Miracle-dz/UniFAR-FTUs huggingface dataset:
Dendritic cell dynamics in blood and lymphoid tissues during pathogenic simian immunodeficiency virus infection

Dendritic cells (DC) are a heterogenous population of antigen presenting cells important in both innate and adaptive immune responses. The two major subsets of DC, CD11c+ myeloid DC (mDC) and CD123+ plasmacytoid DC (pDC), are depleted in the blood of human-immunodeficiency virus (HIV) - 1 infected individuals. It has been proposed that DC loss may be due to lymph node recruitment, direct viral infection, bone marrow suppression or death, although this has not been directly addressed. Using the highly relevant, rhesus macaque/simian immunodeficiency virus (SIV) model of HIV infection, we investigated DC dynamics during acute pathogenic SIV infection and simian AIDS. We hypothesized that SIV infection causes a dysregulation of DC trafficking and death not solely dependent upon direct viral infection. The specific aims of this project are to: 1) determine the phenotypic heterogeneity of DC in blood from healthy macaques and develop a rapid assay for frequent longitudinal quantitation of absolute DC numbers; 2) determine whether mDC and pDC are recruited to lymphoid tissues in simian AIDS; 3) determine the dynamics and possible mechanisms of pDC loss and redistribution to lymphoid tissue during acute SIV infection. We found that rhesus macaque DC were more phenotypically homogeneous than their human counterparts and could be accurately quantified in small volumes of blood. In monkeys with simian AIDS, DC were depleted in both blood and secondary lymphoid tissues associated with increased spontaneous apoptosis. However, the remaining DC were phenotypically normal. During acute SIV infection, pDC responded to infection in a biphasic manner, with rapid mobilization into blood followed by depletion in both blood and lymphoid tissue. However, pDC production from bone marrow was normal and BrdU-labeling indicated increased pDC mobilization and recruitment to lymphoid tissues despite net loss of pDC. In lymph nodes, pDC were directly infected with virus, activated, and undergoing increased levels of apoptosis but retained functional TLR7 signaling. The findings in this study are significant to public health because defining the mechanisms leading to DC loss will offer new opportunities for therapeutic interventions to augment immune responses in HIV-infected individuals.
Assessment of Genetic Variation in Wild Populations of the Redclaw Crayfish (Cherax quadricarinatus, von Martens 1868) by Means of Allozyme and RAPD-PCR Markers

The population structure of the redclaw crayfish (Cherax quadricarinatus) was investigated by analyses of allozymes and RAPD (randomly amplified polymorphic DNA) markers. Electrophoretic analysis of 28 enzyme loci in 12 redclaw populations from the Northern Territory (NT) and North Queensland (NQ) revealed generally low estimates of heterozygosity within each population and low estimates of genetic differentiation among populations except for a fixed allelic difference at the carbonic anhydrase (CA*) locus between NT and NQ populations. Low levels of genetic variability among the NQ populations is possibly a reflection of their recent radiation across the Gulf of Carpentaria after its inundation between 18000 and 6000 BP. RAPD analysis of seven redclaw populations could distinguish each river population and also grouped them according to geographic proximity. RAPD analyses also revealed significant genetic variability both within the species and within individual populations, which could be used to improve their culture. On a preliminary scale, RAPD fragments provided a useful tool for differentiating redclaw strains and constitute a marking system that could be used in crayfish genetic improvement programmes.
The prediction of the voluntary feed intake of dairy cows

SUMMARY Information on the total dry-matter intake (TDMI), concentrates supplied (C), live weight (LW), week of lactation (WL), milk yield (MY) and composition, quality of forage fed to, and parities of, 385 cows from five different sources were assembled to develop appetite prediction equations. The equations were based on multiple regression and least squares constants and were calculated using the data from each source and the data pooled from all sources. The major factors affecting total dry-matter intake (TDMI) were C, LW, WL and MY and for the pooled data these factors explained 73–76% (R2) of the total variation in TDMI. The predictive values of some of the equations were tested against independent sets of data and for groups of cows and individual cows, the equations predicted TDMI within ±1·1 and 1·6 kg, respectively. The application of the equations in the field is discussed and some suggestions made for increasing the R2 of future appetite equations.
A spatially explicit method for evaluating accuracy of species distribution models

Aim Models predicting the spatial distribution of animals are increasingly used in wildlife management and conservation planning. There is growing recognition that common methods of evaluating species distribution model (SDM) accuracy, as a global overall value of predictive ability, could be enhanced by spatially evaluating the model thereby identifying local areas of relative predictive strength and weakness. Current methods of spatial SDM model assessment focus on applying local measures of spatial autocorrelation to SDM residuals, which require quantitative model outputs. However, SDM outputs are often probabilistic (relative probability of species occurrence) or categorical (species present or absent). The goal of this paper was to develop a new method, using a conditional randomization technique, which can be applied to directly spatially evaluate probabilistic and categorical SDMs.
Comment

