Miracle-dz/UniFAR-FTUs huggingface dataset:
The newly extended maize internode: A model for the study of secondary cell wall formation and consequences for digestibility

The upper five internodes were collected from maize (Zea mays L) inbred cell lines Co 125 and W401 harvested at the same developmental stage, 5 days after silking. Each internode was dissected into ten equal lengths labelled A (top) to J (base). The youngest cells were found in section J, which contained the intercalary meristem, and the oldest in section A. Internodes 1, 3 and 5 provided material for chemical analysis and internodes 2 and 4 for degradability measurements. Cell wall material accounted for one-third of dry matter in section J, doubling to two-thirds in the upper half of each internode. Only section J exhibited a polysaccharide profile typical of primary cell walls. In all other sections, 1,4-linked glucose (± 46% of cell wall) and xylan largely free from side chains (± 25% of cell wall) predominated. Net accretion of cell wall polysaccharide reached a maximum by segment G and thereafter little additional carbohydrate was deposited. Lignification appeared to be separated from the biogenesis of structural carbohydrate and continued over much of each internode reaching a maximum in section C. Degradability measurements, made using a modified neutral-detergent cellulase digestibility method, showed substantial differences between sections. In line Co 125, cell wall degradability fell from over 95% in the youngest section (J) to approximately 24% in section B. Internode 4 of line W401 failed to show the same pattern of degradabilities, probably because of a sequential rather than simultaneous pattern of internode elongation. Saponifiable p-coumaric acid appeared to provide a more sensitive marker than lignin of the extent of secondary wall development. The inverse relationship between extent of lignification in each section and its degradability confirmed the value of the internode model for the study of secondary wall formation and its biological consequences.
Exploring phylogeography and species limits in the Altai vole (Rodentia: Cricetidae)

Natural hybridization between species is not a rare event. In arvicoline rodents, hybridization is known to occur in the wild and/or in captivity. In the Microtus arvalis group, cytogenetic studies revealed that there were two distinct chromosomal forms (2n = 46 but a different fundamental number of autosomes). These forms have been attributed to two cryptic species: the common (arvalis) and Altai (obscurus) voles. Recently, individuals with intermediate karyotypes (F1 and backcrosses) were discovered in central European Russia, and, for this reason, other studies have regarded obscurus and arvalis as conspecific. In the present study, to address the question of the species limits in the Altai vole and to infer its evolutionary history, a phylogeographical analysis combined with multivariate morphometric methods and original chromosome data was performed. Two obscurus lineages were identified: the Sino-Russian and South Caucasian lineages. Both lineages are characterized by low genetic diversity, resulting, in the former, from a past bottleneck event caused by encroaching periglacial areas and, in the latter, from recent rapid population divergence. Introgressive hybridization between the Altai and common voles appears to be the result of a secondary contact following the Last Glacial Maximum in central European Russia. Despite the fact that speciation is an ongoing process in most arvicoline species, the common and Altai voles are genetically divergent, morphologically and karyologically distinct, and exhibit contrasting evolutionary histories. For all these reasons, they should be ranked as species: M. arvalis and M. obscurus.
Sparse subspace clustering with one-way selective orthogonal matching pursuit

Orthogonal matching pursuit (OMP) has gained remarkable achievements in the domain of Sparse Subspace Clustering (SSC) for image clustering. However, current methods based on OMP improves the clustering accuracy by adding additional operations, which increase computational complexity. In this paper, a novel SSC algorithm with one-way selective orthogonal matching pursuit (SSC-OWSOMP) is proposed to improve the clustering accuracy without increasing the computational complexity in the SSC-OMP-based methods. In our SSC-OWSOMP, a one-way selective module is designed to avoid mutual selection among data points, which can enrich the information used for clustering without adding additional operations. Experimental results demonstrate that, with the SSC-OWSOMP, not only the clustering accuracy can be improved but also the time complexity be kept, also the SSC-OWSOMP is suitable for the data sets with high sample density.
Ricardo's Numerical Example Versus Ricardian Trade Model: A Comparison of Two Distinct Notions of Comparative Advantage

The so-called Ricardian trade model of contemporary economic textbooks is not a rational reconstruction of Ricardo’s famous numerical example in chapter seven of the Principles. It differs from the latter in terms of the definition of the four numbers, relevant cost comparison, rule for specialisation, assumptions and theoretical implications. Thus, the widespread critique regarding the unrealistic assumptions of the textbook trade model does not apply to Ricardo’s original proof of comparative advantage.
Antioxidant Activity of Hydrolysates Prepared from Flaxseed Cake Proteins Using Pancreatin

