Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic approaches to deciphering genes and ecosystems

A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity(1-4), and in particular how antibiotic producing, sensitive and resistant species coexist(5-11). While cyclic “rock-paper-scissors” interactions can stabilize communities in spatial environments(5-7), coexistence in unstructured environments remains an enigma(8, 12). Here, using simulations and analytical models, we show that the opposing actions of antibiotic production and degradation enable coexistence even in well-mixed environments and despite substantial differences in intrinsic species growth rates. Coexistence depends on 3way interactions where an antibiotic degrading species attenuates the inhibitory interactions between two other species. Unlike in spatial environments where stability can be maintained by a single antibiotic(7), coexistence in well-mixed environments requires at least two antibiotics supporting three or more species. Greater numbers of antibiotics enable more complex communities, with diverse dynamical behaviors ranging from stable fixed-points to limit cycles and chaos, depending on strengths of antibiotic inhibition and degradation. Together, these results show how multi-species antibiotic interactions can generate ecological stability in both spatial and mixed microbial communities, suggesting strategies for engineering synthetic ecosystems and highlighting the importance of toxin production and degradation for microbial biodiversity. Contributions: EDK, KV, RK designed the study; EDK, KV, JZ did the experiments; EDK, KV did the simulations and modeling; EDK, KV, RK analyzed the data and wrote the paper.
Economic viability of cucumber cultivation under NVPH

The economic analysis was conducted for cultivation of parthenocarpic cucumber cv. Dinamik under naturally ventilated polyhouse for two consecutive years, 2013 and 2014. The actual value of economic inputs along with subsidy component (65 and 75%) imparted by Government of Gujarat in coordination with Government of India was considered for fitting into simulation model. The differences in net realization of Rs. 371642.00 (BCR 1.36) and Rs. 164723.00 (BCR 0.55) for the years 2013 and 2014, respectively represented maximum dependency on prevailing market selling rate in respective years besides some minor difference in yield component. BCR of 2.03, 0.95 and 2.17, 1.03 could be anticipated by availing 65 and 75% subsidy in each individual year for a crop of short duration, thus opening new avenues for small farmers of the Gujarat, India.
The effects of population density on the breeding performance of mountain hare Lepus timidus

Feedback between population density and demographic parameters often plays a determining role in population dynamics, and it is particularly important in managing exploited or harvested populations. The mountain hare Lepus timidus is a traditional game species, which is hunted in Scotland for sport and population control. However, information about how population parameters respond to changes in population density is lacking. To assess how reproduction and juvenile recruitment change in response to population density, we sampled 189 hares (88 females and 101 males) from 10 independent private hunting estates. We found a significant negative correlation between population density and the proportion of juveniles recruited into the breeding population, along with a significant interaction between population density and sex, which revealed that the proportion of juvenile females recruited decreases more rapidly with population density compared to the proportion of male juveniles. However, we found no evidence of density-dependent fecundity. Our results suggest density-dependent compensation in this species, acting on recruitment, not fecundity, with rates of juvenile recruitment differing between the sexes. We conclude that the significant correlation between population density and juvenile recruitment may provide harvested populations with the potential for compensatory juvenile recruitment, although harvesting rates need to be accurately estimated to avoid the risk of overharvesting.
Social Caching and Observational Spatial Memory in Pinyon Jays

In the wild, pinyon jays (Gymnorhinus cyanocephalus) live in large, integrated flocks and cache tens of thousands of seeds per year. This study explored social aspects of caching and recovering by pinyon jays. In Experiment 1, birds cached in a large experimental room under three conditions: alone, paired with a dominant, and paired with a subordinate. In all cases, birds recovered caches alone seven days later. Individuals ate more seeds before caching when alone than when paired and started caching sooner when subordinate than when dominant. Pinyon jays accurately returned to sites containing their own caches but not to sites containing caches made by partner birds. However, they went to areas containing partner caches sooner than would be expected, indicating memory for the general areas containing caches made by other pinyon jays. In Experiments 2 and 3 birds were placed closer to each other and allowed to recover one or two days after caching. In Experiment 2, both free-flying and caged observers found caches with accuracies above chance. Cachers made significantly fewer errors than observers. During Experiment 3, caged observers saw the cachers recover some seeds one day after they were cached. On the next day cachers and observers were separately allowed to visit all cache sites. Both cachers and observers performed accurately and did not differ in accuracy. Neither group discriminated between extant and depleted caches. Observational spatial memory in pinyon jays may allow economical cache robbery by wild pinyon jays under some circumstances, particularly shortly after caches are created.
Taxonomic and biological notes on a species of Iphitime (Polychaeta, Eunicida) associated with Pagurus prideaux from western Norway

