Miracle-dz/UniFAR-FTUs huggingface dataset:
Identificación in silico y detección de microRNAs de Taenia solium

Neurocysticercosis (NCC) is a neurological disease caused by the infection in the brain with larvae of Taenia solium. This disease is endemic in developing countries, and in Peru there are regions where 40% of late onset acquired epilepsy are associated with NCC. Clinical manifestations depend on the number of cysts, their location within the brain, and the associated immune response, which is modulated by the parasite through mechanisms that are not very well understood. In the last decade there has been research on how miRNAs from parasites could affect the cellular functions of their hosts. MiRNAs are non-coding ssRNA molecules, about 22 nt long. They are a very important mechanism for post-transcriptional regulation of genetic expression. Additionally, since they have a higher resistance to nucleases than mRNAs, circulating miRNAs are an interesting target for diagnosis and treatment, which are being evaluated in other diseases, including infections by other helminths. In this work, miRNAs expressed by T. solium were sought using an approach based on sequence similarity search, performing a BLAST search on the T. solium genome of pre-miRNAs previously reported in the open access database miRBase; and a structural analysis, using the RNAfold tool to determine the most probable secondary structure of the sequences found through BLAST, and their minimal free energy (MFE) value. 39 pre-miRNA candidates were found in the T. solium genome, homologous to pre-miRNAs previously found in other species. Aditionally, we worked with a collaborator from the Laboratory of Bioinformatics of the Adam Mickiewicz University (Poznań, Polonia), who used on T. solium expressed sequences an algorithm created by his group to construct a new miRNA database, MiRNEST. Six new T. solium miRNA precursor candidates were determined. Their possible gene targets were predicted through the RNAhybrid tool, and we sought to detect three of the six newly predicted sequences in samples of different stages of the parasite life cycle using RT-qPCR. Two of these were detected, although their detection in other helminths showed they were not exclusive of T.solium. Further detection and characterization of T. solium miRNAs in tissue and blood serum of the human host is an important first step to explore the role of these molecules in the host-parasite interaction in NCC, their part in the infection pathology at a molecular level and their potential as diagnostic or treatment monitor tools.
Resource supply drives even spacing of individuals along multiple trait axes in light-limited phytoplankton populations

Individual-level variation arising from responses to environmental gradients influences population and community dynamics. How such responses empirically relate to the mechanisms that govern species coexistence is however not well understood. Previous results from lake phytoplankton communities suggested that the evenness of organisms in multidimensional trait space increases with resource limitation, possibly due to resource partitioning at the individual level. Here we experimentally tested the emergence of this pattern by growing two phytoplankton species (Pseudokirchneriella subcapitata, Microcystis aeruginosa) under a gradient of light intensity, in monoculture and jointly. Under low light (resource) conditions, the populations diversified into a wide range of phenotypes, which were evenly distributed in multidimensional trait space (defined by four pigment-related trait dimensions), confirming the observed field pattern. Our results provide prime experimental evidence that resource limitation induces even spacing of conspecific and heterospecific microbial phenotypes along trait axes, and advances our understanding of trait-based coexistence.
Land use and land cover dynamics in the dehesa of Sierra Morena Biosphere Reserve (Sierra Norte de Sevilla Natural Park, Spain), 1956-2007

The dehesa, a representative savanna-like ecosystem type, has played and plays an important economic, ecological and social role, in addition to the valuable environmental services that it provides. The present study is focused on the analysis of the changes in the land use /cover of the dehesa in the Sierra Norte de Sevilla Natural Park (Sierra Morena Biosphere Reserve) during the last 50 years. In order to estimate the consequences that the change of land uses and, the activities that are carried out on it have on the dynamics of the dehesa, a diachronic analysis was performed for the period 1956-2007 using the digital geographic information available. The most important changes observed were related to: i) the increase of urban areas, water surface area, reforestation areas, eroded areas, mining areas and dumping sites; and ii) the decrease of cultivation areas, dehesa, scrubland and pastureland. The changing dynamics did not strictly respond only to phytosociological aspects, but it is necessary to explain the evolution of the landscape from the complex balance between biophysical and socioeconomic dynamics, where the current environmental changes also make it very difficult to ensure the persistence of this ecosystem. The present legislation promotes the development of a clear and up-to-date diagnosis of the problems that this ecosystem is facing. In this sense, the geographic information systems may be very useful at establishing the guidelines for the conservation and regeneration of the dehesas, and at spreading their environmental values.
Novel Restriction of HIV-1 by Chimeric Human APOBEC3A