Abstract Proteins were isolated from defatted flaxseed cake and hydrolysed with pancreatin. The hydrolysis process was conducted at a stable temperature of 50°C and pH 7.5, and monitored with the pH-stat method. The obtained hydrolysates with a degree of hydrolysis (DH) of 5, 10, 15, 20, 25% were investigated in terms of antioxidant properties. The radical scavenging activity was assayed against DPPH· and ABTS·+, the reducing ability - with FRAP assay, and the capability to bind Fe(II) - by reaction with ferrozine. SE-HPLC analysis was used to determine molecular weight distribution of hydrolysis products. The antiradical activity of pancreatin hydrolysates of flaxseed proteins was increasing along with an increasing DH and for the hydrolysate with DH 25% the EC50 value determined with the DPPH assay accounted for 0.083 mg/assay, and the ABTS·+ scavenging activity - for 0.218 mmol Trolox/g. This hydrolysate was constituted mainly by peptides with low molecular weights (MW) of 0.238-0.556 kDa. In turn, the Fe(II) binding capability increased from 44.5% to 64.9% in the case of hydrolysates with DH 5-20% and decreased in the case of the hydrolysate with DH 25%. A similar de-pendency was observed in the ability of pancreatin hydrolysates of flaxseed proteins to reduce Fe(III). The maximum value of reducing ability reached 0.25 mmol Fe(II)/g for the hydrolysate with DH 20% that was predominated by polypeptides and peptides with MW of 0.238-1.046 Da.
Effects of Platinum Derivatives on the Function and Expression of P-Glycoprotein/MDR1 in LLC-PK 1 Cells: In the Cases of Carboplatin and Nedaplatin

AIM: The aim of this study is to investigate the effects of carboplatin and nedaplatin on the function and expression of P-glycoprotein/MDR1 using porcine kidney epithelial LLC-PK 1 cells, and to compare their characteristics with cisplatin or oxaliplatin. METHODS: The transport activity of MDR1 was examined in LLC-PK 1 and MDR1overexpressing Hvr100-6 cells. The expression level of MDR1 was analyzed with RTPCR and immunoblotting analyses. RESULTS: Neither carboplatin nor nedaplatin affected the accumulation of Rhodamin123 in Hvr100-6 cells, suggesting that both drugs were not the substrates for MDR1. In addition, LLC-PK 1 cells treated for 48 h with 1 ∝M carboplatin did not exhibit any change in subsequent Rhodamine123 transport. Cellular MDR1 mRNA and protein expression was also not altered by carboplatin. In the case of nedaplatin, the accumulation of Rhodamine123 was significantly decreased when LLC-PK 1 cells were pretreated with 1 ∝M of nedaplatin for 48 h, although nedaplatin did not affect the efflux of Rhodamine123. Nedaplatin did not up-regulate both mRNA and protein levels of MDR1. CONCLUSION: Unlike cisplatin and oxaliplatin to induce MDR1, carboplatin and nedaplatin did not affect the function and expression of MDR1 in LLC-PK 1 cells.
APPLICATION OF RESPONSE SURFACE METHODOLOGY TO OPTIMIZE DOCOSAHEXAENOIC ACID PRODUCTION BY SCHIZOCHYTRIUM sp. S31

The optimum concentrations of nutrients (glucose and yeast extract) and cultivation conditions (concentration of sodium chloride, pH and incubation time) on docosahexaenoic acid (DHA) production by Schizochytrium sp. S31 in flasks at 30°C were studied. Experiment design employed fractional factorial design, path of steepest ascent, central composite design and response surface methodology (RSM). The empirical model developed by RSM was adequate to describe the relationships between the studied factors and the response of DHA production. Based on contour plots and canonical analysis, the optimal conditions for maximizing DHA production (516 mg/L) were at 27.98 g glucose/L, 4.52 g yeast extraction/L, 24.82 g sodium chloride/L, pH 6.96 and incubation for 4 days at 30C. Experimental verification of the optimal conditions resulted in about 97% of the predicted DHA production by the model.
Culturable Bacterial Endophytes From Sedimentary Humic Acid-Treated Plants

