Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracing the biogeographical origin of South Asian populations using DNA SatNav

The Indian subcontinent includes India, Bangladesh, Pakistan, Nepal, Bhutan, and Sri Lanka that collectively share common anthropological and cultural roots. Given the enigmatic population structure, complex history and genetic heterogeneity of populations from this region, their biogeographical origin and history remain a fascinating question. In this study we carried out an in-depth genetic comparison of the five South Asian populations available in the 1000 Genomes Project, namely Gujarati Indians from Houston, Texas (GIH), Punjabis from Lahore (PJL), Indian Telugus from UK (ITU), Sri Lankan Tamils from UK (STU) and Bengalis from Bangladesh (BEB), tracing their putative biogeographical origin using a DNA SatNav algorithm - Geographical Population Structure (GPS). GPS positioned >70% of GIH and PJL genomes in North India and >80% of ITU and STU samples in South India. All South Asian genomes appeared to be assigned with reasonable accuracy, along trade routes that thrived in the ancient Mauryan Empire, which had played a significant role in unifying the Indian subcontinent and in the process brought the ancient North and South Indian populations in close proximity, promoting admixture between them, ~2300 years before present (YBP). Our findings suggest that the genetic admixture between ancient North and South Indian populations likely first occurred along the Godavari and Krishna river basin in Central-South India. Finally our biogeographical analyses provide critical insights into the population history and sociocultural forces driving migration patterns that may have been instrumental in shaping the population structure of the Indian subcontinent.
Effect of herbicides on weed infestation and yield in boro rice

A field experiment was conducted at the agronomy field of the Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh, under wet land condition during December 2014 to May 2015. The aim was to see the effects of the weed control treatments on crop growth and yield in boro rice. Five selected herbicides (Metsulfuron-methyl 20 WG at 50 g/ha, pretilachlor 500 EC at 988 ml/ha, bensulfuran methyl 4%+acetachor 14% 18 WP at 800 g/ha, pyrazosulfuron-ethyl 10 WP at 125 g/ha and butachlor 5G at 25 kg/ha) were tested along with two hand weedings. Population density, fresh and dry weight of weed were taken. Eight weed species belonging to five families, namely, Echinochloa colonum, Paspalums crobiculatum, Monochoria vaginalis, Leersia hexandra L. , Scirpus mucronatus L. , Digitaria sanguinalis, Cyperus rotundus and Eclipta alba Hassk were found to grow in the experimental plots. Among the weed control treatments highest grain yield (5.73 t/ha) was produced with the treatment pyrazosulfuron-ethyl 10 WP at 125 g/ha followed by two hand weedings (5.50 t/ha). The increased yield due to application of herbicide contributed mainly from increasing the number of total tillers per plant, effective tillers per plant, filled grains per panicle and 1000-seed weight (g). Maximum benefit: cost ratio with pyrazosulfuron-ethyl 10 WP at 125 g/ha suggested that this herbicidal treatment could be used as an alternative when labour was a limiting factor in producing transplant boro rice.
Summer Pruning of ‘Gala’ Apple: The Relationships between Pruning Time, Radiation Penetration, and Fruit Quality

Trees of apple cv. Gala (Malus domestica Borkh.), which had previously been dormant pruned, were pruned in mid-December (early summer pruned—73 days after full bloom), mid-January (late summer pruned—108 days after full bloom), or were only dormant pruned (control). On 2 harvest dates (late February and early March) fruit from 4 different regions of the tree canopy were assessed for red blush, background color, soluble solids concentration, and fresh weight. Penetration of photosynthetic photon flux density (PPFD) to each region was measured at the summer pruning times and at the First harvest. Summer pruning increased the percentage of red blush—but not background color—for both pruning dates, decreased fresh weight of fruit from the early pruned trees, and decreased the soluble solids concentration of fruit from the late-pruned trees. The percentage of red blush and fruit fresh weight both showed a highly positive correlation with PPFD penetration, but for fruit fresh weight, the correlation also was dependent on the pruning treatment. The concentration of soluble solids also was related to PPFD penetration although, in comparison with fresh weight, the differences were reduced. Background color was relatively independent of tree position or pruning treatment.
The effect of tree size, neighborhood competition and environment on tree growth in an old-growth temperate forest

