Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal Selection of Sabinene Hydrate-Rich Thyme (Thymus vulgaris). Yield and Chemical Composition of Essential Oils

Abstract An inventory of naturally occurring sabinene hydrate (4-thujanol)-rich thyme populations singled out 16 individuals of potential commercial importance. After multiplication by microcuttings and grown in a nursery, we now possess a collection that yields an oil particularly rich in sabinene hydrate (up to 62%). The other constituents commonly found in thyme, 1,8-cineole, linalool, terpinen-4-ol, α-terpineol, geraniol, thymol and carvacrol are present only in small amounts, (trace-5.0%).
Damage by pine weevil Hylobius abietis to conifer seedlings after shelterwood removal

Abstract Pine weevil (Hylobius abietis L.) damage to seedlings after overstorey removal was investigated in a survey study in six shelterwoods in the south–central part of Sweden. The shelterwoods predominantly consisted of Scots pine, except at one site where the shelter trees mainly consisted of Norway spruce. Before final cutting, 10 plots were laid out at each site and measurements of shelter trees and marked seedlings were taken. The seedlings were examined during the 2 years after final cutting. The study showed that removal of shelter trees increases the risk of severe damage by pine weevil and the variable that was most strongly correlated with the risk was the seedling root collar diameter. Both Scots pine and Norway spruce seedlings were severely damaged by pine weevil, and most of the feeding occurred during the first year after cutting. The amount of debarked area was significantly larger for Scots pine than for Norway spruce seedlings. Vitality (growth of the leading shoot before final cutting) of the seedlings also affected the probability of damage. Seedlings with high vitality were less damaged by pine weevil than seedlings with low vitality. For Scots pine the shelterwood density before final cutting was correlated to the intensity of pine weevil feeding after cutting. In conclusion, after the final cutting of a pine or spruce shelterwood, pine weevils will probably invade the area. To avoid serious damage, Norway spruce and Scots pine seedlings should have reached a diameter of at least 10–12 mm.
Testing the role of biological interactions in the evolution of mid-Mesozoic marine benthic ecosystems

Abstract Evaluating the relative importance of biotic versus abiotic factors in governing macroevolutionary patterns is a central question of paleobiology. Here, we analyzed patterns of changes in global relative abundances and diversity of ecological groups to infer the role of biological interactions as driving evolutionary forces in mid-Mesozoic macrobenthic marine ecosystems. Specifically, we tested the hypothesis of escalation, which states that macroevolutionary patterns were controlled by an increasing pressure exerted by enemies on their victims. Associated with evidence of increasing levels of predation and biogenic sediment reworking (bulldozing) is an increasing representation of predation- and disturbance-resistant groups in the fossil record. In particular, we observe increasing proportions of mobile organisms; a decline of vulnerable epifauna living freely on the substrate; and a trend toward infaunalization of the benthos. These trends were most pronounced in the paleotropics, i.e., the region where biological activity is thought to have been highest. The observation that these changes affected several biotic traits and occurred within independent clades argues against the overriding role of a single key adaptive innovation in causing shifts in ecological abundance. Also, changes in the abiotic environment cannot explain these faunal patterns because of lacking cross-correlations with physico-chemical parameters such as global sea level, climate, and seawater chemistry. We conclude that in marine benthic ecosystems of the mid Mesozoic, enemy-driven evolution, or escalation, was a plausible and important factor.
Cambios en el pelaje del roedor subterráneo Ctenomys talarum: posible mecanismo térmico compensatorio

En este trabajo se evaluaron los cambios en densidad y longitud del pelaje dorsal y ventral en el roedor subterraneo Ctenomys talarum, como posible mecanismo compensatorio frente a cambios de temperatura estacionales en el ambiente de la cueva, en especial durante la epoca estival, y durante el periodo de prenez en las hembras, ya que ambas etapas representan desafios para la termorregulacion en esta especie. Se observo que el pelaje ventral fue significativamente mas corto y menos denso que el dorsal en machos, hembras prenadas y hembras no prenadas en las dos estaciones evaluadas. La longitud del pelaje tanto dorsal como ventral en los tres grupos fue significativamente menor durante la estacion de temperaturas mas calidas. En la estacion calida, las hembras prenadas exhibieron un pelaje ventral significativamente mas corto que el pelaje ventral de machos y de hembras no prenadas. Se discuten las posibles ventajas termicas que podrian representar las modificaciones observadas en las caracteristicas del pelaje de esta especie, con enfasis en las restricciones que impone el ambiente subterraneo en cuanto a los mecanismos disponibles de disipacion del calor corporal
Loading beans with sublethal levels of copper enhances conditioning to oxidative stress