The global decrease in soil fertility leads to a new agricultural scenario where eco-friendly solutions play an important role. The plant growth promotion through the use of microbes, especially endophytes and rhizosphere microbiota, has been proposed as a useful solution. Several studies have shown that humic substances are suitable vehicles for the inoculation of plant growth promoting bacteria, and that this combination has an enhanced effect on the stimulation of plant development. In this work, cucumber plants grown hydroponically have been pre-treated with a sedimentary humic acid (SHA) with known plant growth-enhancing effects, and culturable bacterial endophytes have been isolated from these plants. The hypothesis was that this pre-treatment with SHA could lead to the isolation of certain endophytic taxa whose proliferation within the plant could have been promoted as a result of the effects of the treatment with SHA, and that could eventually reinforce a potential synergistic effect of a combined application of those endophytic bacteria and SHA. The culturable endophytes that have been isolated from humic acid-treated cucumber plants have been identified as members of four main phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Isolates were characterized according to the following plant growth-promoting traits: nitrogen fixation/scavenging, phosphate solubilization, siderophore production and plant hormone production. Most of the isolates were able to fix/scavenge nitrogen and to produce plant hormones (indole-3-acetic acid and several cytokinins), whereas few isolates were able to solubilize phosphate and/or produce siderophores. The most promising endophyte isolates for its use in futures investigations as plant growth-promoting bacterial inocula were Pseudomonas sp. strains (that showed all traits), Sphingomonas sp. , Stenotrophomonas sp. strains, or some Arthrobacter sp. and Microbacterium sp. isolates.
Analysis of calcium binding to α‐lactalbumin using a fluorescent calcium indicator

A sensitive and rapid assay of Ca2+ binding to proteins was developed, based on the competition of Ca2+ binding to the protein of interest and fluo-3, a fluorescent Ca2+ indicator. Ca2+ binding to fluo-3 and bovine α-lactalbumin was analyzed at ten different pH values and a range of Na+ and K+ concentrations. We demonstrate that the binding constants of α-lactalbumin, determined by means of the competition assay and using intrinsic protein fluorescence, are the same within experimental error. The dissociation constant of the α-lactalbumin–Ca2+ complex in 50 mM Hepes containing 150 mM Na+ at pH 7.4 and 25°C, was found to be 123 ± 2 nM and 103 ± 43 nM when determined by the competition assay and intrinsic protein fluorescence, respectively. Binding of Ca2+ to α-lactalbumin did not depend on pH in the range 6.6–8.4 and was differently affected by Na+ and K+. EDTA-agarose, a chelating chromatography material, was synthesized and used to remove Ca2+ from buffer and protein solutions. The total concentration of Ca2+ in 50 mM Hepes, containing 150 mM Na+ at pH 7.4, was lowered to 119 ± 13 nM and the number of Ca2+ bound/molecule α-lactalbumin was lowered to 0.069 ± 0.006. No interaction between fluo-3 and α-lactalbumin could be discerned from spectral analysis and fluorescence anisotrophy measurements.
Proterozoic photosynthesis – a critical review

Chlorophyll‐based photosynthesis has fuelled the biosphere since at least the early Archean, but it was the ecological takeover of oxygenic cyanobacteria in the early Palaeoproterozoic, and of photosynthetic eukaryotes in the late Neoproterozoic, that gave rise to a recognizably modern ocean–atmosphere system. The fossil record offers a unique view of photosynthesis in deep time, but is deeply compromised by differential preservation and non‐diagnostic morphologies. The pervasively polyphyletic expression of modern cyanobacterial phenotypes means that few Proterozoic fossils are likely to be members of extant clades; rather than billion‐year stasis, their similarity to modern counterparts is better interpreted as a combination of serial convergence and extinction, facilitated by high levels of horizontal gene transfer. There are few grounds for identifying cyanobacterial akinetes or crown‐group Nostocales in the Proterozoic record. Such recognition undermines the results of various ancestral state reconstruction analyses, as well as molecular clock estimates calibrated against demonstrably problematic Proterozoic fossils. Eukaryotic organisms are likely to have acquired their (stem‐group nostocalean) photoendosymbionts/plastids by at least the Palaeoproterozoic, but remained ecologically marginalized by incumbent cyanobacteria until the late Neoproterozoic appearance of suspension‐feeding animals.
Toll-Like Receptor Ligand Based Adjuvant, PorB, Increases Antigen Deposition on Germinal Center Follicular Dendritic Cells While Enhancing the Follicular Dendritic Cells Network

