Miracle-dz/UniFAR-FTUs huggingface dataset:
Copepods and salmon: characterizing the spatial distribution of juvenile salmon along the Washington and Oregon coast, USA

Yearling Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) were sampled concurrently with physical variables (temperature, salinity, depth) and biological variables (chlorophyll a concentration and copepod abundance) along the Washington and Oregon coast in June 1998–2008. Copepod species were divided into four different groups based on their water-type affinities: cold neritic, subarctic oceanic, warm neritic, and warm oceanic. Generalized linear mixed models were used to quantify the relationship between the abundance of these four different copepod groups and the abundance of juvenile salmon. The relationships between juvenile salmon and different copepod groups were further validated using regression analysis of annual mean juvenile salmon abundance versus the mean abundance of the copepod groups. Yearling Chinook salmon abundance was negatively correlated with warm oceanic copepods, warm neritic copepods, and bottom depth, and positively correlated with cold neritic copepods, subarctic copepods, and chlorophyll a concentration. The selected habitat variables explained 67% of the variation in yearling Chinook abundance. Yearling coho salmon abundance was negatively correlated with warm oceanic copepods, warm neritic copepods, and bottom depth, and positively correlated with temperature. The selected habitat variables explained 40% of the variation in yearling coho abundance. Results suggest that copepod communities can be used to characterize spatio-temporal patterns of abundance of juvenile salmon, i.e., large-scale interannual variations in ocean conditions (warm versus cold years) and inshore-offshore (cross-shelf) gradients in the abundance of juvenile salmon can be characterized by differences in the abundance of copepod species with various water mass affinities.
Map of the Human Genome 3.0

GENOME RESEARCHGeneticists are discovering discrete blocks of DNA that differ from one person to the next. And they may be common enough and account for enough of the genome, researchers concluded at a conference held here last week, that it's time to create a new map of the genome, one that describes its blocky structure. Its creators hope this so-called haplotype map will be a tool for pinning down the genes that contribute to the development of complex diseases such as cancer, diabetes, and mental illness.
UV‐radiation and elevated temperatures induce formation of reactive oxygen species in gametophytes of cold‐temperate/Arctic kelps (Laminariales, Phaeophyceae)

Enhanced UV‐radiation (UVR) through stratospheric ozone depletion and global warming are crucial stressors to marine macroalgae. Damages may arise through formation of reactive oxygen species (ROS) in gametophytes of ecologically important kelps, brown algae of the order Laminariales, Such stress‐induced damages may have a negative impact on their fitness and further impact their following life stages. In our study, gametophytes of three kelp species Alaria esculenta (L.) Grev. , Laminaria digitata (Huds.) Lamour. , Saccharina latissima (L.) Lane, Mayes, Druehl, Saunders from the Arctic, and of L. hyperborea (Gunnerus) Foslie from the North Sea were exposed to photosynthetically active radiation, UV‐A, and UV‐B radiation and four temperatures (2–18°C). ROS are formed predominantly in the peripheral cytoplasm and in chloroplasts especially after exposure to UVR. Superoxide (O2*‐) is additionally formed in small, globular cytoplasmic structures, possibly mitochondria. In the surrounding medium O2*‐‐concentration increased markedly at elevated temperatures and under UV stress in some cases. Ultrastructural damage was negligible pointing to a high stress tolerance of this developmental stage. Our data indicate that stress tolerant gametophytes of three Arctic kelp species should sustain their crucial function as seed bank for kelp populations even under prospective rising environmental perturbations.
GeoSES: A socioeconomic index for health and social research in Brazil

