Miracle-dz/UniFAR-FTUs huggingface dataset:
Glushkov's construction for functional subsequential transducers

Glushkov's construction has many interesting properties and they become even more evident when applied to transducers. This article strives to show the wast range of possible extensions and optimisations for this algorithm. Special flavour of regular expressions is introduced, which can be efficiently converted to $\epsilon$-free functional subsequential weighted finite state transducers. Produced automata are very compact, as they contain only one state for each symbol (from input alphabet) of original expression and only one transition for each range of symbols, no matter how large. Such compactified ranges of transitions allow for efficient binary search lookup during automaton evaluation. All the methods and algorithms presented here were used to implement open-source compiler of regular expressions for multitape transducers.
Evaluation of Milk for Cheese Production Based on Milk Characteristics and Formagraph Measures

Abstract The characteristics of milk, including its clotting ability, were considered in an effort to develop an equation to predict yield of aged Parmesan cheese. The clotting properties of milk were measured using the Formagraph on 279 milk samples from the vats of 12 cheese plants over 12 mo. A significant, nonlinear relationship was found between the Formagraph measure of curd firmness and cheese yield. The relationship between predicted cheese yield and curd firmness depended on fat level. Increasing curd firmness increased cheese yield only at the low fat level. Intermediate values of curd firmness predicted highest cheese yields for the intermediate fat level. At the high fat level, increasing curd firmness resulted in decreasing predicted cheese yields. Cheese yields increased with fat and protein level. It appears that the Formagraph measure of curd firmness is related to cheese yield as an indicator of casein aggregation properties of the milk. No other Formagraph measures were significantly associated with actual aged cheese yield.
Induction of longevity in primed seeds

Abstract Priming of seeds is generally intended to reduce time to germination, often leading to improved emergence. However, as a negative side effect, priming reduces longevity of seeds. We studied the possibilities to obtain primed seeds with reduced time to germination but with longevity similar to that of untreated seeds. For several species tested we found that the desired longevity could be obtained by keeping the seeds, after a priming treatment, under a mild water and / or temperature stress for a period of several hours to days. Time to germination did not increase again due to such a treatment. Optimal duration and degree of water stress were strongly temperature dependent. The methods applied to obtain primed seeds without loss of longevity are very similar to those used to induce desiccation tolerance in germinated seeds.
Notice of Retraction Spermatogenesis-Related Gene Selection by Singular Value Decomposition and Correlation Analysis

The aim of this study is to select significant genes associated with spermatogenesis. We use singular value decomposition to extract the principal component of the DNA microarray dataset and the expression profile of the first eigengene shows the expression tendency of most genes' expression. Basing on this observation, we rank genes using correlation of each gene expression and the first eigengene's profile. Five kinds of correlation methods are considered and experimental results on a real spermatogenesis microarray dataset demonstrate that the cosine correlation method can find 75 informative genes among top 100 probes/genes. The selected significant genes, especially the top 10 probes/genes, are related to spermatogenesis through literature analysis.
Characteristics of refugia used by the threatened Australian growling grass frog (Litoria raniformis) during a prolonged drought

Abstract Context. Because they are dependent on water, drought can have a deleterious impact on aquatic-breeding amphibians. One such species, the threatened growling grass frog (Litoria raniformis) occurs in south-eastern Australia, a region that has recently emerged from a decade-long, severe drought. Aims. We aimed to identify features of drought refugia that facilitate persistence of L. raniformis, so as to provide guidance to natural-resource managers attempting to conserve populations of this species during drought. Methods. We conducted repeat surveys for L. raniformis at 90 water bodies at the end of the ‘millennium drought’. We recorded the following six environmental variables for each water body: origin (natural or not), type (lotic or lentic), proportion of aquatic vegetation cover, conductivity of water, riparian tree-canopy cover and distance to the nearest woodland. We used occupancy models to relate the presence of L. raniformis to these variables, while accounting for uncertain detection. Key results. Water-body type (natural or artificial, lentic or lotic) had minimal influence on the probability of occupancy by L. raniformis. We found a strong negative relationship between occupancy and conductivity of water (a surrogate for salinity), and a positive relationship between occupancy and the proportion of aquatic vegetation. We found a negative relationship between detection and the extent of aquatic vegetation, and a mildly negative effect of canopy cover on occupancy. Conclusions. Habitat characteristics are more important indicators of the quality of drought refugia for L. raniformis than is the type of water body per se. Consequently, we identified aquatic vegetation and salinity as important targets for management when planning the retention, creation or restoration of habitat to facilitate persistence of L. raniformis during drought. Implications. Our results highlighted aquatic vegetation and water-quality parameters that are likely to facilitate the persistence of L. raniformis during drought. Assessing the effectiveness of our recommendations in an experimental framework would ensure that conservation management of this frog can be refined over time.
Evolution of pre‐zygotic and post‐zygotic barriers to gene flow among three cryptic species within the Anastrepha fraterculus complex