The human apolipoprotein B mRNA editing enzyme catalytic peptide-like 3 (APOBEC3; A3) family of proteins are a family of seven cytidine deaminases (A3A, A3B, A3C, A3D, A3F, A3G and A3H) that restrict certain viral infections. These innate defense factors are best known for their ability to restrict the replication of human immunodeficiency virus type 1 (HIV-1) lacking a functional Vif protein (HIV-1Δvif) through the deamination of cytidine residues to uridines during reverse transcription, ultimately leading to lethal G-to-A changes in the viral genome. The best studied of the A3 proteins has been A3G because of its potent activity against HIV-1Δvif. However, one member of this family, A3A, has biological properties that make it unique among the A3 proteins. Despite potent restriction activity when expressed in myeloid cells, human A3A (hA3A) is generally known lacking inhibitory function towards HIV-1Δvif. Previous studies in our laboratory have shown that rhesus macaque A3A (rhA3A) is capable of restricting both simian–human immunodeficiency virus lacking vif gene (SHIVΔvif) and human immunodeficiency virus lacking vif gene (HIV-1Δvif) to a greater extent than hA3A. Chimeric studies by substituting amino acids 25–33 (AC loop 1 region) from rhA3A into hA3A showed that this region is critical in determining the restriction pattern against lentiviruses. Further studies identified three Old World Monkey A3As that were able to restrict HIV-1 replication. Restriction assays with various A3As from hominids, New World monkeys, and Old World monkeys found that agmA3A and colA3A restricted the replication of SHIVΔvif and that all three Old World monkey A3A proteins (agmA3A, colA3A, and rhA3A) restricted HIV-1Δvif to some extent. More impressively, it is also showed that the A3A protein from the black and white colobus monkey (mantled guereza; Colobus guereza; colA3A) potently inhibited
The Food Entrainable Oscillator: The Ghrelin and Growth Hormone Secretagogue Story

Food availability is a potent external cue that can uncouple endogenous rhythmicity from the master circadian oscillator. It is driven by a largely unknown entity that encompasses a network of peripheral and central systems, the food entrainable oscillator (FEO). The orexigenic gut hormone ghrelin is associated with feeding, energy metabolism and has been proposed as an entrainment signal for the FEO. This thesis set out to manipulate the FEO through scheduled feeding paradigms while studying the influence of ghrelin on FEO outputs. Energy utilization patterns in response to a scheduled meal, as examined through indirect calorimetry, exhibited entrainment to the meal timing. We further demonstrated that restricted feeding paradigm entrained the energy utilization patterns, independently of the GHSR and circulating ghrelin. The influence of scheduled meals on the FEO was not limited to a negative energy balance, freely fed CD-1 male mice exhibited food anticipatory activity (FAA) and entrained to a scheduled snack of cookie dough during their non-active phase. Intriguingly, the development and entrainment of FAA is dependent on both the type of scheduled snack and the strain of the animal model used. Circulating ghrelin levels were not necessary in the development or maintenance of the entrainment of the FAA. However, central signaling of ghrelin, through its growth hormone secretagogue receptor (GHSR) may have a role in the development of the FAA in paradigms of a scheduled treats. Taken together these data present evidence that ghrelin and the GHSR are not critical in mediating the systems of the FEO and its respective outputs, under various feeding paradigms.
Morphological and histological description of small metoposaurids from Petrified Forest National Park, AZ, USA and the taxonomy of Apachesaurus

