Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographic Variation and Local Growth Superiority for Coastal Douglas-fir – Rotation-age Growth Performance in a Douglas-fir Provenance Test

Abstract Rotation-age growth performance of 16 provenances and local growth superiority were assessed from a rotation- age reciprocal coastal Douglas-fir [Pseudotsuga menziesii var. menziesii (Mirb.) Franco] provenance test established in the Pacific Northwest of America. Provenance differences for total volume per plot were highly significant. Due to the significant provenance × site interaction effect, the best provenances varied across planting sites in terms of rotation-age volume growth. Local provenance trees exhibited superior volume growth at two of the six planting sites. At the remaining four sites, local provenances performed equally well as average non-local provenances. At the three low-elevation (< 460 m) sites, low-elevation provenances performed significantly better than high-elevation provenances. By contrast, high- and low-elevation provenances had similar growth at the two high-elevation (> 800 m) sites. Southern provenances generally grew faster than northern provenances at the Oregon sites, while northern provenances performed better than southern provenances at the sites in British Columbia. Regression analyses showed that although local growth superiority increased with the geographic distance between provenance’s origin and the test site in general (r=0.47, P<0.001), it only became obvious when the geographic distance is larger than 435 km in latitude or 370 m in elevation. Significant spatial autocorrelation was found via Mantel test, and geographically or climatically closely located provenances tended to have similar rotation-age volume growth. The results suggested that breeding zones larger than the current second-cycle zones would lead to little loss of rotation-age total volume for coastal Douglas-fir in this region.
The complete mitochondrial genome of the green microalgae Dunaliella salina strain SQ

Abstract The complete mitochondrial genome of the microalgae Dunaliella salina strain SQ (GenBank accession number: KX641170) was de novo assembled and annotated using Illumina MiSeq sequencing data. The mitochondrial genome is 41,904 bp long with 31.85% GC content and contains 7 protein-coding genes, 16 introns, 3 ribosomal RNA genes and 3 transfer RNA genes. To date, only two complete mitochondrial genomes of Dunaliella salina strains have been reported, and this genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of Dunaliella salina strains.
In vitro effects of copper nanoparticles on plant pathogens, beneficial microbes and crop plants

Copper-based chemicals are effectively used as antimicrobials in agriculture. However, with respect to its nanoparticulate form there has been limited number of studies. In this investigation, in vitro tests on effect of copper nanoparticles (CuNPs) against plant pathogenic fungi, oomycete, bacteria, beneficial microbes Trichoderma harzianum and Rhizobium spp. , and wheat seeds were conducted. Integration of CuNPs with non-nano copper like copper oxychloride (CoC) at 50 mg/L concentration each recorded 76% growth inhibition of the oomycete Phytophthora cinnamomi in vitro compared to the control. CuNPs also showed synergistic inhibitory effect with CoC on mycelial growth and sporulation of A. alternata . Pseudomonas syringae was inhibited at 200 mg/L of CuNPs. CuNPs were not significantly biocidal against Rhizobium spp. and Trichoderma harzianum compared to CoC. Evaluation of the effect of CuNP on wheat revealed that rate of germination of wheat seeds was higher in presence of CuNPs and CoC compared to control. Germination vigor index, root length, shoot dry weight and seed metabolic efficiency of wheat were negatively affected. At low concentration, CuNPs promoted the growth of the plant pathogenic fungi Botrytis fabae, Fusarium oxysporum f.sp. ciceris, F.oxysporum f.sp. melonis, Alternaria alternate and P. syringae , and sporulation of T. harzianum . Synergistic effect of CuNPs and CoC in inhibiting P. cinnamomi offers a possibility of developing new fungicide formulation for better control of the oomycetes. Non-biocidal effect of CuNPs against beneficial microbes indicates its potential use in the agri-ecosystem.
Canopy height variation and environmental heterogeneity in the tropical dry forests of coastal Oaxaca, Mexico

