Miracle-dz/UniFAR-FTUs huggingface dataset:
Avian Metapneumovirus Reverse Genetics Developments and their Effect on the Performance of Recombinant Live Vaccines

Avian metapneumovirus (AMPV) is an enveloped negative sense single stranded RNA virus which is a major endemic respiratory pathogen of global domestic poultry. Since reverse genetic (RG) techniques have been applied to this pathogen several reports have investigated the effects of single and multiple genomic mutations and gene deletions or insertions on viral biology. The vectoring abilities of subtype A strains have been also investigated. The aim of this study was to develop a new RG system in order to extend this type of studies to the B subtype, gain a better understanding of the viral capacity to accept and express heterologous extra sequences. Initially was performed a nucleotide and amino acid comparison between subtypes A and B, to establish whether subtype A RG components could be partially or fully substituted. Eventually a cDNA copy of subtype B genome was generated and the virus rescued using subtype A and B RG components. The vectoring abilities of subtype B was firstly investigated to accept and express both spike (S1) and nucleocapsid (N) genes of infectious bronchitis virus (IBV). After viruses have been recovered by RG, all recombinants were found to be highly stable during passage in vitro and subsequently tested as candidate vaccines by eye-drop inoculation of one-day-old chickens. When chicks were challenged with IBV, negligible protection and replication results were observed. To improve the ability of the recombinant to induce protective immunity, the sequence of subtype B cDNA was modified in order to increase the replication in the respiratory tract. The new recombinants were rescued and challenge in vivo, showing an increase of the protection. Other strategies were adopted to improve the protection, as increasing the expression of the foreign genes and multiple genes insertions, but in most of the cases the virus rescue proved to be not possible.
Reconstructing the Body Sizes of Quaternary Lizards Using Pholidoscelis Fitzinger, 1843, and Anolis Daudin, 1802, as Case Studies

ABSTRACT Estimating the size of fossil organisms is essential for most paleontological studies, including studies of fossil squamates. Paradoxically, few works about the methods used to achieve this goal have been published. This study focuses on two genera of lizards found in the Lesser Antilles: Pholidoscelis and Anolis. We produced sets of size estimation equations based on skeletal measurements taken on modern specimens. We tested the effect of the anatomical part used and of the species composition of the comparative sample in order to produce reliable and statistically significant equations. We then compared our results with previously published estimates of fossil size for Anolis lizards. We found that past studies were inconsistent with each other in how body size was estimated even if the same value for a measurement was obtained independently. Further, we found that what others have described as Holocene dwarfism for Anolis bimaculatus is likely to reflect a methodological bias, and fossil representatives of this species likely had a similar size to modern individuals. Many conclusions made in previous studies could not be challenged, however, because even though body size estimates are given, the actual measurements made on skeletal elements remain largely unreported in the literature. These results show that more transparency and reproducibility are needed for studies concerning the body size of fossil squamates.
Antimicrobial susceptibility profiles of Staphylococcus spp. from domestic and wild animals

The aim of this study was to determine the prevalence and diversity of veterinary clinical isolates of Staphylococcus and analyze their antimicrobial susceptibility. One hundred Staphylococcus spp. clinical isolates from domestic and wild animals were subjected to partial sequencing of the 16S rRNA gene to species determination. Antimicrobial susceptibility was obtained by a disk diffusion test against six antibiotics: amoxicillin (AMX), cephalexin (LEX), ciprofloxacin (CIP), erythromycin (ERY), gentamicin (GEN) and trimethoprim-sulfamethoxazole (SXT). The most common specie was S. pseudintermedius (61%, 61/100) and resistance to ERY (57%, 57/100), SXT (50%, 50/100) and AMX (46%, 46/100) was detected most frequently. In total, 40% (40/100) of Staphylococcus spp. exhibited a multidrug-resistant (MDR) phenotype. Results of this study emphasize that animals are reservoir of MDR Staphylococcus spp.
Population structure and production of four sibling species of Pseudocalanus spp. in the Chukchi Sea