Tropical tephritids are ideally suited for studies on population divergence and speciation because they include species groups undergoing rapid radiation, in which morphologically cryptic species and sister species are abundant. The fraterculus species group in the Neotropical genus Anastrepha is a case in point, as it is composed of a complex of up to seven A. fraterculus morphotypes proposed to be cryptic species. Here, we document pre‐ and post‐zygotic barriers to gene flow among adults of the Mexican A. fraterculus morphotype and three populations (Argentina, Brazil, and Peru) belonging to two separate morphotypes (Brazilian 1 and Peruvian). We unveiled three forms of pre‐zygotic reproductive isolation resulting in strong assortative mating. In field cages, free‐ranging male and female A. fraterculus displayed a strong tendency to form couples with members of the opposite sex belonging to their own morphotype, suggesting that male pheromone emission, courtship displays, or both intervene in shaping female choice before actual contact and coupling. In addition, males and females of the Peruvian morphotype became receptive and mated significantly later than adults of the Mexican and Brazilian 1 morphotypes. After contact, Mexican females exhibited greater mating discrimination than males when facing adults of the opposite sex belonging to either the Peruvian or the Brazilian 1 morphotype as evidenced by vigorous resistance to penetration once they had been forcefully mounted by heterotypic males. Forced copulations resulted in production of F1 hybrids that were either less viable (and partially fertile) than parental crosses or even sterile. Our results suggest that the Mexican morphotype is a distinct biological entity and that pre‐zygotic reproductive isolation through divergence in courtship or male‐produced pheromone and other mechanisms appear to evolve faster than post‐zygotic isolation in the fraterculus species group.
Genetic variability and structure of Gomortega keule (Molina) Baillon (Gomortegaceae) relict populations: geographical and genetic fragmentation and its implications for conservation

Gomortega keule (Molina) Baillon is a rare Chilean species classified as endangered and currently under conser- vation. Currently, conservation of this species is carried out by private companies and government agencies, but is done so based more on pragmatic criteria than scientifically based strategies. In this context, information concerning the genetic variability of the species among the different populations over its entire distribution range is incomplete, making it difficult to coordinate management and conservation strategies. Here we report a study to evaluate the genetic variability and popu- lation structure of G. keule over its entire distribution in Chile. Twenty-five ISSR primers for 223 individuals from 11 geo- graphical populations were tested to evaluate genetic variability. Results showed a high level of genetic diversity for the species. A high level of genetic differentiation among populations was found, while genetic structure of the geographic populations was also shown by using STRUCTURE 2.1 software. Despite the fact that this species has been highly af- fected by human intervention and habitat destruction, a high level of genetic diversity was present. A likely explanation for this is that it reflects the previous distribution of this long-lived species and the current lack of sexual regeneration. Ge- netic diversity data must be considered in the development of a management strategy for further developing the protected areas, for identifying isolated small populations for conservation, and using larger populations with higher genetic diversity as seed sources for ex situ propagation and replanting.
Pattern and Process in Host-Parasitoid Interactions

Preface 1. Introduction 2. Data and methodology 3. Parasitoid species richness 4. Taxonomic composition and generalist versus specialist parasitoids 5. Host mortality and the impact of parasitoids on host densities 6. Hyperparasitoids 7. Synthesis References Index.
Use of chitin and krill in aquaculture - the effect on gut microbiota and the immune system: a review.