The individual’s socioeconomic conditions are the most relevant to predict the quality of someone’s health. However, such information is not usually found in medical records, making studies in the area difficult. Therefore, it is common to use composite indices that characterize a region socioeconomically, such as the Human Development Index (HDI). The main advantage of the HDI is its understanding and adoption on a global scale. However, its applicability is limited for health studies since its longevity dimension presents mathematical redundancy in regression models. Here we introduce the GeoSES, a composite index that summarizes the main dimensions of the Brazilian socioeconomic context for research purposes. We created the index from the 2010 Brazilian Census, whose variables selection was guided by theoretical references for health studies. The proposed index incorporates seven socioeconomic dimensions: education, mobility, poverty, wealth, income, segregation, and deprivation of resources and services. We developed the GeoSES using Principal Component Analysis and evaluated its construct, content, and applicability. GeoSES is defined at three scales: national (GeoSES-BR), Federative Unit (GeoSES-FU), and intra-municipal (GeoSES-IM). GeoSES-BR dimensions showed a good association with HDI-M (correlation above 0.85). The model with the poverty dimension best explained the relative risk of avoidable cause mortality in Brazil. In the intra-municipal scale, the model with GeoSES-IM was the one that best explained the relative risk of mortality from circulatory system diseases. By applying spatial regressions, we demonstrated that GeoSES shows significant explanatory potential in the studied scales, being a compelling complement for future researches in public health.
Ripening and quality responses of avocado, custard apple, mango and papaya fruit to 1-methylcyclopropene

The potential for the ethylene binding inhibitor, 1-methylcyclopropene, to delay ripening of 'Hass' avocado, 'African Pride' custard apple, 'Kensington Pride' mango and 'Solo' papaya was examined. Fruit were gassed with 25 muL/L 1-methylcyclopropene for 14 h at 20 degreesC, followed by treatment with 100 muL/L ethylene for 24 h, and then ripened at 20 degreesC. Ethylene treatment alone generally halved the number of days for fruit to reach the ripe stage, compared with untreated fruit. 1-Methylcyclopropene treatment alone increased the number of days to ripening by 4.4 days (40% increase), 3.4 days (58%), 5.1 days (37%) and 15.6 days (325%) for avocado, custard apple, mango and papaya, respectively, compared with untreated fruit. Applying 1-methylcyclopropene to the fruit before ethylene prevented the accelerated ripening normally associated with ethylene treatment, so that the number of days to ripening for fruit treated with 1-methylcyclopropene plus ethylene was similar to the number of days to ripening for fruit treated with 1-methylcyclopropene alone. 1-Methylcyclopropene treatment was associated with slightly higher severity of external blemishes in papaya and custard apple, slightly higher rots severity in avocado, custard apple and papaya, and at least double the severity of stem rots in mango, relative to fruit not treated with 1-methylcyclopropene. Thus, 1-methylcyclopropene treatment has the potential to reduce the risk of premature ripening of avocado, custard apple, mango and papaya fruit due to accidental exposure to ethylene. However, additional precautions may be necessary to reduce disease severity associated with 1-methylcyclopropene treatment.
Steroidogenesis in the NCI-H295 Cell Line Model is Strongly Affected By Culture Conditions and Substrain

Abstract Context NCI-H295 cells are the most widely used model for adrenal steroidogenesis and adrenocortical carcinoma and have been used for decades in laboratories worldwide. However, reported steroidogenic properties differ considerably. Objective To evaluate heterogeneity of steroidogenesis among NCI-H295 cell strains, clarify the influence of culture media and test response to inhibitors of steroidogenesis by using liquid chromatography tandem mass spectrometry (LC-MS/MS). Methods NCI-H295 cells were obtained from two cell banks and cultivated in different media. An LC-MS/MS-based panel analysis of thirteen steroids was adapted for cell culture supernatant. Cells were treated with metyrapone, abiraterone and mitotane. Results Mineralocorticoid synthesis was strongly affected by passaging as reflected by reduction of aldosterone secretion from 0.158±0.006 to 0.017±0.001 µg/106 cells (p<0.05). Relevant differences were also found for cells from two vendors in terms of aldosterone secretion (0.180±0.001 vs. 0.09±0.002 µg/106 cells, p<0.05). Selection of medium strongly impacted on cortisol secretion with>4-fold difference (40.6±5.5 vs. 182.1±23 µg/106 cells) and reflected differential activation of the glucocorticoid pathway. Exposure to abiraterone, metyrapone and mitotane resulted in characteristic steroidogenic profiles consistent with known mechanism of drug action with considerable differences in metabolites upstream of the blocked enzyme. Conclusion We demonstrate that steroid hormone secretion in NCI-H295 cells is strongly affected by the individual strain, passage and growing conditions. These factors should be taken into account in the evaluation of experiments analyzing steroid parameters directly or as surrogate parameters of cell viability.
Practice advisory update summary: Patent foramen ovale and secondary stroke prevention

