Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Genome Architecture and Evolutionary Origin of the Yao Silkworm, a Living Fossil of the Domestic Silkworm Bombyx mori (Lepidoptera: Bombycidae)

Abstract The Yao silkworm is a unique silkworm resource producing yellow flat plate silk that has only been reared by the Baiku Yao ethnic group in Nandan County, Guangxi Province, China for a thousand years. Here, we report the mitochondrial genomes (mitogenomes) of five Yao silkworm strains and 10 local Guangxi strains of the domestic silkworm (Bombyx mori) L. (Lepidoptera: Bombycidae), and use the resulting mitogenomes and the available Bombyx mitogenomes to characterize their genome architecture and trace the evolutionary origin of the Yao silkworm. The five Yao silkworm mitogenomes exhibited genome architectures identical to typical set of 37 mitochondrial genes (13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs) and a high level of genome sequence similarity with the domestic silkworm. Mitogenome-based phylogenetic reconstruction provided solid evidence that the Yao silkworm shares a common ancestor with the domestic silkworm. Sliding window analysis uncovered a distinct variation pattern in the mitogenome between the Yao silkworm and the other domestic silkworm strains. The phylogenetic analyses revealed a basal placement of the Yao silkworm among all available domestic silkworm strains, indicating that the Yao silkworm is an ancient population of the domestic silkworm. Our data indicated that the Yao silkworm (B. mori) is a lineage of the domestic silkworm, which for the first time provides insights into the origin of the Yao silkworm.
Study of residential underfloor air distribution (UFAD) systems using a new modelling approach

Although single/multi-zone thermal models have their own advantages, like simple and fast computations of building energy demand, the accuracy of these models is problematic. The assumption of a uniform room temperature reduces the accuracy of the final energy demand results. In fact, the single/multi-zone thermal models are not able to predict indoor thermal behaviours or building energy demands accurately, if a non-uniform environment in a room or building is created by a single or multiple heating, ventilation, and air conditioning (HVAC) systems, i.e. an underfloor air distribution (UFAD) system. The research described in this article investigated the use of a new approach to improve the computational quality and accuracy of the heating energy demands of UFAD systems using an integrated zonal/multi-zone model. Several case studies were carried out, and the results demonstrate not only the advantages of UFAD systems used in a residential house in terms of energy saving, but also the importance of thermostat location in the prediction of building energy consumption. Additionally, the results indicate that the conventional single/multi-zone models are not appropriate to use for UFAD systems in the building energy demand predictions.
High-k perovskite gate oxide for modulation beyond 1014 cm−2

Scaling down of semiconductor devices requires high-k dielectric materials to continue lowering the operating voltage of field-effect transistors (FETs) and storing sufficient charge on a smaller area. Here, we investigate the dielectric properties of epitaxial BaHf0.6Ti0. 4O3 (BHTO), an alloy of perovskite oxide barium hafnate (BaHfO3) and barium titanate (BaTiO3). We found the dielectric constant, the breakdown field, and the leakage current to be 150, 5.0 megavolts per centimeter (MV cm−1), and 10−4 amperes per square centimeter at 2 MV cm−1, respectively. The results suggest that two-dimensional (2D) carrier density of more than n2D = 1014 per square centimeter (cm−2) could be modulated by the BHTO gate oxide. We demonstrate an n-type accumulation mode FET and direct suppression of more than n2D = 1014 cm−2 via an n-type depletion-mode FET. We attribute the large dielectric constant, high breakdown field, and low leakage current of BHTO to the nanometer scale stoichiometric modulation of hafnium and titanium.
Neural Networks Approach for Hyperelastic Behaviour Characterization of ABS under Uniaxial Solicitation

