Miracle-dz/UniFAR-FTUs huggingface dataset:
Population history of European mountain pines Pinus mugo and Pinus uncinata revealed by mitochondrial DNA markers

The dwarf mountain pine (Pinus mugo) and the Pyrenean pine (P. uncinata) constitute a pair of closely related coniferous taxa of poorly resolved evolutionary history and affinity, which inhabit numerous stands scattered over subalpine environments of European mountain ranges. The aim of the study was to investigate their phylogeography and mutual relationships, shedding new light on their taxonomy and the past of the alpine flora. Previous evolutionary reconstructions of the mountain pines relied mainly on bi‐parentally or paternally inherited markers that quickly homogenize between populations, showing rather shallow and recent differentiation of gene pools. Therefore, to contrast these pictures, we analyzed diversity and differentiation within a large set of new mitochondrial loci, inherited in maternal line and distributed by seeds at short geographical distances. Samples of the taxa were taken from 27 natural populations representing their range‐wide distributions—17 populations of P. mugo and 10 of P. uncinata. All markers appeared polymorphic, providing a total of 31 multilocus haplotypes. Two of the loci proved to be species‐diagnostic and nearly fixed between analyzed samples. Distribution of mitotypes indicate that allopatric populations of the taxa constitute separate mitochondrial haplogroups, and the two mountain pines have independent evolutionary history. However, introgression of P. mugo mitotypes by P. uncinata specimens revealed in the species contact zone in Western Alps shows that their speciation is not fully completed.
Up and Down: Trends in Students’ Perceptions about Learning in a 1:1 Laptop Model – A Longitudinal Study

This is a five-year study conducted with junior high school students studying in a 1:1-laptop program in order to test the effects of the program on various measures related to the students: their attitudes, motivation, perceived school norms, self-efficacy, and behavioral intention towards learning with laptops, according to the Theory of Planned Behavior (TPB). These variables were tested at two dimensions: ‘duration of learning’ – the effect of learning in the program on the same students; ‘duration of program in school’ – the effect of the program on different students in different school years. Participants (N=770) answered a questionnaire structured according to motivational and TPB variables. Findings show that attitudes changed over time, but differently for each dimension. For the ‘duration of learning’, attitudes declined between 7 to 9 grade. Structural equation modeling analysis showed that students’ attitudes and self-efficacy explain part of their intention to learn with laptops, therefore ways of maintaining positive attitudes, self-efficacy, and strengthening school norms should be considered. However, for the ‘duration of program in school’, students’ attitudes increased over the years: The attitudes of students who started the program at a later stage were more positive than those who began earlier. This may indicate that students who experience the program at an advanced stage are better prepared, with more realistic expectations. Findings can assist teacher trainers and policymakers with the implementation of similar programs.
Extracts from cultures of Pseudomonas fluorescens induce defensive patterns of gene expression and enzyme activity while depressing visible injury and reactive oxygen species in Arabidopsis thaliana challenged with pathogenic Pseudomonas syringae

Abstract We evaluated the ability of metabolic elicitors extracted from Pseudomonas fluorescens N21.4 to induce systemic resistance (ISR) in Arabidopsis thaliana against the pathogen Pseudomonas syringae DC3000. Metabolic elicitors were obtained from bacteria-free culture medium with n-hexane, ethyl acetate and n-butanol in three consecutive extractions. Each extract showed plant protection activity. The n-hexane fraction was the most effective and was used to study the signal transduction pathways involved by evaluating expression of marker genes of the salicylic acid (SA) signalling pathway (NPR1, PR1, ICS and PR2) and the jasmonic acid/ethylene (JA/ET) signalling pathway (PDF1, MYC2, LOX2 and PR3). In addition, the level of oxidative stress was tested by determining the activity of enzymes related to the ascorbate-glutathione cycle. N-hexane extracts stimulated both pathways based on overexpression of ICS, PR1, PR2, PDF1 and LOX2 genes. In addition, activity of the pathogenesis-related proteins glucanase (PR2) and chitinase (PR3), lipoxygenase and polyphenol oxidase was enhanced together with an increased capacity to remove reactive oxygen species (ROS). This was associated with less oxidative stress as indicated by a decrease in malondialdehyde (MDA), suggesting a causative link between defensive metabolism against P. syringae and ROS scavenging.
Transferability and calibration of airborne laser scanning based mixed-effects models to estimate the attributes of sawlog-sized Scots pines