Despite its importance for carbon storage and other ecosystem functions, the variation in vegetation canopy height is not yet well understood. We examined the relationship between this community attribute and environmental heterogeneity in a tropical dry forest of southern Mexico. We sampled vegetation in 15 sites along a 100‐km coastal stretch of Oaxaca State, and measured the heights of all woody plants (excluding lianas). The majority of the ca. 4000 individuals recorded concentrated in the 4–8 m height range. We defined three plant sets to describe overall community canopy height at each site: a set including all plants, a set made up by the tallest plants representing 10 percent of all individuals, and a set comprising the 10 tallest plants. For each site we computed maximum height and the mean and median heights of the three sets. Significant collinearity was observed between the seven resulting height variables, but null distributions constructed through bootstrap revealed their different behaviors as functions of species richness and density of individuals. Through linear modeling and a model selection procedure, we identified 21 models that best described the variation in canopy height variables. These models pointed out to soil (measured as PC1 of a principal component analysis performed on 10 soil variables), water stress, and elevation as the main drivers of canopy height variation in the region. In the event of increasing water stress resulting from global climate change, the studied tropical dry forests could become shorter and thus decrease their carbon storage potential.
Abnormalities in the Adhesion and Aggregation Profiles of Circulating Monocytes in Psoriasis

By JACKELYN BEZZEG GOLDEN Human psoriasis patients have numerous comorbidities including an increased risk of developing cardiovascular disease (CVD), thus making psoriasis truly more than skin deep. Numerous cellular immune mediators are implicated to initiate, direct, and participate in the chronic inflammation characteristic of psoriasis. A relatively neglected participant in psoriasis pathology is the monocyte. Three main populations of circulating monocytes have been identified in humans based on differential expression of the cell surface markers CD14 and CD16, defining them as “classical” (CD14++CD16-), “intermediate” (CD14++CD16+), and “non-classical” (CD14+CD16++). Intermediate (CD14++CD16+) monocytes are elevated in psoriasis, correlate with psoriasis severity and, interestingly, are predictive of increased CVD risk and outcomes including death, suggesting that monocytes may be an important cellular mediator. A unique feature observed for classical monocytes was a robust relative (p=.006) and absolute (p=.003) increase in circulating CD14+ monocyte-monocyte aggregates (doublets) in both unfractionated whole blood and PBMCs of psoriasis patients. Doublets (from sorted CD14+ cells) have mRNA expression distinct from either classical singlet monocytes or classical singlet monocytes following plastic adherence. Aggregated monocytes overexpress integrins, extracellular matrix proteins, and a unique disintegrin. Cumulative data suggest that psoriasis monocytes
Route of immunization and timing for adjuvant delivery : critical factors for efficient T cell cross-priming

CD8+ T cell responses are crucial in the defense against several infectious agents, as well as for the treatment of cancer. Thus, the development of vaccine strategies capable of eliciting robust CD8+ T cell responses is needed. Antigen cross-presentation is known to be an important mechanism for the activation of antigen-specific CD8+ T cells, and multiple parameters contribute to the efficiency of cross-priming. We examined two of them : the route of immunization and the timing of adjuvant delivery. First, we developed the tetramer-based enrichment strategy, which allowed us to study the endogenous CD8+ T cell response. Then, we investigated the impact of the route of immunization on CD8+ T cell cross-priming. We report that local delivery of cell-associated antigen results in delayed cross-priming due to the increased time required for antigen capture and presentation. In comparison, delivery of systemically disseminated antigen resulted in rapid T cell priming. Surprisingly, local injection of cell-associated antigen, while slower to mount a functional response, resulted in the differentiation of a more robust effector T cell population. We were next interested in evaluating the combination of cell-associated antigen with the delivery of poly I:C, an adjuvant known to induce the production of type I interferons (IFN). We observed an immunization-route-specific effect regarding the timing of innate immune stimulation and identified the optimal time window for adjuvant administration in order to maximize the boosting effects on CD8+ T cell cross-priming. We characterized in detail several effects of poly I:C, as well as type I IFN, exerted on immune cells
Physiological tolerance of the early life history stages of fresh water prawn (Macrobrachium rosenbergii De Man, 1879) to environmental stress