ABSTRACT Metoposaurids are Late Triassic temnospondyls that are abundant components of freshwater depositional settings. Although metoposaurids are represented by hundreds of specimens in collections around the world, the vast majority pertain to large-bodied, relatively mature individuals, and as a result, the early stages of ontogeny are still poorly characterised. Small-bodied metoposaurids from North America have traditionally been assigned to Apachesaurus gregorii, interpreted as a diminutive taxon, but this interpretation has not been rigorously tested. Here we provide a morphological description of two new small-bodied metoposaurid specimens from Petrified Forest National Park, AZ, USA. Both provide various anatomical details that improve our understanding of small-bodied metoposaurids and their taxonomic placement within Metoposauridae. Furthermore, we perform a histological analysis on associated intercentra of these specimens, which indicates that these are relatively immature individuals. These findings support the growing consensus that Apachesaurus is a juvenile metoposaurid, thereby providing additional data regarding the early stages of metoposaurid ontogeny and evidence of the persistence of large-bodied forms into the late Norian. Accordingly, these findings merit a reevaluation of the taxonomic validity and diagnosis of the taxon and of the previous interpretations of its paleobiology.
Epidemiology of bovine tuberculosis and influence of liver fluke co-infection in Cameroon, Central Africa

Background Control of bovine tuberculosis (bTB) and zoonotic tuberculosis (zTB) has relied upon surveillance and slaughter of infected cattle, milk pasteurisation and public health education. In Cameroon, like many other sub-Saharan African countries, there is limited understanding of current cattle husbandry or milk processing practices or livestock keepers awareness of bTB. This paper describes husbandry and milk processing practices within different Cameroonian cattle keeping communities and bTB awareness in comparison to other infectious diseases. Study design A population based cross-sectional sample of herdsmen and a questionnaire were used to gather data from pastoralists and dairy farmers in the North West Region and Vina Division of Cameroon. Results Pastoralists were predominately male Fulanis who had kept cattle for over a decade. Dairy farmers were non-Fulani and nearly half were female. Pastoralists went on transhumance PLOSONE | DOI:10.1371/journal.pone. 0146538 January 8, 2016 1 / 20 OPEN ACCESS Citation: Kelly RF, Hamman SM, Morgan KL, Nkongho EF, Ngwa VN, Tanya V, et al. (2016) Knowledge of Bovine Tuberculosis, Cattle Husbandry and Dairy Practices amongst Pastoralists and SmallScale Dairy Farmers in Cameroon. PLoS ONE 11(1): e0146538. doi:10.1371/journal.pone. 0146538 Editor: Yung-Fu Chang, Cornell University, UNITED STATES Received: June 30, 2015 Accepted: December 18, 2015 Published: January 8, 2016 Copyright: © 2016 Kelly et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Due to ethical restrictions regarding personal identifying information, data are from the CAMbTB study whose authors may be contacted at mark.bronsvoort@roslin.ed.ac.uk and rob.kelly@glasgow.ac.uk for an anonymized dataset. Funding: This work was funded by the Wellcome Trust (WT094945). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. 7.3. PLOS ONE ARTICLE PUBLISHED JANUARY 2016. 240
Detection of tlh and tdh genes in Vibrio Parahaemolyticus inhabiting farmed water ecosystem used for L. Vannamei aquaculture

Vibrio parahaemolyticus is hallophilic gram-negative bacteria that live as natural inhabitant in aquatic environment. All Vibrio parahaemolyticus strain known to have thermolabile hemolysin encoded by tlh gene as species marker. Thermostable direct hemolysin encoded by tdh gene is responsible for regulating virulence factor in Vibrio parhaemolyticus. Aim of this research is to detect tlh and tdh gene from water of L. vannamei aquaculture in Rembang regency. Colonies of green-blueish bacteria grew from isolation of L. vannamei aquaculture water in CD-VP media which was identified as Vibrio parahaemolyticus. Colonies of V. parahaemolyticus grew to be small and green-blueish bacteria colonies in TCBS agar. Result of molecular analysis showed that bacteria isolated from water sample are specifically identified as Vibrio parahaemolyticus bacteria by the detection of tlh gene. Vibrio parahaemolyticus isolated from water of L. vannamei aquaculture detected as tdh negative that indicates tdh gene is not present in isolated bacteria. Vibrio parahaemolyticus isolate were cultured in Wagatsuma agar for tdh gene confirmation test that showed Kanagawa negative result, which indicated that V. parahaemolyticus did not produce thermostable direct hemolysin. These results showed that Vibrio parahaemolyticus isolated from aquatic environment of L. vannamei aquaculture in Rembang regency did not show virulence factors.
Physiological changes in sugarcane in function of air and ground application of fungicide for orange rust control

