Miracle-dz/UniFAR-FTUs huggingface dataset:
Design and Characterisation of a Randomized Food Intervention That Mimics Exposure to a Typical UK Diet to Provide Urine Samples for Identification and Validation of Metabolite Biomarkers of Food Intake

Poor dietary choices are major risk factors for obesity and non-communicable diseases, which places an increasing burden on healthcare systems worldwide. To monitor the effectiveness of healthy eating guidelines and strategies, there is a need for objective measures of dietary intake in community settings. Metabolites derived from specific foods present in urine samples can provide objective biomarkers of food intake (BFIs). Whilst the majority of biomarker discovery/validation studies have investigated potential biomarkers for single foods only, this study considered the whole diet by using menus that delivered a wide range of foods in meals that emulated conventional UK eating patterns. Fifty-one healthy participants (range 19–77 years; 57% female) followed a uniquely designed, randomized controlled dietary intervention, and provided spot urine samples suitable for discovery of BFIs within a real-world context. Free-living participants prepared and consumed all foods and drinks in their own homes and were asked to follow the protocols for meal consumption and home urine sample collection. This study also assessed the robustness, and impact on data quality, of a minimally invasive urine collection protocol. Overall the study design was well-accepted by participants and concluded successfully without any drop outs. Compliance for urine collection, adherence to menu plans, and observance of recommended meal timings, was shown to be very high. Metabolome analysis using mass spectrometry coupled with data mining demonstrated that the study protocol was well-suited for BFI discovery and validation. Novel, putative biomarkers for an extended range of foods were identified including legumes, curry, strongly-heated products, and artificially sweetened, low calorie beverages. In conclusion, aspects of this study design would help to overcome several current challenges in the development of BFI technology. One specific attribute was the examination of BFI generalizability across related food groups and across different preparations and cooking methods of foods. Furthermore, the collection of urine samples at multiple time points helped to determine which spot sample was optimal for identification and validation of BFIs in free-living individuals. A further valuable design feature centered on the comprehensiveness of the menu design which allowed the testing of biomarker specificity within a biobank of urine samples.
Evaluation of organic nutrient-management practices in rice (Oryza sativa) tomato (Lycopersicum esculentum)okra (Abelmoschus esculentus) system under irrigated conditions

A field experiment was conducted during 200506 to 201213 on organic nutrient management in rice (Oryza sativa L.)tomato (Lycopersicum esculentum L.)okra (Abelmoschus esculentus L.) cropping system under irri- gated conditions in a sandy loam soil having pH 5.9 and organic carbon 0.76% at Chiplima, Odisha. Eight treat- ments comprising 5 organic, 2 integrated and 1 inorganic approach of nutrient management were evaluated with 3 replications. Organic source of nutrient supply reduced the system yield by 5.512. 7% compared to the inorganic source in the first year. However, the mean system yield of conversion period (first 3 cropping system cycles) with organic treatment comprising supply of one-third N each through farmyard manure (FYM), green manuring of dhaincha (Sesbania cannabina) or vermicompost and neem oilcake + Azospirillum or Azotobacter + phosphorus solubilizing bacteria (PSB) was at par with inorganic and integrated approach. The mean system yield from fourth to eighth cropping system cycles (after conversion period) with organic source of nutrient supply, i.e. FYM + green manuring or vermicompost + neem oilcake + Azospirillum or Azotobacter + PSB was significantly higher (12%) than that of with inorganic source of nutrient supply, i.e. 100% NPK + ZnSO @ 25 kg/ha to rice and 100% 4 NPK + gypsum @ 110 kg/ha + borax @ 10 kg/ha + ammonium molybdate @ 0.8 kg/ha to both tomato and okra. The organic nutrient-management package increased the soil organic carbon and available N, P and K at the end of eighth cropping system cycle over the initial and the buildup was maximum in the soil applied with one-third N each through FYM, dhaincha/vermicompost and neem oilcake + Azospirillum/ Azotobacter + PSB. The microbial population in terms of colony-forming units increased in a higher rate in soils with organic nutrient-supply system (bacteria 32.4 to 37.1%, fungi 30.2 to 34.4% and actinomycetes 29.3 to 35.9%) compared to the inorganic source of nutrient supply system (bacteria 11.2%, fungi 5.5% and actinomycetes 11.3%) after eighth cropping system cycle over initial status. The microbial biomass carbon of the soils with organic sources of nutrient supply was en- hanced considerably (53.4% to 61.8%) over the initial level (104.7 to 118.2 ? g C/g).
Performance study of onion (Allium cepa L.) varieties for quantitative traits in northern dry zone of Karnataka

