Miracle-dz/UniFAR-FTUs huggingface dataset:
Concurrent Occurrence of Lower Respiratory Aspergillosis and Pneumoconiosis in a Turkey Flock

Abstract This study describes a concurrent occurrence of lower respiratory aspergillosis and pneumoconiosis in a turkey flock. From one flock of 1000 turkeys, 4 clinically affected turkeys were examined pathologically and microbiologically. Clinically affected turkeys showed anorexia, lethargy, drooping of the wing, vomiting, dyspnea and open-beak breathing, or sudden dead. Gross lesions were observed in the air sacs and lungs which presented white to yellowish granulomas of varying size. Microscopic there was multifocal granulomatous airsacculitis and pneumonia. At the center of the granulomas, fungal hyphae were clearly highlighted in the lungs and air sacs by Gomori methenamie silver (GMS) staining. In the microbiological cultivation of the affected lungs and air sacs, Aspergillus fumigatus was isolated on Sabouraud dextrose agar. Furthermore, dark black dust accumulations were present in the cytoplasm of macrophages or interstitial tissue in the lungs and air sacs. There were also fibrosis and lymphohistiocytic cell infiltrations around the particles. Overall, this study could implicated that pneumoconiosis might be a predisposing factor in the development of respiratory aspergillosis in turkeys.
Different pattern of haemagglutinin immunoreactivity of equine influenza virus strains isolated in Poland

Abstract The immunoreactivity of haemagglutinin (HA) polypeptides of equine influenza virus was compared among the strains isolated in Poland, using H3 monoclonal antibody. A stronger signal in immunoblot reaction was observed for A/equi/Pulawy/2008 HA polypeptides compared to A/equi/Pulawy/2006, despite the fact that both strains are phylogenetically closely related and belong to Florida clade 2 of American lineage. The strongest signal, observed in the case of A/equi/Pulawy/2008, seemed to be connected with the presence of G135, I213, E379, and/or V530 instead of R135, M213, G379, and I530 present in A/equi/Pulawy/2006 HA sequence. This implies that point mutations within amino acid sequences of HA polypeptides of equine influenza virus may change their immunoreactivity even when they are not located within five basic antigenic sites.
Reproducing tables in scanned documents

Digitisation is a process of representing real world objects in digital format. The rapid conversion of material available in printed form to editable digital form requires a significant amount of work if we are to maintain the format and the style of the electronic documents similar to their printed counterparts. Most of the existing digitisation procedures cover only text, and they have to go beyond OCR (text only) for making the text inside objects such as tables searchable, while preserving the format and converting the objects to an editable form to modify and reprint the content, for which the processes of detection and recognition are important. In past research the table detection process mostly followed certain assumptions such as i) either having rule lines or no lines and ii) Manhattan or multi-column layout. However, the recognition process assumed that the considered tables have already been detected and fails to preserve their formatting features for future modifications and re-printing. To address these issues, we proposed a simple and fast algorithm using local thresholds for word space and line height, which locates all types of tables and extract their formatting features. From the experiments performed on 353 records, we have achieved a much higher detection ability than the earlier algorithm and is superior as it performs extended layout analysis, elimination of header-footer and bulleted-numbered sections before the reconstruction of tables. While reconstructing the extracted table, the most prominent features of the tables are preserved with the earlier formats. The algorithm has an advantage of linear complexity as it performs the conversion locally.
The Salinity Tolerance of Seeded-type Common Bermudagrass Cultivars and Experimental Selections