Copepods of the genus Pseudocalanus are important members of zooplankton communities in temperate and polar shelf regions, but few studies have focused on their species-specific biology due to the very subtle morphological differences between the species. We assess the distribution, population structure and production of four co-occurring species of Pseudocalanus across the Chukchi Sea during 2004, 2009 and 2012. Our approach used a combination of microscopic identification and species-specific polymerase chain reaction to discriminate between the species. Currently, the arctic P. acuspes dominates the genus (50–90%), with the relative distribution of species closely linked to water mass distribution and variations in physical properties, making Pseudocalanus important indicators of water mass origin. Although the temperate P. newmani had a significant presence throughout the Chukchi Sea, its stage distribution suggests that they recruit poorly in cold waters. Direct temperature-manipulation experiments further suggest that the reproductive activity of the two temperate species is inhibited at low temperatures, while the arctic P. acuspes exhibits reduced fitness and lower reproductive capacity when temperatures are increased to 10°C. Our results suggest that shifting oceanographic patterns and climate warming will have unequal impact on this genus, arising from species-specific differences in life histories and tolerance to environmental conditions.
IMPACT OF AGRICULTURAL SERVICES PROVIDED BY NON-STATE ACTORS ON RURAL LIVELIHOODS: A CASE OF DISTRICT MANSEHRA, KHYBER PUKHTUNKHWA, PAKISTAN

The failure of state actors/institutions in the country in delivering agricultural advisory and extension services to the rural community created a space for non-state actors to deliver these services at the door steps of majority of the rural poor people in order to improve their livelihoods. This situation prevails in all the four provinces of the country especially in Khyber Pakhtunkhwa province, where rural poverty is evident. In order to access the impact of agricultural services rendered by different non-state institutions on the livelihoods of rural poor in this region, the current research study was designed. The study was conducted in district Mansehra (one of the most populated district of Hazara division). Both qualitative and quantitative approaches were used for the collection of data from respondents. The data were collected from the rural community of those villages where the selected non-state organizations were involved in a variety of rural development related activities/tasks. The data were collected from 450 respondents randomly selected from 6 villages. The collected data were analyzed by using computer based statistical software – SPSS. From the results it was concluded that majority of the respondents had age between 36-50 years with secondary educational level. The land holding size of the respondents in the research was very small. It was also concluded that a large majority (>80.0%) of respondents said that agricultural services rendered by non-state institutions like extension education, trainings related to crop & livestock management, poultry & forestry services, vaccination for livestock and awareness campaigns regarding latest agricultural technologies improved their overall agricultural productivity as well as livelihoods. It was also concluded that regarding impacts of agricultural services rendered by non-state organizations, a large majority of the respondents (89.6%) said that their agricultural services increased their agricultural productivity. While exploring the reasons due to which agricultural related services of non-state organizations play role in improving livelihoods of rural people, the results of the study indicated that in extension and education services majority (54.6%) of the respondents said that social organizations provided good quality extension and education related services to the rural community. Finally, it was concluded that agricultural services of non-state organizations were very effective and played a significant role in upgrading the livelihoods of rural poor.
Multiple gene contribution to the phenotypic and genotypic Daptomycin non-susceptible (DNS) variants of Methicillin-Resistant Staphylococcus aureus isogenic strains

Daptomycin (DAP) represents today a valid alternative choice in the treatment of multi-drug resistant (MDR) Staphylococcus aureus infections that do not respond to vancomycin therapy. Knowledge of clinical failure associated with DAP non-susceptibility (DNS) have been accounted in the USA and Europe, and the possibility of glycopeptide induction of low levels of DAP efficacy is worsening this scenario. The phenotypic alterations that characterize DNS S.aureus take place in changes in cell-wall arrangement, turnover, membrane structure and potential, and in modifications of cell autolysis and permeabilization. This study intended to analyze the molecular traits responsible for the phenotypic features of DNS strains, in three sets of isogenic clinical S.aureus in which DNS phenotype arise after DAP therapy. With regard to the genes involved in cell-wall charge, quantitative relative real time RT-PCR data revealed that mprF showed an upregulation in DNS strains presenting a mprF mutation, whereas a downregulation in DNS strains which not presented mutations. All DNS isolates had a dltA up-regulation, while both DNS and hDAP strains presented a cls2 up-regulation. Considering genes involved in the cellwall turnover and autolysis, all DNS isolates exhibited high transcription levels of sceD and atl. Our data confirm the multi-factorial nature of DNS and suggest that the keystone of this phenotype is the mechanism of electrostatic repulsion and, indirectly, a reduction of autolysin activity due mainly to a dltA over expression-dependent, cls2-independent mechanism, as well as to the accumulation of additional secondary factors, such as the presence of mutations correlated with the increased levels of mprF transcription.
Resource allocation pattern under simulated environmental change and seedling establishment of alpine dwarf shrubs in a mid-latitude mountain