Global climate change is transforming life on earth, causing widespread effects on all ecosystems. Among marine ecosystems, estuaries are considered as nursery grounds for marine and fresh water species. M. rosenbergii, a euryhaline species, migrate to the estuaries for breeding and spawning. The subsequent larval rearing takes place by experiencing variations in temperature and salinity conditions. The present study examines the effect of different temperature and salinity on the larval development and survival by observations on stored yolk utilization, cardiac performance, as well as changes in the rate of growth in body appendages and larval activity. The larvae showed 100% mortality at higher temperature (33.5 ± 0.5 °C) in all the salinity conditions (12 PPT, 15 PPT, and 20 PPT). The survival rate varied between 76-96 % on exposure to lesser temperature conditions. Likewise, the post-embryonic yolk lasted for 4 days at ambient temperature (29 °C); whereas, at 33.5 ± 0.5 °C, it lasted only for 2-3 days. There was an increase in total length of larvae, when exposed to higher temperature and salinity, independently or in combination, but at 33.5 ± 0.5 °C under all salinity conditions the larvae died on the 5th day. For the cardiac performance, larval heart beat (fH) significantly increased for higher temperature and salinity conditions (20 PPT; 33.5 °C) and lowered at ambient condition 12 PPT; 29°C. Larval stroke volume Vs, and Cardiac output Q□ were higher in ambient conditions and lowest in higher temperature and salinity conditions. However, temperature and salinity together did not show any significant effect on cardiac performance. On the other hand, the larval activity decreased significantly at higher temperature and salinity conditions, compared to ambient conditions but the interactive effect did not show any change. Thus, the physiological responses to temperature and salinity by the early life stages of M. rosenbergii could restrain the tolerance capability of the organism, thereby interfering in the successful completion of the larval development under the altered climatic conditions.
Does the Novel Class of (2R, 4S)-N-(2, 5-Difluorophenyl)-4-Hydroxy-1-(2, 2, 2-Trifluoroacetyl) Pyrrolidine-2-Carboxamide’s Have Any Effect on Cell Viability and Apoptosis of Human Hepatocellular Carcinoma Cells?

Background: The hepatocellular carcinoma is believed to be the third cause of death due to cancer, worldwide. A new derivative of the (2R,4S)-N-(2,5-difluorophenyl)-4-hydroxy-1-(2,2,2-trifluoroacetyl) pyrrolidine-2-carboxamide compound were synthesized, employing a facile one-pot reaction of trans-4-hydroxy proline and N-(2,5-difluorophenyl)-2,2,2-trifluoroacetimidoyl chloride in the presence of TiO2 as catalysts and sodium hydrogen carbonate. Objectives: Therefore, in the present study we aimed to explore whether if the above new derivative pyrrolidine-2-carboxamide can affect cellular viability and apoptosis in cancerous HepG2 cell line. Methods: HepG2 cells were cultured in RPMI 1640 medium containing fetal bovine serum. Cultured cells were then treated with 7.8 µM to 125 µM of pyrrolidine-2-carboxamide. The toxicity of the compound was assayed by MTT method and detection of annexin V signal, using a flowcytometry system. Results: We found the pyrrolidine-2-carboxamide derived inhibition of HepG2 cells following a dose and time dependent fashion. The highest numbers of dead cells were observed in 125 µM dose, after 48 hours of treatment. Flow cytometric analysis also revealed that massive numbers of apoptotic cells were detectable in response to treatment with this pyrrolidine derivative. Conclusions: Overall, according to the data presented here, the pyrrolidine-2-carboxamide could possibly control cellular viability/apoptosis. Thus it can potentially be concerned as a useful therapeutic tool for hepatocellular carcinoma treatment.
Use of collard green stalks as environmental enrichment for cockatiels ( Nymphicus hollandicus ) kept in captivity