Turfgrass managers are using reclaimed water as an irrigation resource because of the decreasing availability and increasing cost of fresh water. Much attention, thereby, has been drawn to select salinity-tolerant turfgrass cultivars. An experiment was conducted to evaluate the relative salinity tolerance of 10 common bermudagrasses (Cynodon dactylon) under a controlled environment in a randomized complete block design with six replications. ‘SeaStar’ seashore paspalum (Paspalum vaginatum) was included in this study as a salinity-tolerant standard. All entries were tested under four salinity levels (1.5, 15, 30, and 45 dS·m−1) consecutively using subirrigation systems. The relative salinity tolerance among entries was determined by various parameters, including the normalized difference vegetation index (NDVI), percentage green cover determined by digital image analysis (DIA), leaf firing (LF), turf quality (TQ), shoot vertical growth (VG), and dark green color index (DGCI). Results indicated that salinity tolerance varied among entries. Except LF, all parameters decreased as the salinity levels of the irrigation water increased. ‘Princess 77’ and ‘Yukon’ provided the highest level of performance among the common bermudagrass entries at the 30 dS·m−1 salinity level. At 45 dS·m−1, the percent green cover as measured using DIA varied from 4.97% to 16.11% among common bermudagrasses, where ‘SeaStar’ with a DIA of 22.92% was higher than all the common bermudagrass entries. The parameters LF, TQ, NDVI, DGCI, VG, and DIA were all correlated with one another. Leaf firing had the highest correlation with other parameters, which defined its value as a relative salinity tolerance measurement for common bermudagrass development and selection.
Defining rarity and determining the mechanisms of rarity for North American freshwater fishes

Conserving rare species and protecting biodiversity depends on sound information on the nature of rarity. Rarity is multidimensional, presenting the need for a quantitative classification scheme by which to label species as rare or common. I defined rarity for freshwater fishes based on the range extents, habitat breadths, and site abundance and examined the relationship between these dimensions of rarity and imperilment. Imperiled fishes were most often rare by all three dimensions, whereas undesignated species were most often common by all three dimensions. Next, I examined the effect of sampling intensity on observed rarity of stream fish using different numerical and proportional rarity criteria and found that increasing sampling intensity increased the number of species labelled as rare with proportional criteria but did not affect the number of species labelled as rare with numerical criteria. Additional electrofishing passes within a fixed reach increases the likelihood of detecting rare and endemic species. A tradeoff between information collected and sampling resources should be carefully considered in the context of objectives when sampling for rare species. Finally, I examined the effect of regional and watershed habitat variables, biotic interaction variables, and instream habitat variables, on the rare or common status on 23 North American freshwater fishes. I also compared biological and reproductive traits among species classified into the rarity framework. Rarity was successfully explained in 19 of the 23 species and I found that regional and watershed habitat variables were the most important predictors of rarity. I also found that species large body size, high fecundity, and long age at maturity were generally more common by range extent and site abundance while those species that did not guard nests were more frequently rare by site abundance.
Factors influencing the Δ6-desaturation of linoleic acid

A6-desaturase is located in a pivotal position in the metabolism of essential fatty acids and a low activity may lead to coronary heart disease (CHD). Experimental evidence suggests that A6-desaturase is low in humans and data from cross-cultural and case-control studies using fatty acid compositional analyses propose that its activity is reduced by risk markers for CHD. In this thesis the role of some factors implicated in CHD such as diabetes, hypercholesterolaemia and stress are considered and their effect on A6-desaturase activity and tissue fatty acid composition is assessed in the rat. The assay for the A6-desaturation of linoleic acid was re-examined and optimised. Microsomal protein and albumin concentrations were found to be critical because of their substrate binding effects. It was also found necessary to measure the amount of non-esterified linoleic acid in microsomal preparations as it competes with the radioactive substrate. The role of dietary cholesterol on both linoleic acid A6-desaturation and tissue fatty acid composition was assessed. Cholesterol enrichment increased A6-desaturase activity and this was reflected in the increased product-precursor ratio of y-linolenic to linoleic acid in microsomal phospholipids. However, the total amount of long chain polyunsaturated fatty acids derived from linoleic acid, including arachidonic acid, was reduced in cholesterol fed rats, suggesting an impaired A5-desaturase. The increased activity of liver microsomal A6-desaturase was not associated with any significant changes to adipose tissue n-6 fatty acid composition. Further studies were conducted to elucidate possible reasons for the disparity between the present and published studies on the effect of cholesterol. Cholesterol feeding was carried out in grouped and isolated rats and microsomal A6-desaturase reassessed. Although stress caused by isolation reduced A6-desaturase activity, dietary cholesterol increased its activity again. This was observed under both saturating and non-saturating substrate conditions with a good correlation observed between the two. Levels of non-esterified fatty acids in the microsomal preparations were not different
Cardoon (Cynara cardunculus L.) used as vegetable rennet in an Algerian traditional cheese making "Djben"