We introduce the Skill Plot, a method that it is directly relevant to a decision maker who must use a diagnostic test. In contrast to ROC curves, the skill curve allows easy graphical inspection of the optimal cutoff or decision rule for a diagnostic test. The skill curve and test also determine whether diagnoses based on this cutoff improve upon a naive forecast (of always present or of always absent). The skill measure makes it easy to directly compare the predictive utility of two different classifiers in an analogy to the area under the curve statistic related to ROC analysis. Finally, this article shows that the skill-based cutoff inferred from the plot is equivalent to the cutoff indicated by optimizing the posterior odds in accordance with Bayesian decision theory. A method for constructing a confidence interval for this optimal point is presented and briefly discussed.
Phototherapy in the Newborn: An Overview

duction, though one wishes he had discussed the philosophy and broad approach to treatment more fully. He also contributes two chapters, both somewhat speculative: one on treatment by inhibition of renal tubular reabsorption, which certainly has little place in homocystinuria or in hyperprolinaemia indeed, which has yet to be proven as a pathological situation; the other on new and experimental approaches to treatment outlines the several differing and exciting ways in which this is being done. It should be pointed out that nowhere in the book is there any discussion of the effect on the family of prolonged dietary restriction and the possible ways of meeting the problems that arise. This is a suggestion for the second edition! In the chapter on phenylketonuria the focus is on diet and the results of dietary treatment; unfortunately there is no discussion on diagnosis or pathogenesis, including the possible effect of a reduction in available tyrosine. There is considerable information about the calorie, mineral, and amino acid needs of young children with one small omission, the need to add calcium to the diet of children on Cymogran. Professor B. Clayton emphasizes the need for children suffering from inherited metabolic disease to be treated in centres with good facilities and experience, and in his preface Dr. Raine points out that 'success comes more from careful and constant attention to management'. In this context it is hoped that the physician armed with this excellent book will not assume that treatment is easy and so accept full responsibility for the occasional case that comes his way. This should remain a shared exercise with the experienced central unit, which will require at least one copy ofthis book for use in its clinical, dietetic, and biochemical areas.
Bottleneck and gene flow effects impact the genetic structure of seed-propagated apricot populations in Moroccan oasis agroecosystems

In order to highlight the genetic status and origin of Moroccan apricot populations, trees were collected from ten oasis agroecosystems and analysed with AFLP markers. A total of 87 accessions and 12 cultivars grown in Moroccan orchards, including ‘Canino’ and ‘Del Patriarca’ cultivars, were surveyed and compared with in situ Tunisian and ex situ Montfavet (France) collections. Our results highlighted a narrow genetic diversity in the Maghreb region (Tunisia and Morocco) associated with a strong differentiation from the other groups, which supports a bottleneck effect. A similar model was illustrated at a finer geographical scale, i.e. the Draa Valley in Morocco. Genetic structure appeared as two major clusters subdivided into six sub-clusters in which Moroccan germplasm constituted specific groups in comparison with other Mediterranean apricots. Moroccan germplasm was classified into three sub-clusters, two of which were formed by genotypes related to ‘Del Patriarca’ and ‘Canino’, respectively. The present study highlights the wide Moroccan apricot's diversity in traditional agroecosystems, and also suggests a substantial gene flow occurring from recently introduced cultivars (‘Canino’ and ‘Del Patriarca’) to local apricot populations, thus leading to local germplasm diversification through seedling propagation. If we consider its geographical position, the historical diffusion of the species and farming practices, Morocco could be viewed as an additional centre of secondary diversification for apricot. Understanding the origin and specificity of local apricot populations is crucial for managing local collections in regard to adaptive traits for arid and Saharan conditions as well as for introducing local genetic resources into current breeding programmes.
Potential of Fava Bean as Future Protein Supply to Partially Replace Meat Intake in the Human Diet

