Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance and cost benefits of growing pigs fed diets containing graded levels of cassava plant meal

The study evaluated the nutrient digestibility of three standardised Cassava Plant Meals (CPMs) products developed from Tropical Manihot Species (TMS) 30572 with a focus on its efficiency to replace maize completely in the diets of growing pigs and its effect on their growth. The CPM with the best apparent nutrient digestibility (CPM III) was used in the formulation of the basal diet fed to the pigs in the 56-day feeding trial. Twenty growing crossbred pigs (Large White x Hampshire) with initial average weight of 20.00±0.5 kg and of different sexes were randomly allotted to five experimental diets containing 0, 25, 50, 75 and 100 % of maize replaced with CPM as CPM0, CPM1, CPM2, CPM3 and CPM4 respectively. Results showed that cassava plant meal product III (CPM III) had better apparent nutrient digestibility than products I and II. Significant difference ( p <0.05) existed across dietary treatments for average daily weight gain and feed conversion ratio. However, the final weight of pigs on diet CPM2 (50 % replacement) was highest compared to other dietary treatments. Significant differences ( p <0.05) also existed for average daily feed intake across the dietary treatments. Feed conversion ratio, feed intake and weight gain values of CPM2 compared favourably with CPM0, while, CPM2 had the least cost of production. It can be concluded that cassava plant meal could completely replace maize in the diets of growing pigs and significantly reduced cost of production. Keywords: Standardized cassava plant meal; maize; pigs; feed intake; weight gain; cost benefit
Validation of SNP marker linked to alc gene for long shelf life of tomato

ABSTRACT Tomato (Solanum lycopersicum L.) fruits are naturally perishable and have short shelf life. Post-harvest losses can be devastating and can be associated with rapid ripening. The objective of this study was to identify a single nucleotide polymorphism (SNP) marker associated with alc gene conferring long shelf life in tomato. The tomato line CSIR/CRI-AT06 was crossed with Alc-LA3134 to develop an F2 population. A total of 72 plants were screened for the target loci. Genotypic data of the F2 population were generated following the scoring system as [T:A] for heterozygous individuals, [A:A] and [T:T] for plants homozygous for the donor and recipient parents, respectively. An assessment of the Sly10–14 SNP marker was completed by comparing SNP score against fruit shelf life of the 72 F2 entries. The pattern of segregation of SNP marker for the alc gene was tested for goodness of fit to a 1:2:1 ratio using Chi-square test (χ2) test. The results showed that the marker segregated in the expected ratio. The analysis from 72 F2 population plants indicated that SNP marker (Sly 10-14) had significant association with shelf life at 1% significance level. From the analysis, it can be established that a locus linked to Sly10-14 is significant. The homozygous marker (A:A) has an effect of increasing shelf life by 22 days and explains 87% of the observed variation. This marker (Sly10-14) is linked to a gene that controls the shelf life of tomato fruits. The effect of this gene is additive and it increases the shelf life.
Recombinant protein expression in biofilms

Biofilm research is usually focused on the prevention or control of biofilm formation. Recently, the significance of the biofilm mode of growth in biotechnological applications received increased attention. Since biofilm reactors show many advantages over suspended cell reactors, especially in their higher biomass density and operational stability, bacterial biofilms have emerged as an interesting approach for the expression of specific proteins. Despite the potential of biofilm systems, recombinant protein production using biofilms has been scarcely investigated for the past 25 years. Our group has demonstrated that E. coli biofilms were able to produce a model recombinant protein, the enhanced green fluorescent protein (eGFP), at much higher levels than their planktonic counterparts. Even without optimization of cultivation conditions, an attractive productivity was obtained, indicating that biofilm cultures can be used as an alternative form of high cell density cultivation (HCDC). E. coli remains one of the favorite hosts for recombinant protein production and it has been successfully used in metabolic engineering for the synthesis of high value products. This review presents the advantages and concerns of using biofilms for the production of recombinant proteins and summarizes the different biofilm systems which have been described for this purpose. The relative advantages and disadvantages of the four microbial hosts tested for recombinant protein production in biofilms (two bacteria and two filamentous fungi) are also discussed.
Development of Bifunctional Three-Dimensional Cysts from Chemically Induced Liver Progenitors