Airborne laser scanning (ALS) data is nowadays often available for forest inventory purposes, but adequate field data for constructing new forest attribute models for each area may be lacking. Thus there is a need to study the transferability of existing ALS-based models among different inventory areas. The objective of our study was to apply ALS-based mixed models to estimate the diameter, height and crown base height of individual sawlog sized Scots pines ( L.) at three different inventory sites in eastern Finland. Different ALS sensors and acquisition parameters were used at each site. Multivariate mixed-effects models were fitted at one site and the models were validated at two independent test sites. Validation was carried out by applying the fixed parts of the mixed models as such, and by calibrating them using 1â3 sample trees per plot. The results showed that the relative RMSEs of the predictions were 1. 2â6.5 percent points larger at the test sites compared to the training site. Systematic errors of 2. 4â6.2 percent points also emerged at the test sites. However, both the RMSEs and the systematic errors decreased with calibration. The results showed that mixed-effects models of individual tree attributes can be successfully transferred and calibrated to other ALS inventory areas in a level of accuracy that appears suitable for practical applications.Pinus sylvestris
Role and impact of the gut microbiota in a Drosophila model for parkinsonism

Drosophila is poised to be a powerful model organism for studies of the gut-brain axis due to the relative simplicity of its microbiota, similarity to mammals, and efficient methods to rear germ-free flies. We examined the gut-brain axis in Drosophila models of autosomal recessive parkinsonism and discovered a relationship between the gut microbiota and parkin loss of function. The number of live bacteria was increased approximately five-fold in the gut of aged parkin null animals. Conditional RNAi showed that parkin is required in gut enterocytes and not in neurons or muscle to maintain microbial load homeostasis. To examine the significance of gut microbiota, we reared germ-free parkin flies and discovered that removal of microbes in the gut improves the animals’ resistance to paraquat. Sequencing of 16S rDNA revealed microbial species with altered relative abundance in parkin null flies compared to controls. These data reveal a role for parkin activity in maintaining microbial composition and abundance in the gut, suggesting a relationship between parkin function and the gut microbiota, and deepening our understanding of parkin and the impacts upon loss of parkin function.
URBAN GROWTH AND WATER QUALITY IN THIMPHU, BHUTAN

Detailed study was undertaken in 2008 and 2009 on assessment of water quality of River Wang Chhu which flows through Thimphu urban area, the capital city of Bhutan. The water samples were examined at upstream of urban area, within the urban area and its downstream. The water samples were analyzed by studying the physico-chemical, biological and benthic macro-invertebrates. The water quality data obtained during present study are discussed in relation to land use/land cover changes(LULC) and various ongoing human activities at upstream, within the each activity areas and it’s downstream. Analyses of satellite imagery of 1990 and 2008 using GIS revealed that over a period of eighteen years the forest, scrub and agricultural areas have decreased whereas urban area and road network have increased considerably. The forest cover, agriculture area and scrub decreased from 43.3% to 42.57%, 6.88% to 5.33% and 42.55% to 29.42%, respectively. The LULC changes effect water quality in many ways. The water temperature, pH, conductivity, total dissolved solids, turbidity, nitrate, phosphate, chloride, total coliform, and biological oxygen demand were lower at upstream and higher in urban area. On the other hand dissolved oxygen was found higher at upstream and lower in urban area. The pollution sensitive benthic macro-invertebrates population were dominant at upstream sampling sites whereas pollution tolerant benthic macro-invertebrates were found abundant in urban area and its immediate downstream. The rapid development of urban infrastructure in Thimphu city may be posing serious threats to water regime in terms of its quality. Though the deterioration of water quality is restricted to a few localized areas, the trend is serious and needs proper attention of policy planners and decision makers. Proper treatment of effluents from urban areas is urgently needed to reduce water pollution in such affected areas to check further deterioration of water quality. This present study which is based on upstream, within urban area and downstream of Thimphu city can be considered as an eye opener.
Salivary gland macrophages assist tissue-resident CD8+ T cell immune surveillance