Characterization and Control Laboratory Mechanics of Materials and Structures, Ecole Nationale Superior Electricity and Mechanics ENSEM, Road to El Jadida. BP 8118 Oasis, Casablanca, Morocco. Nanotechnology Laboratory and Bioplasturgie, Universite du Quebec en AbitibiTemiscamingue UQAT, 445 University Boulevard, Rouyn-Noranda, Quebec J9X 5E4, Canada. Research Group on Renouvlable Energy and Impact of the Northern Climate Department of Applied Science, University of Quebec at Chicoutimi UQAC Science 555 Boulevard University, Chicoutimi, Quebec G7H 2B1, Canada.
Simultaneous determination of the four key fluoroquinolones and two antipsychotics in fish and shrimp by LC-MS/MS

Abstract In this study, we developed and validated a liquid chromatography triple quadrupole tandem mass spectrometry (LC-MS/MS) method used to simultaneously determine levels of four fluoroquinolones (ofloxacin, norfloxacin, lomefloxacin, and pefloxacin) and two antipsychotics (diazepam and methaqualone) in fish and shrimp. The samples were extracted with a mixture of anhydrous sodium sulfate and acetonitrile, and purified by C18 cartridge solid-phase extraction with an optimized eluent. The MS2 method was applied to recognize the molecular structure of these compounds according to a main fragmentation scheme. The key ions of identification and quantification were deduced from chemical structures. Multiple reaction monitoring was used to quantitatively analyse the compounds of interest. Satisfactory linearities were obtained (R 2 ≥0.99) with the limits of quantitation (LOQs) ranging between 0.03 and 1.96 μg kg−1. The recoveries were 74–122%, with a relative standard deviation (RSD) below 4.9% for these compounds at the spiking level of three, five, and ten times the LODs, respectively. The LC-MS/MS method allows precise and sensitive determination of residues of six important banned veterinary drugs in fish and shrimp tissue. This methodological approach solved the problem imposed by the need for two or more analysis methods to analyse the compounds of interest described in this study.
Examining English Language Arts Teachers: Evidence from National Data

Background: Much of the previous research in teacher attrition and retention focuses on teachers in general, without regard to specific types of teachers. We focus on English language arts (ELA) and English as a second language (ESL) teachers because the United States has stubbornly low achievement in reading, and reading is critical to the success of learning other subjects, and because these are the two groups of teachers most responsible for teaching both native and non-native English speakers to read. Purpose: Our goal is to understand how the demographics and qualifications of ELA and ESL teachers have changed over time, changes in the student characteristics and school conditions in which they teach, their attrition rate, and the factors that are associated with their attrition behaviors. We also pay close attention to teachers in economically disadvantaged schools. Research Design: We use nationally representative data from seven waves of the Schools and Staffing Survey from 1987–1988 to 2011–2012, as well as the 2015–2016 National Teacher and Principal Survey to examine ELA and ESL teachers and their turnover behaviors. We employ sampling weights to make the results nationally representative. We use both descriptive and regression analyses to examine these teachers. Data Analysis: We first describe how characteristics of ELA and ESL teachers and the schools in which they teach have changed from 1988 to 2016. We then examine how these characteristics vary systematically across high- and low-poverty schools and compare the attrition rate for ELA and ESL teachers relative to other teachers. We also examine the factors that are associated with various forms of turnover and how organizational supports may be leveraged to increase retention. Findings: We find the composition of ELA and ESL teachers has changed substantially over time, with more teachers attending selective schools, being certified to teach, and more likely to teach in high-poverty schools. Relatedly, teacher characteristics in high- and low-poverty schools are consistently different across time, and school working conditions play an enhanced role in high-poverty schools rather than in more affluent schools. Conclusions: Although we find ELA teachers turn over at similar rates compared to non-ELA teachers, we find ESL teachers are more likely to leave both their current school and the profession. This is particularly concerning given that the ESL population is increasing while at the same time there is a shortage of trained-ESL teachers.
Analysis of Lactobacillus rhamnosus GG in Mulberry Galacto-Oligosaccharide Medium by Comparative Transcriptomics and Metabolomics

