Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring plant colors.

Plant colors such as 'green leaf' and 'red apple' are often described based on human sense, even in scientific papers. On the other hand, colors are measured based on colorimetric principles in some papers, especially in the studies of horticultural plants. The science of color measurements ('colorimetry') is not included in any of the popular lectures in schools and universities, thus the principles of color measurements would not be understood by most researchers. The present review will overview the principles of colorimetry, and will introduce colorimetric methods which can be used for scientific measurement of plant colors. That is to say, the reflection spectrum of visible light (380-780 nm) is measured at 5-nm intervals on the surface of leaves or petals in 'Spectrometric Color Measurement' (SCM). The spectral data is multiplied with RGB or XYZ color matching functions and integrated to obtain RGB or XYZ intensities. Alternatively, approximate RGB values are directly obtained in 'Photographic Color Measurement' (PCM). RGB/XYZ intensities are further calculated to obtain 'hue', 'saturation', and 'lightness', the three factors of colors. Colorimetric insights into genetic regulations (such as MYB gene) and physiological regulations (such as alexandrite effect) of plant colors are also described.
Evaluation of Dissolution Enhancement of Aprepitant Drug in Ternary Pharmaceutical Solid Dispersions with Soluplus® and Poloxamer 188 Prepared by Melt Mixing

In the present study Aprepitant (APT) ternary solid dispersions (SDs) were developed and evaluated for the first time. Specifically, ternary SDs of APT with Poloxamer 188 and Soluplus® (SOL) were prepared via melt mixing and compared to binary APT/Poloxamer 188 and APT/SOL SDs. Initially, combined thermo-gravimetric and hot-stage polarized light microscopy studies indicated that all tested compounds were thermally stable up to 280 °C, while Poloxamer 188 acted as a plasticizer to SOL by significantly reducing the temperature required to fully solubilize the API during SD preparation. Differential scanning calorimetry combined with wide angle X-ray diffraction studies showed that crystalline API was dispersed in both binary and ternary SDs, while Fourier transformation-infrared spectroscopy studies revealed no molecular interactions among the components. Scanning electron microscopy combined with EDAX element analysis showed that the API was dispersed in nano-scale within the polymer matrices, while increasing APT content led to increasing API nano-crystals within the SDs. Finally, dissolution studies showed that the prepared formulations enhanced dissolution of Aprepitant and its mechanism analysis was further studied. A mathematical model was also investigated to evaluate the drug release mechanism.
An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here I demonstrate an alternative: experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.
Host-selected mutations converging on a global regulator drive an adaptive leap by bacteria to symbiosis

Even though eukaryote health relies on beneficial symbionts, host defenses targeting pathogens create substantial obstacles for the establishment of these essential partnerships. To reveal mechanisms of symbiotic adaptation, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri through Euprymna scolopes squid light organs. Serial passaging of V. fischeri populations through squid hosts produced eight distinct mutations in the binK sensor kinase gene that conferred an exceptional selective advantage demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion behavior which was mediated by symbiotic polysaccharide (Syp). binK variation also produced metabolic convergence with native symbionts, and altered quorum sensing and luminescence. Preexisting coordination of symbiosis traits facilitated an efficient solution where altered function of a regulator was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations. Impact statement Squid selection on non-native Vibrio fischeri drove rapid adaptation through convergent mutations of large effect, unmasking preexisting coordinate regulation of symbiosis. Major subject areas, keywords, and research organism(s) Major subject area: Genomics and evolutionary biology
Assessment of the gene expression profiles of leukocytes from different isolations

BACKGROUND Research on peripheral leukocyte gene expression in human health and disease is growing rapidly. However, how to process sample efficiently, simply and stably, and how to reflect human physiological state preferably remains critical issues in large cohort studies. METHODS We used RNA-seq to explore the differences of gene expression profiles among whole blood (WB) and three groups of leukocytes from buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation. RESULTS The residual globin mRNA in leukocytes from RBC lysis (1.00% ±1.23%) and PBMC isolation (0.06% ± 0.03%) was much less than that in leukocytes from BC extraction (17.48% ± 6.95%) and WB (24.46% ± 6.43%), resulting in higher transcriptome mapping rates and larger numbers of detected genes. The expression of 616 genes associated with leukocyte function was slightly higher in leukocytes from RBC lysis than that from BC extraction and WB, but barely detected in leukocytes from PBMC isolation. CONCLUSIONS We suggest that sample processing based on RBC lysis could allow better applications of gene expression profiling of peripheral leukocytes in large cohort studies.
Coordination of brain wide activity dynamics by dopaminergic neurons

