Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico

Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of niche differentiation among macromycete species within communities in urbanized areas. FEve did not show notable differences along the urbanization gradient, indicating few variations in the distribution of abundances within the occupied sections of the niche space. Similarly, the functional value was markedly higher in the less urbanized site, suggesting greater performance of functional guilds in that area. Our findings suggest that urbanization has led to a loss of macromycete species and a decrease in functional diversity, causing some sections of the niche space to be hardly occupied and available resources to be under-utilized, which could, to a certain extent, affect ecosystem functioning and stability.
The complete chloroplast genome sequence of Prunus glandulosa Thunb. (Rosaceae)

Abstract Prunus glandulosa Thunb. is an ornamental species in the genus Prunus (Rosaceae) mainly distributed in eastern China. It is often cultivated in gardens, roadsides, or shrub clusters. It looks like a cherry but resembles to prunes as well. We obtained the complete chloroplast genome of P. glandulosa using next-generation sequencing technology. The chloroplast genome is 158.078 bp in length with typical tetrad structure. It includes two copies of inverted repeats (IRs, 26.385 bp), a large single copy (LSC, 86.269 bp) and a small single copy (SSC, 19.039 bp). The total GC content is 36.7%, including 85 protein-coding genes (PCGs), 36 transfer RNA genes (tRNA), and eight ribosomal RNA genes (rRNA). The maximum-likelihood phylogeny using the full length of chloroplast genomes indicates that P. glandulosa is closer to prunes than to cherries.
Decoders configurations based on Unet family and feature pyramid network for COVID-19 segmentation on CT images

Coronavirus Disease 2019 (COVID-19) pandemic has been ferociously destroying global health and economics. According to World Health Organisation (WHO), until May 2021, more than one hundred million infected cases and 3.2 million deaths have been reported in over 200 countries. Unfortunately, the numbers are still on the rise. Therefore, scientists are making a significant effort in researching accurate, efficient diagnoses. Several studies advocating artificial intelligence proposed COVID diagnosis methods on lung images with high accuracy. Furthermore, some affected areas in the lung images can be detected accurately by segmentation methods. This work has considered state-of-the-art Convolutional Neural Network architectures, combined with the Unet family and Feature Pyramid Network (FPN) for COVID segmentation tasks on Computed Tomography (CT) scanner samples from the Italian Society of Medical and Interventional Radiology dataset. The experiments show that the decoder-based Unet family has reached the best (a mean Intersection Over Union (mIoU) of 0.9234, 0.9032 in dice score, and a recall of 0.9349) with a combination between SE ResNeXt and Unet++. The decoder with the Unet family obtained better COVID segmentation performance in comparison with Feature Pyramid Network. Furthermore, the proposed method outperforms recent segmentation state-of-the-art approaches such as the SegNet-based network, ADID-UNET, and A-SegNet + FTL. Therefore, it is expected to provide good segmentation visualizations of medical images.
Circular RNA ERBB2 Contributes to Proliferation and Migration of Airway Smooth Muscle Cells via miR-98-5p/IGF1R Signaling in Asthma

Background Asthma belongs to chronic inflammatory respiratory diseases characterized by airway inflammation and remodeling. Circular RNAs (circRNAs) are promising therapeutic targets for various diseases, including asthma. In this work, we aim to investigate the role of circular RNA Erb-B2 receptor tyrosine kinase 2 (circERBB2) during progression of asthma. Methods Human airway smooth muscle cells (ASMCs) were treated with platelet-derived growth factor BB (PDGF-BB) to mimic cell remodeling. The expression of circERBB2, microRNA-98-5p (miR-98-5p), and insulin-like growth factor 1 receptor (IGF1R) was measured by qRT-PCR. Cell proliferation, migration and apoptosis were determined by cell counting-8 (CCK-8), transwell, and flow cytometry. Protein levels of PCNA, MMP-9, IGF1R were evaluated using Western blotting. The levels of tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β), and IL‐6 were detected by enzyme‐linked immunosorbent assay (ELISA). Luciferase reporter gene experiment was adopted to evaluate the targeting relationship between miR-98-5p with circERBB2 and IGF1R. Interaction between RNAs was determined by RNA pulldown and RIP assay. Results The depletion of circERBB2 attenuated the proliferation, migration, and levels of inflammatory factors induced by PDGF-BB and cell apoptosis. CircERBB2 was identified to directly interact with miR-98-5p, and overexpression of miR-98-5p abolished the function of circERBB2 on PDGF-BB-stimulated ASMCs. IGF1R was identified as a target of miR-98-5p, and knockdown of IGF1R relieved the PDGF-BB-induced ASMCs proliferation and migration. Conclusion Our work disclosed that knockdown of circERBB2 suppressed PDGF-BB-caused proliferation, migration and inflammatory response of ASMCs, through regulating miR-98-5p/IGF1R signaling, presented circERBB2 as a promising therapeutic target for asthma.
Take Your Best Shot: Which SARS-CoV-2 Vaccine Should I Get?

