Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into hepatitis B and hepatitis delta virus entry

Notwithstanding the medical importance of the HBV infection, our understanding of how this pathogen enters hepatocytes is incomplete. This reflects a long-lasting dependence of in vitro infection studies solely on primary human hepatocytes, which are difficult to obtain and maintain in a susceptible state. The establishment of a polarizable HBV-susceptible human hepatoma cell line (HepaRG) and the utilization of Tupaia belangeri hepatocytes (PTHs) resolved this issue. Since then, important insight into viral and cellular determinants participating in HBV binding and infection have been achieved. We now know that the large viral surface protein (L) plays a pivotal role in HBV entry. It mediates diverse functions, commencing binding of virions to heparan sulfate proteoglycans at the hepatocytes surface as a prerequisite for entry. Subsequently, (a) highly specific event(s) involving the myristoylated N-terminal preS1 subdomain of L, as well as the cytosolic and antigenic loops of the S-domain, initiates a s.
Soil biota associated with endophyte-infected tall fescue in the field.

Invertebrates present in soil samples taken from plots of tall fescue (Festuca arundinacea) infected with two non-toxic strains of Neotyphodium endophyte (AR501 and AR542) at Aorangi near Palmerston North and one strain (AR501) at Lincoln in Canterbury, together with endophyte-free controls at both sites, were determined in autumn 2002. Roots taken from these samples were stained and checked for the presence of arbuscular mycorrhiza. At Lincoln, numbers of root aphid (Aploneura lentisci) associated with plants infected with AR501 were signifi cantly less than those on endophyte-free plants, while grass grub numbers (Costelytra zealandica) did not differ between treatments. Benefi cial invertebrates, Collembola, mites and earthworms, were not affected by endophyte at either site and neither was colonisation of roots by mycorrhiza.
Performance of a batch-fed High Rate Algal Pond for animal waste treatment

Two 13.1 m2 ponds at Auchincruive, Scotland, were used to treat the diluted liquid phase of separated piggery slurry, in order to identify the climatic and pond operational parameters which influence biomass production and nutrient removal in these systems at a constant areal loading rate. The ponds were operated from April to November at 0.12, 0.24 and 0.34 m depth as batch-fed reactors. Average 5-day biochemical oxygen demand (BOD5) loading was 6.24 g m−2 d−1 and the ponds were mixed at a mean surface velocity of 0.20 m s−1. Dry matter, chlorophyll, optical density (OD560), NO3, NO2, NH4, urea and total phosphorus were determined daily. Temperature, pH, dissolved oxygen and incident irradiance were monitored continuously. Correlation and multiple regression analyses were used to determine significant interactions between environmental factors, biomass production and nutrient removal. Both chlorophyll a and optical density were accurate predictors of dry matter biomass. All measures of pond biomass were .
Grow-out culture of abalone Haliotis tuberculata coccinea Reeve, fed land-based IMTA produced macroalgae, in a combined fish/abalone offshore mariculture system: Effect of stocking density

Haliotis tuberculata coccinea has been identified as a target species for European aquaculture development, in order to fulfil the rising demand for abalone. The effects of different stocking densities on the growth performance, feed utilization and survival of two different initial size groups (30 and 40 mm) of abalones, during the final grow-out to cocktail/market size (45–60 mm), were determined over a 6-month period. Trials were performed in abalone cages installed in a commercial open-sea cages fish farm. Animals were fed the red algae Gracilaria cornea and the green one Ulva rigida, both obtained from a land-based integrated multi-trophic aquaculture system. Survival rates were very high (94–98%) regardless the density employed. Sustained high linear growth was recorded both in shell and weight. However, a 17–19% reduction in weight gain was obtained by doubling the initial stocking density, suggesting a higher competition for space or food. Nevertheless, the high growth performance (70–94 lm day � 1 ; 250–372% weight gain) and survival attained, even at high densities, denoted the suitability of the offshore mariculture system as well as the biofilter produced macroalgae for grow-out culture of H. tuberculata coccinea that overall could reach cocktail/commercial size in only 18–22 months.
Effect of a mannanoligosaccharide-supplemented diet on intestinal mucosa T lymphocyte populations in chickens challenged with Salmonella Enteritidis