Chitin consists of β-1,4-linked N-acetylglucosamine residues and is estimated as the second most abundant biomass in the world after cellulose. However, relatively little chitin is utilized as a material for industrial, agricultural and medical applications and aquacultural purposes. Chitin may be useful as a constitutive material in formulated fish feed, and the interesting effects in fish merit further evaluation. There is evidence that fish and aquatic animals harbour a gut bacterial community that is distinctly different from that reported in the surrounding habitat or in the diet. Thus, the gut environment provides a specific niche, and bacterial activity in the gut is not merely a continuum of that observed in the environment. Today, it is well accepted that the gut microbiota in fish are modulated by dietary manipulations. But to what extent can dietary chitin and krill (chitin-rich) modulate the intestinal microbiota of fish and how do these dietary components affect the immune system? These questions will be discussed in the present review.
Nitrogen stress effects on growth and nitrogen accumulation by field-grown tomato

There are few growth studies evaluating within-season effects of N on vegetative growth and.N accumulation of tomato (Lycopersicon esculentum Mill.). Growth analysis of field-grown tomato for a number of Florida locations and management systems is presented here. Severe N stress resulted in fewer and smaller, but thicker, leaves. With increasing N, average leaf area index (LAI) increased from 0.75 to =3, but radiation use efficiency (RUE) typically increased less then 30%. Lower RUE under N-limited conditions reflected a decrease in N concentration of the most recently matured leaves from 40 mg g -1 to as little as 15 mg g -1 . Over the life of well-fertilized crops, leaf N concentrations dropped from 55 to 65 mg g -1 during initial growth to 20 to 35 mg g -1 at final harvest. Corresponding N concentrations for fruit and for stems were 30 to 35 mg g -1 and 15 to 25 mg g -1 . Severe N stress affected leaf and stem N concentrations most drastically, whereas N in fruits was less variable. With lower N supply (N < 180 kg ha -1 ) under careful management, nitrogen use efficiency (NUE) for field-grown tomato was 0.4 Mg fresh fruit (kg N) -1 and average crop N accumulation increased from 37 to 210 kg N ha -1 as N fertilization increased from 0 to 333 kg N ha -1 . As a fraction of the fertilizer N applied N fertilizer recovery ranged from 0.36 to 0.74 and 0.61 to 0.96 for drip-irrigated and subirrigated crops, respectively.
Risk Factors Affecting the Phenotypic Expression of Heterozy- gous Familial Hypercholesterolemia in Pakistani Population

Familial hypercholesterolemia (FH) is a genetic disorder of lipoprotein metabolism recognized by high plasma concentrations of low-density lipoprotein cholesterol (LDLC), tendon xanthomas, and high risk of early coronary heart disease. The phenotypic expression of FH is variable and several genetic and other risk factors contribute to such variability in clinical expression of the disease. FH is an autosomal disorder characterized by increased levels of total cholesterol (TC), low density lipoprotein cholesterol (LDL-C) and tendinous xanthmata (TX). Clinical phenotype of FH has previously been shown to be associated with increased coronary heart disease (CHD) and premature death. The present study was carried out in a Pakistani population to examine the contribution of environmental factors on the expression of this disease. A detailed examination of the physical and biochemical features of the FH was performed in a cohort of 335 individuals (202 males, 133 females) from Pakistan. Our results indicate that Pakistani females with FH had high levels of TC and LDL-C as compared to Pakistani males. Overall the concentrations of high density lipoprotein cholesterol (HDL-C) were significantly lower for both sexes as compared to the controls (normal). We have also found that high cholesterol levels were associated with increased incidence of CHD in FH Pakistani population where both male and female individuals showed 69% and 31% CHD, respectively. The mean onset age for coronary symptoms was about 38 years in males as compared to 45 years in females. A greater risk of developing CHD has been linked with levels of TC along with a history of smoking in males and presence of hypertension (HTN) in females. Our results indicate that these risk factors possibly affect and contribute in the phenotypic expression of FH in Pakistani population.
Antimitotic agents : effects on double haploid production in wheat