Tissue macrophages and tissue resident memory CD8+ T cells (TRM) play important roles for pathogen sensing and rapid protection of barrier tissues. To date, it is incompletely understood how these two cell types cooperate for efficient organ surveillance during homeostasis. Here, we used intravital imaging to show that TRM dynamically crawled along tissue macrophages in murine submandibular salivary glands (SMG) during the memory phase following a viral infection. Ex vivo confined SMG TRM integrated an unexpectedly wide range of migration modes: in addition to chemokine-and adhesion receptor-driven motility, SMG TRM displayed a remarkable capacity of autonomous motility in the absence of chemoattractants and adhesive ligands. This unique intrinsic SMG TRM motility was transmitted by friction and adaptation to microenvironmental topography through protrusion insertion into permissive gaps. Analysis of extracellular space in SMG using super-resolution shadow imaging showed discontinuous attachment of tissue macrophages to neighboring epithelial cells, offering paths of least resistance for patrolling TRM. Upon tissue macrophage depletion, intraepithelial SMG TRM showed decreased motility and reduced epithelial crossing events, and failed to cluster in response to local inflammatory chemokine stimuli. In sum, our data uncover a continuum of SMG TRM migration modes and identify a new accessory function of tissue macrophages to facilitate TRM patrolling of the complex exocrine gland architecture. One sentence summary Combined in vitro and in vivo imaging of salivary gland-resident tissue memory CD8+ T cells (TRM) uncovers their unique migratory behavior and describes a novel accessory function of tissue macrophages to assist TRM surveillance.
Ultrasonographical and angiographical study on the testes of Large White Yorkshire pig (Sus scrofa).

The present ultrasonographical and angiographical study was conducted on the testes of 10 Large White Yorkshire pigs. The testicular parenchyma appeared homogenous with a coarse medium echo-pattern. The mediastinum testis appeared as a centrally located hyperechoic line extending up to three quarters of the testicular length when imaged in the saggital (longitudinal) plane. The mediastinum testis appeared as circular echogenic area in the mid portion of homogenous testicular parenchyma on transverse sonographic examination. The funicular part of the testicular artery was highly coiled and formed many loops which were irregularly arranged along the whole length of the vascular cone. The marginal portion of the testicular artery was the direct continuation of the funicular portion of the testicular artery on a level with the caput extremity.
Spatial distribution and density of the Lar gibbon Hylobates lar and Siamang Symphalangus syndactylus in relation to canopy structure and disturbance in a lowland dipterocarp forest, Sumatra.