Lactobacillus rhamnosus GG (LGG) has strong acid resistance and can survive passing through the stomach to colonize the intestines, where it promotes the growth of beneficial bacteria. Prebiotics such as mulberry galacto-oligosaccharide (MGO), mulberry polysaccharide solution (MPS), and galactooligosaccharides (GOS) promote LGG proliferation, and MGO has the greatest effect. After culturing LGG with prebiotics, changes in gene expression were studied at the transcriptomic and metabolomic levels. The results showed that, in the stable 24-h growth period of cultivation, ~63 and 132% more differential genes were found after MPS and MGO were added to the MRS medium, respectively, than after GOS was added, and the numbers of up-regulated genes were about 18 and 66% higher with MPS and MGO, respectively, than GOS. Analysis using the KEGG database revealed that, when LGG was cultured with MGO, 120 genes that were up-regulated as the growth rate increased were mainly enriched in pathways such as membrane transport, amino acid metabolism, and carbohydrate metabolism. The genes gatB and gatC were up-regulated for galactose metabolism, and bglA was up-regulated in the glycolysis/gluconeogenesis pathway. The qRT-RCR results, which were in agreement with the RNA-seq, indicated the genes involved in the proliferation effect of LGG were up-regulated. UDP-glucose may be a key metabolite for MGO to promote LGG proliferation.
An Investigation of Working Memory Profile and Fluid Intelligence in Children With Neurodevelopmental Difficulties

The present study aims to evaluate the distinct patterns of working memory (WM) capacity of children with Developmental Language Disorder (DLD), High-functioning children with Autism Spectrum Disorder (ASD) and children with Down syndrome (DS). More specifically, the current study investigates the complex relationship of fluid intelligence and WM between 39 children with DLD, 20 H igh-functioning children with ASD, and 15 children with DS. All children were evaluated in different measures of Phonological Working Memory, Visual-spatial Working Memory whereas Fluid Intelligence was measured with Raven Progressive Matrices. The result analysis revealed a significant difference among the three groups, both among each function separately and the correlations among them, as well. The results revealed that the DLD groups and High-functioning ASD group exhibited a common picture or an overlap of performances in all Phonological and Visuo-spatial working memory measures, except Backward Digit Recall task. As for the DS group research findings revealed different and unique working memory patterns in comparison to DLD group and High-functioning ASD. Their differences have been studied and further conclusions have been drawn about the different patterns of working memory among the three clinical groups. The implications of these findings are discussed in light of support for learning. The common profile that characterize the two developmental conditions and the distinct pattern of working memory performance in DS group underlies the need for further research in the field.
Software Development Statistical Process Control Using Six Sigma Techniques

System developers and managers continually strive to identify, undertake, and realize improvements in software development methods. Measurement-driven software development guides the identification of improvement opportunities and enables the quantitative evaluation of progress and benefits. Six Sigma techniques provide a statistical process control approach for using measurement-driven methods to decrease the variances and shift the means of user-defined metrics such as defect densities, development cycletimes, and resource expenditures. This research investigates the effectiveness of software defection detection using peer reviews across 12 system development phases on 14 large-scale systems. This study analyzes 3418 defects from 731 peer reviews and benchmarks the defect injection and detection performance across the 12 system development phases. Six Sigma techniques including the define-measure-analyze-improve-control (DMAIC) method, root cause analysis, and control charts helped achieve in-phase detection of 95 percent of defects and realize over 50 percent improvements in defect densities and closure cycletimes for certain peer review types.
A non-invasive method for time-lapse imaging of microbial interactions and biofilm dynamics

Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or to competition and the death or displacement of particular organisms or sub-populations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intra- and inter-species interactions in vivo at the microscopic level has remained somewhat limited. Here, we detail BacLive, a novel non-invasive method for tracking bacterial growth and biofilm dynamics using high resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provide examples of how BacLive can be used in the analysis of complex bacterial communities. Importance Communication and interactions between single cells are continuously defining the structure and composition of microbial communities timely and spatially. Methods routinely used to the study of these communities at cellular level rely on sample manipulation what deprives from microscopic time lapse experiments on a given sample. BacLive is conceived as a method for the non-invasive study of the formation and development of bacterial communities, such as biofilms, and the dynamics of formation of specialized subpopulations in time-lapse experiments. In addition we prove that BacLive largely simplifies the analysis of the data generated.
SLC15A4 favors inflammasome function via mTORC1 signaling and autophagy restraint in dendritic cells

Phagocytosis is the first step in the assessment of foreign microbes or particles and enables activation of innate immune pathways such as the inflammasome. However, missing links between phagosomes and inflammasomes remain to be discovered. We show that in murine dendritic cells (DCs) the lysosomal histidine/peptide solute carrier transporter SLC15A4, associated with human inflammatory disorders, is recruited to phagosomes and is required for optimal inflammasome activity after infectious or sterile stimuli. Dextran sodium sulphate-treated SLC15A4-deficient mice exhibit decreased colon inflammation, reduced IL-1β production by intestinal DCs and increased autophagy. Similarly, SLC15A4-deficient DCs infected with Salmonella typhimurium show reduced caspase-1 cleavage and IL-1β production. This correlates with peripheral NLRC4 inflammasome assembly and increased autophagy. Overexpression of constitutively active mTORC1 rescues decreased IL-1β levels and caspase-1 cleavage, and restores perinuclear inflammasome positioning. Our findings suggest that SLC15A4 is a novel link that couples phagocytosis with inflammasome perinuclear assembly and inhibition of autophagy through phagosomal content sensing. Our data also reveal the previously unappreciated importance of mTORC1 signaling pathways to promote and sustain inflammasome activity.
Replacing bar graphs of continuous data with more informative graphics: are we making progress?

Recent work has raised awareness about the need to replace bar graphs of continuous data with informative graphs showing the data distribution. The impact of these efforts is not known. This observational meta-research study examined how often scientists in different fields use various graph types, and assessed whether visualization practices have changed between 2010 and 2020. We developed and validated an automated screening tool, designed to identify bar graphs of counts or proportions, bar graphs of continuous data, bar graphs with dot plots, dot plots, box plots, violin plots, histograms, pie charts, and flow charts. Papers from 23 fields (approximately 1,000 papers/field/year) were randomly selected from PubMed Central and screened (n=227,998). F1 scores for different graphs ranged between 0.83 and 0.95 in the internal validation set. While the tool also performed well in external validation sets, F1 scores were lower for uncommon graphs. Bar graphs are more often used incorrectly to display continuous data than they are used correctly to display counts or proportions. The proportion of papers that use bar graphs of continuous data varies markedly across fields (range in 2020: 4%-58%), with high rates in biochemistry and cell biology, complementary and alternative medicine, physiology, genetics, oncology and carcinogenesis, pharmacology, microbiology and immunology. Visualization practices have improved in some fields in recent years. Fewer than 25% of papers use flow charts, which provide information about attrition and the risk of bias. This study highlights the need for continued interventions to improve visualization and identifies fields that would benefit most.
The Arabidopsis Hop1 homolog ASY1 mediates cross-over assurance and interference