Aims Understanding the controls influencing tree growth is central to forest ecology. Although many factors such as tree size, neighborhood competition and environmental variables, have been proposed as being important in explaining patterns of tree growth, but their relative contributions are still subject to debate. We aimed to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree growth in an old-growth temperate forest in northeast china. Methods We used linear mixed models with data from a 25 ha (500 × 500 m) broad-leaved Korean pine (Pinus koraiensis) mixed forest permanent plot to examine the relative importance of these local drivers on tree growth at three organizational levels (community, guild and species). Subplot was included as a random effect to account for spatial autocorrelation in growth of trees located within the same subplot, and species was included as a random effect to account for variation among species in growth. Important Findings Tree size was typically the most important predictor of growth, followed by neighborhood competition and then soil nutrients. The correlation of tree size to growth varied from strongly positive for large trees and medium trees to slightly positive for small trees. The effect of neighborhood competition on growth showed weak negative density dependence as indicated by slightly negative effect of total basal area of neighbors and the proportion of conspecific neighbors. Environmental factors influenced growth of very common species, smaller tree-size classes and shade-tolerant species. We concluded that the relative importance of variables driving patterns of tree growth varied greatly among tree size classes, shade tolerance and abundance classes in this temperate forest. These results provide critical information for future studies of forest dynamics and offer insight into forest management in this region.
BASAL METABOLIC RATE OF THE RHINOCEROS AUKLET CERORHINCA MONOCERATA, AS MEASURED USING RESPIROMETRY

Marine Ornithology 41: 151–153 (2013) Basal metabolic rate (BMR) is the energy required by an animal when at rest, assuming thermoneutrality and no metabolic work for digestion (Schmidt-Nielsen 1997). BMR has been used to calculate an index of metabolic intensity and of the magnitude of energy expenditure, which is the ratio of field metabolic rate to BMR (Fyhn et al. 2001, Ellis & Gabrielsen 2002). BMR in seabirds differs depending on several ecological traits such as flight activity, migration and breeding stage (Bech et al. 1999, 2002, McNab 2009), as well as physiological states such as size of body components (Daan et al. 1990) and the climate and latitude of their habitat (Ellis 1984). Therefore, measuring the BMR for individual species is important for understanding seabird energetics.
INFLUENCE OF INCREASED PHOTOPERIODS ON GROWTH, FEED CONSUMPTION AND SURVIVAL OF JUVENILE MIRROR CARP (Cyprinus carpio Linnaeus, 1758)

A growth trial was conducted in order to determine the effects of increased photoperiod regimes on growth performance, feed intake and survival of mirror carp (Cyprinus carpio Linnaeus,1758) in laboratory conditions for 90 days. Triplicate groups of fish (6 g mean body weight) were exposed to photoperiod regimes of 12 hours light:12 hours dark (12L:12D), increased photoperiods of 16 hours light:8 hours dark (16L:8D) and continuous light (24L:0D), respectively. At the end of the trial, growth was highest in the group subjected to continuous photoperiod, and appeared significantly different (p0.05) affected by photoperiod treatments. No mortality was observed in the continuous (24L:0D) photoperiod group, however, a mortality of about 3 % was recorded in the other two groups. For a better growth and lower food conversion rate, a continuous (24L:0D) photoperiod exposure is suggested best for rearing of juvenile carp
VARIATIONS IN PLASMA SEX STEROID HORMONES OF THE WILD CASPIAN CYPRINID FISH, KUTUM (RUTILUS FRISII KUTUM)