Summary The relationship between Cu 2+ -overloading and oxidative stress in plant cells was studied. The involvement of Cu 2+ in the reduction of superoxide O 2 − and hydrogen peroxide (H 2 O 2 ) to hydroxyl radical (OH . ), suggest that excess Cu in plants leads to oxidative stress. Cu excess was induced in Phaseolus vulgaris (cv. Pinto ) plants by soaking the roots in a 1 mmol/L Cu(NO 3 ) 2 solution for 24 hours. As a result, Cu content in bean leaves increased from 12 to 23 mg Cu kg −1 DW. Indications for oxidative stress response were detected by monitoring changes in the activities and contents of some components of the antioxidative mechanism. The Cu treatment resulted in doubled activity of ascorbate peroxidase (APX, EC 1.11.1.11) and catalase (EC 1.11.1.6). Excess of copper inhibited glutathione reductase (GR, EC 1.6.4.2) to 60 % of control activity. No differences were found in CuZn-SOD (SOD, EC 1.15.11) and Mn-SOD activity, and glutathione and ascorbate content. Copper overloading affected also, primary reactions of photosynthesis and electron transport as probed by the photochemical energy storage in far-red light. Cu treatment of bean plants resulted in enhanced conditioning to successive methyl viologen and SO 2 treatments as compared to non-treated control.
Ecosystem approach to a global nitrous oxide budget

The authors take an ecosystems approach to explain global nitrous oxide emissions, in much the same way that carbon dioxide and ozone have been previously explained, in terms of budgets, sinks, and sources. He sites the biogenic as well as the anthropogenic sources of nitrous oxides and interaction with oxygen in the atmosphere is the major sink.
Myofibrillar protein degradation of carp (Labeo rohita (Hamilton)) muscle after post‐mortem unfrozen and frozen storage

The degradation of myofibrillar proteins of rohu carp (Labeo rohita (Hamilton)) muscle was analysed after post-mortem storage. Muscle fillets were kept either unfrozen at 2 °C for up to 15 days or frozen at −8 °C or −20 °C for up to 6 months. A co-ordinated histochemical, biochemical and electrophoretic study showed a differential response of the carp muscle, revealing clear degenerative/degradative changes specific to the post-mortem storage temperatures. The myofibrillar protein fractions, namely myosin light chains and α-actinin, showed degradative changes during the above storage conditions, whereas other protein fractions in the high-molecular-weight range fragmented to give lower-molecular-weight proteins. The importance of the post-mortem storage temperature for controlling the degradation of the myofibrillar proteins was emphasised. This is the first report on this popular fish species, known for its culinary importance, showing that specific protein fractions of the myofibrils degrade during post-mortem storage. © 2001 Society of Chemical Industry
Molecular phylogenetic studies in the genus Amanita

A group of 49 Amanita species that had been thoroughly examined morphologically and anatomically was analyzed by DNA sequence comparison to estimate natural groups and phylogenetic relationships within the genus. Nuclear DNA sequences coding for a part of the ribosomal large subunit were determined and evaluated using neighbor-joining with bootstrap analysis, parsimony analysis, conditional clustering, and maximum likelihood methods. Sections Amanita, Caesarea, Vaginatae, Validae, Phalloideae, and Amidella were substantially confirmed as monophyletic groups, while the monophyly of section Lepidella remained unclear. Branching topologies between and within sections could also partially be derived. Subgenera Amanita and Lepidella were not supported. The Mappae group was included in section Validae. Grouping hypotheses obtained by DNA analyses are discussed in relation to the distribution of morphological and anatomical characters in the studied species.
Role of pharmacogenomics in drug development