We set up 11 open-top chambers (OTCs) on a fell-field (1680 m a.s.l.) in the Taisetsu Mountains, northern Japan to assess responses to warming of circumpolar plants growing around their southern distribution margins. The OTCs increased the daily mean air-temperature by 1.7°C throughout the growing season. For five alpine species - two deciduous shrubs: Arctous alpinus and Vaccinium uliginosum and three evergreen shrubs: Ledum palustre subsp. decumbens, Vaccinium vitis-idaea, and Empetrum nigrum var. japonicum - effects of artificial warming on reproductive components were investigated during five (for flower production) or four (for fruit production) years. In addition, seedling establishments were compared among the three vegetation types and bare ground. Flower production in the OTCs was enhanced significantly in both deciduous species over that of control plots. In contrast, comparison to the control plots showed a significant decrease in flower production in the OTCs in two of the evergreen species. Fruit production of V. uliginosum and L. palustre was enhanced in the OTCs relative to the control plots. Both deciduous species allocated their resources to reproduction rather than to vegetative growth. Seedling establishment was very rare and was restricted on bare ground in this study site. We concluded that the difficulty of seedling establishment gives advantage to some species, which show active vegetative growth under global warming, to develop their vegetation cover.
EFFECTS OF SNOW-FREE PERIOD ON THE PHENOLOGY OF ALPINE PLANTS INHABITING SNOW PATCHES

Phenology of alpine plants was studied with reference to the time span of snow-free period by setting six quadrats along a snowmelt gradient. Of the 56 species, 17 inhabited four or more quadrats and their phenology was observed for 3 yr, 1988 to 1990. Contraction of the snow-free period reduced flowering and seeding rates. Phenology of the alpine plants was controlled primarily by (1) growth form, (2) the span of preflowering, and (3) the term for the maturity of seeds. Shrub species, especially evergreen shrubs, took longer for maturing their seeds. They abandoned sexual reproduction and reproduced vegetatively by layering in the short snow-free habitats. Forb and graminoid species opened their flowers even in the
The Gonadal Cycle of the Yellowfin Porgy, Acanthopagrus latus (Houttuyn) Reared in the Net Cage at Tosa Bay, Japan

A study on the gonadal cycle of the yellowfin porgy, Acanthopagrus latus reared in the net cage was carried out. All functional males ranging from 14.0 cm to 33.0 cm SL , had an hermaphroditic gonad and constituted 39 % of the total samples. The size range of females was from 23.0 cm to 38.0 cm SL. The GSI value started to increase in October and was maximum in November . Spawning occurred from the end of October through mid-November . The absolute fecundity was estimated to range from 629•~104 for 26.4 cm SL fish to 1445•~104 for 35.0 cm SL fish . Fish reproduction often becomes deranged when fish are transferred from their natural habitat to the artificial environment, earning them the reputation of being •g difficult to breed in captivity•h. To understand the biological mechanism of the derangement, sufficient information on the annual cycle of gonadal development , sex ratio, fecundity and the time of spawning are considered to be essential for the efficient reproduction of fish. The yellowfin porgy, Acanthopagrus latus is distributed in a wide geographical range, from the coast of the Pacific Ocean in Southern Japan to the Indian Ocean and the Gulf region. This species can be used as a model for the examination of the factors controlling reproduction among the Sparidae, since it can be studied using either reared or wild populations2). Concerning the reared fish, the gradual development of the gonads can be studied over an extended period. Only preliminary studies on some aspects of the reproductive biology of this species from the wild population have been reported2,4,5). This study describes the gonadal cycle of yellowfin porgy in captivity. Materials and Methods Fish used for this study were reared in the floating net cage at Uranouchi Inlet, Tosa Bay for 3-4 years and were fed with fish meal or fish pellet 2-3 times a week during summer until spawning season (OctNov.). In all feeding days, the food was supplied until all the fishes stopped feeding. Feeding activity became lower during spawning season and winter. Sampling was done monthly from 1989 to 1992. Total length, standard length, body weight and gonad weight of each specimen were measured. Changes in the relative gonad weight were calculated using the following formula for gonadosomatic index (GSI) :
Effect of coloured shade net on production of Dracaena fragrans