Chromosome doubling of microspore-derived plantlets and calli is a critical step in haploid breeding programs. For anther culture experiments, colchicine, (S)-N-(5,6,7,9-tetrahydro-1,2,3,10-tetrame-thoxy-9-oxobenzo[a]heptalen-7-yl-acetamide, is the most commonly used compound in doubling the chromosomes of seedlings derived from such experiments. Colchicine, however, is carcinogenic and expensive. We evaluated three antimitotic agent (colchicine ; trifluroryzolin, 2,6-dinitro-N,N-dipropyl-4-(trifluoromethyl)benzenamine (.)
Dose Effect of Cis- and Trans-Encoded HLA-DQαβ Heterodimers in IDDM Susceptibility

Insulin-dependent diabetes mellitus (IDDM) in whites is strongly associated with particular HLA-DQαβ heterodimers composed of a DQα chain with anrginine at residue 52 (Arg52+) combined to a DQβ chain lacking an aspartic acid at residue 57 (Asp57−. With the aim of confirming this association, clarifying which heterodimers account for the highest risk of IDDM and explaining the excess risk of DR3-DQw2/DR4-DQw8,115 unrelated white IDDM patients and 108 unrelated healthy nondiabetic control subjects were studied. With polymerase chain reaction and sequence-specific oligonucleotide probes, both patients and control subjects were typed for their HLA-DQA1 and DQB1 alleles and their DQA1-DQB1 haplotype and genotype frequencies were compared. Four major findings emerged from our analysis. 1) Arg52+ DQα/Asp57− Dβp heterodimers, formed in cis and/r in trans, are strongly associated with susceptibility to IDDM; 97% of patients and 46% of control subjects had at least one such susceptibility heterodimer (relative risk [RR] 32, confidence interval [Cl] 14.25–71.86, P < 10−. 2) The degree of disease susceptibility depends on the number of such DQ heterodimers that a subject can express according to his or her DQA1-DQB1 genotype. The highest RR was observed in patients with four susceptibility DQ heterodimers (RR 41, Cl 17.05–95.9). 3) Only part of the susceptibility DQ heterodimers were significantly increased in patients, conferring IDDM susceptibility of different strength. The strongest association was with the DQA1*0501-DQB1*0302 combination formed in trans position (RR 35.2, Cl 12.88–96.78, P < 10−7). 4) The simultaneous expression of four different susceptibility heterodimers explains the highest risk of DR3-DQw2/DR4-DQw8 heterozygotes. In conclusion, there is a dose effect of cis- and trans-encoded HLA-DQαβ heterodimers in IDDM susceptibility influenced by the diversity of these molecules.
Assessing the general patterns of forest structure: quantifying tree and forest allometric scaling relationships in the United States

Aim Understanding the drivers of forest structure, function and change is a fundamental problem in both theoretical ecology and applied forestry for carbon mapping and monitoring. An important component of forest ecology research often utilizes allometric equations to scale up local measurements to predict large-scale forest and ecosystem-level properties. However, both applied and theoretical allometries in forest ecology (such as metabolic scaling theory, MST) assume that many scaling relationships are insensitive to broad-scale climate gradients or species life histories. We aim to test these assumptions by mapping continental-scale forest allometry across environmental gradients in the United States. Location United States. Methods We fit exponents to two allometric relationships in c. 100,000 Forest Inventory Analysis (FIA) field plots: (1) the relationship between the height of an individual tree and its diameter, and (2) plot-level tree size distributions. We compare fitted exponents to environmental and life-history variables, such as climate, topography and forest structure, in an attempt to explain allometric variability and deviations from theoretically predicted allometries. Results We find that the structural allometry of forests varies strongly as a function of location in the United States. Allometric exponents appear to asymptote at approximately where MST theory predicts with increasing forest height, while deviations from MST are partially explained as a function of environmentally driven recruitment limitations and successional status. Main conclusions While we find support for invariant tree and stand allometric scaling relationships in forests that are in steady state with regard to demography and resources, we also find considerable spatial variability in forest allometric relationships when steady-state conditions are violated. These findings suggest that extensions of metabolic scaling theory should incorporate variation in demographic dynamics in younger successional forests, and factors influencing recruitment limitation.
Growth and morphology of pedunculate oak (Quercus robur L.) and beech (Fagus sylvatica L.) seedlings in relation to shading and drought