Objective To update the 2016 American Academy of Neurology (AAN) practice advisory for patients with stroke and patent foramen ovale (PFO). Methods The guideline panel followed the AAN 2017 guideline development process to systematically review studies published through December 2017 and formulate recommendations. Major recommendations In patients being considered for PFO closure, clinicians should ensure that an appropriately thorough evaluation has been performed to rule out alternative mechanisms of stroke (level B). In patients with a higher risk alternative mechanism of stroke identified, clinicians should not routinely recommend PFO closure (level B). Clinicians should counsel patients that having a PFO is common; that it occurs in about 1 in 4 adults in the general population; that it is difficult to determine with certainty whether their PFO caused their stroke; and that PFO closure probably reduces recurrent stroke risk in select patients (level B). In patients younger than 60 years with a PFO and embolic-appearing infarct and no other mechanism of stroke identified, clinicians may recommend closure following a discussion of potential benefits (absolute recurrent stroke risk reduction of 3.4% at 5 years) and risks (periprocedural complication rate of 3.9% and increased absolute rate of non-periprocedural atrial fibrillation of 0.33% per year) (level C). In patients who opt to receive medical therapy alone without PFO closure, clinicians may recommend an antiplatelet medication such as aspirin or anticoagulation (level C).
Implementation of marker-assisted selection in French dairy cattle.

INTRODUCTION In the last decade, advances in molecular genetics have made it possible to dissect the genetic variability of complex traits into quantitative trait loci (QTL). In dairy cattle, several large QTL detection experiments have been carried all over the world after the pioneering work of Georges et al (1995). Most of them were based on a granddaughter design (Weller et al, 1990) a powerful design exploiting the population structure and the recording systems existing in large dairy breeds. The French granddaughter design included 1554 artificial insemination (AI) bulls distributed into 14 half-sib families, genotyped for 169 markers and evaluated for 24 traits (Boichard et al, 2002). It provided strong evidence for many QTL affecting important traits. Even if the genes involved are still unknown, individual QTL information could enhance selection efficiency. Marker-assisted selection (MAS) is particularly beneficial when the trait is difficult or expensive to measure, when each individual performance brings little information, or, more generally, when the polygenic approach have limited efficiency or a high cost. Therefore, it is believed that MAS could be particularly profitable in dairy cattle. Indeed, this species concentrates many conditions unfavourable to classical selection and, therefore, favourable to MAS: most traits of interest are sex-limited; generation interval is long; bulls should be progeny tested, which is a long and costly step; bull dams are more and more selected before their first lactation on pedigree information only, in order to reduce generation interval; finally, functional traits, such as disease resistance or fertility, have a low heritability but are more and more important in the breeding goal. This paper presents the main characteristics of the marker-assisted selection implemented in France in 2000 by INRA, LABOGENA and UNCEIA for eight breeding companies operating in the three main French dairy cattle breeds (Holstein, Normande, and Montbéliarde).
CC-Chemokine Receptor 6 Is Expressed on Diverse Memory Subsets of T Cells and Determines Responsiveness to Macrophage Inflammatory Protein 3α

CC-chemokine receptor (CCR) 6 is the only known receptor for macrophage inflammatory protein (MIP)-3α, a CC chemokine chemotactic for lymphocytes and dendritic cells. Using anti-serum that we raised against the N-terminal residues of CCR6, we have characterized the surface expression of CCR6 on peripheral blood leukocytes and we have correlated CCR6 expression with responses to MIP-3α. We found that CCR6 was expressed only on memory T cells, including most α4β7 memory cells and cutaneous lymphocyte-associated Ag-expressing cells, and on B cells. Accordingly, chemotaxis of T cells to MIP-3α was limited to memory cells. Moreover, calcium signals on T cells in response to MIP-3α were confined to CCR6-expressing cells, consistent with CCR6 being the only MIP-3α receptor on peripheral blood T cells. Unlike many CC chemokines, MIP-3α produced a calcium signal on freshly isolated T cells, and CCR6 expression was not increased by up to 5 days of treatment with IL-2 or by cross-linking CD3. Despite their surface expression of CCR6, freshly isolated B cells did not respond to MIP-3α. In addition to staining peripheral blood leukocytes, our anti-serum detected CCR6 on CD34+ bone marrow cell-derived dendritic cells. Our data are the first to analyze surface expression of CCR6, demonstrating receptor expression on differentiated, resting memory T cells, indicating differences in receptor signaling on T cells and B cells and suggesting that CCR6 and MIP-3α may play a role in the physiology of resting memory T cells and in the interactions of memory T cells, B cells, and dendritic cells.
PLK2 modulation of enriched TAp73 affects osteogenic differentiation and prognosis in human osteosarcoma

