Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic plasticity of corn leaf aphid Rhopalosiphum maidis under elevated temperature and CO2

In the current context of global climate change, the world average temperature and carbon dioxide (CO2) concentration in the atmosphere has steadily increased. Climate change is also predicted to increase the frequency and magnitude of extreme heat events, which will involve great challenges for most of the ectotherm organisms, such as aphids. As a worldwide pest insect, corn leaf aphid, Rhopalosiphum maidis caused significant damage on cereal crops such as barley, corn, and wheat. R. maidis is also a vector of plant viruses including sugarcane mosaic virus, maize dwarf mosaic virus, which result in economic losses. Similar to all ectotherms, aphids have acute sensory capability for detecting temperature variations. Their small size and high mass-specific metabolic rates makes them sensitive to energy and water balance during exposure to extremes. In this study, thermal tolerance of R. maidis under extreme high temperatures across differential life stages were tested. The critical high temperature (CHT) of R. maidis was between 39.0 to 40.0 °C according kinds of feeding treatments. The upper lethal temperatures (ULTs) of R. maidis were significantly different between feeding and no feeding treatments. In addition, the ULTs varied significantly across life stages with highest ULTs values for 4 instars. Feeding significantly increased the thermal tolerance of aphids. R. maidis exhibit wing polyphenism in response to poor habitat quality. Polyphenism is an important form of adaptation in an adverse environment. Five developmental stages of aphids with increased population densities were investigated under two kinds of temperature patterns. Crowding was found to directly impact winged induction. The 1 and 2 nymphs were more sensitive for alate morphs induction under high density. In addition, temperature played a significant role in wing production, with the 26/39 °C temperature setting inducing higher alate morphs and survival. The increase in concentrations of CO2 not only affects plant growth and development, but also impacts the emission of plant organic volatile compounds. During the dual choice bioassays, the winged and wingless aphids were more attracted by the VOCs of barley seedlings cultivated under ambient CO2 concentrations (aCO2; 450ppm) than barley seedlings cultivated under elevated CO2 concentrations (eCO2; 800ppm), nymphs were not attracted by the VOCs of eCO2 barley seedlings. While 16 VOCs were identified from aCO2 barley seedlings, only 9 VOCs were found from eCO2 barley seedlings. The effect of elevated CO2 on feeding behavior of R. maidis on barley seedlings was tracked using electrical penetration graph (EPG). The nutrient content of host plant and the developmental indexes of aphids under eCO2 and aCO2 conditions were examined. Barley seedlings under eCO2 concentrations had lower contents of crude
StrictCheck: a Tool for Testing Whether a Function is Unnecessarily Strict

In a non-strict functional programming language functions that yield the same result for all total arguments can still differ for partial arguments, that is, they differ in their strictness. Here a tool for Haskell is presented that enables the programmer to easily check whether a given function is least-strict; if it is not least-strict, then the tool suggests how to make it less strict.
Estrogen mediates acute elastic fibre homeostasis in skin

Remodelling of the dermal extracellular matrix makes a major contribution to skin fragility in the elderly. The peri-menopausal period in females is also associated with an age-like phenotype which can be reversed by hormone replacement therapy. This suggests a direct link between circulating hormone levels and tissue ageing. Despite work investigating the role of estrogen as a regulator of collagen fibril abundance and structure, the influence of estrogen on the elastic fibre system remains poorly defined. Here we used an ovariectomised (Ovx) mouse surgical menopause model to show that just 7 weeks of acute hormone deficiency significantly decreased skin tensile strength and elasticity. Systemic replacement of 17β-estradiol to physiological levels protected against these changes to the skin mechanical properties. Moreover, acute hormone deficiency differentially influenced dermal structural networks, significantly decreasing dermal elastic fibre abundance without discernible effect on collagen fibril organisation or abundance. We suggest that this specific elastic fibre proteolysis may be driven by extracellular protease activity, or be a consequence of significant adipocyte hypertrophy. 17β-estradiol supplementation in Ovx mice in vivo protected the elastic fibre system. Treatment of human dermal fibroblasts with 17β-estradiol in vitro induced the selective upregulation of tropoelastin, fibrillin-1 and associated elastic fibre-associated proteins (including EMILINs and fibulins). In summary, these data show that the elastic fibre system is significantly perturbed by estrogen deprivation. Thus, pharmacological intervention may slow the acute effects of menopause and potentially the chronic effects of ageing in skin.
Long Term Safety and Efficacy of Etanercept in Juvenile Idiopathic Arthritis in a Single Center

