Miracle-dz/UniFAR-FTUs huggingface dataset:
A molecular analysis of the phylogenetic position of the suborder Cavernicola within the Tricladida (Platyhelminthes), with the description of a new species of stygobiont flatworm from Benin

This paper presents a new species of cavernicolan planarian from the African continent, which enabled us to determine the position of the suborder Cavernicola within the order Tricladida on a molecular basis. A recent paper suggested a sister-group relationship between Cavernicola and marine triclads. However, our work is the first molecular study to demonstrate unequivocally that the Cavernicola does not group with either the freshwater planarians or the land planarians, i.e. is not closely related to the suborder Continenticola, and corroborates the suggested sister-group relationship with the marine triclads or Maricola. Two possible scenarios are proposed for the evolution of the Cavernicola from marine ancestors. The new species is assigned to the genus Novomitchellia and is characterized by the absence of eyes. Testicular follicles are numerous and only dorsal, extending from behind the ovaries to the posterior end of the body. The vasa deferentia separately penetrate the penis bulb and the seminal vesicle. The penis papilla is very short and blunt, and the penis bulb musculature is weak. A long and narrow copulatory bursa is situated behind the gonopore. The common oviduct is orientated perpendicularly to the short bursal canal.
Retrieval of omnidirectional slope spectrum of sea roughness by underwater solar path images: theory and numerical experiment (one-dimensional sea roughness)

This paper reveals the theoretical possibilities of using the underwater solar path images (USPI) to retrieve the wind wave spectra, including situation when surfactant film is on the sea surface. It contains a theoretical model of USPI, an algorithm for retrieval wave spectra through statistical moments of USPI, and results of testing proposed algorithm using numerical simulation. The last one was based on the Elfouhaily wind wave spectrum and the Ermakov model of thin surfactant film. The use of modeling made it possible to establish the main difficulties in achieving a solution of challenging, and also to offer an alternative method. The obtained results confirm the efficiency of the developed method.
IMBIBITION TEMPERATURE AFFECTS ON SEEDLING VIGOR : IN CROPS AND SHRUBS

Imbibition at cold temperatures reduces seedling vigor of some species, but is beneficial to others. We used 3 rangeland shrubs and 8 agronomic crop species to test for a general relationship between imbibition temperature (5 to 30°C) and seedling vigor measured as post-germination growth; and to test for an effect of imbibition temperature on seed water uptake and dry weight loss during imbibition. Imbibition temperatures between 5 and 15°C were correlated with greater seedling length of the shrubs while most crops were favored by imbibition temperatures between 20 and 30°C. Winter wheat (Triticum aestivum L.) response to imbibition temperature was similar to that of the shrubs. Generally, shrubs had lower post-germination growth than crops, and during imbibition most crop seeds lost less weight than shrub seeds. Winter wheat had high weight loss as well as high seedling vigor. Seed water content generally increased with increasing imbibition temperature; however, winter wheat, kochia (Kochia prostrata (L.) Schrad. ), and big sagebrush (Artemisia tridentata Nutt.) had significantly less water when imbibed at 30°C than when imbibed at lower temperatures. The differences due to temperature suggest the relationship between imbibition temperature and seedling vigor is a general phenomenon related to the physiology of water uptake and to seed respiration (as indicated by weight loss). Therefore, we recommend that optimum imbibition temperatures be defined by species and incorporated into seed-testing guidelines. This appears particularly important for species that do not have a long history of cultivation and whose response to temperature may differ significantly from that of crops.
Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXM’s performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample.
BIOEFFICACY OF Millettia pachycarpa BENTHAM AGAINST TOBACCO CATERPILLAR, Spodoptera litura (FABRICIUS)

M. pachycarpa leaves were shade dried and extracted with different solvents of varying polarity. The leaf powder was firstly extracted with hexane solvent which yielded crude hexane extract. The hexane extract was then partitioned with methanol to give hexane and aqueous methanolic extract. The plant material remained after extraction with hexane was re-extracted with methanol and to obtain crude methanol extract. The methanol extract was then concentrated under vacuo to one third of the volume, diluted with water and then serially partitioned with hexane, dichloromethane, ethyl acetate and butanol and respective extracts were obtained as hexane extract, dichloromethane extract, ethyl acetate extract and butanol extract. The hexane fractions arising from crude hexane and methanol extracts after partitioning were clubbed together. The dichloromethane portion of methanol extract after initial TLC was subjected to column chromatography hexane: ethyl acetate solvent systems to obtain different fractions. these fractions were analyzed for their active constituents by HPLC
The Himalayan Uplift and the Evolution of Aquatic Biodiversity Across Asia: Snowtrout (Cyprininae: Schizothorax) as a Test Case