Several neuropsychiatric conditions, such as addiction, schizophrenia, and depression may arise in part from dysregulated activity of ventral tegmental area dopaminergic (THVTA) neurons, as well as from more global maladaptation in neurocircuit function. However, whether THVTA activity affects large-scale brain-wide function remains unknown. Here, we selectively activated THVTA neurons in transgenic rats and measured resulting changes in whole-brain activity using stimulus-evoked functional magnetic resonance imaging (fMRI). Selective optogenetic stimulation of THVTA neurons not only enhanced cerebral blood volume (CBV) signals in striatal target regions in a dopamine receptor dependent fashion, but also engaged many additional anatomically defined regions throughout the brain. In addition, repeated pairing of THVTA neuronal activity with forepaw stimulation, produced an expanded brain-wide sensory representation. These data suggest that modulation of THVTA neurons can impact brain dynamics across many distributed anatomically distinct regions, even those that receive little to no direct THVTA input.
The Envelope Proteome Changes Driven by RamA Overproduction in Klebsiella pneumoniae that Enhance Acquired β-Lactam Resistance

OBJECTIVES In Klebsiella pneumoniae, overproduction of RamA results in reduced envelope permeability and reduced antimicrobial susceptibility but clinically relevant resistance is rarely observed. Here we have tested whether RamA over-production can enhance acquired β-lactam resistance mechanisms in K. pneumoniae and have defined the envelope protein abundance changes seen upon RamA overproduction during growth in low and high osmolarity media. METHODS Envelope permeability was estimated using a fluorescent dye accumulation assay. Antibiotic susceptibility was measured using disc testing. Total envelope protein production was quantified using LC-MS/MS proteomics and transcript levels quantified by Real Time RT-PCR. RESULTS RamA overproduction enhanced β-lactamase mediated β-lactam resistance, in some cases dramatically, without altering β-lactamase production. It increased production of efflux pumps and decreased OmpK35 porin production, though micF over-expression showed that OmpK35 reduction has little impact on envelope permeability. A survey of K. pneumoniae bloodstream isolates revealed ramA hyperexpression in 3 out of 4 carbapenemase producers, 1/21 CTX-M producers and 2/19 strains not carrying CTX-M or carbapenemases. CONCLUSIONS Whilst RamA is not a key mediator of antibiotic resistance in K. pneumoniae on its own, it is potentially important for enhancing the spectrum of acquired β-lactamase mediated β-lactam resistance. LC-MS/MS proteomics analysis has revealed that this enhancement is achieved predominantly through activation of efflux pump production.
Developing Self-adaptive Software System: A Case Study

Current trends in software system, such as cloud and big data platform, are leading to rapid and continuing changes. At the same time, these systems will have to react to these changes at runtime to satisfy the potential Quality of Service (QoS). Self-adaptation is recognized as a practical way for a software system to meet QoS requirements. The Development of self-adaptive software is generally more challenging and more difficult due to their high complexity. To address these challenges, this paper reviews the related research of self-adaptive software system and reports a case study that investigates a selfadaptive concurrency controller for database system. Through the case we illustrate how to develop a self-adaptive software system. Compared with other traditional method, the experimental results demonstrate that our self-adaptive controller can effectively improve the database performance by adjusting the MPL value based on workload changes and QoS requirements. Finally some future trends in this area are prospected and discussed.
Resting-state functional connectivity, cortical GABA and neuroactive steroids in peripartum and peripartum depressed women: a functional magnetic imaging and resonance study