An experiment was conducted to study the effect of different coloured shade-nets on production and quality of Dracaena fragrans. Plants were grown under different coloured shade-nets, viz. red, green, black, and white with 50% shading intensity along with control (without shade net). Different weather parameters and plant growth parameters were measured at different crop growth stages. Coloured shade net exhibited special optical properties and also influenced the microclimate. Cut greens grown under coloured shade-nets gave better performance in terms of plant height, number of leaves, biomass, leaf area, photosynthetic rate, harvest index etc. compared to control. All the shade-nets reduced temperature, light intensity and improved relative humidity. Red and white shade-nets gave higher photosynthetically active radiation (PAR, μmol/m2/s) and transmittance than other coloured nets. Plants grown under red and white shade-nets exhibited better plant height, leaf number, leaf chlorophyll content, leaf area, fresh weight, dry weight, photosynthetic rate and transpiration. The harvest index was superior under red shade net. Red and white shade-nets were found superior in improving plant and weather parameters and hence they can be used in place of the commercially used green shade net for improved growth of dracaena.
Effect of the extract and compound from Solanum nigrum Linn on Tetranychus cinnabarinus

The carmine spider mite Tetranychus cinnabarinus (Boisduval) is a serious pest affecting various glasshouse vegetables, fruits and crops and causes significant damage to crop yields and quality by piercing and sucking foliar tissues. The control of this mite primarily involves the application of synthetic chemical pesticides. In this study, a Solanum nigrum L. extract was evaluated for its potential acaricidal activity against adult female T. cinnabarinus in laboratory conditions, and the S. nigrum extract showed marked efficacy in controlling the carmine spider mite both in vitro and in potted seedlings. Furthermore, the active compound, a phytostanol ester (β‐sitosterol‐3‐O‐heptadeca‐8Z, 11Z‐dienoate), was isolated from the petroleum ether‐soluble fraction of S. nigrum extract via repeated column chromatography and identified based on its physiochemical properties and spectral data. At 7 days after treatment in a potted seedling experiment, the LC50 values of the S. nigrum extract and active compound were found to be 4.70 and 1.85 g/l, respectively. All of these results demonstrated that the S. nigrum extract and its active component exhibit the potential for use as new natural acaricides for controlling carmine spider mites.
Efeito de alguns extratos vegetais na eclosão, mobilidade, mortalidade e patogenicidade de Meloidogyne exigua do cafeeiro

As part of a work aiming to develop new methods to control Meloidogyne exigua in coffee plants that are not toxic to human beings or to the environment, methanolic and aqueous plant extracts were prepared from Cajanus cajan (L.) Mill. , Crotalaria juncea L. , Ficus elastica Roxb. , Ruta graveolens L. , Stylosanthes guianensis (Aubl.) Sw. , Leucaena leucocephala (Lam.) Dewit. , Punica granatum L. , Allium cepa L. , Allium sativum L. , Brachiaria decumbens Stapf. , Catharantus roseus G. Don and Tagetes minuta L. All extracts presented toxic effects on M. exigua when submitted to in vitro assays with eggs and second-stage juveniles of that nematode. As those from A. cepa and R. graveolens afforded the best results, these were employed in an in vivo assay with six-month-old coffee plants inoculated with M. exigua eggs. This prompted the reduction of gall numbers without any toxic effect on coffee plants.
Evaluating old and novel proxies for in vitro digestion assays in wild ruminants

