Miracle-dz/UniFAR-FTUs huggingface dataset:
Bloodlines: mammals, leeches, and conservation in southern Asia

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to find mammals in a given area. While these invertebrate-parasite-derived DNA (iDNA) methods are promising, most of the leech species utilized for this type of survey remain unevaluated, notwithstanding that their diversity varies substantially. Here we examine approximately 750 individual leech specimens in the genus Haemadipsa across a large range in southern Asia (Bangladesh, Cambodia, and China), specifically reviewing the diversity of mammals they feed on and their own genetic structuring. Leeches were found to feed on a considerable variety of mammals, corroborating prior studies. Additionally, leeches were found to have fed both on bats and on birds, neither of which has previously been recorded with this method. The genetic structuring of the leeches themselves revealed 15 distinct clades of which only two precisely corresponded to previously characterized species, indicating that much work is needed to finalize classifications in this genus. Most importantly, with regards to mammal conservation, leeches in these clades appear to feed on a broad range of mammals.
Application of treated wastewater on yield and heavy metals content of seeds in sunflower cultivars.

Treated wastewater could be considered as a new water resource in agriculture especially in arid and semi-arid regions of the world such as Iran. Two one-year field experiments were carried out to determine the effects of municipal treated wastewater on yield and seed heavy metals content of sunflower cultivars, in Research Farm of Yazd Municipal Wastewater Purification Station during 2015 and 2016. The climate of the region was hot and dry according to Koppen climate classification system. Experiment was arranged as split plot based on randomized complete block design with three replicates. Treatments were three irrigation water types as main plot consisted (“WW”: irrigation with treated municipal wastewater thoroughly, “WW/FW”: irrigation with treated wastewater/fresh water alternatively and “FW”: irrigation with fresh water thoroughly) and three sunflower cultivars (Azargol, Record, and Farrokh) as subplots. The following parameters were assessed: plant height (cm), head diameter (cm), seed numbers per head, unfilled seeds per head, seed and biological yield (kg/ha) and seed heavy metals content. Results showed that the highest plant height (194 cm) obtained in Record and the highest head diameter (21.5 cm) obtained in Farrokh cultivars, which were irrigated by WW. Treated municipal wastewater also increased seed yield by 10.7% compared to FW treatment. The highest (5029 Kg/ha) and lowest (3734 Kg/ha) seed yield were obtained in Azargol and Farrokh that irrigated with WW and WW/FW treatment, respectively. However, application of treated municipal wastewater lead to accumulation of trace elements (Fe, Mn, Zn, Cu, Cd, Pb, and As) in seeds; but, the values of all the elements were below the permissible limits recommended by World Health Organization. It is concluded that WW could be used for irrigating sunflower crop without worrying about the accumulation of toxic substances.
The separation of auditory experience and the temporal structure of MEG recorded brain activity

Do brain oscillations limit the temporal dynamics of experience? This pre-registered study used the separation of auditory stimuli to track perceptual experience and related this to oscillatory activity using magnetoencephalography. The rates at which auditory stimuli could be individuated matched the rates of oscillatory brain activity. Stimuli also entrained brain activity at the frequencies at which they were presented and a progression of high frequency gamma band events appeared to predict successful separation. These findings support a generalised function for brain oscillations, across frequency bands, in the alignment of activity to delineate representations.
Considerations on the future biomass production potential of Iceland, and what role that could have in future fuel supply and carbon balances

ABSTRACT This study suggests that Iceland may be able to produce sufficient liquid hydrocarbon fuels from biological sources in the future to substitute the Icelandic 2016 consumption of fossil fuels, by using forest products. The authors evaluate a strategy to put forest on up to 35,000 km2 in Iceland to 2050. The preliminary study shows that Iceland could reach climate neutrality around 2050 and be a significant net carbon sequester for the next 250 years. Approximate estimates suggest that the total forest biomass production could reach about 10 million m3yr−1, comprising 3.1 million m3yr−1 of roundwood, 3.1 million m3yr−1 for generic biomass, and about 4.2 million m3yr−1 woody material for biofuel use. This could result in a net annual carbon dioxide sequestration of 2–2.5 mill ton CO2 yr−1 by 2100. The calculations suggest that such an afforestation and land restoration undertaking would be long term profitable in economic terms and that the payback time would be about 2050. The method applied in this study is that of a static mass balance calculations at different time points into the future. Parallel to this work, a full integrated regional forest production model is being developed and will be applied to this issue.
Combining Computer Simulation with Physical Simulation: An Attempt to Validate Turf Runoff Models

