Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative splicing QTLs in European and African populations using Altrans, a novel method for splice junction quantification

With the advent of RNA-sequencing technology we now have the power to detect different types of alternative splicing and how DNA variation affects splicing. However, given the short read lengths used in most population based RNA-sequencing experiments, quantifying transcripts accurately remains a challenge. Here we present a novel method, Altrans, for discovery of alternative splicing quantitative trait loci (asQTLs). To assess the performance of Altrans we compared it to Cufflinks, a well-established transcript quantification method. Simulations show that in the presence of transcripts absent from the annotation, Altrans performs better in quantifications than Cufflinks. We have applied Altrans and Cufflinks to the Geuvadis dataset, which comprises samples from European and African populations, and discovered (FDR = 1%) 1806 and 243 asQTLs with Altrans, and 1596 and 288 asQTLs with Cufflinks for Europeans and Africans, respectively. Although Cufflinks results replicated better across the two populations, this likely due to the increased sensitivity of Altrans in detecting harder to detect associations. We show that, by discovering a set of asQTLs in a smaller subset of European samples and replicating these in the remaining larger subset of Europeans, both methods achieve similar replication levels (94% and 98% replication in Altrans and Cufflinks, respectively). We find that method specific asQTLs are largely due to different types of alternative splicing events detected by each method. We overlapped the asQTLs with biochemically active regions of the genome and observed significant enrichments for many functional marks and variants in splicing regions, highlighting the biological relevance of the asQTLs identified. All together, we present a novel approach for discovering asQTLs that is a more direct assessment of splicing compared to other methods and is complementary to other transcript quantification methods.
Identifying variable sea ice carbon contributions to the Arctic ecosystem: A case study using highly branched isoprenoid lipid biomarkers in Cumberland Sound ringed seals

We analyzed liver samples from 322 ringed seals (Pusa hispida) collected from Cumberland Sound (southeast Baffin Island) to test our ability to differentiate between carbon sources in near apex predators. Highly branched isoprenoids (HBIs) were present in all samples, and their distributions were consistent with recognized seal habitat use. HBI distributions in mature seals (≥ 5 yr) confirmed a less variable carbon source during winter, consistent with geographically restricted sexually mediated territorialism. In contrast, HBI distributions were more variable for immature seals (< 5 yr old), consistent with increased movements and body growth—mediated habitat selection. The ubiquitous presence of sea ice—derived HBIs (e.g., the ‘Ice Proxy with 25 carbons’) in every seal collected throughout January—December indicates that springtime sea ice primary production remains important for ringed seals throughout the year. HBI distributions remain largely unaltered by trophic transfer, enabling them to document short‐term (< 4 weeks) and seasonal changes in carbon. This important characteristic of HBIs facilitated interpretation of sea ice—derived carbon use by seals over annual and interannual timeframes and identified strong associations between sea ice carbon use and insolation as well as sea ice extent. Analysis of HBI distributions could be used to monitor and predict the response of Arctic organisms to reducing sea ice extent and the associated decline in future sea ice primary production over a range of temporal scales.
Effects of Tree Invasion on the Habitat Use of Sand Lizards

Abstract: The introduction of exotic tree species may interfere with conservation efforts for natural habitats, including grasslands in coastal sand dunes. Natural plant cover is used by several species in coastal dunes of Buenos Aires, Argentina, among them the lizard Liolaemus wiegmannii. Here we study the habitat use and abundance of this lizard inhabiting a psammophytic grassland within this ecosystem, where Acacia longifolia was recently introduced. Surveys and lizard sampling were conducted along 40 transects distributed in four independent zones of 75 ha, each with a different degree of invasion impact. We measured structural and thermal features in relation to A. longifolia and native plants. The lizard L. wiegmannii was three times more abundant in zones with ≤ 25% coverage of A. longifolia. The Jacobs selectivity index showed that all age classes selected native shrubs and avoided A. longifolia trees. These results were similar in greenhouse experiments. However, we found no differences in the use of any of these plants' (introduced or native) leaf litter. Structural and thermal characteristics of the habitat under the shrubs seemed to be more favorable for the physiological performance and behavior of L. wiegmannii, whereas the lower temperatures under A. longifolia might explain the lower presence of lizards in areas where this tree was introduced.
Atypical carotenoids for the Rhodophyceae in the genus Gracilaria (Gigartinales)