Les effets d'ombrage a differents degres en combinaison avec un traitement de dessechement sur la croissance et la morphologie de plants de chene pedoncule et de hetre ont ete etudies en conditions experimentales. La reaction du chene et du hetre s'est trouvee identique a l'ombrage mais elle etait differente quant au dessechement. L'ombrage reduit la croissance mais il augmente l'allocation de matiere seche a la tige et aux branches, de meme qu'au feuillage mais il la reduit pour les racines d'un diametre de 2 mm.
Evaluation of transgenic sugarcane plants engineered for resistance to mosaic and canegrubs

Transgenic sugarcane plants have been engineered witlz genes for resistance to either sugarcane rnosaic virus or sugarcane whitegrubs. Plants transforined with the coat protein gene of SCMV display three resistarzce phenotypes aper challenge inoculation witlz a viral preparation in glasshouse trials; inrnzunity, recovery and 'atypical: but only show the iinrnune and atypical resistance phenotypes in field trials. There appears to be little correlation between either transgene copy number or transcript level and resistance. Tlze resistance of sugarcane to canegrubs has also been signiJicantly enhanced in pbnts transfortned with constructs to express the potato proteinase inhibitor 11 or the Galantlzus nivalis lectirz. Canegrubs fed on plants of one transgenic line gained as little as 4.2% of the weight of canegrtlbs fed on untransforrned control plants. IL 1
Comparative Leaching of Chalcopyrite by Selected Acidophilic Bacteria and Archaea

A systematic study of the bioleaching of chalcopyrite (CuFeS 2 ) was conducted using axenic cultures of 11 species of acidophilic Bacteria and Archaea to obtain a direct comparison of the microbial chalcopyrite leaching capabilities of the different cultures and to determine the factors that affect Cu release. The characteristics of chalcopyrite leaching by the moderate thermophile Sulfobacillus thermosulfidooxidans , the mesophile Acidithiobacillus ferrooxidans , and the thermophile Acidianus brierleyi were used to elucidate the leaching process. Moderately thermophilic cultures of Sulfobacillus acidophilus, Acidimicrobium ferrooxidans , and Acidithiobacillus caldus were used to study the effects of different metabolic capabilities and relate those to leaching efficiency. The greatest rate of Cu solubilization from chalcopyrite was achieved at high temperatures (up to 70°C) at redox potentials below +550 mV (Ag/AgCl). The enhanced Cu solubilization observed at high temperatures resulted from accelerated chemical reaction rates, rather than from the rates at which individual acidophiles generated the mineral leaching reactants such as Fe 3+ .
The dynamics of collapse in world fisheries

The fear of a rapid depletion of world fish stocks because of over-exploitation is increasing. Analysis of 1519 main series of the FAO world fisheries catch database over the last 50 years reveals that 366 fisheries’ collapses occurred, that is nearly one fishery of four. The robustness of this result is tested by performing several complementary analyses using different conservative options. The number of collapses has been stable through time since 1950s indicating no improvement in the overall fisheries management. Three typical patterns emerge from the analysis of catch series during the period preceding the collapses: smooth collapse (33%), i.e. a long regular decline, erratic collapse (45%), i.e. a fall after several ups and downs, and a plateau-shaped collapse (21%), i.e. a sudden fall after a relatively long and stable persistence of high level of catches. Using a simple mathematical model, we relate the plateau-shaped collapses (which are, by nature, the most difficult to predict) to surreptitiously increasing exploitation and a depensatory mechanism at low population levels. Thus, a stable level of catch over several years is shown to conceal the risk of a sudden collapse. This jeopardizes the common assumption that considers the stability of catch as a goal for fisheries sustainability.