The objective of this study was to evaluate the influence of collard green stalks as environmental enrichment on the behavior of cockatiels (Nymphicus hollandicus) maintained in captivity. Sixteen birds were housed individually in cages and fed a commercial diet for parrots and seed mix, with water ad libitum during 12 days in climatic chamber with temperature and relative humidity simulating tropical conditions. The animals (n = 8) were divided into two groups, control and enriched, and the experimental period was divided into two phases (during and after enrichment) of four days each. The collard green stalks were used as enrichment only during the first period of the experiment, daily changed and maintained only during the day. The stalks increased the feed intake and decreased the sleep activities. No effect was observed on the body surface temperature, locomotion, maintenance and other resting activities. Small undesirable activities were detected. It was concluded that collard green stalks can be used as environmental enrichment, becoming part of food preferences of cockatiels. However, its use does not significantly alter the behavior of birds kept in captivity
Complete mitochondrial genome of the apple snail Pomacea diffusa (Gastropoda, Ampullariidae) with phylogenetic consideration

Abstract We present the complete mitochondrial genome of Pomacea diffusa in this study. The results show that the mitochondrial genome is 16,640 bp in length, which is comprised of 13 protein-coding genes, two rRNA genes, and 21 tRNA genes. The nucleotide compositions of the light strand are 39.62% of A, 30.13% of T, 16.02% of C, and 14.24% of G. Except eight tRNA (Glu, Gly, Trp, Cys, Tyr, Met, Thr, Val) on the light strand, the rest are encoded on the heavy strand. All the protein-coding genes start with ATC initiation codon, and two types of inferred termination codons are TAA and TAG. There are 26 intergenic spacers and two gene overlaps. The phylogenetic analysis shows that P. diffusa clusters with P. canaliculata and P. maculata with high bootstrap support, which is consistent with the morphological and molecular evidence.
Purification of progenitor photoreceptors derived from the directed differentiation of human pluripotent stem cells

Cell therapy has the potential to treat a wide variety of unmet therapeutic indications that affect a growing number of people globally. Many of these therapies require purification steps to separate specific cell types from heterogeneous populations. This thesis investigates current affinity purification platforms to isolate human pluripotent stem cell-derived progenitor photoreceptors for the treatment of retinal dystrophies, and introduces a novel purification technology which possess bioprocessing and clinical advantages over current techniques. Successful production of progenitors was achieved using both induced pluripotent stem cells (iPSC) and human embryonic stem cells (hESC). By controlling the cell aggregation step and other iterative improvements to the retinal differentiation, 35.7% of cells generated expressed Cone-Rod Homeobox (CRX)-positive – a key marker to define progenitor photoreceptors. The critical performance metrics of fluorescent-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS) were then derived through experimentation. Sort purity, progenitor yield and viable cell recovery of CD73-positive cell populations – a surface marker shown to co-express with CRX - were measured, and demonstrated that high purity separations above 90% were attained. However, both methods suffered from low cell recoveries with over 30 or 40% of cells (for FACS and MACS respectively) lost through the numerous processing steps involved in labelling cells with either a fluorescent or paramagnetic tag, washing and sorting samples. Cell labelling also leaves the product with a bound cellular label, complicating additional processing and potentially causing toxic clinical affects. A novel purification technology was assessed with SpheriTech affinity beads that possess bioprocess and clinical advantages over current purification methods. Cells are unmodified through isolation, with the positively selected cell type remaining label-free after processing. Consequently, cells experience minimal process steps so the time, risk, cost burden of purification and cell loss is reduced. Comparable purity with all separations was observed, however progenitor yield was noted to be lower with SpheriTech affinity beads than for FACS and MACS. To assess the impact different purification technologies have upon the complete bioprocess in an iPSC-derived therapy, an economic cost-modelling tool was created. By inputting experimentally-derived data into an integrated model, the cost of goods (COG) per dose was evaluated when using each of the three affinity purification methods. FACS was found to be economically favourable only at small production scales due to throughout limitations, with MACS presenting the most cost effective technology at all other scales. However, if progenitor yield could be increased to improve process yields through further process development, SpheriTech would compete with MACS across all scales tested.
Consequences of High-Density Fish Culture as Monitored By Growth, Behavior and Immune Responses of Nile Tilapia (Oreochromis niloticus)