Received:March 4, 2019, Revised:May 17, 2019, Accepted:June 3, 2019 Corresponding to:Kwang Nam Kim http://orcid.org/0000-0003-4024-5128 Department of Pediatrics, Hallym University Sacred Heart Hospital, 22 Gwanpyeong-ro 170beon-gil, Dongan-gu, Anyang 14068, Korea. E-mail:kwangnamkim@naver.com Copyright c 2019 by The Korean College of Rheumatology. All rights reserved. This is an Open Access article, which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. Original Article pISSN: 2093-940X, eISSN: 2233-4718 Journal of Rheumatic Diseases Vol. 26, No. 3, July, 2019 https://doi.org/10.4078/jrd.2019. 26.3. 200
Realidade e desafios de infecções emergentes por Rhodotorula spp. em pacientes hospitalizados

Rhodotorula spp. is an emerging yeast responsible for causing opportunistic infections in humans. It currently appears as an etiological agent in septicemia, onychomycosis, meningitis, ventriculitis, pneumonia, peritonitis and endophthalmitis. In the hospital scenario, this fungus is responsible for 2% of the cases of fungemia according to several epidemiological studies. It is estimated that in cases with more severe complications mortality is 15%. This study aims to know the epidemiological, clinical and therapeutic profile of infections caused by Rhodotorula spp. in the hospital environment. A bibliographic review of scientific articles and case reports published between the years 2008 and 2018 was prepared from three databases: Latin American and Caribbean Literature in Health Sciences (Lilacs), Medical Literature Analysis and Retrieve System Online (Medline) and Sientific Eletronic Library Online (Scielo). It can be verified in the analysis of the cases that the patients affected by Rhodotorula spp. are preferably immunocompromised adults over 40 years of age and carriers of chronic diseases or invasive devices. Reports of these infections are more concentrated in the Asian and European continents. The pathogenic species prevalent in humans were Rhodotorula mucilaginosa in cases of invasive infections and Rhodotorula glutinis as the cause of superficial infections. In Brazil cases are concentrated more in the Southeast and South regions. The laboratory diagnosis is based on conventional methods of identification such as blood cultures and biochemical tests. Molecular techniques serve as a complement for species confirmation, but because of their high cost they are not used routinely. The most commonly used antifungal was amphotericin B Liposomal for an average of two weeks. In general, 80% of the patients had a good prognosis without recurrence after adequate antifungal therapy. The rapid isolation of this yeast and the knowledge of its susceptibility profile are fundamental for the favorable clinical outcome. Identify the origin of the infection and promote preventive actions in hospital settings in order to control infections caused by Rhodotorula spp. is challenging for both researchers and health professionals.
Exosomes in the Repair of Bone Defects: Next-Generation Therapeutic Tools for the Treatment of Nonunion

Nonunion with bone defects, a common complication after long bone fracture, is a major challenge for orthopaedic surgeons worldwide because of the high incidence rate and difficulties in achieving successful treatment. Bone defects are the main complications of nonunion. The conventional biological treatments for nonunion with bone defects involve the use of autologous bone grafts or bone graft substitutes and cell-based therapy. Traditional nonunion treatments have always been associated with safety issues and various other complications. Bone grafts have limited autologous cancellous bone and there is a risk of infection. Additionally, problems with bone graft substitutes, including rejection and stimulation of bone formation, have been noted, and the health of the stem cell niche is a major consideration in cell-based therapy. In recent years, researchers have found that exosomes can be used to deliver functional RNA and mediate cell-to-cell communication, suggesting that exosomes may repair bone defects by regulating cells and cytokines involved in bone metabolism. In this review, we highlight the possible relationships between risk factors for nonunion and exosomes. Additionally, we discuss the roles of exosomes in bone metabolism and bone regeneration.
Comparative Analysis of Phytochemicals Screening, Proximate and Elemental Analysis of Anacardium occidentale L. Nuts and Carica papaya Seeds