The Himalayan uplift, a tectonic event of global importance, seemingly disseminated aquatic biodiversity broadly across Asia. But surprisingly, this hypothesis has yet to be tested. We do so herein by sequencing 1,140 base-pair of mtDNA cytochrome-b for 72 tetraploid Nepalese/Bhutanese Snowtrout (Schizothorax spp.), combining those data with 67 GENBANK® sequences (59 ingroup/8 outgroup), then reconstructing phylogenetic relationships using maximum likelihood/ Bayesian analyses. Results indicate Snowtrout originated in Central Asia, dispersed across the Qinghai-Tibetan Plateau (QTP), then into Bhutan via south-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). The headwaters of five large Asian rivers provided dispersal corridors into southeast Asia. South of the Himalaya, the YLTR transitions into a westward-flowing Brahmaputra River that facilitated successive colonization of Himalayan drainages: First Bhutan, then Nepal, followed by far-western drainages subsequently captured by the Indus River. We found greater species-divergences across rather than within-basins, implicating vicariant evolution as a driver. The Himalaya is a component of the “third-pole” [Earth’s largest (but rapidly shrinking) glacial reservoir outside the Arctic/Antarctic]. Its unique aquatic biodiversity must not only be recognized (as herein) but also conserved through broad, trans-national collaborations. Our results effectively contrast phylogeography with taxonomy as a necessary first step in this process. The Himalaya is the most extensive and recently evolved mountain system on Earth (length=2400km; width=240km; elevation=75-8800m), with a global significance underscored by its large-scale lithospheric, cryospheric, and atmospheric interactions [1]. These have not only driven global climate, but also defined the cultural and biological endemism of the region [2]. Massive, tectonically derived mountain chains such as the Alps and the Himalaya are hypothesized as being fundamental to the formation of global biodiversity gradients via vicariance and local adaptation, with a significantly stronger signal in terrestrial rather than aquatic systems [3]. Here we test how orogeny (the deformation and folding of Earth’s crust by lateral compression) has contributed to the diversification of freshwater fishes broadly across Asia. We do so by evaluating the phylogeography of an endemic high-elevation fish, the Snowtrout (Schizothorax: Cyprinidae).
Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes

Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performing distinct functions. In each case, these large periodic transcriptional programs are controlled by gene regulatory networks (GRNs), and it has been shown through genetics and chromosome mapping approaches in model systems that at the core of these GRNs are small sets of genes that drive the transcript dynamics of the GRNs. However, it is unlikely that we have identified all of these core genes, even in model organisms. Moreover, large periodic transcriptional programs controlling a variety of processes certainly exist in important non-model organisms where genetic approaches to identifying networks are expensive, time-consuming, or intractable. Ideally, the core network components could be identified using data-driven approaches on the transcriptome dynamics data already available. This study shows that a unified set of quantified dynamic features of high-throughput time series gene expression data are more prominent in the core transcriptional regulators of cell and circadian cycles than in their outputs, in multiple organism, even in the presence of external periodic stimuli. Additionally, we observe that the power to discriminate between core and non-core genes is largely insensitive to the particular choice of quantification of these features. There are practical applications of the approach presented in this study for network inference, since the result is a ranking of genes that is enriched for core regulatory elements driving a periodic phenotype. In this way, the method provides a prioritization of follow-up genetic experiments. Furthermore, these findings reveal something unexpected—that there are shared dynamic features of the transcript abundance of core components of unrelated GRNs that control disparate periodic phenotypes.
PHYLOGENETIC RELATIONSHIPS IN THE CRASSULACEAE INFERRED FROM CHLOROPLAST DNA

A restriction-site analysis of chloroplast DNA from 44 species, representing 19 genera and all six subfamilies of the Crassulaceae was conducted using 12 restriction endonucleases. A total of 969 variable sites was detected, 608 of which were phylogenetically informative and used in parsimony analysis. Estimated values of nucleotide sequence divergence were used to construct a distance tree by the neighbor-joining method. Maximum sequence divergence in the family was --7%. Different tree inference methods yielded only moderately different topologies. The amount of support for the monophyletic groups obtained in the Wagner parsimony analysis was evaluated by bootstrap and decay analysis. There is very strong support for a basal division of the family, which separates the monophyletic subfamily Crassuloideae from all other taxa. Four of the six traditionally recognized subfamilies are indicated to be polyphyletic. These include the Cotyledonoideae, Sempervivoideae, Sedoideae, and Echeverioideae. The Kalanchoideae and the genera Cotyledon and Adromischus exhibit low levels of cpDNA sequence divergence relative to one another, suggesting a relatively recent radiation. The genera Sedum and Rosularia are indicated to be polyphyletic. Sedum comprises sister taxa of most of the other genera of the family.
Avaliação técnico-econômica da colheita manual e mecanizada da cana-de-açúcar (saccharum spp) na região de Bandeirantes: Pr