Postpartum depression (PPD) is associated with abnormalities in resting-state functional connectivity (RSFC) but the underlying neurochemistry is unclear. We hypothesized that peripartum GABAergic neuroactive steroids (NAS) are related to cortical GABA concentrations and RSFC in PPD as compared to healthy comparison women (HCW). To test this, we measured RSFC with fMRI and GABA+/Creatine (Cr) concentrations with proton magnetic resonance spectroscopy (1H MRS) in the pregenual anterior cingulate (pgACC) and occipital cortices (OCC) and quantified peripartum plasma NAS. We examined between-group differences in RSFC and the relationship between cortical GABA+/Cr concentrations with RSFC. We investigated the relationship between NAS, RSFC and cortical GABA+/Cr concentrations. Within the default mode network (DMN) an area of the dorsomedial prefrontal cortex (DMPFC) had greater connectivity with the rest of the DMN in PPD (peak voxel: MNI coordinates (2, 58, 32), p=0.002) and was correlated to depression scores (peak HAM-D17 voxel: MNI coordinates (0, 60, 34), p=0.008). pgACC GABA+/Cr correlated positively with DMPFC RSFC in a region spanning the right anterior/posterior insula and right temporal pole (r=+0.661, p=0.000). OCC GABA+/Cr correlated positively with regions spanning both amygdalae (right amygdala: r=+0.522, p=0.000; left amygdala: r=+0.651, p=0.000) as well as superior parietal areas. Plasma allopregnanolone was higher in PPD (p=0.03) and positively correlated with intra DMPFC connectivity (r=+0.548, p=0.000) but not GABA+/Cr. These results provide initial evidence that PPD is associated with altered DMN connectivity; cortical GABA+/Cr concentrations are associated with postpartum RSFC and allopregnanolone is associated with postpartum intra-DMPFC connectivity.
Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. ABSTRACT Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 102 to 103 genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10−5). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [CT] values, <30) and 6/13 samples with low viral titers (CT values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
Digital-compatible high-performance operational amplifier with rail-to-rail input and output ranges

This paper presents a CMOS buffer amplifier which operates on a single 5-V power supply. The uniquely symmetrical design adds the following advantages: rail-to-rail linear, symmetrical operation at both the input and output; the output stage allows the use of gate channel capacitors of standard MOSFET's as the compensation capacitor saving die area from 80%/spl sim/93% in a standard single polysilicon digital process; large gain-bandwidth product; high power supply rejection ratio; good common-mode rejection ratio; and easy compact layout suitable for design automation (layout as a parametric cell, allows easy adaption to changing processes). The buffer is capable of driving 300 /spl Omega//spl par/100 pF with a loaded gain-bandwidth product of more than 4 MHz and a fully loaded slew rate of greater than 4 V//spl mu/S. >
Radiosumin, a Trypsin Inhibitor from the Blue-Green Alga Plectonema radiosum

Radiosumin, a novel potent trypsin inhibitory dipeptide, was isolated from the freshwater blue-green alga Plectonema radiosum (NIES-515). Its structure was elucidated to be 1 on the basis of 2D NMR data and chemical degradation. The IC50 of 1 against trypsin was 0.14 μg/mL.
General Approach to the Total Synthesis of Macroline-Related Sarpagine and Ajmaline Alkaloids1

Described in this review is a general and efficient strategy for the synthesis of macroline-related sarpagine and ajmaline alkaloids. The tetracyclic ketone in the parent system, as well as the alkoxy substituted series served as templates for the synthesis of these complex molecules. The palladium-mediated enolate cross coupling process, regiospecific hydroboration, and Tollens reaction are some of the key transformations that have been employed for further functionalization of these templates. Synthetic routes that have been improved, in order to obtain gram quantities of these alkaloids form a part of this review.
Load control strategies for mixed services in WCDMA

The QoS concept for UMTS/IMT-2000 has recently been standardized by the 3/sup rd/ Generation Partnership Project (3GPP). This paper describes the functionality needed within the UTRAN to enable the provisioning and maintenance of QoS for services with different requirements. Load control strategies based on resource reservation that enable quality guarantees to data services have been developed and evaluated, and the system performance has been analysed through simulations involving a simple scenario with a real-time and non real-time services mix. The results show an improvement in non real-time services quality, which becomes quite independent of the real-time load.
Utilization of Pomegranate Peels to Increase the Shelf Life of Chicken Burger during Cold Storage