Chemically induced liver progenitors (CLiPs) have promising applications in liver regenerative medicine. Three-dimensional (3D) structures generated from liver progenitor cells possess wide applications in cell transplantation, disease model, and drug testing. Here, we report on the spontaneous formation of 3D cystic structures comprising maturing rat CLiPs on gelatin-coated dishes. Our 3D cysts contained Alb+/+CK19+/− and Ck19+/+Alb+/− cells. These cell types gradually diverged into specialized mature cells, as demonstrated by the expression of mature biliary markers (Cftr, Ae2, and Aqp1) and hepatic markers (Alb and Mrp2). The 3D cysts also expressed functional multidrug resistance protein 1 (Mdr1), as indicated by epithelial efflux of rhodamine. Furthermore, we observed bile canaliculi functions between hepatocytes and cholyl-lysyl-fluorescein extrusions, indicating that the functional characteristics of 3D cysts and active bile salt export pump (Bsep) transporters were intact. Thus, our study revealed a natural characteristic of rat CLiPs to spontaneously form 3D cystic structures accompanied with cell maturation in vitro, offering a platform for studies of liver development and drug screening.
Distribution and dispersal of Urophora cardui (Diptera, Tephritidae) in Finland in 1985-1991

Distribution and dispersal of Urophora cardui (Diptera, Tephritidae) in Finland in 1985- 1991. - Entomol. 2:211- 216. Urophora cardui (Linnaeus) was reported for the first time from Finland in 1981, from the city of Helsinki. During the years 1985- 1991 the distribution and dispersal of the species was monitored by searching for galls which the fly larvae cause on stems of the thistle Cirsium arvense. In 1986 galls were ob served at a distance of 18- 36 km from the center of Helsinki, and by 1991 the distance had increased to 37-55 km along the main roads. Annual dispersal of the fly was found to correlate strongly with the warmth of summers: after a cold summer the area occupied by the fly actually decreased, but in a warm summer new galls were found up to 16 km further from city center than the year before.
Application of cow manure and inorganic fertilizer in one season and carryover of effects in sesame on tropical ferruginous soils

The aim of this research was to find whether Sesamum radiatum growth requires cow manure and nitrogen-phosphorus-potassium (NPK) fertilizers. We examined the survey vegetable over two growing seasons on ferruginous soil: from June to December in 2009 (Season 1) and 2010 (Season 2). We used cow manure (0, 20, 30 and 40 t.ha-1) and NPK 10:10:20 (0, 50, 100 and 150 kg.ha-1) during season 1 and no amendments during season 2 to determine if application of amendments would carry through to a second season as partially described by effects on soil and yield. A randomized complete block designed through three replications is performed. Parameters such as pH, Organic carbon, Nitrogen, phosphorus, exchangeable bases (Ca2+, K+, Mg2+), cation exchange capacity, base saturation and yields were identified. Cow manure significantly affected height, leaves yields while NPK had a lowly significant effect on total yield, stems yield and base saturation and highly significant effect on leaves yields, sum of bases and cation exchange capacity. Both cow manure and NPK fertilizers significantly affected magnesium and organic carbon. 20 tâˆ™ha-1 of cow manure and 100 kg.ha-1 of NPK produced the best yield in the second season and our results opened up encouraging perspectives in using magnesium, organic or inorganic fertilizers for sesame growth. The outcomes provided important prerequisite for effective cultivation of the survey leafy vegetable and it is expected to be applied in research for cultivars suitable to modern planting systems and food purposes. Key words: Amended soil, unamended soil, yield, growing seasons, leafy vegetable.
Understory Vegetation Dynamics across a Poplar Plantation Chronosequence in Reclaimed Coastal Saline Soil