The flowers of cardoon are typically used in Algeria, for traditional cheese making of "Djben" usually manufactured with raw ewe'’s milk. This plant (Cynara cardunculus L.), used for milk-clotting, is widely distributed in Mediterranean countries . It grows wild and abundantly in dry, uncultivated places, producing flower all summer. The present study was carried out in order to study the aptitude of the cardoon to coagulate cow’s, ewe's and goat's milks in the traditional cheese making. First, extractions carried out from various parts of the plant, indicate A coagulating activity only with the flower collected at an advanced stage of development. Second, the most firmness of cheese texture was obtained with ewe's milk cheese. The coagulant agent seems to show a greater affinity for the ewe's milk where its action is found to be much better. The organoleptic characteristics of cheese performed with the three types of milk differs notably, particularly the consistency and the bitterness flavor in cow’s milk cheese. The ewe's milk cheese was the most appreciated by the jury.
Taxonomic delimitation of the rare, eastern North American endemic lichen Santessoniella crossophylla (Pannariaceae)1

Abstract The taxonomic delimitation and generic placement of Santessoniella crossophylla (Old Gray Crosslobes), a cyanolichen endemic to eastern North America, are revisited based on newly generated nrITS and mtSSU sequences. A population from Nova Scotia whose identification as S. crossophylla has been questioned is confirmed as belonging to the species. The monospecific genus Rockefellera is introduced to accommodate lichens ascribable to S. crossophylla in light of molecular results herein presented. The new name honors the Rockefeller family for their century-long support of North American conservation efforts, particularly with respect to national parks.
Characterization of a Thylakoid-Bound lsoprene Synthase in Salix discolor Chloroplasts

lsoprene synthase is an enzyme that is responsible for the production of the volatile C5 hydrocarbon, isoprene, in plant leaves. lsoprene formation in numerous C3 plants is interesting because (a) large quantities of isoprene are emitted, 5 x IOl4 g of C annually, (b) a plant may release 1 to 8% of its fixed C as isoprene, and (c) the function of plant isoprene production is unknown. Because of the dependence of foliar isoprene emission on light, the existence of a plastidic isoprene synthase has been postulated. To pursue this idea, a method to isolate chloroplasts from Salix discolor was developed and shows a plastidic isoprene synthase that is tightly bound to the thylakoid membrane and accessible to trypsin inactivation. The thylakoid-bound isoprene synthase has catalytic properties similar to known soluble isoprene synthases; however, the relationship between these enzymes is unknown. The discovery of a thylakoidbound isoprene synthase with a stromal-facing domain places it in the chloroplast, where it may be subject to numerous direct and indirect light-mediated effects. lmplications for the light-dependent regulation of foliar isoprene production and its function are presented.
Effect of dietary β-glucan supplementation on growth performance, nutrient digestibility, and characteristics of feces in weaned pigs

ABSTRACT A total of 150 crossbred weaned pigs [(Yorkshire × Landrace) × Duroc] with an average body weight of 6.75 ± 0.49 kg were used in a 6-wk trial to determine the effects of dietary supplementation of β-glucan on growth performance, nutrient digestibility, and characteristics of feces (fecal score, microbiota, moisture, and pH) in weaned pigs. The corn-soybean meal based dietary treatments included: 1) antibiotic (30 ppm Tiamulin), 2) 0% β-glucan, 3) 0.1% β-glucan, 4) 0.2% β-glucan, and 5) 0.4% β-glucan. Dietary supplementation with β-glucan resulted in no significant differences in growth performance, nutrient digestibility, or characteristics of feces compared with that of Tiamulin supplementation. Pigs fed β-glucan exhibited a linearly increasing average daily gain and feed/gain ratio. Dietary supplementation of β-glucan linearly increased apparent total tract digestibility of dry matter and energy during 1–14 and 1–42 d as dietary β-glucan increased from 0.1 to 0.4%. In addition, pigs fed β-glucan had linearly decreasing coliform bacterial counts. In conclusion, dietary supplementation with β-glucan from rice bran improved growth performance, nutrient digestibility and coliform bacteria in weaned pigs, and β-glucan had the same effect as Tiamulin supplementation on growth performance, nutrient digestibility, and characteristics of feces. Thus, we suggest that β-glucan from rice bran can be used as an alternative to antibiotics, and will improve productivity of weaned pigs.
Gross and Biometrical Studies on Male Reproductive System of Adult Local Fowl of Uttarakhand (Uttara Fowl)

