inherited rod-cone degenerations, inherited macular degeneration, age-related macular degeneration, and proliferative vitreoretinopathy. Recent studies in post-mortem eyes have found upregulation of critical epithelial-mesenchymal transition (EMT) drivers such as TGF-β, Wnt, and Hippo. As RPE cells become less differentiated, they begin to exhibit the defining characteristics of mesenchymal cells, namely, the capacity to migrate and proliferate. A number of preclinical studies, including animal and cell culture experiments, also have shown that RPE cells undergo EMT. Taken together, these data suggest that RPE cells retain the reprogramming capacity to move along a continuum between polarized epithelial cells and mesenchymal cells. We propose that movement along this continuum toward a mesenchymal phenotype be defined as RPE Dysfunction. Potential mechanisms include impaired tight junctions, accumulation of misfolded proteins and dysregulation of several key pathways and molecules, such as TGF-β pathway, Wnt pathway, nicotinamide, microRNA 204/211 and extracellular vesicles. This review synthesizes the evidence implicating EMT of RPE cells in post-mortem eyes, animal studies, primary RPE, iPSC-RPE and ARPE-19 cell lines.
Frequency-Specific Resting Connectome in Bipolar Disorder: An MEG Study

Background Bipolar disorder (BD) is a serious psychiatric disorder that is associated with a high suicide rate, and for which no clinical biomarker has yet been identified. To address this issue, we investigated the use of magnetoencephalography (MEG) as a new prospective tool. MEG has been used to evaluate frequency-specific connectivity between brain regions; however, no previous study has investigated the frequency-specific resting-state connectome in patients with BD. This resting-state MEG study explored the oscillatory representations of clinical symptoms of BD via graph analysis. Methods In this prospective case-control study, 17 patients with BD and 22 healthy controls (HCs) underwent resting-state MEG and evaluations for depressive and manic symptoms. After estimating the source current distribution, orthogonalized envelope correlations between multiple brain regions were evaluated for each frequency band. We separated regions-of-interest into seven left and right network modules, including the frontoparietal network (FPN), limbic network (LM), salience network (SAL), and default mode network (DMN), to compare the intra- and inter-community edges between the two groups. Results In the BD group, we found significantly increased inter-community edges of the right LM–right DMN at the gamma band, and decreased inter-community edges of the right SAL–right FPN at the delta band and the left SAL–right SAL at the theta band. Intra-community edges in the left LM at the high beta band were significantly higher in the BD group than in the HC group. The number of connections in the left LM at the high beta band showed positive correlations with the subjective and objective depressive symptoms in the BD group. Conclusion We introduced graph theory into resting-state MEG studies to investigate the functional connectivity in patients with BD. To the best of our knowledge, this is a novel approach that may be beneficial in the diagnosis of BD. This study describes the spontaneous oscillatory brain networks that compensate for the time-domain issues associated with functional magnetic resonance imaging. These findings suggest that the connectivity of the LM at the beta band may be a good objective biological biomarker of the depressive symptoms associated with BD.
Calculation of Drug Dosage In Chronic Kidney Disease

Kidneys are the main organ in fluid and electrolyte homeostasis. It also have an important role in eliminating various types of drugs. Drug elimination in the kidney is affected by plasma drug concentrations, plasma protein binding, and kidney function. Glomerular filtration rate (GFR) represents the kidney function. Thus by knowing it, drug dosage can be determined. Chronic kidney disease alter the effect of drug, some decrease drug effect but more often increase drug toxicity. Chronic kidney disease affect the pharmacodynamic and pharmacokinetic of drug. Therefore, providing an optimal treatment for CKD patient, knowledge of the pharmacokinetic and pharmacodynamic changing in CKD is needed. Exploring the patient’s history and carrying out complete physical examination is important before giving the drug to patients with impaired kidney function. In addition, identifying drugs that have the potential to cause nephrotoxicity and drug interactions is also important. The body response to drugs in patient with CKD is very varied, complex, and individual. Dosage must be based on several factors, not only glomerular filtration rates but also other comorbid diseases, interactions with other drugs and clinical condition of the patient.
Application of Exogenous dsRNAs-induced RNAi in Agriculture: Challenges and Triumphs