A pratica da queima antes da colheita da cana-de-acucar vem sendo muito questionada, tanto pelo poder publico quanto pela sociedade, preocupada com as questoes ambientais. A colheita mecanizada da cana sem queima e apontada como um dos possiveis metodos para evitar a queima, e ainda nao esta sendo utilizada na regiao de Bandeirantes-PR. Neste trabalho avaliou-se a viabilidade tecnica-economica da utilizacao de colhedoras automotrizes de cana-de-acucar sem queima em toletes, comparando com o custo da colheita manual da cana queimada, de modo a fornecer subsidios que auxiliem no planejamento de investimentos agricolas. As determinacoes de campo foram realizadas em area pertencente a Usina de Acucar e Alcool Bandeirantes. As variedades de cana-de-acucar, S accharum spp, utilizadas foram: RB 72-454, SP 81-3250 e RB 85-5113, plantadas em espacamento de 1,40 m em nitossolos com declividade inferior a 12%. Foram encontrados valores de 3,06 US$. t -1 para o custo da colheita mecanizada da cana sem queima e de 4,14 US$. t -1 para a colheita manual da cana queimada, observando-se uma reducao de 32,74% em favor do custo da tonelada colhida mecanicamente. A capacidade operacional da maquina, estimada a 5,39 km.h -1 e com eficiencia de campo de 60%, foi calculada em 0,45276 ha.h -1.
Part I: Ectoparasite prevalences in sheep and in goats in and around Wolaita soddo, Southern Ethiopia

Cette etude conduite entre Novembre 2006 et Mai 2007 a pour objectifs d'identifier les ectoparasites et de determiner leur frequence chez les petits ruminants de la region de Wolaita Soddo (sud de l'Ethiopie). La presence d'ectoparasites ou de lesions cutanees a ete recherchee sur 214 moutons et 102 chevres des 2 sexes (169 femelles et 147 mâles) divises en jeunes et en adultes (72 et 244 animaux respectivement). La prevalence globale des ectoparasites a ete de 55.7 % (147 moutons et 29 chevres infestes), les moutons etant significativement plus souvent infestes que les chevres. En outre, au sein de la population ovine, une plus forte prevalence a ete observee chez les femelles (p < 0.05). Les principaux ectoparasites identifiees dans cette zone geographique ont ete les tiques (Rhipicephalus, Boophilus et Amblyomma) et les puces (Ctenocephales felis et canis a un moindre degre). L'infestation par les tiques s'est averee significativement plus frequente chez les ovins (31.78 %) que chez les caprins (18.63 %) et serait independante de l'âge ou du sexe. En revanche, les taux d'infestation par les puces etaient equivalents dans les 2 populations de ruminants, les femelles (essentiellement chez les chevres) ou les jeunes (surtout chez les ovins) etant infestes de facon privilegiee. Un seul cas de gale (Demodex caprae) a ete diagnostique chez une chevre et la pediculose due a Damalinia ovis n'a ete observee que chez les ovins avec une frequence relativement elevee (25.70 %). Bien que ces resultats soulignent une meilleure resistance des caprins aux ectoparasitoses et une frequence relativement faible des tiques dans le Sud de l'Ethiopie alors que la prevalence de la pediculose semble fortement soumise aux conditions climatiques durant la periode d'etude, cette etude montre que les ectoparasitoses affectent frequemment les petits ruminants et doivent etre urgemment controlees.
Quantitative analysis of cold hardening and dehardening in Lolium

A quantitative analysis of the process of hardening and dehardening is described for contrasting varieties of L. perenne and L. multiflorum. The data for L. perenne varieties are taken from a previous publication and new data are presented for L multiflorum. The analysis is discussed in terms of its potentiel to distinguish between proposed mechanisms of cold hardening and dehardening between varieties and species.
Gastropod shell utilisation pattern by the hermit crab Clibanarius symmetricus (Anomura: Diogenidae) in an Equatorial Amazon estuary