Abstract It has been generally accepted that the carotenoids of the rhodophycean algae are α-carotene, β-carotene, lutein, and zeaxanthin. However, one report on a species of Gracilaria indicated that antheraxanthin, an epoxide, was the major carotenoid. We have confirmed this report and have examined twenty-one other samples (mostly unialgal cultures, some field material) representing at least another eight species of Gracilaria. All of these samples contained antheraxanthin, and many also had the diepoxide, violaxanthin. This is the first report of the latter compound for this genus. Our data indicate that carotenoid epoxides are probably more common in the Rhodophyceae than is generally indicated, and phylogenetic schemes based on pigment composition must be modified accordingly to accommodate these compounds in the Rhodophyceae.
The knowledge transfer process in Six Sigma subsidiary firms

Although the operative benefits of the Six Sigma methodology in the business world are well accepted, the long-term benefits of the initiative are currently under discussion. This paper aims to analyse how Six Sigma methodology is related to the knowledge transfer process, a source of competitive advantage. For this purpose, we observe how team management in Six Sigma firms differs statistically from the team management proposed by other quality management initiatives, and how Six Sigma team management is related to the knowledge integration and knowledge transfer processes. An ANOVA analysis and Partial Least Squares approach were used to analyse data from 53 European Six Sigma firms, confirming the hypotheses developed. The results confirm that Six Sigma methodology offers new possibilities to companies and that implementation of Six Sigma has a positive effect on the variables that influence long-term organisational performance, such as knowledge management. Relevant academic contributions and implicat.
Examining possible foraging differences in urban and rural cave cricket populations: Carbon and nitrogen isotope ratios (δ 13 C, δ 15 N) as indicators of trophic level

Division of Biodiversity and Ecological Entomology, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL 61820 ( sjtaylor@uiuc.edu phone: 217-649-0240 ) Zara Environmental, LLC, Buda, TX 78610 ( jean@zaraenvironmental.com phone: 512-295-5333 ) Isotope Geochemistry Laboratory, Illinois State Geological Survey, 615 E Peabody Dr., Champaign, IL 61820 ( hackley@isgs.uiuc.edu phone: 217-244-2396 )
Deep Convolutional Neural Networks and Data Augmentation for Acoustic Event Detection

We propose a novel method for Acoustic Event Detection (AED). In contrast to speech, sounds coming from acoustic events may be produced by a wide variety of sources. Furthermore, distinguishing them often requires analyzing an extended time period due to the lack of a clear sub-word unit. In order to incorporate the long-time frequency structure for AED, we introduce a convolutional neural network (CNN) with a large input field. In contrast to previous works, this enables to train audio event detection end-to-end. Our architecture is inspired by the success of VGGNet and uses small, 3x3 convolutions, but more depth than previous methods in AED. In order to prevent over-fitting and to take full advantage of the modeling capabilities of our network, we further propose a novel data augmentation method to introduce data variation. Experimental results show that our CNN significantly outperforms state of the art methods including Bag of Audio Words (BoAW) and classical CNNs, achieving a 16% absolute improvement.
Survival of ovulated oocytes of the European catfish (Silurus glanis) after in vivo and in vitro storage or exposure to saline solutions and urine