Vaccines are arguably one of the greatest advancements in modern medicine. Subunit vaccines comprise the majority of current preparations and consist of two main components—antigen and adjuvant. The antigen is a small molecule against which the vaccine induces an immune response to provide protection via the immunostimulatory ability of the adjuvant. Our laboratory has investigated the adjuvant properties of Toll-like receptor (TLR) ligand-based adjuvants, especially the outer membrane protein from Neisseria mengingitidis, PorB. In this current study we used PorB, along with CpG, an intracellular TLR9 agonist, and a non-TLR adjuvant, aluminum salts (Alum), to further investigate cellular mechanisms of adjuvanticity, focusing on the fate of intact antigen in the germinal center and association with follicular dendritic cells (FDCs). FDCs are located in the B cell light zone of the germinal center and are imperative for affinity maturation. They are stromal cells that retain whole intact antigen allowing recognition by the B cell receptor of the germinal center B cells. Our studies demonstrate that TLR ligands, but not Alum, increase the FDC network, while PorB and Alum increased colocalization of FDC and the model soluble antigen, ovalbumin (OVA). As PorB is the only adjuvant tested that induces both a higher number of FDCs and increased deposition of antigen on FDCs, it has the greatest ability to increase FDC-antigen interaction, essential for induction of B cell affinity maturation. These studies demonstrate a further mechanism and potential superiority of PorB as an adjuvant and its influence on antibody production.
Productive Performance and Immunocompetence of Commercial Laying Hens Given Diets Supplemented with Eucalyptus

2 Abstract: A study was conducted to determine the effect of Eucalyptus leaf powder supplementation on productive performance and immune response of brown Hy-line laying hens. Sixty brown Hy-line layers were equally divided into four groups. They were fed diet containing 0, 1, 2 and 3g Eucalyptus leaf powder/kg diet form 46 to 54 weeks of age. Egg production (weight and number) was recorded daily. Body weight and feed consumption were recorded every 4 weeks. Cell mediated immunity was determined at 54 weeks of age. At the end of the experiment, internal and external egg quality measurements were determined. The present results revealed that supplementation of Eucalyptus at the rate of 3g/kg diet significantly increased egg number compared to the other groups. Likewise, the hens fed a diet containing 3g Eucalyptus produced significantly higher egg mass compared to remaining groups. However, there was no significant difference among treated groups for egg weight. There was no significant difference among treated groups for all egg quality traits, except for breaking strength. Whereas the eggs produced from hen fed a diet containing 3g Eucalyptus had a significantly higher breaking strength compared to other treated groups. With respect to immune response, it could be noticed that the hens fed diets supplemented with 2 or 3g Eucalyptus were significantly hyper responder to PHA-P injection compared to other groups. Moreover, the Eucalyptus supplementation at the rate of 2 and 3g/kg diet significantly decreased the H/L ratio of laying hens. In summary, the current experiment has shown that the inclusion of Eucalyptus at the level of 3g/kg diet is useful for improving the productive performance and immunity of commercial laying hens.
Breast Cancer With a HER2 IHC2+ and FISH HER2/CEP17 Ratio ≥2.0 and an Average HER2 Gene Copy Number <4.0 per Tumor Cell: HER2 mRNA Overexpression Is a Rare Event