Aims: The aim of this study was comparative analysis of phytochemicals screening, proximate and elemental analysis of Anacardium occidentale L nut and Carica papaya seeds extracts. Study Design: The samples were cleaned, washed with water, dried, and grinded with a laboratory mortar and pestle, packed in an air tight container and stored ready for further analysis. Place and Duration of Study: The research was conducted at the Chevron Biotechnology Centre, Modibbo Adamawa University of Yola, Nigeria which lasted for about three months. Methodology: The nuts were manually separated from fruit pulp, cleaned, washed with water, dried, roasted and grinded with a laboratory mortar and pestle, packed in an air tight container and stored ready for further analysis. Results: The result of Anacardium occidentale L nut phytochemicals screening showed that with Glycosides (-), Tannins (+), flavonoids(+++), Alkaloids(++), Saponins(-) and the proximate composition (%) were as follows: moisture content (9.7 ± 0.2), ash content (3.46±0.3), crude fat (26.79± 0.5), crude protein (14.26 ± 0.01) carbohydrate (by difference) (45.78± 0.01) Calorific (Energy) value 482.00 Kcal. The mineral analysis (mg/100g) revealed that magnesium (3.50 ± 0.01), Manganese (2.00 ± 0.01), Nickel (3.22 ± 0.01) and Cobalt (0.13 ±0.01) while the phytochemical screening for Carica papaya seeds extracts also showed Glycosides (+), Tannins (++), flavonoids(++), Alkaloids(++), Saponins(-) for the moisture content (8.59 ± 0.3), ash content (4.09±0.16), crude fat (15.60± 0.2), crude protein (15.84 ± 0.01) carbohydrate (by difference) (41.63) Calorific (Energy) value 1549.25 Kcal. The mineral analysis (mg/100g) revealed that magnesium (3.02 ± 0.02), Manganese (0.22 ± 0.01), Nickel (3.41 ± 0.01) and Cobalt (0.18 ± 0.01). Conclusion: The study therefore indicates that the Anacardium occidentale L nut and Carica may not provide all the nutrients required by human in the right proportion though it contains an appreciable quantity of some essential nutrients like Fats, Proteins, Carbohydrate and some minerals.
KUZULARA KURU OTA İLAVE OLARAK VERİLEN KONSANTRE YEMİN BESİ PERFORMANSI VE BAZI RUMEN PARAMETRELERİNE ETKİSİ

Bu arastirmada, kuzulari yalniz kuru ot ve kuru ota ilave olarak farkli miktarda konsantre yem ile beslemenin yem tuketimi, canli agirlik, yemden yararlanma orani ile rumen sivisi pH, TUYA ve NH3-N degerleri uzerine etkisi arastirilmistir. Deneme, yalniz kuru ot tuketen grup (Kontrol) ve kuru ota 150 g (Grup 1) ile 300 g (Grup 2) konsantre yem ilave edilen gruplar olmak uzere toplam uc grup halinde 50 gun sureyle yurutulmustur. Arastirma sonunda Kontrol, Grup 1 ve Grup 2’ deki kuzular, gunluk olarak 904, 974 ve 1052 g yem tuketmis olup 31.7, 33.0 ve 36.6 kg canli agirliga ulasmistir. Gunluk canli agirlik artisi deneme sonu itibariyla gruplarda 118, 144 ve 215.3 g olarak belirlenmistir. Gruplarda toplam yem tuketimi konsantre yem ilavesi yapildikca artmis, ancak kuru ot tuketimi azalmistir. Konsantre yem ilavesi yemden yararlanma oraninin iyilestirmistir. Denemede ozellikle kuru ota ilave olarak verilen gunluk 300 g konsantre yem, canli agirlik ve gunluk canli agirlik artisi bakimindan diger gruplardan onemli farklilik gostermistir (P<0.05). Kuru ota ilave olarak konsantre yem verilmesi, hayvanlardan alinan rumen sivisi pH degerini azaltmistir. Rumen sivisi TUYA, NH3-N degerleri ise rasyona katilan konsantre yem miktarina gore artis gostermistir. Bu artis 300 g konsantre yem saplementasyonu yapilan grupta onemli duzeye ulasmistir (P<0.05). Sonuc olarak, kuru ota ilave olarak 150 ve 300 g konsantre yem verilmesi hayvanlarin besi performansi ve rumen parametreleri uzerine olumlu etkiler yapmistir. Ozellikle 300 g konsantre yem verilmesi gunluk canli agirlik artisi ile rumen amonyak azotunda daha fazla artisa neden olmustur.
Effect of chitosan coating on the shelf life of ready-to-eat bovine meatballs and the control of Listeria monocytogenes growth on their surface during refrigeration storage