Predicting the off-target movement of agrochemicals applied to turf is an essential component for assessing risk to aquatic environments. For surface transport, a fully validated model does not exist. Such a model is required to make cost effective risk assessments and regulatory evaluations. To address this deficiency, a turf model validation program is outlined in this paper. The effect of turf characteristics on the fate and movement of pesticides is presented followed by the discussion of the selection for a proper turf runoff model. The design and implementation of small plot runoff studies and their usefulness in model validation are discussed. The procedures of model calibration and model verification are explained for model validation purpose.
Estimation of Genetic Parameters for 305 Days Milk Yields and Calving Interval in Xinjiang Brown Cattle

This study was conducted to estimate variance components and genetic parameters for 305 days mature equivalent milk yields (MEM) and calving interval (CAI) of registered Xinjiang Brown cattle. The total records were 3940 including 2579 for 305-day MEM and 1970 for CAI, which were collected from Xinjiang Urumqi Cattle Breeding farm in China with calving records from 1990 to 2008. Genetic parameters were obtained by multiple trait derivative-free restricted maximum likelihood (MTDFREML) using animal model. The model included year, season, parity and calving interval of calving for 305 days MEM, and year, season and parity of birth for CAI as fixed effects. Heritability for 305 days MEM was moderate (0.39) and in the same range of parameters estimated in management systems with medium production levels. Heritability of calving interval was small (0.02) as fertility traits for Xinjiang Brown cattle. Estimates of genetic and environmental correlations between 305 days MEM and CAI were 0.47 and 0.37, respectively. Estimates of genetic variation and heritability indicated that selection would result in genetic improvement of production traits. Estimates of both heritability and genetic variation for CAI were small, which indicates that genetic improvement would be difficult.
Génération d'anticorps monoclonaux neutralisants et dérive antigénique du virus influenza pandémique A(H1N1) 2009

v Table des matières . vii Liste des tableaux . xi Liste des figures . xiii Liste des abréviations . xv Remerciements . xxi Avant-Propos . xxiii 1. Chapitre 1 : Introduction . 1 1.1 Historique du virus influenza . 1 1.2 Structure et classification . 2 1.2. 1 Le génome viral . 4 1.2. 1.1 Polymérase (PA, PB1 et PB2) . 5 1.2.2. 2 Nucléoprotéine (NP) . 6 1.2.2.3 Matrice (M1 et M2) . 6 1.2.2.4 Protéines Non-Structurales (NS1 et NS2/NEP) . 6 1.2.2.5 Neuraminidase (NA) . 7 1.2.2.6 Hémagglutinine (HA) . 10 1.3 Cycle réplicatif . 10 1.4 Hémagglutinine . 14 1.4. 1 Variants antigéniques de la HA . 18 1.4. 2 Sites antigéniques de la HA . 20 1.4. 3 Site d’attachement (RBS) . 23 1.4. 4 Sites de glycosylation . 25 1.4. 5 La tige HA2 de fusion . 26 1.5 Épidémiologie de l’influenza . 27 1.5. 1 Glissement ou dérive antigénique . 28 1.5. 2 Cassure antigénique . 30 1.5. 3 Grandes épidémies et pandémies . 30
Isolation and Identification of Yeasts from Indoor Swimming Pools in Duhok City With Special Concern to The Effect of Some Disinfectant Agents