Gross and biometrical study was conducted on male reproductive system of 12 apparently healthy adult male Uttara fowl birds. The testicles were elongated bean shaped and creamy in appearance. The left testis was larger and heavier, while the right one was smaller and lighter. The epididymis was located on the dorsomedial aspect of the testis. The anterior part was closely associated with the adrenal gland and it was particularly extensive for left epididymis. The paired ductus deferens was convoluted and wavy in adult birds. It began at the caudal end of the epididymis and extends to the cloaca parallel to the respective ureter.
Is it possible to obtain zero estimates of genetic diversity? A case study of the Nigerian indigeneous goat breeds at the β-lactoglobulin gene locus

The current investigation was conducted to appraise the genetic diversity and genetic distance of three goat populations namely; Red Sokoto, Sahel and West African Dwarf (WAD), in Nigeria, making use of blood samples collected from 20, 20 and 20 individual from which blood DNAs were extraction, respectively. The DNAs extracted were used to study polymorphism at the β-lactoglobulin gene locus using RLFP-PCR process. Results revealed that the mean total number of alleles was 1 while the effective number of alleles was also 1. The percentage of polymorphic locus was 0% while Shannon's information index, observed homozygousity, expected heterozygosity, unbiased expected heterozygosity and inbreeding coefficient (F) were all observed to be 0.000. The pairwise Fst was 0.000 between all the breeds of goats. Variation within and between the populations of goats was 0% at p>0.05. The genetic distance between the goat breeds was 0.000. The present study revealed that RLFP-PCR may not be a powerful tool for the study of the β-lactoglobulin gene locus and hence other methodologies should be employed for a broader judgment on the genetic status of the goat population at the locus.
Automated computation of two-dimensional fetch fields: case study of the Salto Caxias reservoir in southern Brazil

ABSTRACT Marques M, Andrade FO. 2017. Automated computation of two-dimensional fetch fields: case study of the Salto Caxias reservoir in southern Brazil. Lake Reserve Manage. 33:62–73. This work described and applied a computational model, OndaCad, developed to automate Saville's method for fetch evaluation in sinuous inland waterbodies. The OndaCad model is part of a web-based system being developed to estimate induced mixing length and sediment resuspension by effects of wind-generated waves. The model, written in AutoLisp language, allows the agile calculation of fetch on a structured computational mesh that encloses the waterbody. The fetch was determined automatically at each mesh node by using a fine resolution Saville's method, and the solution was displayed on thematic maps as a 2-dimensional fetch field. The model was applied to the case study of Salto Caxias reservoir located in southern Brazil. Two-dimensional fetch fields were calculated for 16 wind directions, and the largest fetches and their locations were identified. The model was able to process 16 maps of fetch in ∼6 hours using a personal computer. The significant wave heights associated with the fetch fields for the north-oriented winds were obtained using parametric equations that assumed variable coefficients dependent on the wind velocity magnitude. Validation of the results was performed against numerical model data for steady state and uniformly distributed winds of 10, 15, and 20 m/s. The significant wave height comparisons indicated errors <10% for the reservoir central area.
The utility of mortality hazard rates in population analyses