Although the understory vegetation abundance, diversity, and composition associated with stand development in natural forests have been well reported, only a few studies have examined the age-related changes of understory vegetation in fast-growing planted forests in reclaimed soils. This study measured the understory vegetation and soil variables in 8-, 12-, and 18-year-old poplar plantations in reclaimed coastal saline soil of Eastern China. This study examined how the abundance, diversity, and composition changed with stand development and the soil variables. Further, structural equation modeling (SEM) was used to evaluate the direct and indirect factors influencing the abundance and plant diversity throughout stand development. Herb abundance was significantly higher in the youngest and oldest stands, whereas shrub abundance was higher in the middle-aged stands. Shannon’s diversity index was significantly higher in the youngest stand for herbs, whereas it was highest in the middle-aged stands for shrubs. A multivariate analysis revealed that the herb and shrub composition were influenced by the stand age, total soil carbon and soil pH. The most parsimonious SEM model showed the negative direct effects of the stand age and the negative indirect effects of the stand age via the soil variables on shrub abundance, shrub diversity, and herb diversity, suggesting that the increase of overstory biomass with the stand age reduces resources available for the understory. Our results revealed that understory diversity and composition might change with stand development mediated by the changes in understory light and soil resources in fast-growing plantations.
Single Cell RNA-sequencing reveals cellular heterogeneity, stage transition and antigenic variation during stress adaptation in synchronized Plasmodium falciparum

The malaria parasite has a complex life cycle exhibiting phenotypic and morphogenic variations in two different hosts. Phenotypic cell-to-cell variability can be an important determinant of cellular adaptation, stress tolerance and immune evasion in the host. To investigate cellular heterogeneity, we performed single cell RNA-sequencing (scRNA-seq) of 4949 and 6873 synchronized Plasmodium cells in control and under temperature stress condition (phenocopying the cyclic bouts of fever experienced during malarial infection). High-resolution clustering of scRNA-seq datasets and a combination of gene signatures allow identification of cellular heterogeneity and stage transition during stress adaptation. We identified a subset of parasites primed for gametogenesis and another subset primed for stress adaptation. Interestingly, temperature stress inducted the process of gametogenesis by upregulation of master regulator (AP2-G) of sexual conversion. Moreover, pseudotime analysis indicated bifurcation for cell-fate decision to gametogenesis at two different stages of intra-erythrocytic cycle. Furthermore, we identified a rare population of cells, which is only emerged during the stress condition, showing the reactive state of the pathogen against the temperature stress condition. Interestingly, genes associated with the gametogenesis, chaperon activity and maintenance of cellular homeostasis showed maximum variation under temperature stress condition. We also developed an online exploratory tool (website: http://bit.ly/plasmo_sync), which will provide new insights into gene function under normal and physiological stress condition. Thus, our study suggests that the variability and versatility of the maintenance of cellular homeostasis should enable cells to survive under different stress conditions, and may act as an important stimulator of development of drug-resistance in Plasmodium falciparum.
B Cell Compartmentalization in Blood and Cerebrospinal Fluid of HIV-Infected Ugandans with Cryptococcal Meningitis