The present study was conducted to study the level of yeast contamination in indoor public swimming pools in Duhok city. A total of 230 samples (50 water sample) were taken from swimming pool water and (180 swab samples) were taken from walls, flour of bathrooms, dressing rooms and flour around the pool in five indoor public swimming pools from September 2014 to February 2015. All samples were examined for the presence of yeasts using three culture media (Potato Dextrose Agar, Malt Extract Agar and Sabouraud's Dextrose Agar). The highest number of Yeast genera was in November (6) followed by October (5), December and January (4) while the lowest number was in September (3). Eleven (11) isolates yeasts were selected randomly for in vitro sensitivity to the disinfectant agents {Chlorine, Chloroxylenol and Hydrogen peroxide (H2O2)}. All tested isolates were highly sensitive to chlorine, Chloroxylenol and H2O2. The MIC value of chlorine for most of them was 0.01 % and for Chloroxylenol was 0.1 % except Candida tropicalis and C. glabrata. Regarding the effect of H2O2 the MIC value ranged from 0.1% - 12.8 %.
New species of the Rhinella crucifer group (Anura, Bufonidae) from the Brazilian Cerrado

A new species of Rhinella of Central Brazil from the Rhinella crucifer group is described. Rhinella inopina sp. nov. is restricted to the disjunct Seasonal Tropical Dry Forests enclaves in the western Cerrado biome. The new species is characterized mainly by head wider than long, shape of parotoid gland, and oblique arrangement of the parotoid gland. Data on natural history and distribution are also presented.
Aspects and prospects of algal carbon capture and sequestration in ecosystems: a review

ABSTRACT Long-term storage of carbon dioxide (CO2) and other forms of carbon in non-atmospheric reservoirs is called carbon sequestration. Selective anthropogenic enrichment of the atmospheric carbon pool is causing dire environmental problems, thereby necessitating remediation by mitigation. Algae possess efficient carbon concentrating mechanisms and consequently high photosynthetic rates which make them suitable candidates for biosequestration of CO2. Globally, nearly half of the atmospheric oxygen is generated by algal photosynthesis despite the fact that algae account for less than 1% of photosynthetic biomass. In water bodies, algae are responsible for creating the ‘biological pump’ that transports carbon from the upper sunlit waters to the depth below. A diverse array of photoautotrophs ranging from prokaryotic cyanobacteria to eukaryotic algae such as Chlorophytes, and even protists like euglenoids, contribute to this ‘biological pump’. It operates in a variety of aquatic ecosystems ranging from small freshwater ponds to the oceans where it has been most extensively studied. Two separate but intricately linked processes constitute this ‘biological pump’, viz. the ‘organic carbon pump’ and the ‘calcium carbonate pump’. The present review discusses the natural CO2 sequestration processes carried out by algae and cyanobacteria in their native ecosystems.
Amino acid homeostasis in Caenorhabditis elegans lacking the intestinal peptide transporter PEPT-1 and identification of PEPT-1 modulator proteins

The intestinal peptide transporter PEPT-1 is responsible for the absorption of amino acids in di- and tripeptide bound form. The present work used the model organism Caenorhabditis elegans to assess the role of the two amino acid transporters AAT-6 and Y4C6B.2 and whether those are able to compensate the lack of the peptide transporter. Moreover, a RNAi-screen was used to identify new proteins (F26E4.12, ZC416.6, R11H6.1) that appear to specifically regulate PEPT-1 function most likely via altered cellular amino acid concentrations and the signal transduction pathway involving TOR (target of rapamycin) complex 1 and 2.
Assessment of the reactions of pure lines selected from Turkish bread wheat landraces against bunt disease (Tilletia foetida) with the GGE-biplot method

Abstract The present research was conducted to determine the reactions of 200 pure lines selected from bread wheat landraces collected from 18 provinces and seven regions of Turkey against bunt disease (Tilletia foetida) under field conditions for 3 years. Bunt disease reactions of pure lines were assessed based on the infected spike/total spike ratio. For visually assessed materials, the GGE-biplot method, where G = genotype effect and GE = genotype-by-environment effect, was used to group the reactions against bunt disease. Fifty-nine pure lines showed high resistance (with infection rates ranging from 0.1 to 10%); 24 in the moderate resistance (with infection rates ranging from 10.1 to 25%); 75 in the moderate susceptibility (with infection rates ranging from 25.1 to 45%); 38 in the susceptibility (with infection rates ranging from 45.1 to 70%) and finally four in the highly susceptibility (with infection rates of >70.1%). PC1 and PC2 of the GGE-biplot graph created over the years explained 76.49% of the total variation. The GGE-biplot graph provided efficient identification of resistant genotypes. The lowest PC1 values and PC2 values close to 0.0 explained the resistance of pure line to bunt disease best. The resistance of pure lines to bunt disease over the biplot decreased from the first section through the last section. Based on the results of present study, 19 pure lines (located within the first circle of the biplot graph) were selected for resistance breeding programmes against the diseases.
The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)