Survival of Silurus glanis ovulated oocytes (ova) measured by the capacity of normal development i.e. percentage of normal and abnormal hatched larvae after in vivo and in vitro storage and exposure to sperm activating or immobilizing solutions and urine was studied. In the case of ovulated oocytes left in the ovaries, total hatching and abnormal hatched larvae (in % of hatching) were respectively 74 and 8.2% immediately after ovulation, 77 and 8.6% after 2 h, 54 and 18% after 4 h, and 38 and 50% after 6 h of storage. Four and 6 h stay of ovulated oocytes in ovaries resulted in a significant increase of abnormal hatched larvae ( p in vitro, the capacity to undertake a full embryonic development after fertilization was not significantly changed either after 8.5 h at 19 °C or 3.5 h at 25 °C; there was no ova survival at all after 3.5 h storage at 8 °C, 12 h at 19 °C and 8.5 h at 25 °C. There was a significant increase of abnormal larvae after 3.5 h at 25 °C (74%, p p < 0.05). Exposure of non inseminated ova to water buffered to pH 7.0 (5 mM Tris-HCl) to sperm activating solution (17 or 41 mM NaCl, 5 mM Tris-HCl, pH 8.0) or to immobilizing solution (200 mM NaCl, 30 mM Tris-HCl, pH 7.0) resulted in a regular and rapid decrease of their capacity of development; this was 10% of normal hatched larvae within 4 min in water, and within 6-8 min in the NaCl solutions. A similar situation was observed after exposure to urine with a loss of embryonic development of 30% within 3 min. These results indicate that all steps of the whole procedure of gamete collection and artificial insemination should be carried out rapidly as soon as possible after ovulation.
Isolation, characterization and phylogenetic analysis of Bagy-2 retrotransposon envelope-domain in the Egyptian cotton G. barbadense

In this study, the presence of Bagy-2 env domains in the Egyptian cotton, G. barbadense, using modified PCR program was investegated Comparative DNA sequence of cotton env clones revealed the presence of sequence length polymorphisms and deletions. Nevertheless, the coding information seems to be preserved. The ratio of synonymous to nonsynonymous changes indicates that the env domain in cotton is evolving under purifying selection. Moreover, env sequences in cotton have evolved under functional constraints and likely to play a role in the life cycle of these elements. Our phylogenetic analysis illustrates that cotton env sequences closest homologue is that of barley Bagy-2 retroelement.
Effects of carbonized rice hull and wood charcoal mixed with pyroligneous acid on the yield, and antioxidant and nutritional quality of rice

The effects of mixture of rice hull charcoal and pyroligneous acid (MRPA) and mixture of wood charcoal and pyroligneous acid (MWPA) with reduced rate of chemical fertilizer on the yield, and antioxidant and nutritional quality of rice were investigated. Results showed that RF (Recommended N-P-K fertilizer application = 110-55-48 kg ha-1) generally had higher agronomic and yield components than MWPA and MRPA treatments while MWPA was more effective in improving the yield of rice than MRPA. The total phenolic compounds and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical electron-donating ability were improved at higher application rate of MWPA while xanthine oxidase (XO) inhibition was improved at lower MWPA. In the case of nutritional quality of rice, total amylose content increased while lipid content decreased at lower MWPA. Fatty acid contents were generally high at the combined treatments of organic material and chemical fertilizer than at chemical fertilizer alone. Furthermore, the results revealed that MWPA was more appropriate to use than MRPA in increasing both the antioxidant property and nutritional quality of rice.
Examining the Ecological Quality of Küçükçekmece District Parks in Istanbul in Terms of Permeability and Natural Vegetation

Kucukcekmece, is one of the important districts to define the city of Istanbul at the international level with its historical, cultural, and natural values. In this study, the parks in Kucukcekmece District were examined in terms of ecological quality, principles, and standards. Ecological quality is a composite of the structural and functional features determining the habitat values of a landscape. An objective evaluation on the ecological quality of parks is important from the point of rehabilitation from an existing situation, and providing areas which will have high habitat value in the future. Recovery in the existing park area will generate a livable urban atmosphere. In line with this basic comprehension, the ecological quality of the parks in Istanbul's Kucukcekmece District was examined. There are four principles determining ecological quality of an area: vegetative production, water, permeability (soil), and natural vegetation cover (biological diversity). This research was done in two phases regarding the permeability and natural vegetation cover using ecological quality principles. In the first phase of the study, a vegetation list was provided by the Park and Garden Department of the Kucukcekmece Municipality. The park names and size were acquired from the "Kucukcekmece District green corridor Transformation Project". The space where the soil surface is covered by soil material, or is suppressed because of overuse and can not sustain plant growth is accepted as an impermeable soil surface. Whether there is a relation between park areas and permeable surface areas was examined using the Spearman correlation test. Whether permeability ratio of parks changes according to their location was analyzed using the Chi-Square test. In the second stage of the study, the existing vegetation cover was analyzed on-site. Existing vegetation cover analysis is made according to trees, shrubs, bushes, flowers, and trailings. Findings of, this study show that the average permeability ratio is 35.19% and the naturality ratio is 52% in the 63 parks under examination. This study shows that the permeable land surfaces of the parks remain incapable of sustaining vegetative growth and therefore the habitat values of the park areas, which can have an economic, social and ecologic contribution to the urban environment, will reduce. Result of this study will contribute to the sampling used for the ecological quality principles in other parks in other districts. The study reveals the importance of the ecological quality factors that need to be taken into consideration in the design and planning of parks.
Effects of epibiotic Enteromorpha spp. on the mole crab Emerita analoga in the Peruvian central coast