Forest structure is an important factor in the persistence of arboreal primates, and understanding the relationship between primate populations and habitat characteristics is essential for their conservation. Indonesia is experiencing one of the highest rates of deforestation globally, and with such a large amount of historical logging having taken place, only ~3.8% of the remaining forest is classified as primary. Sumatran lowland forests are one of the most threatened habitat types, though few studies have been conducted on primate populations within this habitat. The aim of the study was to ascertain forest vegetation structure between four different land units (hills, plains, alluvial and hill-swamp), and identify which structural variables are important indicators of habitat suitability for the two sympatric gibbon species, the lar gibbon Hylobates lar, and the siamang Symphalangus syndactylus. The field study was conducted from 1st March to 1st August 2016 within the Sikundur region of the Gunung Leuser National Park, North Sumatra, where both large and small-scale logging practices have been undertaken. At ten forest survey locations, auditory sampling methods using fixed points counts were used to produce hylobatid density estimations, and 4-6 vegetation plots per site were undertaken to identify differences in forest structure. Lar gibbon densities ranged from 1.19 – 3.56 groups/km2 and were found to be correlated with median tree height and crown area (F(9)= 5.604, p = 0.031, R2 = 0.459), and negatively correlated with frequency of trees <20m (F(9)= 6.775, p = 0.035, R2 = 0.616), and with canopy connectivity <15% (F(9)= 22.45, p =0.001, R2 = 0.737). Siamang densities ranged from 0.40 – 2.11 groups/km2, and were correlated with frequency of trees between 10-20m in height (F(9)= 5.576, p = 0.046, R2 = 0.411), and with canopy connectivity between 50% -75% (F(9)= 5.930, p = 0.041, R2 = 0.426). These results indicate these hylobatid species exhibit a degree of tolerance and behavioural flexibility to habitat disturbance, though the preservation of tall trees and the provision of a significant amount of canopy connectivity is required for their continued presence in lowland forests. It is hoped that the results of this study will contribute to the preservation of Sumatran’s lowland forest, and the gibbon species that inhabit them.
KARAKTERISTIK BAKTERI ASAM LAKTAT YANG DIISOLASI DARI SUSU KUDA SUMBA

The purpose of this study was to isolate and identify the lactic acid bacteria found in Sumba mares milk. This research will be carried out from September to November 2017 at the Veterinary Laboratory of the Livestock Service Office of East Nusa Tenggara Province. The research stages are isolation of lactic acid bacteria from Sumba mares milk by growing lactic acid bacteria on MRS agar media, and identifying lactic acid bacteria with gram staining, catalase test, motility test, and total plate count testing. Based on the results of the study, the presence of lactic acid bacteria originating from Sumba mares milk was characterized by the presence of colonies of lactic acid bacteria from Sumba mares milk which grew on MRS media agar as a selective medium for lactic acid bacteria. Based on the results of testing the characteristics of lactic acid bacteria Sumba mares milk has Gram positive, the negative results in the catalase test are characterized by not forming gas bubbles when the bacteria are added with H2O2. Based on the motility test obtained negative results or bacteria are non-motile and the number of lactic acid bacteria that can be a total picture of lactic acid bacteria that exist in Sumba mares milk in milliliter of milk. The conclusion are lactic acid bacteria isolated from Sumba mares milk has characteristic as Gram positive, basil or stem shaped, negative catalase and non motile, and has a total lactic acid bacteria of 3.5 x 108 cfu/ml (est).
Genetic diversity and characteristics of gyrA gene in Neisseria spp

Background Neisseria meningitidis bacteria characterized by clonal complex (CC4821) showed a high resistance rate to quinolones. The aim of this study was to assess whether the DNA gyrase A gene from N.meningitidis CC4821 strains collected in China featured any specific characteristics compared to other Neisseria species. Two hundred fifty two gyrase gene sequences were analyzed, among them 77 generated in this study from N.meningitidis CC4821 strains collected in China between 1978 and 2016. Results The quinolone resistance-related gene, coding for the DNA gyrase subunit A (GyrA) protein, was highly divergent within the N.meningitidis strains whereas N. gonorrhoeae and N.lactamica counterparts appeared well conserved. Only one position, 91 (83 in E.coli gyrA gene), was linked to quinolone resistance, all resistant strains featuring the substitution T91I. The E.coli position 87, which was mutated in quinolone-resistant strains, was also divergent (position 95) in some Neisseria resistant strains. Moreover, twenty eight additional putative resistance markers were identified. Finally, putative recombination events between N.meningitidis and either N.subflava, or N.lactamica or N.cinerea as well as between N.meningitidis strains were reported. Conclusions Analyzing the evolution of gyrA gene within Neisseria spp. is critical to monitor the quinolone resistance phenotype and the acquisition of new resistance markers. Such studies are necessary for the control of the meningococcal disease and the development of new drugs targeting DNA gyrase.
Sex-associated differences in cytomegalovirus prevention: Prophylactic strategy is associated with a strong kidney function impairment in female renal transplant patients