Steroid hormones in plasma play an important role in reproductive cycles of animals especially during the final maturation stages. Steroid hormones synchronize gonad developments depending to fish species reproductive strategies. The wild Cyprinid fish, Kutum (Rutilus frisii kutum) is an ecologically and economically important fish species which inhabit in southern coastline of the Caspian Sea in Iran. Over the past few decades, natural reproduction of this species dramatically impaired due to the urbanization, civilization close to the land and shallow water in south western of the Caspian Sea. Therefore annual sex steroid hormones and gonads development were measured to assess the annual reproductive biology of female Kutum. In this study for the first time, our aims were to determine the annual variations in sex steroid hormones; 17 β Estradiol (E2), Progesterone (P) and testosterone (T) and gonad development of female Kutum. Our results showed that plasma steroid levels in females manifested in two phases in annual reproductive cycle; the resting phase (June - February) being characterized with the lowest level of steroid hormones and the peak reproduction activity phase (March–May) with simultaneously a significant increase in level of E2, P and T in plasma. Interestingly, comparing with other Teleost fish species the baseline level of E2 in plasma of Kutum during the resting phase to some extent was also huge. Increase in concentration of plasma E2 was in accordance with an increase of gonadosomatic index during spawning season. Our results contribute to our knowledge about the reproductive biology of Kutum and calls further long-term investigation.
Survey of container breeding mosquito larvae (Dengue vector) in Tiruchirappalli district, Tamil Nadu, India

Dengue is currently one of the most important arboviral diseases, with 2.5 billion people living in areas of risk and many millions of cases occurring each year. A prospective study was carried out in survey of container breeding mosquito larvae and identifying the dengue vector (Aedes species) distributed throughout Tiruchirappalli district, Tamilnadu, India. Aedes mosquito larvae were collected randomly during September 2012 to March 2013 from different natural and artificial containers and the water container index (CI) was calculated. Totally 118 water containers were inspected, among which 38 containers were recorded as positive for dengue vector. The collected larvae were raised to adults for identification. The dengue vector survey reveals the presence of two dominant mosquito species namely Aedes aegypti (45%) and Aedes vittatus (45%). Our study concludes that the Aedes aegypti and Aedes vittatus was most predominant container breeding mosquito in Tiruchirappalli district. Thus the study reveals the mosquito breeding habitat identification is helpful in creating of awareness and control of mosquito borne disease like dengue.
Catalase Activity of Rice Seed Embryo and Its Relation to Germination Rate at a Low Temperature

Germination ability of rice seeds at a low temperature varies with the cultivars. However, the biochemical mechanism of this difference has not been clarified. To analyze the role of active oxygen-scavegning enzymes in germination at a low temperature, calatase activity in rice seed embryo was determined. The specific activity of catalase increased during germination and the rate of increase was high in cultivars with a high germination ability at a low temperature. Catalase activity was detected even in the embryo of dry seeds (before imbibition). This initial level of catalase also varied with the cultivars and there was a positive correlation between initial level of catalase activity and germination rate at a low temperature. Such a relation was not observed between the superoxide dismutase activity of dry seed embryo and germination rate at a low temperature. It was also found that cultivars with a high initial level of catalase activity in the embryo could germinate even in a 3 % hydrogen peroxide solution. These charac-teristics reflect one of the genetic traits of rice.
Small Changes in Vegetation Structure Create Great Changes in Amphibian Ensembles in the Colombian Pacific Rainforest