The chromosome axis plays a crucial role in meiotic recombination. Here, we study the function of ASY1, the Arabidopsis homolog of the yeast chromosome axis associated component Hop1. Specifically, we characterized cross-over (CO) distribution in female and male meiosis by deep sequencing of the progeny of an allelic series of asy1 mutants. Combining data from nearly 1000 individual plants, we find that reduced ASY1 activity leads to genomic instability and sometimes drastic genomic rearrangements. We further observed that COs are less frequent and appear in more distal chromosomal regions in plants with no or reduced ASY1 activity, consistent with previous analyses. However, our sequencing approach revealed that the reduction in CO number is not as dramatic as suggested by cytological analyses. Analysis of double mutants of asy1 with mutants with three other CO factors, MUS81, MSH4 and MSH5 as well as the determination of foci number of the CO regulator MLH1 demonstrates that the majority of the COs in asy1, similar to the situation in the wildtype, largely belong to the class I, which are subject to interference. However, these COs are redistributed in asy1 mutants and typically appear much closer than in the wildtype. Hence, ASY1 plays a key role in CO interference that spaces COs along a chromosome. Conversely, since a large proportion of chromosomes do not receive any CO, we conclude that CO assurance, the process that ensures the obligatory assignment of one CO per chromosome, is also affected in asy1 mutants. Significant statement The regulation of the number and placement of cross-overs (COs) during meiosis is critical to ensure meiotic fidelity and promote new genetic combinations. Here, we investigated the function of one of the proteins of the chromosome axis, which plays a key role in CO formation: ASY1. Our results show that COs in asy1 mutants are positioned closer to each other than in the wildtype and that, despite a roughly similar number of COs, not every chromosome receives a CO. With this, our results shed light on the mechanisms regulating two important but still poorly understood aspects of meiosis: CO assurance, which safeguards at least one CO per chromosome pair, and CO interference, which prevents two COs from occurring close to each other.
Mesoaccumbal glutamate neurons drive reward via glutamate release, but aversion via dopamine co-release

Ventral tegmental area (VTA) projections to the nucleus accumbens medial shell (NAc) drive reward-related motivation. Although dopamine neurons are predominant, a substantial glutamatergic projection is also present, and a subset of these populations can release both dopamine and glutamate. Optogenetic stimulation of VTA glutamate neurons supports self-stimulation, but can also induce place avoidance, even in the same assay. Here, we parsed the selective contribution of glutamate or dopamine co-release from VTA glutamate neurons to reinforcement and avoidance. We expressed Channelrhodopsin (ChR2) in VTA glutamate neurons, in combination with CRISPR/Cas9 to disrupt either the gene encoding vesicular glutamate transporter 2 (VGLUT2) or Tyrosine hydroxylase (Th). Selective disruption of VGLUT2 abolished optogenetic self-stimulation, but left real-time place avoidance intact, while CRISPR/Cas9 deletion of Th preserved optogenetic self-stimulation but abolished place avoidance. Our results demonstrate that glutamate release from VTA glutamate neurons is positively reinforcing, but that dopamine release from these same neurons can induce avoidance behavior.
Cell size and actin architecture determine force generation in optogenetically activated adherent cells

Adherent cells use actomyosin contractility to generate mechanical force and to sense the physical properties of their environment, with dramatic consequences for migration, division, differentiation and fate. However, the organization of the actomyosin system within cells is highly variable, with its assembly and function being controlled by small GTPases from the Rho-family. How activation of these regulators translates into cell-scale force generation and the corresponding sensing capabilities in the context of different physical environments is not understood. Here we probe this relationship combining recent advances in non-neuronal optogenetics with micropatterning and traction force microscopy on soft elastic substrates. We find that after whole-cell RhoA-activation by the CRY2/CIBN optogenetic system with a short pulse of 100 milliseconds, single cells contract before returning to their original tension setpoint with near perfect precision on a time scale of several minutes. To decouple the biochemical and mechanical elements of this response, we introduce a mathematical model that is parametrized by fits to the dynamics of the substrate deformation energy. We find that the RhoA-response builds up quickly on a time scale of 20 seconds, but decays slowly on a time scale of 50 seconds. The larger the cells and the more polarized their actin cytoskeleton, the more substrate deformation energy is generated. RhoA-activation starts to saturate if optogenetic pulse length exceeds 50 milliseconds, revealing the intrinsic limits of biochemical activation. Together our results suggest that adherent cells establish tensional homeostasis by the RhoA-system, but that the setpoint and the dynamics around it are strongly determined by cell size and the architecture of the actin cytoskeleton, which both are controlled by the extracellular environment.