This study was conducted to utilize the pomegranate peels to reduce the microbial load and extend shelf life of chicken burgers during cold storage (2-10 days) at (4±1°C). Some chemical properties e.g. acid value, peroxide value and thiobarbituric acid (TBA) of lipid extracted from chicken burger samples, which were prepared with percentages 0, 10, 20 and 30 % (w/w) of additive pomegranate peels r were studied. Sensory attributes (appearance, odor, texture and taste) of chicken burgers during cold storage were evaluated. Flavonoids and phenolic compounds were determined by high performance liquid chromatographic method (HPLC) using ultraviolet detector set at 330 and 280 nm, respectively. Total bacterial count, psychrophilic bacteria, spore-forming bacteria, total molds and yeasts count of chicken burger samples were determined during cold storage. The results showed that additive pomegranate peels to chicken burgers samples during its preparation decreased the acid, peroxide and TBA values of their lipids and retarded the growth of total molds & yeasts, total bacterial, psychrophilic bacteria and spore-forming bacteria of chicken burgers samples during cold storage for concentration 10, 20 and 30 % (w/w) of additive pomegranate peels. The applied additive also improved the appearance, odor, texture and taste of the chicken burgers samples of interest. It was concluded that the activity of pomegranate peels, as natural antioxidant and antimicrobial assay to control microbial load of chicken burgers samples, could be conducted as a food additive to enhance the safety of consumable chicken products.
Continuum approximations for lattice-free multi-species models of collective cell migration

Abstract Cell migration within tissues involves the interaction of many cells from distinct subpopulations. In this work, we present a discrete model of collective cell migration where the motion of individual cells is driven by random forces, short range repulsion forces to mimic crowding, and longer range attraction forces to mimic adhesion. This discrete model can be used to simulate a population of cells that is composed of K ≥ 1 distinct subpopulations. To analyse the discrete model we formulate a hierarchy of moment equations that describe the spatial evolution of the density of agents, pairs of agents, triplets of agents, and so forth. To solve the hierarchy of moment equations we introduce two forms of closure: (i) the mean field approximation, which effectively assumes that the distributions of individual agents are independent; and (ii) a moment dynamics description that is based on the Kirkwood superposition approximation. The moment dynamics description provides an approximate way of incorporating spatial patterns, such as agent clustering, into the continuum description. Comparing the performance of the two continuum descriptions confirms that both perform well when adhesive forces are sufficiently weak. In contrast, the moment dynamics description outperforms the mean field model when adhesive forces are sufficiently large. This is a first attempt to provide an accurate continuum description of a lattice-free, multi-species model of collective cell migration.
A comprehensive delay macro modeling for submicrometer CMOS logics

The increasing need for high-performance, cost-effective, application-specific integrated circuits, associated to the reduction of design cycle time, compels designers to manage and optimize the circuit speed performance at each step of the design flow. Circuits are usually designed at gate level; the gate selection or sizing and their placement are driven by estimated delay, hence the need for accurate estimations at the logical level. In the submicrometer range, the gap between gate-level logical estimations and transistor-level electrical simulations dramatically increases. We propose here a comprehensive analytical modeling of the speed performance of CMOS gates with an accuracy comparable to electrical simulators. A design-oriented expression of delay is first developed for CMOS inverters, considering input slope, input-to-output capacitance coupling, and short-circuit current effects. The extension to more complex gates is proposed using a serial array reduction technique taking account of the gate input dependency and the input-slope-induced nonlinearity. Validations are obtained over a large range of design, load, and input slope conditions by comparison with SPICE simulations (level 6 with 0.65-/spl mu/m foundry specified card model) used as a reference.
An investigation into the phenotype, function and immunomodulatory properties of in vitro expanded iNKT cells

Invariant natural killer T (iNKT) cells are endowed with features of both innate and adaptive immunity. They are activated by the recognition of glycolipid agonists presented by CD1d which makes them excellent candidates for cellular therapies. In order to investigate the ability of iNKT cells to suppress experimental acute Graft versus host disease (GVHD), iNKT cells were first expanded in vitro, which is likely to be required prior to their use as a cellular therapeutic. Interestingly, the expanded cells showed increased frequencies of IL-10, IL-13 and IL-17 producing cells and were found to robustly suppress alloreactive T cell proliferation in vitro compared to freshly isolated cells. However, in a model of acute GVHD induced by alloantigen-reactive TCR-transgenic T cells neither freshly isolated nor expanded iNKT cells suppressed GVHD, although some survival benefit was seen following the activation of host iNKT cells. These data indicate that iNKT cells can be expanded ex vivo, that they can acquire different functional properties and that such cells robustly suppress alloreactive T cell proliferation in vitro. Therefore, further investigation into the suppressive behaviour of these cells is warranted despite a failure to suppress acute GVHD in the current study.