This study determines the composition of amphibian ensembles along a vegetation gradient in the coastal Pacific rainforests in Colombia. Eight environmental and structural variables were measured to characterize the species' habitats and to determine which was most important in structuring amphibian patterns. After a total of 432 man-hours sampling effort, 513 individuals from 32 amphibian species were found. Although the species richness was similar among the vegetation cover types, the composition of the ensembles and total amphibian abundance were different in each case. In addition, a strong relationship was found between changes in the vegetation structure and the amphibian pattern, with the canopy cover being the key variable in the composition of the ensembles for each cover type. Habitats with over 76% canopy cover, combined with a high density of individual woody plants (> 176 individuals per 500 m2) and a high depth of leaf litter (> 16 cm), provide the necessary habitat conditions for typical rainforest composition of amphibian species. However, for amphibian ensembles to have a mature forest composition, the habitat must have a canopy cover over 89%, a density of woody plants exceeding 231 individuals per 500 m2, and a leaf litter depth above 23 cm. Therefore, future studies of amphibian succession and restoration in tropical forests must determine the changes in vegetation structure, rather than the possible direct effect of microclimatic variables.
Evaluation of Anti-inflammatory Effects of Steroids and Arthritis-Related Biotherapies in an In Vitro Coculture Model with Immune Cells and Synoviocytes

Background During rheumatoid arthritis (RA), steroids and biotherapies are used alone and combined. Efficacy has been established in clinical trials but their differential effects at the cellular level are less documented. The aim was to study these cellular effects using an in vitro model with synoviocytes interacting with peripheral blood mononuclear cells (PBMC) to reproduce the interactions in the RA synovium. Methods Activated-PBMC were cocultured with RA synoviocytes during 48 h. A dose–response of methylprednisolone (MP) was tested and different biotherapies (Infliximab, Etanercept, Adalimumab, Tocilizumab, Abatacept, and Rituximab) were added alone or in combination with MP. Cytokine production (IL-17, IL-6, IL-1β, IFN-γ and IL-10) was measured by ELISA. Results Addition of MP to cocultures inhibited the production of all cytokines. The response to the biotherapies alone was treatment-dependent. IL-17 production was inhibited only by Tocilizumab (p = 0.004), while IL-6 was decreased only by Infliximab (p ≤ 0.002). IL-1β level was affected in all conditions (p ≤ 0.03). IFN-γ production was mainly decreased by Infliximab (p = 0.004) and IL-10 by Infliximab and Tocilizumab (p ≤ 0.004). The combination MP and biotherapies did not induce an additional effect on pro-inflammatory cytokine inhibition. The combination MP and biotherapies induced a higher IL-10 secretion than MP alone, mainly with Rituximab. Conclusion Steroids inhibited the secretion of all cytokines, and low doses were as potent. The anti-inflammatory effect of biotherapies was dependent on their mechanism of action. MP and biotherapy combination did not enhance the inhibitory effect on pro-inflammatory cytokines but could have a beneficial effect by increasing IL-10 production.
Effects of dietary α-tocopherol acetate, pomegranate peel, and pomegranate peel extract on phenolic content, fatty acid composition, and meat quality of broiler chickens

ABSTRACT This study investigated the effect of dietary α-tocopherol (α-Toc), pomegranate peel extract (PPE), and pomegranate peel (PP) on phenolic content and breast meat quality of broilers during 11 days of storage with the addition of α-Toc, PPE, and PP. Broilers were fed eight dietary treatments, including: control diet, α-Toc diet (200 mg/kg), PPE diets (100, 200, and 300 mg/kg), and PP diets (1, 2, and 3 g/kg) during 0–42 days. The extents of lipid oxidation in samples were assessed by measuring thiobarbituric acid-reactive substances and the 1, 1-Diphenyl-2-picrylhydrazyl radical-scavenging activities were determined. The feed efficiency was improved significantly in chickens fed diet containing 0.2 g/kg PPE, and the growth performance of chickens was impaired in chickens fed with PP diet. Long-chain polyunsaturated fatty acids n-3 were increased in breast muscles of broilers fed α-Toc and high levels of PPE diets (P < .05). Total phenolic contents and antioxidant activity in the breast meat were improved significantly when chickens fed diets containing α-Toc and PPE (P < .05). In conclusion, dietary supplementation with 200 and 300 mg/kg PPE may improve the antioxidant potential and quality indices of broilers breast meat. The antioxidant potential of PPE was equal to that of α-Toc in refrigerated meat.
Genetic parameters of purebred and crossbred Milking Criollos in tropical Mexico