Epibiotic interactions between macroalgae and crustaceans have rarely been described. We examined the interaction between the mole crab, Emerita analoga and the opportunistic algae Enteromopha spp. in a sandy beach of the central coast of Peru. Enteromorpha spp. was found fouling the carapace of the mole crab that provides the only stable substrate to spore settlement in the beach environment. Epibiosis prevalence was up to 2.1%, and affected mainly larger, ovigerous females. Prevalence presented a seasonal pattern, with peaks during summer. Mole crab body condition was higher when fouled, whereas fecundity was not affected. Fouled mole crabs burrowed at lower speed, which was reversible by the removal of epibiotic algae. The burrowing depth was not affected by epibiosis. Contrary to the expected, the effects of algal epibiosis on demographic and life history parameters of mole crabs, with the exception of body condition, were mainly neutral but important on behavioural traits.
FURTHER LIGNANS FROM OCOTEA DUCKEI

Yangambin, epiyangambin and episesartemin were isolated from the leaves of Ocotea duckei Vattimo. They were identified and characterized by mass spectrometry and nuclear magnetic resonance spectrometry (1 H and 13 C) with the aid of two-dimensional techniques (1 H- 1 H COSY-45 and HMBC). The presence of epiyangambin and episesartemin in Ocotea duckei has not been previously reported.
Methyl iodide, an ozone-safe alternative to methyl bromide as a soil fumigant.

Methyl iodide was tested as a possible replacement for methyl bromide as a soil fumigant due to the scheduled removal of methyl bromide from the market. Methyl iodide is a better methylating agent than methyl bromide; it is rapidly destroyed by UV light and therefore unlikely to be involved in stratospheric ozone depletion. In laboratory and field trials, we tested methyl iodide alone or in comparison with methyl bromide for effectiveness in controlling the fungi Phytophthora citricola, P. cinnamomi, P. parasitica, and Rhizoctonia solani; the nematode Heterodera schachtii; and the plants Abutilon theophrasti, Chenopodium album, C. murale, Convolvulus arvensis, Cyperus rotundus, Poa annua, Portulaca oleracea, and Sisymbrium irio. In addition, we compared methyl iodide for biocidal effectiveness with seven other alkyl iodides. In both laboratory and field trials, when compared at equivalent molar rates, methyl iodide was equal to or better than methyl bromide in controlling the tested soilborne plant pathogens and weeds. When compared with other alkyl iodides, methyl iodide was the most effective fumigant.
Association study of disrupted-in-schizophrenia-1 gene single nucleotide polymorphism with schizophrenia in Han Chinese population