An investigation was conducted to ascertain the production potentials of different genotypes of onion (Allium cepa L.) were carried out in Main Horticultural Research and Extension Centre, University of Horticultural Sciences, Bagalkot during 2016. Experiment was conducted with nine different varieties of onion. Among them, growth parameters like, more number of leaves were observed in Arka Bindu (12.62), highest plant height is seen in Arka Bheema (59.12cm) and the highest leaf length reported in Arka Kalyan (50.37). No.of ringsthe highest is seen in Arka Pragati (10.50) and lowest in Arka Kalyan (7.70). TSS was found highest in Arka Keetiman (14.70 o B). Among yield parameters, bulb weight was the highest in Arka Pragati (212.62 g), total weight was reported highest in Arka Pragati (12.75 kg). Thus onion is an important crop with many medicinal values, it has good yield and quality attributes. Thus identification of promising varieties as a commercial crop for the area with high yield and quality fruits would help the farmers in its adoption and improving their economic status.
Using genomic information to conserve genetic diversity in livestock

Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity.
The nocturnal zonation of decapods in the subtidal zone within the reef seascape—abiotic factors defining habitats

the reef seascape—abiotic factors defining habitats Bruno Welter Giraldes,* Petrônio Alves Coelho Filho, David M. Smyth, and Petrônio Alves Coelho Environmental Science Center (ESC), Qatar University (QU). Al Hala St 2713, Doha, Qatar Laborat orio de Carcinologia, Museu Oceanogr afico “Dr. Petrônio Alves Coelho”, Departamento de Oceanografia, Universidade Federal de Prnambuco (UFPE). Avenida Arquitetura, s/n, Cidade Universit aria, Recife, PE, Brasil Departamento de Engenharia de Pesca, Universidade Federal de Alagoas. Avenida Divaldo Suruagy, s/n, Centro, Penedo, AL, Brasil *Corresponding author: tel: þ974-4403-6859; fax þ974-4403-3940; e-mail: bweltergiraldes@qu.edu. qa. Deceased.
Phytotoxicity of Herbicides to Spring Flowering Bulbs

Biennial application for two years of nine commonly used turf and ornamental herbicides were evaluated for phytotoxicity to fourteen species of spring flowering bulbs. OH 2 significantly damaged foliage of Anemone ‘Rosea’, Crocus ‘Cream Beauty’, Endymion ‘Blue’, Hyacinthus ‘Ostara’, Iris reticulata ‘Harmony’, Muscari armeniacum, Narcissus ‘Geranium’, Ornithogalum umbellatum, Scilla ‘Spring Beauty’, Triteleia ‘Queen Fabiola’, and the Tulipa ‘Golden Apeldoorn’, ‘Purissima’, and ‘Paul Richter’. Ronstar damaged the foliage of Crocus ‘Cream Beauty’, Crocus ‘Remembrance’, Endymion ‘Blue’, Hyacinthus ‘Ostara’, Iris ‘Harmony’, Muscari armeniacum, Narcissus ‘Geranium’, Ornithogalum umbellatum, Scilla ‘Spring Beauty’, Trietleia ‘Queen Fabiola’, and the Tulipa ‘Golden Apeldoorn’, ‘Purissima’, and ‘Paul Richter’. Muscari foliage was damaged by Balan, Dacthal, Devrinol, Fusilade and Poast. Hyacinthus ‘Ostara’ foliage was damaged by Balan. Anemone ‘Rosea’ foliage was injured by Betasan and Pennant. Tulipa ‘Paul Richter.
A Review on the Phylogeography of Potentially Chemoautotrophic Bacteria from Major Vent and Seep Fauna and Their Contribution to Primary Production

ABSTRACT Though geochemically and microbially well-defined, the phylogeographic data of microbial symbionts in these highly productive vent and seep systems require a closer examination and synthesis. QIIME analysis of 16S rDNA of bacterial associates of major fauna from 1995 to 2015 was thus undertaken to examine phylogeography of their microbial symbionts along with host specificity. While phylotypes were generally unrelated, bivalve Calyptogena exhibited vertical transmission sharing similar symbionts in geographically separated geosystems. Different species of tubeworms possessed identical symbionts through horizontal acquisition at geographically distinct Guaymas basin vent and the Arctic seep. Vents were more versatile with both mobile and sessile fauna hosting ecto- and endo-symbionts. Comparatively, seeps were more specialized with sessile animal hosts with endosymbionts. C-fixation rate measurements are still scanty for sediments, bedrocks and serpentine systems; vent, seep, anoxic and oxic basins were shown to fix up to 22, 325, 96, and 37,400 g C m−3 y−1, respectively. Estimation of chemosynthetic primary production rates in chemoautotrophic ecosystems could endeavor to improve existing biogeographic models by coupling volcanism and plate-tectonics to global climate and phylogeography.
The small-scale kinematics of a variable-density turbulent jet