Background. Three vaccines against SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) have now received emergency use authorization by the US Food and Drug Administration. Patients may have the opportunity to make a choice about which vaccine they prefer to receive. Vaccine hesitancy is a hurdle to the development of widespread immunity, with many patients struggling to decide whether to get vaccinated at all. Objective. Develop a decision model exploring the question, “Should I get vaccinated with mRNA or adenovirus vector vaccine (AVV) if either is available now? ”Design. Markov state transition model with lifetime time horizon. Data Sources. MEDLINE searches, bibliographies from relevant English-language articles. Setting. United States, ambulatory clinical setting. Participants. Previously uninfected, nonimmunized adults in the United States. Interventions. 1) Do Not Vaccinate, 2) Vaccination with mRNA Vaccine, 3) Vaccination with Adenovirus Vector Vaccine. Main Measures. Quality-adjusted life years (QALYs). Key Results. Base case—for a healthy 65-year-old patient, both vaccines yield virtually equivalent results (difference of 0.0028 QALYs). In sensitivity analyses, receiving the AVV is preferred if the short-term morbidity associated with each vaccine dose exceeds 1.8 days. Both vaccines afford an even greater benefit compared with Do Not Vaccinate if the pandemic is in a surge phase with a rising incidence of infection or if the current 7-day incidence is greater than the base case estimate of 105 cases per 100,000. Conclusions. Preferred vaccination strategies change under differing assumptions, but differences in outcomes are negligible. The best advice for patients is to get vaccinated against COVID-19 disease with whatever vaccine is available first. Providing mRNA vaccine to the remaining eligible US population would result in an aggregate gain of 3.92 million QALYs. Highlights Question: Now that three vaccines have received emergency use authorization to prevent SARS-CoV-2, should I get vaccinated with either the mRNA (Moderna or Pfizer) or the adenovirus vector (Janssen/Johnson & Johnson) vaccine if either one is available now? Findings: In our base case, for a healthy 65-year-old patient, an mRNA vaccine is very slightly preferred over the adenovirus vector vaccine by 0.0028 QALYs, or slightly more than 1 day. However, both vaccines afford a substantial benefit compared with not getting vaccinated. Meaning: In conclusion, although different vaccine strategies are preferred under different modeling assumptions, in the final analysis the differences in outcomes are extremely small. Our best advice is to simply get vaccinated with whatever is available the soonest!
Ubiquitous Conjugative Mega-Plasmids of Acinetobacter Species and Their Role in Horizontal Transfer of Multi-Drug Resistance

Conjugative mega-plasmids play a special role in adaptation since they carry a huge number of accessory genes, often allowing the host to develop in new niches. In addition, due to conjugation they are able to effectively spread themselves and participate in the transfer of small mobilizable plasmids. In this work, we present a detailed characterization of a recently discovered family of multiple-drug resistance mega-plasmids of Acinetobacter species, termed group III-4a. We describe the structure of the plasmid backbone region, identify the rep gene and the origin of plasmid replication, and show that plasmids from this group are able not only to move between different Acinetobacter species but also to efficiently mobilize small plasmids containing different mob genes. Furthermore, we show that the population of natural Acinetobacter strains contains a significant number of mega-plasmids and reveal a clear correlation between the living conditions of Acinetobacter strains and the structure of their mega-plasmids. In particular, comparison of the plasmids from environmental and clinical strains shows that the genes for resistance to heavy metals were eliminated in the latter, with the simultaneous accumulation of antibiotic resistance genes by incorporation of transposons and integrons carrying these genes. The results demonstrate that this group of mega-plasmids plays a key role in the dissemination of multi-drug resistance among Acinetobacter species.
Fecal Shedding of 2 Novel Live Attenuated Oral Poliovirus Type 2 Vaccine Candidates by Healthy Infants Administered Bivalent Oral Poliovirus Vaccine/Inactivated Poliovirus Vaccine: 2 Randomized Clinical Trials