Abstract On the basis of 658 specimens collected over an 11 year period, the symbiotic eunicid polychaete, Iphitime paguri Fage & Legendre, 1934, is redescribed, and its biology in its presumed preferred host, Pagurus prideaux Leach, 1815, is outlined. The main ecological part is based on sampling of Pagurus on five occasions throughout a year in Raunefjorden, southwest of Bergen. Iphitime paguri turned out to have a strong sexual dimorphism, both in outer appearance and in the morphology of the jaws. Both juveniles and mature individuals of both genders are described. The infestation rate of Pagurus prideaux was very high (as opposed to the low reported infestation rate in Pagurus bernhardus, generally regarded as the host of this species) and the symbiotic polychaetes turned out to have a distinct pattern of host utilization in different life stages. Ripe males and females were, at certain times of the year, generally found more or less intertwined in the apex of the gastropod shell inhabited by its host. Small larval stages were found in the same place. Intermediate size groups were found in the gill chamber and in a sulcus on the carapax of the pagurid host.
Epidemiology and Economic Benefits of Treating Goat Coccidiosis

ABSTRACT Received: Revised: Accepted: December 23, 2010 December 28, 2010 December 30, 2010 Key words: Coccidiosis Economic benefits Epidemiology Goat A study was carried out to determine the prevalence of Eimeria species and to compare the efficacy of Toltrazuril and Amprolium against coccidosis. Of the total 121 fecal samples examined for Eimeria, 67 (55.99%) were found infected with four species of Eimeria. Amongst the identified species, E. ninakohlyakimovae was the commonest one (49.25%) followed were E. arloingi, E. caprina and E. hirci with prevalence of 44.78, 25.37 and 19.40%, respectively. Kids had significantly (P<0.05) higher prevalence of Eimeria than adults. Higher prevalence of Eimeria was observed in female goats. Forty five Eimeria positive animals were randomly divided into three equal groups, i.e., groups A to C. Group A was treated with Amprolium (2g/40kg BW) and group B was treated with Toltrazuril (15mg/kg BW) for three days each while no drug was given to Group C. On day 7 post treatment, all goats of group B stopped shedding oocysts while 8 (53.33%) goats of group A stopped shedding oocysts. After the treatment, goats of group B gained 2.2 kg body weight over a period of 15 days compared 1.2 kg weight in group A. The lowest weight gain (0.5 kg) was in goats of group C (untreated control). No significant difference in milk yield of the three groups was recorded. It can be concluded that control of goat coccidiosis through single treatment of Toltrazuril is economically beneficial. ©2011 PVJ. All rights reserved
Mitochondrial DNA Phylogeography of the North American Brown Bear and Implications for Conservation

The historical distribution of the brown bear (Ursus arctos) in North America included Alaska, western Canada, the western and midwestern states, plus northern Mexico. Currently, the brown bear is limited to Alaska, the Canadian provinces of the Yukon, Northwest Territories, British Columbia, and Alberta, and six threatened subpopulations in the lower 48 states. To examine the evolutionary history of U. arctos in North America and to assess the genetic divergence between individuals from different geographic regions, we obtained 294 nucleotides of mitochondrial DNA sequence data from the control region for 317 free‐ranging brown bears. Twenty‐eight unique sequences, or mitochondrial DNA haplotypes were detected. The average sequence divergence between haplotypes was high (4.3%), and some haplotypes differed by as many as 23 nucleotides. Phylogenetic analyses using maximum parsimony revealed four major mitochondrial DNA phylogeographic groups, or clades. The significant phylogeographic structure detected in brown bears strongly contrasts with results obtained for other large carnivores and suggests limited female‐mediated gene flow. The mitochondrial DNA phylogeographic clades do not correlate with taxonomic classifications for U. arctos, and we hypothesize that the clades were formed prior to migration of this species into North America. We suggest evolutionarily significant units for conservation in three geographic regions: (1) the Alaskan islands of Admiralty, Baranof, and Chichagof; (2) mainland Alaska, Kodiak Island, and northern Canada; and (3) southern British Columbia, southern Alberta, and the states of Idaho, Montana, and Wyoming.
ANTHELMINTIC ACTIVITY OF TRACHYSPERMUM AMMI (L) EXTRACT

Objective: The anthelmintic activities of alcoholic and aqueous extract of seeds of Trachyspermum ammi L. were evaluated separately on Indian adult earthworm p.posthuma (Annelida). Methods: For this work seeds were extracted separately with ethanol and distilled water by soxhalation and maceration method with various concentration (10,20,40mg/ml) of each extract were tested for anthelmintic activity which involve the determination of time of paralysis and time of death of worms. Results: All extract were able to show anthelmintic activity at all concentration. The activities are well comparable with standard drug albendazole as positive control. Tween 20 with distilled water (for alcoholic extract) and distilled water (for aqueous extract) were used as negative control did not show any anthelmintic activity. Conclusions: Seeds of Trachyspermum ammi L showed good anthelmintic activity against Indian earthworm. Dose dependent activity was observed in plant extract.
Land use pattern and sustainability of food crop production in the fadama of Southern Guinea Savanna of Nigeria