Purpose: For breast cancer, accurately illustrating HER2 characteristics is a critical precondition for evaluating the prognosis and predicting the efficacy of anti-HER2 therapy. Our purpose was to expose HER2 mRNA expression through an in situ hybridization assay (RNAscope), to aid the identification of HER2 status in breast cancers with a previously controversial classification for patients suffering from a HER2 IHC2+ and HER2/CEP17 ≥2.0 and a <4.0 mean HER2 gene copy number/cell (entitled FISH group 2 by update 2018 HER2 testing guideline). Methods: A total of 8,983 cases of breast cancer with a known HER2 status detected by initial IHC, and a necessary reflex FISH assay for those with IHC2+, were retrospectively analyzed. Then, 41 cases of HER2 IHC2+ in the FISH group 2 were collected and a RNAscope was performed. Results: The incidence of breast cancers with IHC2+ and in the FISH group 2 was 0.46% (41/8,983) in our single-institutional study cohort. In most of the cases (27/41, 65.9%), low levels of HER2 mRNA expression (score 1 and 2 by RNAscope) were demonstrated. Only one case (1/41, 2.4%) of high-level HER2 mRNA expression (score 4 by RNAscope), harboring a FISH HER2/CEP17 ratio of 2.06 and an average HER2 copy number of 3.70, was revealed. One case with the highest FISH HER2/CEP17 ratio of 3.90, showed the lowest level of HER2 mRNA expression (score 1 by RNAscope). Two cases with the same highest average HER2 signals/cell (3.95) by FISH possessed score 3 and score 2 with RNAscope, respectively. No cases with a score of 0 by RNAscope occurred in our sample. In the majority of cases (35/41, 85.4%), hypodisomy of chromosome 17 (average CEP17 signals/cell ≤1.75) was observed. There was no significant relationship between the mRNA expression and FISH results (average HER2 signals/cell, average CEP17 copy number, or HER2/CEP17 ratio) and clinicopathological features (ER and PR statuses, Ki 67 index, tumor size, and lymph node metastasis) in our population. Conclusion: HER2 mRNA overexpression was not a feature in our group of patients. Based on our data, breast cancers with HER2 IHC2+ and in FISH group 2 support a categorization of HER2 negative.
THE EFFECT OF WATERLOGGING ON INFECTION OF EUCALYPTUS MARGIN AT A SEEDLINGS BY PHYTOPHTHORA CINNAMOMI

Summary Three- to four-month-old Eucalyptus marginata Donn ex Sm. (jarrah) were grown in the glasshouse in peat/sand at 20° C root temperature, infected with zoospores of Phytophthora cinnamomi Rands, added either 10 cm below the soil surface or flooded onto the soil, and various waterlogging regimes were imposed. When plants were infected but not waterlogged, the proportion of infected root length adjacent to the point where zoospores were added was low. More lesions were formed per metre root length on tap roots than on lateral roots, but lesions on lateral roots were longer than on tap roots. When plants were waterlogged for a 4 d period before the addition of zoospores, there was no increase in root infection. When plants were waterlogged at the same time or after the pots were inoculated, there was a significant increase in the proportion of root length infected. This was due to an increase in the number of lesions and not, in four of the five harvests, to an increase in lesion length. When inoculation and waterlogging were imposed at the same time, the increased number of infections was probably due both to the increased attraction of zoospores to anaerobically respiring roots and to increased zoospore motility in flooded soil. When waterlogging was imposed several days or weeks after the plants had been infected, the increased number of lesions was unlikely to have been due to residual zoospores in the soil, because their numbers declined exponentially. It was also unlikely to have been due to sporangia developing de novo on the roots after waterlogging had been imposed, because the O2 concentration of the soil solution was inadequate. It is probable, therefore, that the new infections originated from zoospores liberated from sporangia already formed on lesions before waterlogging was imposed. When plants were infected but not waterlogged, there was no effect on the leaf diffusive resistance, leaf relative water content and shoot xylem pressure potential between 1 and 28 d. When plants were flooded, the daily water loss decreased more rapidly and plants died more rapidly in the inoculated and waterlogged treatments than in the treatments which were only waterlogged. Infection by P. cinnamomi did not affect the proportion of xylem vessels occluded with tyloses in seven of the eight unflooded, and seven of the eight flooded, comparisons.
Permutation-Based Residential Short-term Load Forecasting in the Context of Energy Management Optimization Objectives

What makes a household-level short-term load forecast "good"? Individual household load profiles are intermittent, as distinct peaks correspond to specific activities in the household. Using traditional point-wise error metrics to assess household-level forecasts may lead to, for instance, double-digit mean absolute percentage errors. One reason is a double penalty incurred if a peak is forecasted correctly in amplitude, but with a small delay in time. An adjusted forecast error measure based on local permutations was proposed to assess household-level forecasts by optimally aligning the peaks bounded by a displacement limit. This work shows how the choice of this parameter leads to different "best" forecasts in terms of specific applications, namely the optimization objectives of an energy management system. For that, different parameterizations of the Local Permutation Invariant (LPI) distance are compared within k-Nearest Neighbors as a forecasting model for three different optimization objectives. A simulation study on 100 households of the CER dataset shows that the optimal parameterization can decrease the peak load on average by over 22.5% compared to the Euclidean distance. However, for increasing self-sufficiency and minimizing costs, no significant improvements can be achieved. This implies that household-level forecasts should generally be evaluated in terms of their application, as traditional metrics as a proxy may not express its "goodness" adequately.