Activated B cells modulate infection by differentiating into pathogen-specific antibody-producing effector plasmablasts/plasma cells, memory cells, and immune regulatory B cells. In this context, the B cell phenotypes that infiltrate the central nervous system during human immunodeficiency virus (HIV) and cryptococcal meningitis coinfection are ill defined. ABSTRACT Activated B cells modulate infection by differentiating into pathogen-specific antibody-producing effector plasmablasts/plasma cells, memory cells, and immune regulatory B cells. In this context, the B cell phenotypes that infiltrate the central nervous system during human immunodeficiency virus (HIV) and cryptococcal meningitis coinfection are ill defined. We characterized clinical parameters, mortality, and B cell phenotypes in blood and cerebrospinal fluid (CSF) by flow cytometry in HIV-infected adults with cryptococcal (n = 31) and noncryptococcal (n = 12) meningitis and in heathy control subjects with neither infection (n = 10). Activation of circulating B cells (CD21low) was significantly higher in the blood of subjects with HIV infection than in that of healthy controls and greater yet in matched CSF B cells (P < 0.001). Among B cell subsets, elevated frequencies of memory and plasmablasts/plasma cells most clearly distinguished the CSF from blood compartments. With cryptococcal meningitis, lower frequencies of expression of the regulatory protein programmed death-1 (PD-1) on plasmablasts/plasma cells in blood (median, 7%) at presentation were associated with significantly decreased 28-day survival (29% [4/14 subjects]), whereas higher PD-1 expression (median, 46%) characterized subjects with higher survival (88% [14/16 subjects]). With HIV infection, B cell differentiation and regulatory markers are discrete elements of the circulating and CSF compartments with clinical implications for cryptococcal disease outcome, potentially due to their effects on the fungus and other local immune cells.
Social bonding induces changes in brain functional connectivity in male and female monogamous voles: a longitudinal fMRI study

Microtus ochrogaster, the prairie vole, has become a valuable rodent model to study complex social behaviors, including enduring social bonding. Previous studies have related pair bonding in the prairie vole with plastic changes in several brain regions. However, the network interaction between these regions and their relevance to such socio-sexual behaviors has yet to be described. In this study, we used resting state functional magnetic resonance imaging (rsfMRI) to explore the longitudinal changes in the functional interactions of a set of brain regions previously associated with pair bonding in prairie voles. Specifically, 32 prairie voles were scanned at baseline, after 24 hours and two weeks of cohabitation and mating with a sexual partner (16 male-female pairs). Between 48 and 72 hours of cohabitation voles showed significant preference for the partner over a stranger, confirming pair bond formation; however, individual variability was observed. Network based statistics showed no sex differences in functional connectivity, but revealed a common network with significant longitudinal changes between sessions, including the anterior cingulate cortex (ACC), anterior olfactory nucleus (AON), dentate gyrus (DG), dorsal hippocampus (dHIP), lateral septum (LS), medial prefrontal cortex (mPFC), retrosplenial cortex (RSC), ventral hippocampus (vHIP), and ventral tegmental area (VTA). Furthermore, baseline functional connectivity in three sub-networks including the ACC, nucleus accumbens (NAcc), basolateral amygdala, and DG (ACC-NAcc-BLA-DG), the medial amygdala (MeA)-ventral pallidum (VP), and RSC-VTA, predicted the onset of affiliative behavior (huddling latency) in the first hours of cohabitation, even before sexual experience. Finally, a relationship was found between the strength of the pair bond (partner preference index) with long-term changes in the functional connectivity between the ventral pallidum and medial amygdala (MeA-VP). Overall, our findings revealed the association between network-level changes and the process of social bonding, and provide a novel approach to further investigate the neurophysiology of complex social behaviors displayed in the prairie vole.
Determination of grapefruit (
 Citrus paradisi
 ) peel extract bio‐active substances and its application in Caspian white fish (
 Rutilus frisii kutum
 ) diet: Growth, haemato‐biochemical parameters and intestinal morphology