SUMMARY Salmonellosis is one of the most common worldwide zoonosis, and the Enteritidis and Typhimurium serotypes are most prevalent. In this study, we evaluated the effects of a diet supplemented with mannanoligosaccharides (MOS) on CD3+ ,C D4+ ,C D8+, and goblet cell counts in the intestines of broilers vaccinated and challenged with Salmonella Enteritidis. The evaluation was based on randomized experiments including 45 chickens divided into 3 experimental groups. Group 1 received a nonsupplemented control diet. Group 2 received a diet supplemented with 1 kg MOS/t from d 1 to 21 and 0.5 kg MOS/t from d 22 to 56. Group 3 received a diet supplemented with 2 kg MOS/t from d 1 to 21 and 1 kg MOS/t from d 22 to 56. Chickens fed the lower level of MOS demonstrated reduced fecal shedding of Salmonella 14 d after being challenged (P < 0.05). Both groups of MOS-supplemented chickens showed an increase in CD4+ and CD8+ cell counts in the ileal and cecal mucosa after being challenged with Salmonella Enteritidis (SE). Supplementation with MOS increased the specific T lymphocyte infiltration in the intestinal mucosa of chickens vaccinated and challenged with Salmonella Enteritidis.
The recognition of infraspecific taxa in Juniperus brevifolia (Cupressaceae)

Based on morphological, genetic and ecological data, we describe new infraspecific taxa of the Azorean endemic Juniperus brevifolia . J. brevifolia subsp. maritima is an erect shrub or small tree, found in Flores, Terceira, Pico and Sao Jorge , in coastal scrubs below 100 m. J. brevifolia subsp. brevifolia occurs in all islands of the archipelago except Graciosa, between 300 and 1500 m. J. brevifolia subsp. brevifolia var. brevifolia is a small to medium tree found between 300 and 1000 m. J. brevifolia subsp. brevifolia var. montanum is a small prostrate shrub, common in mountain scrubs and blanket bogs, between 850 and 1500 m. The most striking morphological differences of subsp. maritima are the larger leaves, seed cones and seeds. Phenological patterns of the subspecies also differ, notably in the periods of seed maturation and pollination. The distribution of taxa within islands is peripatric. Coastal populations (subsp. maritima ) are small and isolated from the usually much larger subsp. brevifolia populations, above 300 m. In subsp. brevifolia the varieties are parapatric, since their ranges are adjacent to each other, occurring together in narrow contact zones.
Size- and sex-based habitat partitioning by Lepetodrilus fucensis near hydrothermal vents on the Juan de Fuca Ridge, Northeast Pacific

This study examines habitat partitioning by a hydrothermal vent limpet, Lepetodrilus fucensis, along environmental gradients and among vents with differing levels of flux. To test for spatial patterns in size structure, two distances from isolated vent flows were sampled (0–25 cm and 51–75 cm). Lepetodrilus fucensis displays a size gradient: juveniles are rare in flow (relative abundance 95%, 2616 ± 2002 individualsdm–2). Next, sex-based habitat partitioning was examined. High flux locations are female-biased (proportion male = 0.34 ± 0.07), whereas males are overrepresented peripherally and at waning vents (0.64 ± 0.08). The spatial mismatch between the sexes within a vent is driven by differential habitat occupation at decimetre scales. One hypothesis to explain this pattern is that females suffer a higher cost of reproduction and outcompete males for habitats with high food availability. Indeed, relatively higher percentages of females in waning vents had empty gonads in comparison with males (32%–78% vs. 0%–16%, respectively). Furthermore, females transplanted to the vent periphery for one year displayed much lower survivorship than males (2% vs. 27%). This finding suggests that differential survivorship between the sexes when food is limited can yield male-biased populations at waning vents.
Observations on the predation of the snail Huttonella bicolor on the snail Allopeas gracile