Records on total of 1746 calvings of principally Milking Criollos and their crosses were collected between 1972 and 1990 at the experiment station of the Mexican Association of Animal Production on the Gulf Coast of Mexico. Traits of interest were 305-day milk yield, days in lactation, number of services per lactation (raised to power 1/2), age at first calving and lifetime milk yield. Data were analysed by restricted maximum likelihood (REML) under an individual animal model based on 584 animals of which 146 were female ancestors and 35 were male ancestors. Heritabilities of 305-day milk and age at first calving were 0·17 and 0·07, respectively, but heritabilities of other traits were close to zero. Genetic trend in the Milking Criollos for 305-day milk was small and not significant (0·76 (s.e. 2·38) kg/year). Of crosses with Criollo sires, those involving Holstein and Canadienne breeding had highest 305-day and lifetime milk yields and those involving Brown Swiss and native Mexican (mostly Oaxaca) had lowest yields. Jersey crosses were intermediate for 305-day yield. The F 1 Criollo × Jersey cross had highest lifetime yield, but backcrosses involving Jersey breeding were poor for lifetime milk. Additive breed effects for Jersey and Canadienne, relative to Milking Criollo, were 88 (s.e. 91) and 227 (s.e. 74) kg 305-day milk, respectively. Heterosis was 144 (s.e. 55) kg (11·6%) for 305-day milk, 16–4 (s.e. 9·6) (5·0%) for days in milk, −0·107 (s.e. 0–042) (7·7%) for number of services per lactation raised to power 1/2, −25·6 (s.e. 41·4) days (2•3%) for age at first calving and 1789 (s.e. 664) kg (60·0%) for lifetime milk. A plan was designed to develop a nucleus breeding scheme utilizing multiple ovulation and embryo transfer technology (MOET) for the genetic improvement of the Milking Criollo breed in Mexico.
Surface-sediment diatom assemblages and water chemistry from 42 subarctic lakes in the southwestern Yukon and northernBritish Columbia, Canada

Abstract Modern diatom assemblages were related to surface-water chemistry from 42 lakes in the southwestern Yukon and in northern British Columbia. The lakes were alkaline (pH ranged from 7.5 to 9.4) with high specific conductance (mean = 379 µS cm-1). The lakes spanned a relatively wide range of trophic conditions, with the majority being oligotrophic or meso-eutrophic. Lake water depth, alkalinity, lake surface area, and Mg accounted for most of the variation in the diatom assemblages. Diatom assemblages most closely resembled those of the southern interior of British Columbia, where high conductance lakes are numerous, although many of the taxa were common to other northern regions, including Siberia, Alaska, and other parts of the Yukon. These data may be used in conjunction with other data from northern regions, including the Yukon and Alaska, to provide broader descriptions of environmental preferences of diatom taxa by extending the range of environmental variables such as alkalinity and specific conductance.
A STUDY OF PEDAL LACERATION IN ACTINIANS

1. The change in the form of a laceration piece, leading up to the acquisition of the typical actinian shape, takes place through the upgrowth of the tissue about the orifice where it was torn off from the parent.2. The permanent mesenteries arise as new growths in the undifferentiated tissues of the oral end of the laceration piece.3. The first twelve mesenteries do not appear in the sequence followed by those in egg embryos.4. As development goes on the old mesenteries—those brought over from the parent when the fragment was torn off—become restricted to a proportionately shorter and shorter part of the base of the young actinian until they are finally entirely resorbed.5. The mesenteric filaments are formed, just as in egg embryos, from a downgrowth of the ectodermal lining of the stomodeum. Their trilobed condition arises through the differentiation of this tissue.6. The tissues of the most actively growing part of a laceration piece become very thin; the ectoderm and the entoderm lose all apparent ce.
Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes

The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization- mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.