In recent years, RNA interference (RNAi) machinery has widely been explored by plant biologists for its potential applications in disease management, plant development, and germplasm improvement. RNAi-based technologies have mainly been applied in the form of transgenic plant generation and host-induced-gene-silencing (HIGS). However, the approval of RNAi-based transgenic plants has always been challenging due to the proclaimed concerns surrounding their impacts on human health and the environment. Lately, exogenous applications of double-stranded RNAs (dsRNAs), short interfering RNAs (siRNAs), and hairpin RNAs (hpRNAs) has emerged as another technology that could be regarded as more eco-friendly, sustainable, and publicly acceptable than genetic transformation. Inside the plant cell, dsRNAs can undergo several steps of processing, which not only triggers RNAi machinery but may also involve transitive and systemic silencing, as well as epigenetic modifications. Therefore, along with the considerations of proper exogenous applications of dsRNAs, defining their final destination into plant cells is highly relevant. In this review, we highlighted the significance of several factors that affect dsRNA-induced gene silencing, the fate of exogenous dsRNAs in the plant cell, and the challenges surrounding production technologies, cost-effectiveness, and dsRNAs stability under open-field conditions. This review also provided insights into the potential applications of exogenous dsRNAs in plant protection and crop improvement.
Investigation of computational flow field over a re-entry capsule at high speed

Manned space programme has become inevitable in the modern world. One important aspect in such endeavors is getting the crew back to home safe and sound. Re-entry capsules are widely used for bringing back astronauts back to the Earth. The re-entry mission is a very crucial one, with speeds up to 30 times than that of sound and temperatures hot enough to ionize air. The study and design of a re-entry capsule has to be done with utmost concern over the life of returning asronauts. In this paper, simulations carried out over a re-entry vehicle for various free-stream conditions such as subsonic, supersonic and hypersonic flow regimes. Results were obtained by solving compressible Navier-Stokes equation with k-omega turbulent model. Simulations were carried out for various inlet conditions corresponding to an altitude of a re-entry vehicle by using CFD code SU2. The geometrical parameters of a re-entry vehicle such as spherical nose radius and cone angle were varied and the effects of the aerodynamic phenomena such as shock wave, flow separation and wake formation over a downstream of a module were studied. In this paper, the results pertaining to the pressure distribution, the Mach contour and temperature over a module is presented.
The Role of HLA-G in Human Papillomavirus Infections and Cervical Carcinogenesis

Human leukocyte antigen (HLA)-G, a non-classical HLA-class I molecule, has a low polymorphism frequency, restricted tissue distribution and immunoinhibitory property. HLA-G expression in tumor cells and cells chronically infected with virus may enable them to escape from host immune surveillance. It is well-known that the HLA-G molecule is a novel biomarker and potential therapeutic target that is relevant in various types of cancers, but its role in cervical cancer has not been fully explored. In this review, we aim to summarize and discuss the immunologic role of the HLA-G molecule in the context of HPV infections and the process of cervical cancer carcinogenesis. A better understanding of the potential impact of HLA-G on the clinical course of persistent HPV infections, cervical epithelial cell transformation, tumor growth, recurrence and metastasis is needed to identify a novel diagnostic/prognostic biomarker for cervical cancer, which is critical for cervical cancer risk screening. In addition, it is also necessary to identify HLA-G-driven immune mechanisms involved in the interactions between host and virus to explore novel immunotherapy strategies that target HLA-G/immunoglobulin-like transcript (ILT) immune checkpoints.
Pre-meiotic, 24-nt reproductive phasiRNAs are abundant in anthers of wheat and barley but not rice and maize

Two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs and their patterns of accumulation have been described in maize and rice anthers. Their precise function remains unclear, but some studies have shown that they support male fertility. The important role of phasiRNAs in anthers underpins our current study to their characterization in wheat and barley anthers. In this study, we staged anthers at every 0.2 mm of development for one wheat and two barley varieties. We isolated pre-meiotic (0.2 mm, 0.4 mm and 0.6 mm), meiotic (0.8 mm, 1.0 mm and 1.4 mm) and post-meiotic (1.8 mm) anthers for which we then investigated accumulation patterns of RNAs, including reproductive phasiRNAs. We annotated a total 12,821 and 2,897 PHAS loci in the wheat and barley genomes, respectively. When comparing the total number of PHAS loci in genomes of maize, rice, barley and wheat, we characterized an expansion of reproductive PHAS loci in the genomes of Poaceae subfamilies from Panicoideae to Oryzoideae and to Poideae. In addition to the two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs, previously described in maize and rice anthers, we described a group of 24-nt phasiRNAs that accumulate in pre-meiotic anthers. The absence of pre-meiotic 24-nt phasiRNAs in maize and rice suggests a divergence in grass species of the Poideae subfamily. Additionally, we performed a co-expression gene analysis describing the regulation of phasiRNA biogenesis in wheat and barley anthers. We highlight AGO9 and AGO6 as candidate binding partners of pre-meiotic and meiotic 24-nt phasiRNAs, respectively. One sentence summary In wheat and barley anthers, 24-nt reproductive phasiRNAs are abundant in both meiotic and pre-meiotic stages.
Response of carbon and nitrogen allocation in two hybrid poplar clones to soil nitrogen in Northern China