Edible chitosan coating on the surface of ready-to-eat (RTE) bovine meatballs was evaluated for its effect on their shelf life and the control of Listeria monocytogenes at 5 °C. L. monocytogenes was inoculated onto the surface of RTE bovine meatballs with and without edible chitosan coating. The samples were stored at 5 °C. Total aerobic viable count (TVC) and the bacterial counts of L. monocytogenes, lactic acid bacteria and Enterobacteriaceae were determined on days 0,1,7,14,21 and 28. The sensory characteristics were also evaluated at the same time spots by semi trained panelists. The results of the microbiological analysis depicted that the use of edible chitosan membranes reduced all of the microbial populations that were enumerated, and retarded their growth leading to the conclusion that they can prolong the shelf life of these products by 14 days. Moreover, the population of the inoculated L. monocytogenes was about 2 log CFU/g lower in the meatballs coated with chitosan, indicating an inhibitory effect of chitosan in the growth of L. monocytogenes. The sensory analysis showed that the samples coated with chitosan were satisfactorily accepted by the panelists even at day 28, in contrast to the samples without chitosan (control samples) which were unacceptable at day 14. These results indicate that edible chitosan coatings represent a potential agent in controlling L. monocytogenes on the surface of RTE meatballs as well as other RTE meat products, prolonging their shelf life without affecting their sensory characteristics.
Higher quality de novo genome assemblies from degraded museum specimens: a linked-read approach to museomics

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historic specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges. Linked-read or ‘synthetic long-read’ sequencing technologies, such as 10X Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded specimens. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four published genomes assembled from a single shotgun library and four deer mouse (Peromyscus spp.) genomes assembled using 10X Genomics technology. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher quality, measured by larger N50 values and greater gene content. Although not without caveats, our results suggest that linked-read sequencing technologies may represent a viable option to build de novo genomes from historic museum specimens, which may prove particularly valuable for extinct, rare, or difficult to collect taxa.
F factor plasmid-mediated Epstein-Barr virus genome introduction establishes an EBV positive NPC cell model

Background Most Epstein-Barr virus (EBV)-positive cells lose the EBV episomes upon prolonged propagation. Purpose The purposes of this study were to establish a simple cell model for nasopharyngeal carcinoma (NPC) research by introducing a plasmid with the EBV genome into NPC cells and then to investigate the resulting changes in malignant biological behaviour and NPC-associated signalling pathways. Methods HONE1 NPC cells were transfected with F-factor plasmids including the EBV genome (HONE1-EBV cells). Then cell proliferation, migration, cell cycle distribution and apoptosis were evaluated in vitro by using CCK8, transwell and flow cytometry assays respectively. EBV-encoded proteins and cell signal tranducting proteins were detected by western blot assays. EBV-encoded RNAs were detected by in situ hybridization. EBV particles were assayed by transmission electron microscope (TEM). The morphology of cells were detected by immunofluorescence assays for alpha-tubulin. Results Latent membrane protein 1 (LMP1), latent membrane protein 2A (LMP2A), Epstein-Barr nuclear antigen 1 (EBNA1) and EBV-encoded small RNAs (EBERs) were successfully expressed in HONE1-EBV cells. No EBV particles were founded by TEM. Introduction of the EBV genome significantly promoted proliferation, cell cycle progression and migration and inhibited apoptosis in HONE1 cells. Immunofluorescence assays showed that the morphology of HONE1-EBV cells changed into spindle. Furthermore, EBV genome introduction significantly inhibited the JAK/STAT signalling pathway, while it activated the PI3K-AKT and NF-κB signalling pathways in HONE1 cells. Conclusion These findings suggest that F-factor plasmid-mediated EBV genome introduction was successful in constructing an EBV positive cell model, which showed deteriorated biological behavior and activated NPC-associated signalling pathways. This model can serve as a good tool for studying EBV in NPC, but the subtle differences in cancer-associated pathways must be considered.
Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed

Oat ranks sixth in world cereal production and has a higher content of health-promoting compounds compared to other cereals. However, there is neither a robust oat reference genome nor transcriptome. Using deeply sequenced full-length mRNA libraries of oat cultivar Ogle-C, a de novo high-quality and comprehensive oat seed transcriptome was assembled. With this reference transcriptome and QuantSeq 3’ mRNA sequencing, gene expression was quantified during seed development from 22 diverse lines across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes, we identified 22 major temporal co-expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered, and termed genetic co-expression (GCoE) sets. 17 of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non-permutation analyses. Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p-values than permutation analysis. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. This study expands our understanding of physiological processes that occur during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.
Isocitrate Lyase and Succinate Semialdehyde Dehydrogenase Mediate the Synthesis of α-Ketoglutarate in Pseudomonas fluorescens

Glycerol is an important by-product of the biodiesel industry and its transformation into value-added products like keto acids is being actively pursued in order to improve the efficacy of this renewable energy sector. Here, we report that the enhanced production of α-ketoglutarate (KG) effected by Pseudomonas fluorescens in a mineral medium supplemented with manganese (Mn) is propelled by the increased activities of succinate semialdehyde dehydrogenase (SSADH), γ-aminobutyric acid aminotransaminase (GABAT), and isocitrate lyase (ICL). The latter generates glyoxylate and succinate two key metabolites involved in this process. Fumarate reductase (FRD) also aids in augmenting the pool of succinate, a precursor of succinate semialdehyde (SSA). The latter is then carboxylated to KG with the assistance of α-ketoglutarate decarboxylase (KDC). These enzymes work in tandem to ensure copious secretion of the keto acid. When incubated with glycerol in the presence of bicarbonate (HCO3−), cell-free extracts readily produce KG with a metabolite fingerprint attributed to glutamate, γ-aminobutyric acid (GABA), succinate and succinate semialdehyde. Further targeted metabolomic and functional proteomic studies with high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and gel electrophoresis techniques provided molecular insights into this KG-generating machinery. Real-time quantitative polymerase chain reaction (RT-qPCR) analyses revealed the transcripts responsible for ICL and SSADH were elevated in the Mn-supplemented cultures. This hitherto unreported metabolic network where ICL and SSADH orchestrate the enhanced production of KG from glycerol, provides an elegant means of converting an industrial waste into a keto acid with wide-ranging application in the medical, cosmetic, and chemical sectors.
Epidemiology of Carbapenemase-Producing Klebsiella pneumoniae in a Hospital, Portugal

We aimed to provide updated epidemiologic data on carbapenem-resistant Klebsiella pneumoniae in Portugal by characterizing all isolates (N = 46) recovered during 2013–2018 in a 123-bed hospital in Lisbon. We identified blaKPC-3 (n = 36), blaOXA-181 (n = 9), and blaGES-5 (n = 8) carbapenemase genes and observed co-occurrence of blaKPC-3 and blaGES-5 in 7 isolates. A single GES-5–producing isolate co-produced the extended-spectrum β-lactamase BEL-1; both corresponding genes were co-located on the same ColE1-like plasmid. The blaOXA-181 gene was always located on an IncX3 plasmid, whereas blaKPC-3 was carried on IncN, IncFII, IncFIB, and IncFIIA plasmid types. The 46 isolates were distributed into 13 pulsotypes and 9 sequence types. All isolates remained susceptible to ceftazidime/avibactam, but some exhibited reduced antimicrobial susceptibility (MIC = 3 mg/L).