Legumes have the potential to support global protein production by partially replacing meat and dairy products in the human diet. This will not only help meeting the increasing worldwide demand for proteins, but could contribute towards mitigating the threat imposed to the environment by current agricultural practices in higher-economy countries (dependence on fossil fuel energy and harmful emissions). Among the legumes, fava bean (Vicia faba L.) is a valuable crop. It is a rich source of proteins, fiber, and other non-nutrient compounds considered beneficial for health. Although a popular source of proteins in many parts of the world, especially in the Middle East, Mediterranean area, and South America, it has yet to be fully exploited in markets where meat is the predominant source of proteins in the diet. Here, fava bean cultivation could not only make a valuable contribution towards protein self-sufficiency, but could potentially play a role in alleviating the rise in chronic diseases. In addition, fava bean enables symbiotic fixation of atmospheric nitrogen and can provide a more environmentally friendly substitution for industrial N-fertilizers with associated improvements in resource efficiency and production costs. From both a food security and environmental sustainability perspective, encouraging both production and consumption of fava bean is a timely and important target. This review focuses on the potential of fava bean as a functional food ingredient to partially replace meat in the human diet.
DETECTING POPULATION TRENDS IN MIGRATORY BIRDS OF PREY

Abstract Counts of visible migrants at traditional watchsites throughout North America provide an opportunity to augment population-monitoring efforts for birds of prey. We analyzed hourly counts of migrating raptors at one inland (Hawk Mountain Sanctuary, Pennsylvania) and one coastal (Cape May Point, New Jersey) watchsite in northeastern North America. Hourly counts of migrants have been collected for 38 years at Hawk Mountain Sanctuary and for 28 years at Cape May Point. We compared effort-adjusted, arithmetic-mean passage rates to five geometric-mean indexes for 12 species. We used reparameterized polynomial regression to estimate trends in the indexes and to test the significance of trends from 1976–1978 (average index over three-year period) to 2001–2003. Effort-adjusted, arithmetic-mean indexes corresponded to more sophisticated indexes on the complete data sets but did not perform well on simulated data with missing observation days. We recommend the use of a regression-based, date-adjusted index for the analysis of hawk-count data. This index produced trends similar to other geometric-mean indexes, performed well on data sets simulating reduced sampling frequency, and outperformed other indexes on data sets with large blocks of missing observation days. Correspondence between trends at the watchsites and trends from Breeding Bird Surveys (BBSs) suggests that migration counts provide robust estimates of population trends for raptors. Furthermore, migration counts allow the monitoring of species not detected by BBS and produce trends with greater precision for species sampled by both methods. Analysis of migration counts with appropriate methods holds considerable promise for contributing to the development of integrated strategies to monitor raptor populations. Detección de Tendencias Poblacionales en Aves de Presa Migratorias
Induction and characterization of hepatic metallothionein expression from cadmium-induced channel catfish (Ictalurus punctatus)

Two low-molecular-weight proteins of approximately 10,000 daltons (DA) were isolated from the hepatic tissue of catfish intraperitoneally injected with CdCl{sub 2} (5 mg/kg). Each protein was significantly induced following Cd treatment. Bound Cd, co-eluted from DEAE anion-exchange HPLC with rabbit hepatic metallothioneins I and II, did not possess UV absorption indicative of aromatic amino acids and corresponded to the expression of two mRNA transcripts of approximately 400 base pairs, which hybridized to a full-length cDNA probe to winter flounder metallothionein (MT). Because these data indicated that these two low molecular weight proteins were hepatic MT isoforms, induction of MT mRNA expression was studied in livers of channel catfish exposed to aqueous CdCl{sub 2} utilizing the ribonuclease protection assay. Following a 7-d exposure to 10, 50, and 100 {micro}g/L CdCl{sub 2}, expression of two MT mRNAs increased in a dose-dependent manner (MT-a, r{sup 2} = 0.95; MT-b, r{sup 2} = 0.98). Each transcript was maximally induced 48 h after exposure to 100 {micro}g/L CdCl{sub 2} and then gradually declined to approximately 20% above controls after 96 h and maintained this level of expression for 7 d. Although MT expression is rapidly induced in channel catfish by Cd, and MT mRNA measurementmore » is a sensitive indicator of MT induction, the use of hepatic MT of channel catfish may not be a sensitive bioindicator of short-term, low-level aqueous exposures of Cd. « less
Structure, expression and function of the Phantastica gene in Antirrhinum organ development

The mutant phenotype of the PHANTASTICA (PHAN) gene had indicated that PHAN was required for dorsoventrality of leaves, bracts and petal lobes in Antirrhinum majus. Here it was shown that at low temperature, phan mutants carrying a likely null allele also stopped organ initiation and growth, and the shoot apical meristem arrested. These effects were reversed when plants were returned to a higher temperature. This indicated that PHAN is also required redundantly for earlier elaboration of the proximodistal axis of all organs and for meristematic function. PHAN was shown to encode a novel MYB-related transcription factor. In situ hybridisation revealed that P11AN mRNA was first expressed in leaf initials before they became morphologically distinct from the meristem. Comparisons of the expression patterns of PHAN and floral homeotic genes revealed that PHAN is expressed in floral organ initials at, or before, the time that their identities are specified within the meristem. The early and specific expression pattern of PHAN, its requirement for elaboration of the two axes unique to lateral organs and the regulatory activity of its product suggest that it specifies the identity of lateral organ initials as distinct from the meristem and stem. The requirement for PHAN in maintenance of the shoot apical meristem appears to be non cell-autonomous and therefore to involve PHAN-dependent signalling from organ initials. To characterise the relationship between PHAN and other genes involved in meristem function, the expression pattern of an Antirrhinum homologue of the Arabidopsis SHOOTMERISTEMLESS (STM) gene, AmSTM, was determined. This showed that AmSTM was expressed in a domain complementary to that of PHAN. Evidence suggesting that PHANis required for expression of AmSTM was obtained.
Male‐producing thermal ecology of a southern loggerhead turtle nesting beach in Brazil: implications for conservation