We present the experimental results of a turbulent variable-density (VD) jet inside a wind tunnel. Our goal is to study the differences in the kinematics and dynamics of the small scales between constantand VD flows – the knowledge is important to the development of physics-based turbulence closure models. To obtain the full velocity gradient tensor (VGT) needed in the analysis, we used time-resolved stereoscopic particle image velocimetry (SPIV) together with the Taylor’s frozen turbulence hypothesis to reconstruct the jet volume at a streamwise location that was sixteen jet diameters (16D) from the jet nozzle. We found the following for the dense SF6 jet: (1) it experiences less fluid deformation (left panel in figure 3), (2) it has a weaker normalized vortex-stretching term, and (3) conditional statistics based on the different quadrants in the QR-plot show that it has stronger enstrophy production/destruction contributions to the total ωisi jω j than that observed in the air jet.
A novel protocol for studying bee cognition in the wild

Understanding how animals perceive, learn and remember stimuli is critical for understanding both how cognition is shaped by natural selection, and how ecological factors impact behaviour. However, the majority of studies on cognition involve captive animals in laboratory settings. While controlled settings are required to accurately measure aspects of cognition, they may not yield realistic estimates of learning performance in natural environments. Wild bees offer a useful system in which to study cognitive ecology and comparative cognition more broadly: they encompass around 20,000 species globally, varying in characteristics such as life‐history strategy, degree of sociality and dietary specialization. Yet, the limited number of protocols currently available for studying insect cognition has restricted research to a few commercially available bee species, in almost exclusively laboratory settings. We present a protocol (Free‐Moving Proboscis Extension Response [FMPER]) to measure wild bees’ colour preferences, learning performance and memory. We first used laboratory‐reared bumblebees Bombus impatiens to establish that FMPER yielded results consistent with learning theory. We then successfully tested wild honeybees Apis mellifera in the laboratory and Bombus vosnesenskii at field sites. Free‐Moving Proboscis Extension Response is straightforward to implement, is low cost, and may be readily adapted to other flower‐visiting insects. We believe it will be useful to a broad range of evolutionary biologists, behavioural ecologists and pollination ecologists interested in measuring cognitive performance in the wild and across a broader range of species.
Vitamin D status in growing dairy goats and sheep: influence of UVB radiation on bone metabolism and calcium homeostasis

The aim of this study was to investigate how controlled UVB irradiation in combination with reduced nutritional vitamin D (vitD) supply affects vitD status and Ca metabolism of growing goats and sheep. The hypothesis was that, like dairy cows, goats and sheep are able to compensate for the missing nutritional supply of vitD through endogenous production in the skin, with the consequence of a high vitD status and a balanced Ca homeostasis. Sixteen lambs and 14 goat kids aged 3 and a half months were housed in an UVB free environment and fed hay and a vitD-free concentrate over a period of 13 wk. One group of each species was exposed to UVB lamps daily during individual feeding; the other groups served as controls. Serum, urine, and feces samples were taken at the start and at a monthly interval. Serum was analyzed for vitD metabolites, bone markers, growth hormone, insulin-like growth factor I, Ca, and P. Apparent digestibility and urinary excretion of Ca and P were determined. The left metatarsus was analyzed by peripheral quantitative computer tomography for bone mineral density before starting and at the end of the trial. In wk 13, all animals were slaughtered and samples of skin, rumen, duodenum, kidney, and bone (metatarsus) were collected. Content of sterols of vitD synthesis in the skin, Ca flux rates in rumen and duodenum, expression of vitD receptor in duodenum and kidney, renal and intestinal gene expression of Ca transport proteins, and renal enzymes related to vitD metabolism were determined. The UVB exposure led to lower 7-dehydrocholesterol content in the skin and a better vitD status (higher serum 25-hydroxyvitamin D), but no signs of vitD deficiency were seen in the control groups and no effect of irradiation was detected in the analyzed parameters of Ca homeostasis. Differences between the 2 species were detected: lambs had a higher increase of bone mineral density, lower values of bone markers, growth hormone, and insulin-like growth factor I in serum and higher tachysterol and lower lumisterol content in skin compared with goat kids. The results indicated that growing lambs and goat kids are able to compensate for a vitD-reduced diet by cutaneous vitD synthesis when exposed to UVB irradiation and therefore to keep a high vitD status. In contrast, when a reduced vitD diet is combined with missing UVB exposure, the vitD status drops, but the experimental time was probably too short to induce a vitD deficiency or an effect on Ca homeostasis.
Evaluation of Indigenous Fungal Isolates, Metarhizium anisopliae M34412, Beauveria bassiana B3301 and Nonluraea rileyi N812 for the Control of Helicoverpa armigera (Hubner) in Pigeonpea Field