Cytomegalovirus (CMV) syndrome or disease, a serious health hazard after renal transplantation, can be prevented using the antiviral drug (val)ganciclovir. (Val)ganciclovir is typically administered following a prophylactic or a pre-emptive strategy. The prophylactic strategy entails early universal administration, the pre-emptive strategy early treatment in case of infection. However, it is not clear which strategy is superior with respect to transplantation outcome and viral clearance. We have retrospectively analysed 540 patients from the multicentre Harmony study: 308 were treated according to a prophylactic, 232 according to a pre-emptive strategy. As expected, we observed an association of prophylactic strategy with lower incidence of CMV syndrome, delayed onset and lower viral loads compared to the pre-emptive strategy. However, the prophylactic strategy was associated with higher incidence of acute rejection (P=0.002) and – for female patients – a strong impairment of glomerular filtration rate (eGFR) one year post-transplant (P<0.001, median difference: 18.5 mL·min−1·1.73m−2). Additionally, the prophylactic strategy was associated with increased incidence of severe BK virus reactivation. Our results suggest for the first time that the prophylactic strategy might lead to inferior transplantation outcomes, providing evidence for a strong association with sex. ClinicalTrials.gov number: NCT00724022
Sensory information from a slipping object elicits a rapid and automatic shoulder response

Humans have the remarkable ability to hold, grasp, and manipulate objects. Previous work has reported rapid and coordinated reactions in hand and shoulder muscles in response to external perturbations to the arm during object manipulation; however, little is known about how somatosensory feedback of an object slipping in the hand influences responses of the arm. We built a hand-held device to stimulate the sensation of slipping at all five fingertips. The device was integrated into an exoskeleton robot that supported it against gravity. The setup allowed us to decouple somatosensory stimulation in the fingers from forces applied to the arm— two variables that are highly interdependent in real-world scenarios. Fourteen participants performed three experiments in which we measured their arm feedback responses during slip stimulation. Slip stimulations were applied horizontally, in one of two directions, and participants were either instructed to follow the slip direction, or to move the arm in the opposite direction. Participants showed responses within ∼67 ms of slip onset when following the direction of slip, but significantly slower responses when instructed to move in the opposite direction. Arm responses were modulated by the speed but not the distance of the slip. Finally, when slip stimulation was combined with mechanical perturbations to the arm, we found that sensory information from the fingertips significantly modulated the shoulder feedback response. Overall, the results demonstrate the existence of a rapid feedback system that stabilizes hand-held objects. NEW & NOTHEWORTHY We tested whether the sensation of an object slipping from the fingers modulates shoulder feedback responses. We found rapid shoulder feedback responses when participants were instructed to follow the slip direction with the arm. Shoulder responses following mechanical joint perturbations were also potentiated when combined with slipping. These results demonstrate the existence of fast and automatic feedback responses in the arm in reaction to sensory input to the fingertips that maintain grip on hand-held objects.
Diversity of Arbuscular Mycorrhizal Fungi in Agroforestry, Conventional Plantations and Native Forests in Roraima State, Northern Brazil

Arbuscular mycorrhizal fungi (AMF) are important components of the soil microbiota in terrestrial ecosystems, under the influence of various factors such as soil use and management, and can be adapted to a structure and diversity of fungal communities. The aim of this survey was to evaluate the influence of different systems of land use and management on AMF diversity in the Roraima State, Brazil. We collected soil samples in agroforestry, conventional soybean planting, conventional corn and native forest. After 150 days of incubation in a greenhouse, we extracted the spores in order to evaluate AMF, volume and to determine taxonomic identification. We found 16 species of AMF and the genus Acaulospora was the most frequent, followed by Glomus. Soil under agroforestry system had the highest species richness and the native forest, the lowest. On the other hand, soybean and corn areas presented greater density values than agroforestry system and native forest. In the agroforestry system, SOM attributes, Al3+ and H + Al had influence in AMF species richness. Thus, agroforestry constitute sustainable alternative influencing AMF communities in these ecosystems.