Abstract Background Primary intestinal immunity through viral replication of live oral vaccine is key to interrupt poliovirus transmission. We assessed viral fecal shedding from infants administered Sabin monovalent poliovirus type 2 vaccine (mOPV2) or low and high doses of 2 novel OPV2 (nOPV2) vaccine candidates. Methods In 2 randomized clinical trials in Panama, a control mOPV2 study (October 2015 to April 2016) and nOPV2 study (September 2018 to October 2019), 18-week-old infants vaccinated with bivalent oral poliovirus vaccine/inactivated poliovirus vaccine received 1 or 2 study vaccinations 28 days apart. Stools were assessed for poliovirus RNA by polymerase chain reaction (PCR) and live virus by culture for 28 days postvaccination. Results Shedding data were available from 621 initially reverse-transcription PCR–negative infants (91 mOPV2, 265 nOPV2-c1, 265 nOPV2-c2 recipients). Seven days after dose 1, 64.3% of mOPV2 recipients and 31.3%–48.5% of nOPV2 recipients across groups shed infectious type 2 virus. Respective rates 7 days after dose 2 decreased to 33.3% and 12.9%–22.7%, showing induction of intestinal immunity. Shedding of both nOPV2 candidates ceased at similar or faster rates than mOPV2. Conclusions Viral shedding of either nOPV candidate was similar or decreased relative to mOPV2, and all vaccines showed indications that the vaccine virus was replicating sufficiently to induce primary intestinal mucosal immunity.
A novel dynamic integral sliding mode control for power electronic converters

The key characteristics of the sliding mode control (SMC) are the ability to manage unmodeled dynamics with rapid response and the inherent robustness of parametric differences, making it an appropriate choice for the control of power electronic converters. However, its drawback of changing switching frequency causes critical electro-magnetic compatibility and switching power loss issues. This paper addresses the problem by proposing a dynamic integral sliding mode control for power converters having fixed switching frequency. A special hardware test rig is developed and tested under unregulated 12.5-22.5 V input and 30 V output. The experimental findings indicate excellent controller efficiency under wide range of loads and uncertain input voltage conditions. In addition, the findings indicate that the closed-loop system is robust to sudden differences in load conditions. This technique provides an improvement of 24.52 % in the rise time, 20.10 % in the settling time and 42.85 % in robustness of the controller as compared to conventional controllers. Furthermore, the comparison with the existing fixed-frequency sliding mode control techniques is presented in a tabular form.
Thermodynamic analysis and performance improvement of Irem geothermal power plant in Turkey: A case study of organic Rankine cycle

Renewable and environmentally friendly energy sources are becoming increasingly important nowadays. This growth in importance also has an effect on the energy conversion systems using more eco‐friendly and renewable energy sources (geothermal, wind, solar) than fossil fuels, the use of which has been reduced these days (oil, coal, natural gas, etc.). From this perspective, renewable energy sources and the conversion efficiency of the facilities which use these sources have also gained importance. The purpose of this study is to calculate the energy and exergy efficiency of the Irem binary cycle geothermal power plant located in Germencik‐Aydın, Turkey geothermal area. Data measured in the power plant were used in the calculations, and correlations were developed depending on the ambient temperature. In addition, exergoeconomic analysis was performed by taking into account the total cost of the power plant (investment and maintenance costs). The greatest energy (97,805.34 kW) and exergy (6463.8 kW) losses were observed in the air‐cooled condenser. The first law efficiency and the second law efficiency of the power plant were found to be 5.89% and 33.8%, respectively. Furthermore, a model was proposed for 6 different refrigerants with the purpose of investigating the availability of the waste heat and consists of a numerical thermodynamic optimization of the model in this study. © 2017 American Institute of Chemical Engineers Environ Prog, 37: 1523–1539, 2018
Betting Against the Odds: The Mysterious Case of the Clinical Override in Risk Assessment of Adult Convicted Offenders

Various tools were designed to guide practitioners in the risk assessment of offenders, including the Level of Service and Case Management Inventory (LS/CMI). This instrument is based on risk assessment principles prioritizing the actuarial approach to clinical judgment. However, the tool’s architects allowed subjective judgment from the practitioners—referred to as clinical override—to modify an offender’s risk category under certain circumstances. Few studies, however, have examined these circumstances. Therefore, the current study used decision tree analyses among a quasi-population of Quebec offenders (n = 15,744) to identify whether there are offenders more likely to be subjected to this discretion based on their characteristics. The results suggest that, although the override is rare, it occurred under few specific combinations of circumstances. More precisely, these findings propose that the utilization of the clinical override stems from a perceived discrepancy between risk prediction and management.
Astaxanthin Supplementation Increases Glutathione Concentrations but Does Not Impact Fat Oxidation During Exercise in Active Young Men.