The application of fungicides in different operating conditions is a usual practice for maintaining the productive potential in sugarcane varieties considered susceptible to orange rust, however, the physiological effects provided by the different application methods are unknown. The objective of this study was to evaluate the photosynthetic responses (gas exchange and chlorophyll content) in the SP81-3250 sugarcane variety, in function of different operational conditions of the aerial and ground application of fungicide in the orange rust control. Two application of fungicides of the chemical groups Strobilurins and Triazoles were carried out in the experimental units in different treatments. In the aerial applications, two application rates (30 and 40 L ha) and three nozzle orientations (0o, 90o and 135o) and in the ground application was used 200 L ha and flat fan spray nozzles with air induction (AI11004-VS). Gas exchange evaluations were performed with an IRGA and amount of chlorophyll a and b with a chlorophyll meter. Data were analyzed using Student's t-test for independent samples, at 0.05 significance. The aerial application provided better photosynthetic responses and chlorophyll a and b contents in leaf limb compared to ground application. Significant differences were detected in gas exchange and chlorophyll content between application rates and angulation of the spray nozzles in the boom. Fungicide applications provided increments of more than 19 t ha compared to the control, depending on the spraying technique employed. Aerial application with 30 L ha and 0° of deflection is a viable option to provide safer applications as a function of the larger droplet size.
Tropical Leafy Vegetables as Valuable Sources of Carotenoids and Phenolics

Leafy vegetables play an important role as essential components of diet for rural populations in tropical Africa. This study was undertaken to provide a more comprehensive characterization of carotenoids and phenolics in these neglected plant foods. For this, 12 leafy vegetables widely consumed in Côte d’Ivoire were selected, washed and oven-dried (50°C/3 days) before High-Performance Liquid Chromatography (HPLC) analysis of carotenoids and phenolics compounds. Carotenoids contents were significantly different (p ˂ 0.05) with lutein (43.68 ± 4.89 – 513.91 ± 5.68 μg/g dw) and all trans-β-carotene (22.62 ± 1.54 – 222.61 ± 5.63 μg/g dw) as major constituents. The calculated retinol activity equivalent (RAE) of β-carotene-rich leafy vegetables in this study ranged between 1.54 and 2.52 mg/100 g. The values of total phenolics ranged from 179.66 ± 11.33 mg/100 g dw in Corchorus olitorius to 436.48 ± 1.73 mg/100g dw in Abelmoschus esculentus. Three (3) flavonoids: quercetin (0.79 – 8.36 μg/g dw), catechin (0.39 – 5.65 μg/g dw) and kaempferol (0.76 – 29.11 μg/g dw) were quantified in the selected leafy vegetables. Chlorogenic acid (0.94 – 17.01 μg/g dw) was the most quantified phenolic acid in the leaves. Antioxidant activity evaluation of the leaves showed that 2,2-Diphenyl-1-Picrylhydrazyl (DPPH) radical scavenging activity ranged between 19.63 and 65% with Solanum melongena showing the highest value (65%). For 2,2’-Azino-Bis(3-ethylbenzothiazoline-6-sulphonic acid) or ABTS scavenging activity, Myrianthus arboreus recorded the highest value (76.66%) compared to other leaves. All these results suggest that the studied leafy vegetables are potential sources of carotenoids and phenolics and their consumption in sufficient amount may contribute to human health improvement.
Effect of pH-values on gelation properties of myosin extracted from high-pressure treated pre-rigor rabbit muscle

Myosin was extracted immediately from pre-rigor rabbit muscles (PRRMs) after high-pressure (HP) treatment (200 MPa, 25 °C for 15 s) to investigate the effect of pH (5.0, 5.5, 6.0, 6.5 and 7.0) on gel properties under the defined parameters. The water characteristics of the formed gel was modified as the pH altered. Improved water-holding capacity (WHC) was observed as the pH increased away from 5.5 and the highest value was reached at pH 7.0 (P<0.05). Assessment of rheological properties and secondary structures demonstrated that the thermal-induced aggregation of myosin after 50 °C was hindered at pH 6.5 and 7.0, and the unfolding of myosin conformational structures was intensified. Moreover, rapid exposure of buried amino groups in the temperature range between 40 °C and 70 °C occurred at pH 6.5 and 7.0, which contributed the formation of gel. These alternations give partial interpretation to the quality of gels obtained and verified the importance of monitoring the pH when applying HP treatment to the production of meat products.
Increased Obesity Is Causal for Increased Inflammation—A Mendelian Randomisation Study