In this study, total phenolic and flavonoid contents of grapefruit peel extract (GPE) were equal to 117.3 ± 0.3 µg of gallic acid/mg and 39.30 ± 0.1 µg of quercetin/mg respectively. Caspian white fish (n = 180, 4 ± 0.9 g body weight) was fed with supplemented diets, including 0, 6.25, 12.5 and 25 mg of GPE/kg for 60 days at 25 ± 1°C. The growth performance was markedly improved in fish fed with 25 mg/kg of GPE compared to others (p < 0.05). Moreover, fish fed with 25 mg/kg of GPE showed a significant increase in red blood cell (2.65·106 cell/mm3), white blood cell (17.75·103 cell/mm3), packed cell volume (48%) and haemoglobin concentrations (8.75 g/dl) compared to the control (p < 0.05). However, the highest alanine aminotransferase (140 U/L), alanine transaminase (14.5 U/L), and alkaline phosphatase (18.5 U/L) were observed in control group. Morphological analysis of intestine revealed the highest amount of villus width (8.4 µM), height (32.86 µM) and surface area (342.7 µM2) in fish fed with 25 mg/kg of GPE (p < 0.05). In conclusion, supplementing feed with GPE at 25 g/kg can improve growth performance and haemato‐biochemical parameters of Caspian white fish fry.
Genome-wide association analyses of multiple traits in Duroc pigs using low-coverage whole-genome sequencing strategy

High-density markers discovered in large size samples are essential for mapping complex traits at the gene-level resolution for agricultural livestock and crops. However, the unavailability of large reference panels and array designs for a target population of agricultural species limits the improvement of array-based genotype imputation. Recent studies showed very low coverage sequencing (LCS) of a large number of individuals is a cost-effective approach to discover variations in much greater detail in association studies. Here, we performed cohort-wide whole-genome sequencing at an average depth of 0.73× and identified more than 11.3 M SNPs. We also evaluated the data set and performed genome-wide association analysis (GWAS) in 2885 Duroc boars. We compared two different pipelines and selected a proper method (BaseVar/STITCH) for LCS analyses and determined that sequencing of 1000 individuals with 0.2× depth is enough for identifying SNPs with high accuracy in this population. Of the seven association signals derived from the genome-wide association analysis of the LCS variants, which were associated with four economic traits, we found two QTLs with narrow intervals were possibly responsible for the teat number and back fat thickness traits and identified 7 missense variants in a single sequencing step. This strategy (BaseVar/STITCH) is generally applicable to any populations and any species which have no suitable reference panels. These findings show that the LCS strategy is a proper approach for the construction of new genetic resources to facilitate genome-wide association studies, fine mapping of QTLs, and genomic selection, and implicate that it can be widely used for agricultural animal breeding in the future.
Macroecology of ground beetles: Species richness, range size and body size show different geographical patterns across a climatically heterogeneous area

Ecogeographical patterns have been widely studied in endothermic vertebrates, but relatively few studies have simultaneously examined patterns and causes of gradients in species richness, range size and body size in ectothermic insects. We examined patterns in species richness, mean range size and mean body size of ground beetle assemblages across the biogeographical provinces of Northern Europe, a region that was mostly covered by ice sheets during the latest Ice Age and that presents strong contemporary climatic gradients.
Meta‐analyzing the likely cross‐species responses to climate change

Abstract Ecological Niche Models (ENMs) have different performances in predicting potential geographic distributions. Here we meta‐analyzed the likely effects of climate change on the potential geographic distribution of 1,205 bird species from the Neotropical region, modeled using eight ENMs and three Atmosphere‐Ocean General Circulation Models (AOGCM). We considered the variability in ENMs performance to estimate a weighted mean difference between potential geographic distributions for baseline and future climates. On average, potential future ranges were projected to be from 25.7% to 44.5% smaller than current potential ranges across species. However, we found that 0.2% to 18.3% of the total variance in range shifts occurred “within species” (i.e., owing to the use of different modeling techniques and climate models) and 81.7% to 99.8% remained between species (i.e., it could be explained by ecological correlates). Using meta‐analytical techniques akin to regression, we also showed that potential range shifts are barely predicted by bird biological traits. We demonstrated that one can combine and reduce species‐specific effects with high uncertainty in ENMs and also explore potential causes of climate change effect on species using meta‐analytical tools. We also highlight that the search for powerful correlates of climate change‐induced range shifts can be a promising line of investigation.
Exogenous interferons for the prevention of respiratory viral infections: evaluation of different aspects in vitro

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