This study investigated the effects of 6 mg/day of astaxanthin supplementation on markers of oxidative stress and substrate metabolism during a graded exercise test in active young men. A double-blind, randomized, counterbalanced, cross-over design was used. Fourteen men (age = 23 ± 2 years) supplemented with 6 mg/day of astaxanthin and a placebo for 4 weeks, with a 1 week washout period between treatments. Following each supplementation period, a fasting blood sample was obtained to measure markers of oxidative stress: glutathione, hydrogen peroxide, advanced oxidation protein products, and malondialdehyde. Participants also completed a graded exercise test after each treatment to determine substrate utilization during exercise at increasing levels of intensity. Glutathione was ∼7% higher following astaxanthin compared with placebo (1,233 ± 133 vs. 1,156 ± 185 μM, respectively; p = .02, d = 0.48). Plasma hydrogen peroxide and malondialdehyde were not different between treatments (p > .05). Although not statistically significant (p = .45), advanced oxidation protein products were reduced by ∼28%. During the graded exercise test, mean fat oxidation rates were not different between treatments (p > .05); however, fat oxidation decreased from 50 to 120 W (p < .001) and from 85 to 120 W (p = .004) in both conditions. Astaxanthin supplementation of 6 mg/day for 4 weeks increased whole blood levels of the antioxidant glutathione in active young men but did not affect oxidative stress markers or substrate utilization during exercise. Astaxanthin appears to be an effective agent to increase endogenous antioxidant status.
Genetic Studies of Metabolomics Change After a Liquid Meal Illuminate Novel Pathways for Glucose and Lipid Metabolism

Humans spend the greater part of the day in a postprandial state. However, the genetic basis of postprandial blood measures is relatively uncharted territory. We examined the genetics of variation in concentrations of postprandial metabolites (t = 150 min) in response to a liquid mixed meal through genome-wide association studies (GWAS) performed in the Netherlands Epidemiology of Obesity (NEO) study (n = 5,705). The metabolite response GWAS identified an association between glucose change and rs10830963:G in the melatonin receptor 1B (β [SE] −0.23 [0.03], P = 2.15 × 10−19). In addition, the ANKRD55 locus led by rs458741:C showed strong associations with extremely large VLDL (XXLVLDL) particle response (XXLVLDL total cholesterol: β [SE] 0.17 [0.03], P = 5.76 × 10−10; XXLVLDL cholesterol ester: β [SE] 0.17 [0.03], P = 9.74 × 10−10), which also revealed strong associations with body composition and diabetes in the UK Biobank (P < 5 × 10−8). Furthermore, the associations between XXLVLDL response and insulinogenic index, HOMA-β, Matsuda insulin sensitivity index, and HbA1c in the NEO study implied the role of chylomicron synthesis in diabetes (with false discovery rate–corrected q <0.05). To conclude, genetic studies of metabolomics change after a liquid meal illuminate novel pathways for glucose and lipid metabolism. Further studies are warranted to corroborate biological pathways of the ANKRD55 locus underlying diabetes.
Variability in Quantity and Quality of Early Linguistic Experience in Children With Cochlear Implants: Evidence from Analysis of Natural Auditory Environments

Objectives: Understanding how quantity and quality of language input vary across children with cochlear implants (CIs) is important for explaining sources of large individual differences in language outcomes of this at-risk pediatric population. Studies have mostly focused either on intervention-related, device-related, and/or patient-related factors, or relied on data from parental reports and laboratory-based speech corpus to unravel factors explaining individual differences in language outcomes among children with CIs. However, little is known about the extent to which children with CIs differ in quantity and quality of language input they experience in their natural linguistic environments. To address this knowledge gap, the present study analyzed the quantity and quality of language input to early-implanted children (age of implantation <23 mo) during the first year after implantation. Design: Day-long Language ENvironment Analysis (LENA) recordings, derived from home environments of 14 early-implanted children, were analyzed to estimate numbers of words per day, type-token ratio (TTR), and mean length of utterance in morphemes (MLUm) in adults’ speech. Properties of language input were analyzed across these three dimensions to examine how input in home environments varied across children with CIs in quantity, defined as number of words, and quality, defined as whether speech was child-directed or overheard. Results: Our per-day estimates demonstrated that children with CIs were highly variable in the number of total words (mean ± SD = 25,134 ± 9,267 words) and high-quality child-directed words (mean ± SD = 10,817 ± 7,187 words) they experienced in a day in their home environments during the first year after implantation. The results also showed that the patterns of variability across children in quantity and quality of language input changes depending on whether the speech was child-directed or overheard. Children also experienced highly different environments in terms of lexical diversity (as measured by TTR) and morphosyntactic complexity (as measured by MLUm) of language input. The results demonstrated that children with CIs varied substantially in the quantity and quality of language input experienced in their home environments. More importantly, individual children experienced highly variable amounts of high-quality, child-directed speech, which may drive variability in language outcomes across children with CIs. Conclusions: Analyzing early language input in natural, linguistic environments of children with CIs showed that the quantity and quality of early linguistic input vary substantially across individual children with CIs. This substantial individual variability suggests that the quantity and quality of early linguistic input are potential sources of individual differences in outcomes of children with CIs and warrant further investigation to determine the effects of this variability on outcomes.