Mortality is a key process in ecology and evolution, and much effort is spent on development and application of statistical and theoretical models involving mortality. Mortality takes place in continuous time, and a fundamental representation of mortality risks is the mortality hazard rate, which is the intensity of deadly events that an individual is exposed to at any point in time. In discrete‐time population models, however, the mortality process is represented by survival or mortality probabilities, which are aggregate functions of the mortality hazard rates within given intervals. In this commentary, we argue that focussing on mortality hazard rates, also when using discrete‐time models, aids the construction of biologically reasonable models and improves ecological inference. We discuss three topics in population ecology where mortality hazard rates can be particularly useful for biological inference, but are nevertheless often not used: (a) modelling of covariate effects, (b) modelling of multiple sources of mortality and competing risks, and (c) elasticity analyses of population growth rate with respect to demographic parameters. To facilitate estimation of cause‐specific mortality hazard rates, we provide extensions to the R package marked. Using mortality hazard rates sometimes makes it easier to formulate biologically reasonable models with more directly interpretable parameterizations and more explicit assumptions. In particular, interpretations about relative differences between mortality hazard rates, or effects of relative changes in mortality hazard rates on population growth (elasticities), are often more meaningful than interpretations involving relative differences in survival (or mortality) probabilities or odds. The concept of hazard rates is essential for understanding ecological and evolutionary processes and we give an intuitive explanation for this, using several examples. We provide some practical guidelines and suggestions for further methods developments.
Isolation and characterization of a Serratia marcescens with insecticidal activity from Polyphylla olivieri (Col.: Scarabaeidae)

Members of the genus Serratia are known for their abilities to infect insects. In this study, a red‐pigmented S. marcescens was isolated and characterized from the infected larvae of Polyphylla olivieri using bacterial cultivation, phylogenetic analysis as well as bioassays against larvae of the two insect pests, Plodia interpunctella and Ephestia kuehniella. Comparative 16S rRNA and groEL gene sequence BLAST analyses strongly suggested that the isolated strain should be placed in the genus Serratia, sharing high sequence similarities with several strain of S. marcescens associated with insects. Phylogenetic analysis placed the isolated bacterium with other S. marcescens bacteria in a clade with high bootstrapping values. To assess pathogenicity of the S. marcescens isolate, the bacterial cells were either injected into the haemolymph of the fifth‐instar larvae or added to the diets of insects. Survival curves of the control insects and those challenged with six different concentrations of S. marcescens showed that the S. marcescens isolate significantly reduced survival rates of the larvae. The LC50s of the bacterium on P. interpunctella and E. kuehniella were 1992.26 and 1.09 × 104 (CFU/μl) for injection bioassays at 6 h post‐injection, and 4.48 × 104 and 1.96 × 105 (CFU/10 μl) for feeding bioassays at 24 h post‐feeding, respectively. Injection of the bacterial culture supernatant into the larvae led to continuous bleeding from the site of injection, while injection of heat‐treated culture supernatant of the bacterium did not cause continuous bleeding. Together, our results showed the possibility of using this S. marcescens isolate in microbial control of the insect pests after addressing the safety concerns. Moreover, it might be considered as a source of useful bioactive molecules and genes with application in insect control and biotechnology via developing insect‐resistant plants.
High quality RNA from hydroponically grown grapevine roots suitable for gene expression studies

Abstract Objectives Grapevine root system plays a great role in sensing and adapting to abiotic and biotic stresses. Identification of candidate genes involved in the tolerance to abiotic stress is becoming a crucial strategy to select and breed resilient genotypes. However, obtaining high quality RNA from grapevine roots under hydroponic culture is difficult. Hence, we have developed a new extraction procedure to improve RNA quality for root gene expression studies. Methods Conventional RNA extraction methods using CTAB are not suitable for gene expression studies and need to be improved. Here we report the application of a CTAB- based method for RNA extraction using an additional clean-up purification step. Results The RIN value of the resulting RNA indicated that our procedure allowed the purification of high RNA quality and quantity. Hence, the clean-up purification step efficiently eliminated contaminants which inhibit downstream applications. Derived RNA was successfully used for differential gene expression analysis in salt stressed grapevine by Northern Blot hybridizations. Conclusion In this study, we developed an efficient RNA isolation protocol from hydroponic cultivated grapevine roots which yielded RNA suitable for gene expression studies. This will open large perspectives in grapevine functional genomics with the identification of pertinent genes of agronomic interest.