The response of poplar to nitrogen (N) fertilizer application varies with clones. Our objective was to quantify differences in resource allocation in two hybrid poplar clones due to nitrogen conditions. A two clone (46 and 107)-by-three nitrogen conditions (poor, medium and rich) factorial randomized design was replicated three times and undertaken in Mentougou District, Beijing, China. Biomass, TNC concentration and N concentration were determined at harvest maturity. Results revealed that clone 107 exhibited greater biomass in leaves and roots but less biomass in stems than clone 46 under poor and medium soil nitrogen conditions. Total non-structural carbohydrate allocation, especially the starch allocation in roots of clone 107 was greater than that in clone 46. Nitrogen concentration in leaves and stems were lower in clone 107 compared with clone 46, but higher nitrogen allocation in leaves and roots as well as N use efficiency of leaves and roots were detected in clone 107. There was no difference of endogenous resources between the two clones under rich soil nitrogen conditions. Our results suggest that clone 107 is more sensitive to poor N conditions than clone 46.
Comparative phylogeography reveals how a barrier filters and structures taxa in North American warm deserts

The study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns, and understand the statistical power of differentiating alternative diversification modes. We incorporate published datasets to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan deserts of North America, to synthesize phylogeographic structuring across the community with respect to organismal functional traits. We then use a simulation and machine learning pipeline to assess the power of phylogeographic model selection. Taxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses vary concordantly with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation-by-environment are the primary mechanisms purported to structure taxa. Simulations reveal that in spatially-explicit isolation-with-migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation-by-distance can confound the interpretation of evolutionary history and model selection by producing easily-confusable results. By synthesizing phylogeographic data for the Cochise Filter Barrier we show a pattern where barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying the modes of differentiation across the barriers for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.
GATA4, expressed in Barrett’s esophagus and esophageal adenocarcinoma, can block squamous epithelial cell gene expression in human esophageal cells

Metaplasia often involves a change from one cell type to another that was present during organogenesis. The embryonic esophagus is initially lined by columnar cells that are replaced by squamous cells, and metaplasia in Barrett’s esophagus (BE) involves a change from squamous to columnar cells in the setting of gastroesophageal reflux. Here, we explored the effect of ectopic expression of the essential developmental transcription factor GATA4 on squamous epithelial cell gene expression using human esophageal squamous epithelial cells. We found that GATA4 protein, although absent in mature human esophageal squamous epithelium, was present in BE and esophageal adenocarcinoma (EAC). Moreover, acid and bile induced GATA4 mRNA in esophageal squamous epithelial cells. Ectopic GATA4 expression in esophageal squamous epithelial cells generally compromised squamous cell marker gene expression, although the extent varied between cell lines studied. We observed GATA4 occupancy in the p63, KRT5, and KRT15 gene promoters, suggesting that GATA4 can directly repress expression of typical squamous epithelial cell marker genes. Overall, our data suggest a mechanism whereby GATA4 expression in abnormal esophageal cells, possibly induced by reflux, supports a columnar metaplastic cell identity by repressing expression of key genes required to program stratified squamous epithelial cell identity.
DEVELOPMENT OF AN INTERACTIVE ONLINE ETHICS SCENARIO ACTIVITY FOR ENGINEERING STUDENTS

This paper describes development and deployment of an online interactive ethical decision-making simulation. This tool was piloted in a first-year introduction to engineering course at the University of British Columbia. It used a “choose your own adventure” style of decision-making and narrative to add realism and engagement to what was otherwise viewed by students as dry, uninteresting content. After storyboarding using sticky notes and Visio, the final tool used by students was implemented and deployed using a survey tool (Qualtrics). It featured a scenario with initially incomplete information and the appearance of unethical behaviour by others. It included decision-based branching, but also randomization such that different groups had the story unfold differently, even if they made the same initial decisions. Student feedback on this tool was very positive, suggesting this style of interactive online ethics simulation could be an effective tool for enhancing engagement and learning.
The Determination of Sex and Polymorphism in Microevolution

Abstract Environmental instabilities may be grouped into three broad categories each with different conseqences for the organism which has to survive the stress of these instabilities. On one side are irreversible changes of the environment which will lead to complete adaptive compliance or conformity of the population, brought about by natural selection. On the other side are short-term recurrent instabilities, fluctuations, or oscillations; if their cycle is short enough so that all phases are experienced by all individuals of each generation, natural selection will promote the ability of each individual to withstand the whole range of environmental recurrent fluctuations. Between these extremes are recurrent instabilities that are not experienced by all individuals, or by each generation; here natural selection will evolve mechanisms that prevent the population from conforming with any temporary selection pressure. Polymorphism is such a mechanism, specifically polymorphism based on a gene potency balance system modelled on the same principles as the system that determines sex, the most common example of polymorphism. Instances of such polymorphism in a genus of tortricid moths include haemolymph pigment, adult wing colour, and rate of larval development. The latter exemplifies polymorphism of a quantitative character.