Objective To analyze the association between single nucleotide polymorphisms (SNPs) in DISC1 gene. Methods The studied sample consisted of 528 patients with schizophrenia (264 males and 264 females) and 528 healthy controls (264 males and 264 females). Two function SNPs were selected and genotyped by Illumina Golden Gate assay. Genotype and allele frequencies were compared between patients and controls to assess the association to schizophrenia. The clinical features of the hospital first patients were further examined with the Positive and Negative Syndrome Scale (PANSS) before treatment with antipsychotics. Results Two SNPs were genotyped in subjects. A significant association was found between rs3737597 and schizophrenia in genotype(387∶133∶8, 350∶164∶14) and allele frequencies (907∶149, 864∶192, P<0.05). Moreover, the haplotypes, A-A constructed from two SNPs showed significant differences between cases and controls (P<0.05). For rs821616, there were significant difference in positive syndrome score, delusions and poor rapport between patients with genotypes AA or not. Conclusion This study describes a positive association between DISC1 and schizophrenia in the Han Chinese population and DISC1 is the susceptible gene in schizo phrenia. Key words: Schizophrenia; Disrupted-in-schizophrenia-1; Association; Positive and negative syndrome scale
Uncertainties in projecting climate-change impacts in marine ecosystems

Projections of the impacts of climate change on marine ecosystems are a key prerequisite for the planning of adaptation strategies, yet they are inevitably associated with uncertainty. Identifying, quantifying, and communicating this uncertainty is key to both evaluating the risk associated with a projection and building confidence in its robustness. We review how uncertainties in such projections are handled in marine science. We employ an approach developed in climate modelling by breaking uncertainty down into (i) structural (model) uncertainty, (ii) initialization and internal variability uncertainty, (iii) parametric uncertainty, and (iv) scenario uncertainty. For each uncertainty type, we then examine the current state-of-the-art in assessing and quantifying its relative importance. We consider whether the marine scientific community has addressed these types of uncertainty sufficiently and highlight the opportunities and challenges associated with doing a better job. We find that even within a relatively small field such as marine science, there are substantial differences between subdisciplines in the degree of attention given to each type of uncertainty. We find that initialization uncertainty is rarely treated explicitly and reducing this type of uncertainty may deliver gains on the seasonal-to-decadal time-scale. We conclude that all parts of marine science could benefit from a greater exchange of ideas, particularly concerning such a universal problem such as the treatment of uncertainty. Finally, marine science should strive to reach the point where scenario uncertainty is the dominant uncertainty in our projections.
The impact of power line-related mortality on the Cape Vulture Gyps coprotheres in a part of its range, with an emphasis on electrocution

Summary The global population of the Cape Vulture Gyps coprotheres, a threatened southern African endemic, is known to be impacted by electrocutions and collisions on power line infrastructure, but to date this impact has not been estimated or quantified. Using data in a national database from the period prior to our study, conducted in the Eastern Cape Province of South Africa, we estimated a mean annual mortality rate from power line-related mortality of around 14 vultures per year. After applying an adjusted rate based on the results of a landowner survey, this estimate increased to around 80 vultures per year (i.e. a 5.7 fold increase). For a number of reasons, the estimated mean annual mortality rate is considered to under-represent the true situation, and must therefore be considered a minimum value. A simple model was constructed and run to investigate the potential impact of the mortality rate from electrocution on the study population. It distinguishes between vulture subpopulations in areas of high and low electrocution threat, and a migratory subpopulation that moves between these two areas. The model, simulated over 50 years and applying a constant theoretical maximum annual growth rate of 2%, indicates positive growth of the population in those areas where the electrocution threat from power lines is low, whereas the population in those areas where this threat is high is predicted to crash to extinction, from electrocution mortality alone, within a 20–35 year period. The regional population is predicted to show positive growth over the 50 year period. However, for a number of reasons that relate to the nature of certain parameters used in the model, the simulations must be considered to be conservative, at best. In addition, other unnatural mortality factors (notably inadvertent poisoning, drowning in high-walled farm reservoirs, harvesting for the traditional medicine trade, local food shortage), which are additive to power line-related mortality have not been taken into account. Management recommendations aimed at obtaining an improved estimate of the mean annual mortality rate from power lines, and at ameliorating the impact of electrocutions on the regional Cape Vulture population, are briefly mentioned. These address the former by documenting ways to improve the quantity and quality of the field data, and the latter by identifying areas where urgnt action needs to be taken to reduce or avoid the electrocution of vultures, by mitigating extant ‘unsafe’ power line infrastructure, and by ensuring that that only ‘safe’ infrastructure is used for new power lines.