The predatory snail Huttonella bicolor (Hutton 1834) (Gastropda: Streptaxidae) was encountered along with Allopeas gracile (Hutton 1834) (Gastropoda: Subulinidae) during a survey of small land snail species from several terrestrial habitats in Kolkata, India. An evaluation of the predation of H. bicolor as a function of prey size and predator density was carried out using A. gracile as a model prey snail. The predatory interactions were noted with an increasing ratio of 1, 2 and 4 H. bicolor against 10 A. gracile of varied size classes in a defined terrarium. At the end of a 48 h period of exposure, H. bicolor was observed to consume on an average 5.32 ± 0.50 snails depending on the size class and the predator density. The predation pattern varied significantly with the prey size class, as revealed through the logistic equation, y (prey-consumed) = 1 / (1 + exp (-(0.97–0.71*size class-prey))). In a separate experiment, it was observed that the presence of H. bicolor induced a reduction in the fecundity in A. gracile, as revealed through the logistic regression, y (egg laid) = 1 / (1 + exp(-(3.45–0.67*predator-density))). The direct effect of predation and indirect effect of oviposition reduction reflect the efficacy of H. bicolor on population regulation of A. gracile. In view of conservation biological control, the use of the snail H. bicolor as a biocontrol agent may prove beneficial in situations where A. gracile is a pest.
The fatty acid composition of muscles and fat depots of ostriches as influenced by genotype

Three genotypes of ostrich (South African Black, Zimbabwean Blue Necks and crosses between Zimbabwean Blue Neck males x South African Black females) were used to investigate the influence of genotype on the fatty acid composition of the musculus gastrocnemius and musculus iliofibularis, and abdominal and breast fat depots. Total saturated fatty acids in both the m. gastrocnemius and m. iliofibularis were higher in crosses (36.4% and 35.9%) than in South African Black ostriches (32.9% and 30.4%), whereas mono-unsaturated fatty acids were highest in South African Black ostriches. Total polyunsaturated fatty acids in the m. gastrocnemius were lowest in South African Black ostriches (26.5%) compared with the Zimbabwean Blue Necks (33.2%). Neither the ratio of polyunsaturated to saturated (0.73 to 0.99) nor n-6 to n-3 (1.6 to 2.2) fatty acids were influenced by genotype, although the ratio of polyunsaturated to saturated fatty acids in Zimbabwean Blue Necks was higher in the m. gastrocnemius (0.99) than in the m. iliofibularis (0.73). Differences in individual fatty acids were prominent in the breast fat, and total saturated and mono-unsaturated fatty acids differed between genotypes in both breast and abdominal fat. Only the ratio of polyunsaturated to saturated fatty acids in the fat depots differed between South African Black (0.48) and Zimbabwean Blue Neck ostriches (0.42). The latter ratio was higher in the breast (0.50) than abdominal (0.42) fat in Zimbabwean Blue Necks. These results indicate that crossbreeding of different genotypes of ostriches reared under similar conditions does influence the overall fatty acid profiles of meat and fat.
Metamorphic Changes in the Velar Musculature, Head and Shell of some Prosobranch Veligers

The velum of Lacuna vincta (Montagu) and Nassarius incrassatus (Ström) is retracted into the shell by 2 dorsal and 2 ventral groups of muscles, bilaterally arranged, which are components of the larval retractor muscle. Each dorsal group passes forward from its area of origin on the shell to the dorsal part of the head where some fibres insert and adjacent ones enter the velar fold. The velum is bilobed in Lacuna and the muscles radiate through the dorsal half of the lobe to insert on the anterior and posterior surfaces and ciliated edge, whereas Nassarius has 4 long velar lobes, 2 dorsal and 2 ventral, and the muscles form a median bundle from which fibres radiate to similar insertions. Each ventral group of muscles passes through the nerve ring lateral to the developing radular sac in Lacuna and to the developing proboscis in Nassarius, and muscles accompanying them insert on the sac and proboscis wall. Anterior to the ring some muscles insert on the lips and the buccal wall posterior to the oral sphincter and alongside attachments of muscles from the foot. The majority pass to the mentum, a median protuberance of the lower lip with non-vibratile cilia, where right and left ventral cephalic retractors and muscles from the foot converge. The pedal muscles attach here and from this area muscles radiate to multiple insertions on the head and ventral half of the velum. This arrangement of the ventral muscles allows the increased angle of mobility required by the ventral areas of the velum in swimming and feeding and the intimate contact between velum and foot.
The taxonomy of Chenopodium desiccatum and C. nitens, sp. nov.1