ABSTRACT Clibanarius symmetricus is a diogenid hermit crab that is highly abundant in rocky intertidal environments, including the rock outcrops of Amazon estuaries. This study characterises the C. symmetricus shell utilisation pattern in the Marapanim River estuary, Pará, Equatorial Amazon, based on the hypothesis that occupancy patterns would differ, in relation to biometry and diversity of occupied shells, from those of other regions in the range of this species due to the distinct and unique environmental characteristics of equatorial estuaries. Monthly samplings were carried out from August 2006 to July 2007, in the upper and lower areas of the mid-littoral during low tides. A total of seven gastropod species were found as shells occupied by hermit crabs: 93.33% were Thaisella trinitatensis shells, 2.00% Nassarius vibex, 2.00% Neritina virginea, 1.33% Natica marochiensis, 0.67% Parvanachis obesa, and, occasionally, Littorina flava and Phalium granulatum shells, each with only one occurrence (0.33%). Juveniles [cephalothoracic shield length (CL) of less than 3.6 mm] occupied a higher variety of shells, while adults occupied shells with larger meristic variation. Males occupied larger shells. The length of the animal was influenced by shell measurements (total width, aperture width and weight). Clibanarius symmetricus showed occupancy patterns generally similar to those of specimens of the same species previously studied in the Brazilian subtropical region, and this occupancy is explained by shell availability, shell size and weight, and hermit size. However, this study showed lower occupied shell species diversity, and the species with highest occupancy frequency (T. trinitatensis) was not reported in any previous studies on this hermit crab. In addition, the studied population differed in occupancy patterns, with differences between males and females, and between juveniles and adults.
Nitrogen stimulation of periphyton biomass in rivers: Differential effects of ammonium-N and nitrate-N

The ecological effects of wastewater treatment plant (WWTP) discharges into rivers typically include elevated periphyton biomass resulting from enrichment by dissolved reactive phosphorus (DRP), dissolved inorganic nitrogen (DIN), or both. WWTP discharges may transfer DIN to receiving water as ammonium-N (NH4-N) and, following nitrification steps, nitrate-N (NO3-N). The potential for NH4-N to exacerbate nuisance periphyton biomass compared to NO3-N is not well understood. Theoretically, NH4-N is the more energy-efficient source of N for algae, but its effect on algal growth rates depends on concentration, interaction with NO3-N, and environmental conditions, such as temperature. We investigated the relative importance of NH4-N and NO3-N in WWTP discharges by tracking periphyton biomass and algal assemblage composition in streamside channels for 27 d under 500 µg DIN/L comprising different proportions of NH4-N: 0.5% (low-NH4, ambient levels of NH4-N, 2.2 µg/L), 30% (medium-NH4, 160 µg/L), and 77% NH4-N (high-NH4, 389 µg/L). The DIN treatments had replete DRP (25 µg/L) and were compared to controls with no enrichment (control) and DRP enrichment only (P-control). Biomass was measured as chlorophyll a (Chl a) and ash-free dry mass (AFDM), which showed contrasting responses to different proportions of NH4-N enrichment. Chl a was higher under high-NH4 than under low-NH4 (p < 0.01, 50% higher at maximum Chl a on d 20). Under medium-NH4 and low-NH4, Chl a was not different from the controls and P-controls (p > 0.15). AFDM did not differ among the 3 DIN treatments (p > 0.11) but was higher in all DIN treatments than in the controls (p < 0.05). Algal assemblage composition discriminated the controls from all other treatments and the low-NH4 from high-NH4 treatments. The assemblage analyses indicated that high-NH4 favored enhanced cell division rates in small diatoms, especially Encyonema minutum. Higher Chl a/unit volume of small taxa than larger taxa likely explained elevated Chl a under high-NH4. The results illustrated that, with replete DRP, elevating DIN through enrichment with NH4-N may cause additional increases in periphyton biomass as Chl a compared to elevating DIN through NO3-N enrichment. Consequently, enhanced management to specifically reduce NH4-N outputs in WWTP discharges may assist in the control of nuisance periphyton downstream.
The polychaete cryptofauna from Cozumel Island, Mexican Caribbean

The polychaete cryptofauna collected in dead coral substrates in the shelf of Cozumel Island, Mexican Caribbean is analyzed here. Samples were taken with SCUBA diving on transects perpendicular to the coastline (depths 2 to 22 m). Nineteen families, 36 genera and 42 species were found. The Eunicidae dominate in density and species richness with a mean density of 315 ind m -2 (seven species), followed by the Syllidae with 94 ind m -2 (five species) and the Amphinomidae with 73 ind m -2 (three species). Eunice cariboea, a characteristic species of coral reef areas in the Gulf of Mexico (representing here 36% of the total collected, and Syllis (Typosyllis) ortizi are the dominant species in Cozumel. There is some effect related to depth and anthropogenic influence, on the density and species richness because the lowest values were found in the shallower sampling zones (approximately 332 ind m -2 and 20 species, versus 931 ind m -2 and 32 species, in the deeper zones) and the populations' composition at each site is quite different. Compared with other areas sampled in the extensive Mexican coral reef environments in the Gulf of Mexico, in Cozumel the densities of polychaetes and species richness are high.