An assessment of the sustainability of food crop production in the fadamas of Southern Guinea Savanna of Niger State, Nigeria was carried out within the framework of small-scale farming households utilizing fadama for the cultivation of food crops. The study determined profitability of food crop production in the fadama and identified the pattern of land use and management and its effects on sustainability of fadama. A two- stage simple random sampling technique was used to obtain 149 food crop farming households interviewed for the study. The data were analyzed by using descriptive statistics such as frequency distribution, mean, standard deviation, in addition estimates of crop diversification index (CDI), nutrient intake index (NII), Ruthberg index, farm budgeting model was made. A typical household hectared seventeen persons and planted an average of 3.44 ha scattered in three plots. The major enterprises were sole crop rice and maize – based mixtures in about 0.70 and 2.59 ha respectively. Estimated mean CDI was 0.651 implying stability of income and sustainability of mixed crop enterprises while mean NII was 1.89 showing that combined crops hectareve low tendency to deplete soil nutrient. The Ruthberg index value of 0.393 implied that a six years fallow period alone may not be adequate to restore natural fertility. The farm budget analysis showed thectaret the sampled fadama food crop farming household hectared positive net return for all enterprises. Maize/cowpea enterprise hectared the highest gross margin of N25, 663/ ha while leafy vegetables (for example spinach) hectared the highest return on investment (2.39). The average return on investment for all the farms studied was 1.89. Mixed cropping the dominant cropping system generally adopted by the fadama farming households gave higher gross margin per hectare. The study concluded that production of food crop in the fadama of the Guinea Savanna of Niger State, Nigeria is sustainable. Mixed cropping, consolidation of household resources, increased use of animal traction and organic fertilizer as well as integrated pest management is recommended. In order for the foregoing to be effective, they must be accompanied by improved extension service delivery, aggressive adult education programme, regulated use of agro-chemical, improved access to credit and availability of subsidized inputs.
Helminth parasites of the Newfoundland short-finned squid, Illex illecebrosus illecebrosus (LeSueur) (Cephalopoda: Decapoda)

Five genera of cestode parasites were found in the short-finned squid. Representatives of three of these, Pelichnibothrium speciosum, Monticelli, Scolex polymorphus Rudolphi, and Nybelinia sp. are new host records. The other two genera are Phyllobothrium and Dinobothrium, both of which have previously been described from Illex illecebrosus illecebrosus. The specimens of Dinobothrium collected were identified to the species level, Dinobothrium plicitum Linton, for the first time. Contrary to conclusions drawn by other workers, the plerocercoids of Phyllobothrium sp. do not wander freely about the body of the squid in nature, but are restricted to the caecum. The wandering of plerocercoids referred to above is probably a function of rising temperature over the period between time of capture of the squid and time of examination.
Wool production of different breeds of mixed-age ewes on hill country

Abstract Greasy fleece weight, staple length, quality number, character, and severity of staple unsoundness and cotting were recorded from Romney, Coopworth, Perendale, Cheviot, and Dorset-Romney ewes over 7 years. All breeds were grazed together except during mating. Romney had the heaviest fleece weight followed by Coopworth, Perendale, Dorset-Romney and Cheviot. Fleece weights increased to 3 or 4 years of age and declined to 5 years of age, Coopworth and Perendale showing the greatest decline. All breeds except Romney showed a decline in fleece weight associated with fertility status, dry ewes having the heaviest fleeces. Romney ewes rearing their own single lamb had higher fleece weights than dry ewes. The subjectively assessed fleece characteristics were not influenced by fertility status. Romney and Coopworth had a higher proportion of cotted fleeces than the other breeds and Cheviot had the highest proportion of fleeces with staple unsoundness. Increased staple unsoundness was associated with lower.
RE-EVALUATION OF TORTELLA (MUSCI, POTTIACEAE) IN CONTERMINOUS U.S.A. AND CANADA WITH A TREATMENT OF THE EUROPEAN SPECIES TORTELLA NITIDA