There are three subtypes of undifferentiated human conventional osteosarcoma (HCOS): osteoblastic osteosarcoma (OOS), chondroblastic osteosarcoma (COS), and fibroblastic osteosarcoma (FOS). HCOS also exhibits heterogeneous pathological maldifferentiation in individual patients. Currently, the mechanism regulating HCOS differentiation remains unclear, and therapies are ineffective. Osteopontin (OPN) and osteocalcin (OCN) are markers of osteoblast maturation, and their expression is inhibited in HCOS. A previous study found that PLK2 inhibited TAp73 phosphorylation and consequent anti‐OS function of TAp73 in OS cells with enriched TAp73. TAp73 was also reported to regulate bone cell calcification. Here, OOS was found to have higher TAp73 levels and PLK2 expression than those in COS, which is correlated with HCOS maldifferentiation according to Spearman analysis and affects patient prognosis according to Kaplan‐Meier survival analysis. In the conventional OS cell‐line Saos2 and in patient‐derived xenograft OS (PDX‐OS) cells, increased PLK2 expression owing to abundant TAp73 levels affected OPN and OCN content as measured by RT‐PCR and Western blotting, and alizarin red staining showed that PLK2 affected calcium deposition in OS cells. In addition, PLK2 inhibition in PDX‐OS cells prohibited clone formation, as indicated by a clonogenic assay, and sensitized OS cells to cisplatin (CDDP) (which consequently limited proliferation), as shown by the CCK‐8 assay. In an established PDX animal model with abundant TAp73 levels, PLK2 inhibition or CDDP treatment prevented tumor growth and prolonged median survival. The combined therapeutic effect of PLK2 inhibition with CDDP treatment was better than that of either monotherapy. These results indicate that increased PLK2 levels due to enriched TAp73 affect osteogenic differentiation and maturation and OS prognosis. In conclusion, PLK2 is a potential target for differentiation therapy of OS with enriched TAp73.
Advances in Extrusion 3D Bioprinting: A Focus on Multicomponent Hydrogel‐Based Bioinks

3D bioprinting involves the combination of 3D printing technologies with cells, growth factors and biomaterials, and has been considered as one of the most advanced tools for tissue engineering and regenerative medicine (TERM). However, despite multiple breakthroughs, it is evident that numerous challenges need to be overcome before 3D bioprinting will eventually become a clinical solution for a variety of TERM applications. To produce a 3D structure that is biologically functional, cell‐laden bioinks must be optimized to meet certain key characteristics including rheological properties, physico‐mechanical properties, and biofunctionality; a difficult task for a single component bioink especially for extrusion based bioprinting. As such, more recent research has been centred on multicomponent bioinks consisting of a combination of two or more biomaterials to improve printability, shape fidelity and biofunctionality. In this article, multicomponent hydrogel‐based bioink systems are systemically reviewed based on the inherent nature of the bioink (natural or synthetic hydrogels), including the most current examples demonstrating properties and advances in application of multicomponent bioinks, specifically for extrusion based 3D bioprinting. This review article will assist researchers in the field in identifying the most suitable bioink based on their requirements, as well as pinpointing current unmet challenges in the field.
Effect of Dietary Microalgae on Growth Performance, Profiles of Amino and Fatty Acids, Antioxidant Status, and Meat Quality of Broiler Chickens