In vitro digestion assays provide useful data for wild ruminant ecologists. It remains highly constraining, however, to conduct these assays in the field. We evaluated various proxies for in vitro digestion assays that use ruminal liquor from wild ruminants. The ruminal liquor of freshly killed white-tailed deer (Odocoileus virginianus) was used to measure in vitro true digestibility (IVTD), total gas, and volatile fatty acids (VFA) production of dominant summer and winter forage. We evaluated the ability of 4 proxies to predict these digestibility variables: 1) IVTD, total gas, and VFA produced with cow ruminal liquor; 2) acid detergent fiber (ADF) concentration; 3) CO2 production from soil–forage mixtures; and 4) predictive models based on near infrared spectra (NIRS) of forages. Predictions using NIRS were best correlated with all deer digestibility variables (each r2 > 0.93) with limited bias across forage species. Forage ADF and CO2 production from soil–forage mixtures were related with all digestibility variables (r2 = 0.62–0.95). Digestion assays using cow ruminal liquor was relatively good for predicting IVTD (r2 = 0.94) from deer ruminal liquor, but the weakest for predicting total gas (r2 = 0.63) and VFA production (r2 = 0.44). Calibrated NIRS models could substantially improve the prediction of in vitro digestibility variables. If access to NIRS technology or the ability to collect reference data with deer inocula for NIRS calibrations is impractical, forage ADF or CO2 production from soil–forage mixtures remain acceptable alternatives. Comparing the digestion kinetics and VFA production of wild and domestic ruminants is an innovative avenue for better understanding the adaptive ecophysiology of digestion by different herbivores. © 2016 The Wildlife Society.
Study of volatile alcohols and esters from the subcutaneous fat during ripening of Iberian dry-cured ham. A tool for predicting the dry-curing time

Variations in the amounts of volatile alcohols and esters from subcutaneous fat have been assessed during the dry-curing process (1022 days) of Iberian ham according to a purge and trap-gas chromatography-mass spectroscopy method, using the same hams throughout the process. During processing time, the subcutaneous adipose tissues of ten hams obtained from five Iberian pigs fed on acorns and pasture were sampled and analyzed once per month. Fifteen alcohols and five esters have been identified. All volatile alcohols detected in this work have been previously identified by other authors on Iberian ham, except 3-buten-2-ol, 5-methyl-3-hexanol and 2-isononanol. A linear discriminant analysis (LDA) was applied and the two discriminant functions were obtained using backward stepwise analysis retaining the following variables: butyl ester formic acid, 1-penten-3-ol, methyl ester 2-propenoic acid, 5-methyl-3-hexanol, 1-nonanol, ethyl ester pentanoic acid, ethyl ester hexanoic acid, 2-isononanol, ethanol and 3-buten-2-ol. A complete separation among the three periods was obtained, suggesting that the retained variables are powerful descriptors to distinguish samples from these three dry-curing stages.
Precommercial thinning in mixed-species conifer plantations affected by armillaria and heterobasidion root diseases in West-Central Oregon and Washington: 30-year results

Four 10- to 20-year-old plantations were precommercially thinned to determine the effects on tree growth and mortality caused by armillaria and heterobasidion root diseases. The plantations represented different species compositions with one each of (1) coastal Douglas-fir and noble fir, (2) Douglas-fir and western hemlock, (3) pure Douglas-fir, and (4) Shasta red fir and mountain hemlock. After 30 years, the probabilities of leave-tree survival and actual leave-tree survival (trees/ha [TPH]) were significantly (P ≤ 0.05) higher in thinned versus unthinned plots in one of the four plantations with no significant differences in the other three plantations. Most tree mortality was caused by armillaria root disease. Despite the high frequency of Heterobasidion occidentale in overstory stumps, only two leave trees in one plantation were killed by this fungus after 30 years. Quadratic mean diameter (QMD) growth and basal area (BA) (per ha) growth of leave trees were significantly (P ≤ 0.05) greater in thinned than in unthinned plots in one plantation for QMD and in three plantations for BA. Precommercial thinning does not appear to exacerbate the incidence of leave-tree mortality from armillaria or heterobasidion root diseases after 30 years, and leave-tree QMD and BA growth increased significantly in most but not all plantations for the tree species sampled. Armillaria and heterobasidion root diseases are not an impediment to precommercial thinning in plantations or stands similar to those we studied.