An experiment was performed in a twelve weeks period at three varied stocking densities: low density (LD, 100 fish m-3), medium density (MD, 200 fish m-3) and high density (HD, 400 fish m-3) to analyze the biological performances and ingestive behaviour, of Nile tilapia (Oreochromis niloticus) and Lately, fish were challenged with Aeromonas hydrophila to evaluate the cumulative mortality (%). Stocking density had no effect on survival rate, the final weight markedly reduced with increased density, ingestive behaviour was higher in fish reared in MD than fish reared in LD, however, fish at HD have a higher feed intake (%) and feed conversion ratio. Fish at LD showed marked higher levels of total protein, albumin and globulin compared with those reared at HD. plasma glucose and cortisol levels were high in HD contrast to LD and MD groups. LD fish had higher RBCs and WBCs parallel to MD and HD. similarly, lymphocytes, neutrophils, and monocytes (%) decreased with increasing density. In addition, Serum antioxidant and lysozyme enzymes were considerably (P
Endemic Top Predator Response to Goat Eradication on Santiago Island: the Galapagos Hawk and its Diet.

The eradication of invasive species is becoming a common approach for the conservation of native communities around the world. However, few of the programs complete exhaustive studies and monitoring of the impact of these eradications. The current study is one component of a long-term monitoring of the Galapagos Hawk (Buteo galapagoensis) before, during and after the eradication of goats (Capra hircus) on Santiago Island in 2006. As the herbivory pressure was released, we foresaw that the rapid vegetation recovery would affect the hunting success of the Galapagos Hawk on its preferred terrestrial prey. We performed a comparative study on the feeding ecology of the hawk by direct observation of prey delivered to nests pre(1999-2000) and post-goat eradication (2010-2011). We predicted that the Galapagos Hawk would adapt to its new environment by shifting its diet composition, from predominantly terrestrial prey before goat removal to a more arboreal prey base after goat removal, and that the effect would differ across habitat types. Additionally, we were interested in assessing the response of introduced rats (Rattus rattus) to the removal of goats. Contrary to our primary hypothesis, we were unable to find overall changes diet composition of terrestrial and arboreal prey. Nonetheless, the consumption of terrestrial prey did vary between vegetation types, confirming the influence of vegetation on the amount of prey consumed. Even though terrestrial prey consumption did not change much, it consisted of a much higher proportion of introduced rats. However, rat-trapping indicated no increases in abundance of rat populations, which coupled with the increased consumption of rats by hawks, suggests top predator control on the rodent invader. Moreover, it appears that the hawk’s ability to hunt arboreal prey is hampered in areas with high vegetation, as consumption of arboreal prey in the higher transition zone habitat after eradication is significantly lower than before. Consequently, hawks in densely vegetated territories now depend largely on introduced rodents as a food source. Overall, we observed how the territorial population of the top predator in this community has, so far, been able to withstand these changes by adjusting to a new diet and possibly exert top down control on other potentially threatening invaders. Thus, we have learned that special consideration should be given to natural trophic interactions to understand the potential effects of invasive species eradication.
A novel approach to reveal spike coding in rat oxytocin cells

The methods proposed here adopt a direct approach to describe spike interval patterning because this constitutes the information that reaches the axon terminals. An information model has been developed in which spike patterning increases the predictability of interspike intervals (ISIs). Log ISI histogram probability distributions were used to evaluate the entropy, an absolute measure of the disorder of the interval distribution. Very regular intervals exhibit minimal disorder and convey only frequency information.