Simple Summary The use of feed additives with no side effectsfor enhancing growth performance and improving meat quality in broilers chickens is an essential research topic. In these regards, this study aimed to evaluate the impact of three species of microalgae namely Chlorella vulgaris (CV), Spirulina platensis (SP) and Amphora coffeaformis (AC) on growth performance, profiles of fatty and amino acids, antioxidant status and meat quality of breast muscles. The results demonstrated that the inclusion of studied microalgae notably AC has a positive effect on performance, antioxidant status and meat quality of breast muscle in broiler chickens. Abstract The study used 96 broiler chickens to evaluate the impact of three species of microalgae on performance, profiles of fatty and amino acids, antioxidants, and meat quality of breast muscles. Birds were divided into four groups (24 birds/each) with 4 replicates (6 birds each). Birds in the first group were fed basal diet and served as a control (C). Birds of 2–4 groups were fed basal diet mixed with same dose (1 g/kg diet) of Chlorella vulgaris (CV), Spirulina platensis (SP), and Amphora coffeaformis (AC). At the age of 36 days, performance parameters were reported, and breast muscle samples were collected and stored frozen at −80 °C. AC shared CV in the superiority of increasing final body weight and body weight gain compared to SP and control. AC shared SP in the superiority of increasing the level of essential fatty and amino acids and decreasing the microbial growth in breast muscle compared to CV and control. All studied microalgae reduced malondialdehyde (MDA) and protein carbonyl (PC) levels, cooking loss, and aerobic plate count (APC) and increased the superoxide dismutase (SOD) activities in breast muscle compared to control. The current study indicated that studied microalgae, notably AC, can be used to enhance performance and meat quality in broilers chickens.
From Vitamin C to Metabolite Repair: The Role of Novel Sugar Nucleotide Phosphorylases

Author(s): Adler, Lital Noah | Advisor(s): Clarke, Steven G | Abstract: The pcm-1 gene in the soil nematode Caenorhabditis elegans that encodes the L- isoaspartyl methyltransferase has roles in protein repair as well as in the worm's insulin-like signaling pathway. Interestingly, the pcm-1 gene displays overlapping exon sequences with a previously undescribed gene (mcp-1, C10F3.4) that is transcribed from the opposite strand. This rare topology in the C. elegans genome (less than 0.05% of all genes) led us to ask whether the expression of the pcm-1 and mcp-1 genes may be co-regulated or whether their products may have a related function. PSI-BLAST analyses revealed that MCP-1 has homologs in plants, vertebrates and invertebrates and that all the homologs share a conserved HIT (histidine triad) motif. Mutations in the Arabidopsis thaliana homolog, vtc2, lead to vitamin C deficiency in these plants. In this thesis, I have characterized the enzymatic activity of VTC2 from A. thaliana as a GDP-L-galactose phosphorylase, the last missing step in the Smirnoff-Wheeler pathway for vitamin C biosynthesis in plants. Additional work has been done to show that the green alga Chlamydomonas reinhardtii shares homologs with all of the genes in the Smirnoff-Wheeler pathway as well as the specific activity of GDP-L-galactose phosphorylase.While vitamin C is an apparent important antioxidant and enzymatic cofactor in C. elegans, no reports had been made as to the ability of this nematode to produce it. In my work I found out that C. elegans extracts contain low levels of vitamin C. Nevertheless, as levels of vitamin C in the mcp-1 deletion strain are not different from the values in the control animals and as C. elegans lack key homologs in the biosynthesis pathway, I concluded that mcp-1 was not involved in vitamin C synthesis in C. elegans.Enzymatic analysis revealed that C. elegans ’ mcp-1 and its mammalian homologs encode GDP-D-glucose phosphorylases. mcp-1 mutant worms that lacked this activity accumulated GDP-D-glucose. This unique metabolite, which shares high similarity with GDP-D-mannose, does not have a reported role in invertebrates or mammals. With my collaborators, I suggested that GDP-D-glucose could compete with GDP-D-mannose for binding to glycosyltransferases in the first steps of protein N-glycosylation in the cell, thus potentially replacing mannose residues with glucose residues in a step that could lead to N-glycosylation defect. Thus, MCP-1 may serve as a metabolite repair enzyme that eliminates adventitiously formed GDP-D-glucose from the cytosol to ensure correct protein N-glycosylation. I have tested this hypothesis by observing morphological changes in mcp-1 mutant worms and by directly comparing the N-glycan profiles of mcp-1 and control animals.