The moss genus Tortella (Pottiaceae) is re-examined for continental North America north of Mexico. Tortella alpicola is distinguished from T. fragilis as an uncommon but widespread taxon. Tortella japonica is considered to be a minor variant of T. humilis. Tortella rigens is new to the United States on the basis of comparison of American material with that of Europe, previous reports being erroneous. Tortella nitida is redescribed from authentic material and is excluded from the North American flora. The hitherto European Tortella tortuosa var. fragilifolia is reported from American plant populations. Tortella inclinata var. densa is reported as new to North America as a comb. nov. The bipolar distribution of Tortella fragilis is confirmed. Tortella inclinata var. inclinata is excluded from the flora of Arctic North America—specimens on which the species were cited were found to be T. inclinata var. densa instead. This study of the genus Tortella in continental North American north of Mexico was especially undertaken to address certain problematic taxa. An attempt was made to resolve past ambiguities by focusing on anatomical and morphological characters, for example to distinguish between the relatively common T. fragilis (Drumm.) Limpr. and a hitherto relatively unknown element in Tortella, T. alpicola Dix. Zander (1994d) added Tortella japonica (Besch.) Broth. to the Mexican flora, drawing attention to the relationship between the Japanese and Mexican floras. This created problems in separation of similar specimens with a broad distribution in Canada and the United States from the widespread northern hemisphere species T. humilis (Hedw.) Jenn. The decision that these two taxa are conspecific reveals greater variability in Tortella humilis than previously recognized, and
Isolation of fruit ripening genes from Carica papaya var. Eksotika 1 cDNA libraries (Pemencilan gen pemasakan Carica papaya var. Eksotika 1 daripada perpustakaan cDNA)

As an initiative to discover genes that are associated with the fruit ripening process, the expressed sequence tags (ESTs) analysis was conducted on the local papaya variety Eksotika I. Single pass sequencing was performed on a total of 2,150 ESTs from early ripe and ripe Carica papaya var. Eksotika I cDNA libraries. Homology search on ESTs with BLASTX algorithm against SwissProt non-redundant amino acid database revealed 71.1% of the papaya ESTs sequences matched the registered proteins with a cut off value of 1 x 10E -5 . Analysis of KEGG and UniProt showed that there were 129 transcripts or 22 unigenes involved in fruit ripening processes such as ethylene biosynthesis pathway, fruit softening and aroma. The ESTs profiling data revealed a general picture of papaya gene expression and regulation pattern particularly of genes related to fruit ripening. The results obtained in this study can facilitate the follow up on gene expression studies using DNA microarray and contribute to the development of new markers for comparative and functional genomics studies of other tropical fruit crops.
A phylogeny of the leptostraca (Crustacea) with keys to families and genera

Walker-Smith, G.K. and Poore, G.C. B. , 2001. A phylogeny of the Leptostraca (Crustacea) with keys to families and genera. Memoirs of Museum Victoria 58(2): 383–410. A phylogenetic analysis of the Leptostraca Claus, 1880 is undertaken using 32 of the 41 known species (including 4 undescribed species). The value of outgroups for deriving a plausible phylogeny in a group whose affinities remain contentious is discussed. A hypothetical ancestor is considered the best solution to the problem and states were scored based on general principles of crustacean evolution as evidenced by a wide variety of taxa. States of the 43 characters used in the analysis are detailed. The new phylogenetic hypothesis is compared with those of Olesen (1999). We conclude that a phylogeny based on species-level taxa and many informative characters is more likely to represent true evolutionary relationships than one based solely on genera and few characters. A new classification based on the phylogeny is derived with a new family, Paranebaliidae, being erected for Paranebalia Claus, 1880 and Levinebalia Walker-Smith, 2000. Nebaliopsididae Hessler, 1984 is supported for Nebaliopsis Sars, 1887. A restricted Nebaliidae Samouelle, 1819 for the remaining genera (Speonebalia Bowman, Yager and Iliffe, 1985, Nebaliella Thiele, 1904, Dahlella Hessler, 1984 and Nebalia Leach, 1814). Sarsinebalia Dahl, 1985 is synonomised with Nebalia. New keys and family and generic diagnoses are presented. All known species are listed with notes on distribution.
Potential bioactive compound from marine actinomycetes against biofouling bacteria

In the present study, 25 bacterial isolates were recovered from fouling samples collected from Parangipettai coastal area. Based on their adherence property, three isolates were characterized and identified as Bacillus sp. (BB11), Serratia sp. (BB13) and Alteromonas sp . (BB14). Six out of 20 actinomycete extracts showed inhibition of biofouling bacteria in disc diffusion method. Strain R1 extract showed maximum inhibition against all the biofouling bacteria tested. Culture filtrate and ethyl acetate extract from strain R1 showed 13-15 mm inhibition against biofouling bacteria. Reduction in biofilm formation was also observed in cover slip method. Active antifouling compound was purified using TLC and detected by bioautography. Based on chemical screening, the active compound was tentatively identified as sugar containing molecule. potential actinomycete strain R1 was characterized and identified as Streptomyces filamentosus (R1). Present study concluded that the marine actinomycete, Streptomyces filamentosus (R1) will be a potential source for the development of eco-friendly antifouling compounds. This will be a better alternative to the pollution causing synthetic antifoulants.