Abstract Fruits and seeds of the genus Chenopodium have been considered taxonomically important but have not been fully studied or utilized. We discuss the importance of describing fruit and seed morphology at low magnification to improve the identification and taxonomy of North American taxa of Chenopodium, which in a large part remains unresolved. A new species, Chenopodium nitens Benet-Pierce & M. G. Simpson, is described, integrating these reproductive characters with general vegetative characters.
VASCULAR ANATOMY OF THE FLOWER OF HYACINTHOIDES NON‑SCRIPTA (L.) CHOUARD EX ROTHM. A NEW INSIGHT ABOUT A COMPLEX PLACENTATION PATTERN IN ASPARAGACEAE

Floral vasculature and gynoecium architecture were revised in Hyacinthoides non-scripta (L.) Chouard ex Rothm. Receptacle exhibits the usual regular vascular groundplan for monocots, while carpels are united at the ovary bases and by their styles, but very loosely in their middle region, so that a basket-like capsule is ripened. The septal nectary is well developed with two apertures at the ovary base and below the style insertion. Vasculature demonstrated basal ovules pairs sheltered by each carpel are in fact cauline. Thus floral axis appears to be involved in the congenital intercarpellary fusion, an unrecognized feature until now in the core-Asparagales.
Evaluating the Restoration Potential of 19 Ohio Reservoirs

ABSTRACT Eighty-four percent of Ohio's lakes and reservoirs are eutrophic. Significant reductions in nutrient loading are usually the object of lake restoration projects. However, variations in attainable nutrient concentrations, based on regional differences in watershed characteristics and land use, often are not considered. The purpose of this project was to evaluate the “ecoregion” concept for estimating which surveyed Ohio reservoirs might have the greatest potential for reduction in phosphorus concentrations. Ecoregional watershed characteristics dictate the practical lower or attainable limits of stream nutrient concentrations that can be reached. Attainable reservoir phosphorus concentrations were estimated from stream phosphorus concentration data that represent the best water quality in each Ohio ecoregion and by the use of a loading model. The reservoirs with actual summer 1989 phosphorus concentrations that exceeded predicted attainable concentrations by the greatest amounts were considered to.
Closing the circle: how ecologists can prepare their own quality control material to increase confidence in stable isotope data

Stable isotope analysis (SIA) is widely used in ecology but is usually performed by specialist facilities. Consequently, the reliability of SIA data depends completely on the facility's quality systems unless ecologists take steps themselves. Although widely recommended, practical advice on how to do this is lacking. Here, we outline preparation of 150 vials of an in‐house quality control material (QCM) based on air‐dried soil as an exemplar and describe methods of data analysis applicable to any QCM matrix. Homogeneity testing of the candidate material involves duplicate analysis of 10 randomly chosen vials, a Cochran test for outliers and 1‐way anova. Given that many ecologists find SIA expensive, we propose that an ecologist preparing a soil QCM pretest for homogeneity using a simple colorimetric analysis of a soil quantity (bicarbonate‐extractable P) sensitive to inhomogeneity. Once pretest homogeneity has been established, homogeneity under SIA can be tested. We obtained a 1‐way anova P value of 0·824 in our laboratory pretest, then 0·782 (δ13C) and 0·125 (δ15N). QCM stability should also be confirmed. Submission of each batch of samples for SIA should be accompanied by a vial of the QCM, labelled as a normal sample. Control charting of the results then allows detection of within‐batch issues encompassing any component of the analytical process (transport to the laboratory, sample preparation and subsampling, sample analysis, results calculation and reporting) and assessment of long‐term analytical control. Any issue thus identified can form the basis of a conversation with the SIA laboratory about the affected batch of samples.
Variation of heartwood phenolics and oak lactones between the species and phenological types of Quercus petraea and Q. robur

Summary Pressler cores were taken of Quercus petraea and Q. robur trees from young German provenance stands and mature mixed plantations in England. The concentration of total phenolics extracted from the outer heartwood was measured and significant differences found between the two species. Concentrations of oak lactones, measured from provenance samples, also varied significantly between the species. However, the difference in total phenolics between species was much lower among the trees from the mixed plantations than from the provenance trials. Q. petraea was characterized by lower levels of total phenolics but greater concentrations of oak lactones than Q. robur. A comparison between late and early flushing Q. petraea trees found no significant difference in total phenolics between these phenological types.
CHEMICAL COMPOSITION AND INSECTICIDAL ACTIVITY OF THE ESSENTIAL OIL OF ANETHUM GRAVEOLENS L.