The major nesting areas for loggerhead turtles in Brazil are estimated to produce about 90% female hatchlings on account of their warm temperatures. In the present study, sand temperatures were monitored at the southern cooler end of the nesting range (Comboios, Espiríto Santo): the temperatures were cool enough to produce a far greater proportion of males than at the major beaches further north. Particular beaches may be thermally suited for the production of a particular sex. Protection of rookeries that appear minor in terms of numbers of turtles nesting could be important for the health of a larger population by insuring that there is an appropriate sex ratio. Temperatures were also monitored in a central guarded hatchery, set back from high seas. The hatchery was thermally similar to zones on the beach where turtles commonly lay, indicating that this conservation practice is unlikely to introduce any large distortions of sex ratio on this beach.
Consistent functional response of meadow species and communities to land-use changes across productivity and soil moisture gradients

Questions Wet meadows have traditionally been managed at low intensity, promoting the co-existence of a variety of plant species. The remaining fragments of these meadows are now being degraded by either mowing abandonment or by agricultural intensification, such as increased fertilization. We tested the theoretical expectation that certain functional traits can explain vegetation changes along gradients of productivity and soil moisture in response to these land-use changes. Location Železne hory Mts. , Czech Republic, Central Europe. Methods We set up a long-term experiment where we applied a full factorial design of fertilization and abandonment to 17 traditionally mown wet meadows covering a broad range of productivity and soil moisture conditions found within the region. Plant functional traits that cover different aspects of plant ecological strategies – plant height, specific leaf area (SLA), leaf dry matter content (LDMC), seed mass and clonality – were used to explain both species and whole community response to land-use change. We employed linear mixed effect models to test for the consistency of functional changes across different productivity and soil moisture conditions. Results We found that the functional response of species and whole communities to land-use change was consistent across meadows differing substantially in their productivity and soil moisture. Specifically, irrespective of the local conditions, both fertilization and abandonment selected for tall species within communities, highlighting the effect of increased competition for light. Traits related to a more exploitative strategy in species (higher SLA, more prominent clonal growth and smaller seeds) were consistently favoured with increased fertilization. Conclusions We show that within a given region with a common land-use history, certain functional traits consistently explain and can help to predict changes in plant communities caused by land-use change, irrespective of different productivity and soil moisture conditions. Our results demonstrate a simple way to use functional traits in applied nature conservation. We hope this will encourage practitioners to use functional traits to complement existing knowledge on composition and productivity of considered habitats to enhance the planning of management practices. We encourage practitioners to build regional trait databases to actively use trait information for the purpose of habitat management.
Immunohistochemistry as a tool for the accurate diagnosis of diseases in reptiles

Increased efforts have been devoted in recent years to the study of reptile medicine and surgery, including medical management, pathological studies, and diagnosis of diseases in reptiles. Immunohistochemistry has proved to be a powerful tool for the accurate diagnosis of a number of important diseases in humans and domestic animals, depending on the production of appropriate primary antibodies and the availability of monoclonal antibodies. Although molecular techniques for pathogens identification have been recently developed, the diagnosis of pathogens in reptiles is usually achieved by isolation, culture or histopathology. However, immunohistochemistry allows the demonstration of antigens of specific pathogens in paraffin-embedded histological sections, being the major advantage the possibility to directly associate a specific pathogen with histologic lesions. Using different clinical cases of bacterial, viral, mycotic and parasitic diseases in reptiles we review the basics of the immunohistochemistry. Clinical cases include immunohistochemical detection of Salmonella sp. in snakes, ophidian paramyxovirus in snakes, pathogenic fungi in sea turtles, and filarial nematodes in lizards. Efforts should be made to develop standardized and commercially available specific polyclonal and monoclonal antibodies against pathogens described in reptiles. We conclude that immunohistochemistry is an optimal tool for the accurate diagnosis in reptiles, emphasizing the usefulness of the microscopic studies in reptile pathology.