Inflammation is endemic to obesity and type 2 diabetes (T2D) but it is unclear if it is a cause or a consequence. If the latter, then inflammation may increase the risk of obesity and diabetes complications. Large genome-wide association studies (GWAS) of inflammation and cardiometabolic traits can be used to investigate causal mechanisms. Summary statistics were assembled from GWAS of 49 cytokine (N=840-80,000) and 20 cardiometabolic traits (N=2,447-465,333). Shared genetic background was measured using LD score regression. Polygenic scores (PGS) were generated from GWAS data for 49 cytokines (representing inflammation) and 20 cardiometabolic traits and used in two-way Mendelian Randomisation (MR) analyses. Causal relationships were identified using summary statistics for all traits, and individual data (UK Biobank, N=465,333) to test the association of cytokine PGS with body mass index (BMI) and T2D. LD score regression analysis demonstrated that BMI and T2D shared a genetic background with acute phase cytokines. However, MR analyses showed that genetically-driven variation in cytokine levels were not associated with increased BMI or T2D risk. This argues against a causal role for inflammation (as represented by these cytokines) in the development of obesity and T2D. In contrast, genetically driven obesity was associated with increased inflammation: a PGS for increased BMI was associated with increased C-reactive protein (Beta [95% CI], 0.40 [0.34,0.46], p=1.3×10-36) and activated plasminogen inhibitor (Beta [95% CI], 0.39 [0.19, 0.59], p=7.8×10-5) levels. Genetically-driven variation in cytokine levels were causally linked with chronic kidney disease in subjects with T2D: fibroblast growth factor 2 (OR[95% CI], 0.58[0.46,0.72], p=1.8×10-6) and interleukin 13 (OR[95% CI], 1.28[1.15,1.43], p=7.0×10-6) We conclude that chronic inflammation is a consequence, rather than a cause, of T2D and obesity, and may contribute to some of their complications. Disclosure N. van Zuydam: None. M. Wielscher: None. M. McCarthy: Research Support; Self; Eli Lilly and Company, Takeda Pharmaceuticals U.S.A. , Inc., Novo Nordisk A/S. Advisory Panel; Self; Novo Nordisk A/S, Pfizer Inc. Research Support; Self; Pfizer Inc., Sanofi, Boehringer Ingelheim GmbH, AstraZeneca, Merck Sharp & Dohme Corp. M. Jarvelin: None.
Chl Fluorescence Parameters and Leaf Reflectance Indices Allow Monitoring Changes in the Physiological Status of Quercus ilex L. under Progressive Water Deficit

Extreme droughts and heat events, frequently produced in Mediterranean climates, induce anomalies in the ecosystem–atmosphere CO2 fluxes. In order to mitigate the consequences on forests and agriculture, managers must have a better knowledge of the ecosystem by monitoring plant status. Water status is commonly observed measuring water potential but when the extreme event is over, this parameter cannot show managers the recovery of other physiological processes such as photosynthesis. To address this problem, we have evaluated the Quercus ilex L. water status and photosynthetic capacity throughout an intense water scarcity event and a subsequent re-watering. Photosynthetic capacity was evaluated through chlorophyll fluorescence parameters and leaf reflectance indices. We found that all fluorescence parameters changed as water potential decreased and they did not completely recover after re-watering. Among the reflectance indices, the physiological reflectance index (PRI) varied similarly to fluorescence, obtaining a strong correlation with the non-photochemical quenching (NPQ). We proposed using PRI to detect the level of photosynthetic capacity in Q. ilex, as it is much easier-to-handle. We also concluded that intense droughts and heat stress not only might reduce photosynthetic capacity through changes in Chl fluorescence parameters during the stress period, but might also affect photosynthetic capacity once the plant water status is recovered.