We describe a new species of litter frog from western Brazilian Amazon previously referred to as Allobates femoralis (Boulenger 1883). The new species is allopatric to A. femoralis and its known occurrence is restricted to terra-firme forests on the left bank of the upper Madeira River and southeastern State of Acre. This species is distinguished from A. femoralis and from other species in the A. femoralis group by presenting two-note advertisement calls and conspicuous reddish-orange color on ventral surfaces of hind limbs and posterior abdomen. Phylogenetic analyses based on a fragment of the 16S rRNA mitochondrial gene suggest the new species is the sister group to a clade referred to as A. femoralis occurring in southern State of Acre, from which it is distinguished by six unambiguous nucleotide substitutions, in addition to exclusive advertisement calls and color patterns. The new species is more distantly related to A. femoralis sensu stricto occurring near the A. femoralis type locality in the Peruvian Amazon. Summarizing evidence from molecular phylogenetic analysis, genetic distances and available data on advertisement calls, we identify one possible case of genetic introgression between lineages in this group and highlight the potential for the description of more species within the A. femoralis complex.
Soybean (Glycine max) Yield and Quality Responses Associated with Wild Poinsettia (Euphorbia heterophylla) Control Programs

In field studies conducted over 2 yr, POST applications of chlorimuron, imazaquin, fomesafen, or acifluorfen following PRE applications of clomazone, metribuzin, or metribuzin plus chlorimuron enhanced wild poinsettia control when compared with the PRE herbicides applied alone. Wild poinsettia control was highest for imazaquin compared with other PRE treatments and with the exception of fomesafen, applications of POST herbicides following imazaquin PRE did not improve weed control. With the addition of POST herbicides, soybean yields were generally not increased, but moisture content in one year and foreign material content both years were reduced. In other studies, early POST applications (2 to 8 cm) of fomesafen, imazaquin, acifluorfen, lactofen, and chlorimuron controlled wild poinsettia better than late POST applications (10 to 15 cm) in only one year. Soybean yields both years were generally similar regardless of herbicide application time.
NDC80 clustering modulates microtubule dynamics under force

Multivalency, the presence of multiple interfaces for intermolecular interactions, underlies many biological phenomena, including receptor clustering and cytosolic condensation. One of its ultimate purposes is to increase binding affinity, but systematic analyses of its role in complex biological assemblies have been rare. Presence of multiple copies of the microtubule-binding NDC80 complex is an evolutionary conserved but poorly characterized feature of kinetochores, the points of attachment of chromosomes to spindle microtubules. To address its significance, we engineered modules allowing incremental addition of NDC80 complexes. The modules’ residence time on microtubules increased exponentially with the number of NDC80 complexes. While modules containing a single NDC80 complex were unable to track depolymerizing microtubules, modules with two or more complexes tracked depolymerizing microtubules and stiffened the connection with microtubules under force. Cargo-conjugated modules of divalent or trivalent NDC80 stalled and rescued microtubule depolymerization in a force-dependent manner. Thus, multivalent microtubule binding through NDC80 clustering is crucial for force-induced modulation of kinetochore-microtubule attachments.
SWORD: GENETIC ALGORYTHM TOOL FOR PROTEIN-RNA INTERACTION MOTIFS RECOGNITION

Recognition of potential for protein-RNA interaction is an important problem in bioinformatics. The solution may present a clue for understanding gene regulation. Formalization of the problem leads to in silico search for a complex motif in the 15-letter UIPAC alphabet in RNA sequences considering their secondary structure. The genetic algorithm with island modification was used to solve the related discrete optimization problem. The algorithm named SWORD was implemented on GPU and CPU. The comparison has shown a significant performance advantage of the GPU implementation. The algorithm was applied for searching RNA-motifs interacting with Hu antigen R (HuR) protein. The result achieved is better than that obtained in the previous work based on fitness-function criterion.
Highly efficient extraction of EPA/DHA‐enriched oil from cobia liver using homogenization plus sonication