The essential oil of seeds of Anethum graveolens L. growing in Pakistan was obtained by hydrodistillation. It was analysed by GC-MS. Components were identified and R-(-)-carvone(38.899%), apiol (30.812%), limonene(15.938%) and trans-(+)-dihydrocarvone (10.999%) were the main components. The essential oil was found to be toxic to Periplanata americana L. , Musca domestica L. and Tribolium castaneum. The mean mortality ranged from 25 to 100% for the different insects. In conclusion, the essential oil of A.graveolens may have the potential to be developed as a natural insecticide against various insects.
Synthesis of deoxy analogues of (2→8)-linked 3-deoxy-α-D-manno-oct-2-ulopyranosylonic acid (Kdo) disaccharides for binding studies with Chlamydia specific monoclonal antibodies

Deoxy analogues of the Chlamydia-specific, α-(2→8)-linked Kdo disaccharide epitope modified at the pyranose ring of the terminal Kdo unit have been prepared. Utilizing the 3,5-dideoxy-D-arabino-oct-2-ulosonate bromide donor [1] and the acceptor [2] under Helferich conditions, the 5-deoxy-α-Kdo-(2→8)-α-Kdo disaccharide [3] was obtained as the minor product together with unsaturated, α-(2→8)-glycosidically and (4→8)-ether-linked derivatives [5] and [7] as the major components. Deprotection afforded the disaccharide allyl glycosides [4], [6], and [8]. Further transformation of protected intermediates by hydrogenation followed by deblocking gave the propyl glycosides [12], [14] and [17]. The compounds may be used for binding studies with Chlamydia-specific and cross-reactive, Kdospecific monoclonal antibodies.
A heuristic simulation model of Lake Ontario circulation and mass balance transport

The redistribution of suspended organisms and materials by large-scale currents is part of natural ecological processes in large aquatic systems but can contribute to ecosystem disruption when exotic elements are introduced into the system. Toxic compounds and planktonic organisms spend various lengths of time in suspension before settling to the bottom or otherwise being removed. We constructed a simple physical simulation model, including the influence of major tributaries, to qualitatively examine circulation patterns in Lake Ontario. We used a simple mass balance approach to estimate the relative water input to and export from each of 10 depth regime-specific compartments (nearshore vs. offshore) comprising Lake Ontario. Despite its simplicity, our model produced circulation patterns similar to those reported by more complex studies in the literature. A three-gyre pattern, with the classic large counterclockwise central lake circulation, and a simpler two-gyre system were both observed. These qualitative simulations indicate little offshore transport along the south shore, except near the mouths of the Niagara River and Oswego River. Complex flow structure was evident, particularly near the Niagara River mouth and in offshore waters of the eastern basin. Average Lake Ontario residence time is 8 years, but the fastest model pathway indicated potential transport of plankton through the lake in as little as 60 days. This simulation illustrates potential invasion pathways and provides rough estimates of planktonic larval dispersal or chemical transport among nearshore and offshore areas of Lake Ontario.
Marine bacteria and biogeochemical cycling of iron in the oceans

Prokaryotic microbes play a critical role in oceanic Fe cycling. They contain most of the biogenic Fe in offshore waters and are responsible for a large portion of the Fe uptake by the plankton community. In the subarctic North Pacific, surface populations of heterotrophic species assimilate more than 50% of the dissolved Fe and thus compete directly with phytoplankton for this limiting resource. In oligotrophic tropical and subtropical waters, photosynthetic bacteria become more important in Fe cycling as the number of unicellular cyanobacteria increases and the nitrogen-fixing Trichodesmium, which contains most of the biogenic Fe in the mixed layer, becomes abundant. Like their terrestrial counterparts, heterotrophic and phototrophic marine bacteria produce Fe-binding siderophores that are involved in Fe acquisition. Evidence exists that bacteria may modify Fe chemistry in the sea through the production of these ligands and thereby play a significant role in regulating production of eukaryotic phytoplankton.