The effectiveness of oil-based conidia formulations of indigenous fungal isolates Metarhizillm anisopliae M34412, Beallveria bassiana 83301 and Nomuraea rileyi N812 were evaluated against Helicoverpa armigera (Hubner) infestation on pigeon pea under field conditions. The M. allisopliae M34412 conidia in the oil formulation (7:3, diesel: Sunflower oil) were found to be most effective in controlling H. armigera . The results were compared with other control agents such as, endosulfan and Ha NPV ( H. armigera Nuclear Polyhedrosis Virus). The per cent efficacies were, . W. anisopliae,/i> 66.74, endosulfan 62.58, N. rileyi 60.88 and HaNPV 55.58. B. bassiana preparation was found to be relatively less effective (51.25% efficacy). The effectiveness of all the control agents based on per cent pod damage and yield has also been discussed.
Motion-based frame interpolation for film and television effects

Frame interpolation is the process of synthesising a new frame in-between existing frames in an image sequence. It has emerged as a key algorithmic module in motion picture effects. In the context of this special issue, this study provides a review of the technology used to create in-between frames and presents a Bayesian framework that generalises frame interpolation algorithms using the concept of motion interpolation. Unlike existing literature in this area, the authors also compare performance using the top industrial toolkits used in the post production industry. They find that all successful techniques employ motion-based interpolation, and the commercial version of the Bayesian approach performs best. Another goal of this study is to compare the performance gains with recent convolutional neural network (CNN) algorithms against the traditional explicit model-based approaches. They find that CNNs do not clearly outperform the explicit motion-based techniques, and require significant compute resources, but provide complementary improvements in certain types of sequences.
Incidence, severity, and relationship of broiler footpad lesions and gait scores of market‐age broilers raised under commercial conditions in the southeastern United States

SUMMARY The prevalence and severity of footpad dermatitis (FPD) and gait score (GS) as an indicator of lameness in commercial broiler production in the United States has not been widely reported. The objectives of this field study were to determine the prevalence and severity of FPD and lameness in commercial broilers, as well as the relationship between FPD and GS under the production conditions typical of the southeastern United States. Observations were collected from an integrated broiler complex producing a light broiler (1.94 to 2.22 kg) and an integrated broiler complex producing a heavier broiler (3.62 to 3.76 kg). Data were collected from 554 farms, 16,697 houses, and 166,977 broilers, representing over 328 million birds over the 3‐year span of the study. Light broilers had significantly better FPD and GS than heavier broilers. Additionally, there was a strongly significant association between FPD and GS within a complex. There were significantly greater odds of GS worsening as FPD worsened and significantly high odds of FPD becoming more severe as GS worsened.
Seasonality and interindividual variation in mandrill feeding ecology revealed by stable isotope analyses of hair and blood

Mandrills are large‐bodied terrestrial forest primates living in particularly large social groups of several hundred individuals. Following these groups in the wild to assess differences in diet over time as well as among individuals is demanding. We here use isotope analyses in blood and hair obtained during repeated captures of 43 identified free‐ranging mandrills (Mandrillus sphinx) from Southern Gabon, to test how dietary variation relates to the season as well as an individual's age and sex. We measured the stable carbon (δ13C‰) and nitrogen (δ15N‰) isotope ratios in 46 blood and 214 hair section samples as well as from a small selection of mandrill foods (n = 24). We found some seasonal isotopic effects, with lower δ13C values but higher δ15N values observed during the highly competitive long dry season compared to the fruit‐rich long rainy season. Variation in δ13C was further predicted by individual age, with higher δ13C values generally found in younger individuals suggesting that they may consume more high canopy fruit than older individuals, or that older individuals consume more low canopy foliage. The best predictor for δ15N values was the interaction between age and sex, with mature and reproductively active males revealing the highest δ15N values, despite the observation that males consume substantially less animal food items than females. We interpret high δ15N values in these mature male mandrill blood and hair sections to be the result of nutritional stress associated with intense male–male competition, particularly during mating season. This is the first study showing isotopic evidence for nutritional stress in a free‐ranging primate species and may spark further investigations into male mandrill diet and energy balance.