Cobia, Rachycentron canadum, is a species of marine finfish with emerging global potential for offshore aquaculture. The fillet processing by-product, cobia liver, can be considered an accessible source of EPA/DHA-enriched oil. Oils are mainly extracted with hexane in the oil industry; however, extractability is greatly decreased in wet biomass as the hydrophilic surface hinders the penetration of hexane into the tissue matrix. In this study, the feasibility of agitated extraction (AE), ultrasonic extraction (UE), Soxhlet extraction (SE), homogenizer extraction (HE), and homogenizer extraction plus sonication (HES) was evaluated. HE and HES showed higher extraction efficiency than AE, UE, or SE. The highest yields: 45.7% and 50.2%, were obtained from using HE for 2 min and HES for 120 min, respectively. Both yields were close to the fat content of cobia liver, indicating that the lipids were effectively extracted. The fatty acid profiles revealed that the highest contents of 5.2% eicosapentaenoic acid (EPA) and 19.7% docosahexaenoic acid (DHA) were obtained from HE and HES, respectively. These results demonstrated that HE and HES were highly efficient and the most useful among all tested methods for lipid extraction from wet biomass. Practical applications: Increasing the value of low quality processing waste is important in the food and nutraceutical industries. Cobia liver, comprising 5% of total fish mass, is a potential source of EPA/DHA-enriched fish oil. EPA and DHA decompose easily when exposed to high temperatures for a long time. HE has an advantage over traditional extraction methods due to its ability to operate at a low temperature for a short period (2 min), thereby preventing EPA and DHA decomposition. Cobia are already bred in the aquaculture industry; their livers are readily available by-products obtained after fillet processing. The oils extracted from cobia liver have high levels of EPA and DHA, therefore it is an excellent raw material to produce EPA/DHA-enriched oil. Wet biomass contains a high amount of moisture, creating mass transfer resistance for hexane penetration into the tissue matrix. Homogenizer extraction grinds the tissue matrix, disrupting the cell and dispersing the water into solvent phase. Schematic representation of the extent of cell disruption during homogenizer extraction shows its effect on the rate of lipid release.
The presence of the brown bear Ursus arctos in Holocene Britain: a review of the evidence

1. The brown bear, Ursus arctos, was Holocene Britain’s largest carnivoran and has appeared in recent rewilding discussions. 2. Despite widespread interest, we know very little about the species in Holocene Britain as few studies have been undertaken. This paper draws together information on the brown bear to examine the presence and extinction of bears through examination of the archaeological and palaeontological evidence. 3. Data were collected from published literature and museum catalogues. Information on the chronological date of the sites, number of specimens, and the body parts present were particularly sought. 4. A total of 86 sites were identified, 57 are well dated, 27 are of uncertain date but likely to be Holocene, and two have uncertain identifications. Very few specimens from non-archaeological sites (i.e. fens and caves) are well-dated, skewing the data towards anthropogenic sites such as settlements, castles, and graves. 5. Analysis of body part representation shows that the bear bones found in the Bronze Age, Iron Age and most of the early medieval period are from skins. All body parts are present during the Romano-British, medieval, and post-medieval period, indicating that live bears were present, and were probably imported for entertainment. 6. It seems the brown bear was rare throughout the Holocene, and based on current evidence two extinction scenarios can be put forward: extinction in the late Neolithic/early Bronze Age, or extinction in the early medieval period.
Limited polymorphism in two spittlebugs, Philaenus spumarius (Linnaeus) and P. signatus Melichar (Hemiptera: Cercopidae), in island populations from Western Turkey

Two colour polymorphic spittlebug species, Philaenus spumarius and Philaenus signatus were recorded for the first time in Gökçeada, Turkey. Three non-melanic – POP (populi), TYP (typicus), and VIT (vittata) – and three melanic MAR – (marginellus), FLA (flavicollis), and LCE (leucocephalus) – colour/pattern phenotypes of P. signatus were found. Philaenus spumarius was represented only by POP and TYP, which are expressed by a single pigmentation allele. The other six alleles were absent on this island, although they are found in most populations throughout the world. Stochastic events such as random genetic drift may be the reason for shaping the polymorphism of these two sympatric species in Gökçeada. Thus, the absence of pigmentation alleles possibly indicates the founder effect.