Pharmacogenomics is charged with the task of uncovering genetic variations that underlie responses to drugs. While the results in the field have been slow in coming, more recent high‐throughput screening methods and data‐mining approaches are expected to effectively expedite the drug development process in the near future. While these new techniques are likely to reduce costs, the selection of the most pertinent study cohort with respect to the biological mechanism of the study compound is a critical element in risk management. Enrichment of the study cohort with carriers of “at‐risk” variants in genes that reside within and/or influence the biological pathway targeted by the drug candidate, would be expected to lower the risk of drug failure, while both delivering faster and better results at lower costs. In this context, at deCODE Genetics, Inc., the powerful coupling of family‐based linkage to ultra‐high throughput genotyping, gene array, and proteomics technology, together with innovative bioinformatic resources, provides a focused integrative strategy for pinpointing disease‐causing genes that may generate validated drug targets and genes that are responsible for differential response to drugs. deCODE has compiled one of the world's most comprehensive collection of population data on genealogy, genotypes, and phenotypes. This combination of resources provides an effective system for uncovering genes that predispose to disease or regulate drug response. In addition, this approach allows for the development of novel therapeutic strategies and diagnostic tests that, apart from being applicable to assessment of disease susceptibility and clinical response to drugs, provide for an effective clinical trial design, ultimately leading to safer and more efficacious drugs for patients. Drug Dev. Res. 62:86–96, 2004. © 2004 Wiley‐Liss, Inc.
Endogenous polyamines in apple and their relationship to fruit set and fruit growth

The distribution of free and bound polyamines was investigated from blooming until harvest on flower, fruitlets and fruits of Malus domestica Borkh cv. Golden Delicious, Relationships between polyamines and fruit set and growth were also investigated. The level of free polyamines was high only during the first weeks after full bloom and then decreased gradually. The amount of bound trichloroacetic acid-insoluble polyamines was much higher than free polyamines. Bound spermine in particular showed a high value for almost 40 days after full bloom, while spermidine and putrescine were no longer detectable even a few days after full bloom. In relation to fruit set, it was possible to observe that abscission peaks took place when free polyamine levels were low or decreasing. Insofar as fruit growth is concerned, the most substantial variations in polyamine levels occurred very early in the season when fruit dry weight and protein amount were also changing rapidly and fruit diameter was almost impossible to measure.
Hair cell progenitors: identification and regulatory genes

Hair cell loss in higher vertebrates appears to be permanent. Progenitors that are quiescent in the organ of Corti are the best candidates for the restoration of the different cell types in the organ of Corti. However, little is known about the presence of these progenitors and their capacity to differentiate into hair cells. This review will first highlight recent findings concerning the identification of progenitor cells that are able to proliferate and to differentiate into hair cells. Principal factors impinging on this process are then reviewed. Auditory hair cell progenitors have been identified and, under appropriate conditions, are capable of proliferating and differentiating into hair cells. Characterization of signals that maintain, expand and regulate these progenitors will be essential for the biomedical application of stem cell populations to restore hearing.
Physical and Sensory Characteristics of Chiffon Cake Prepared with Erythritol as Replacement for Sucrose

ABSTRACT: The effects of erythritol on physical and sensory characteristics of chiffon cakes were studied. The results showed that chiffon cakes prepared with 25%, 50%, 75%, and 100% replacement of sucrose with erythritol were lighter in crust and crumb and less sweet in crumbs than those with sucrose. There were no differences in the specific gravity of cake batter, volume, and moisture content between cakes prepared with sucrose or erythritol. Results from sensory evaluation also showed no significant differences in crumb color, moistness, and tenderness for any cakes.
Rice Bran as the Major Energy Source for Laying Hens

Abstract The purpose of these experiments was to devise a successful diet for laying hens with rice bran as the major energy source. Three experiments were conducted with commercial strain-cross White Leghorn-type pullets, starting at 20 weeks of age. A control group fed a standard breeder diet was used in each experiment. In Experiment 1, pullets fed a diet with 81.5% rice bran laid significantly fewer eggs than pullets fed a standard breeder diet. The progeny of the pullets fed 81.5% rice bran showed feather defects. Adding zinc carbonate to the maternal diet eliminated the feather defects. In Experiment 2, diets containing 79.0 to 81.5% of rice bran were supplemented with zinc carbonate. There was no significant difference in egg production between the high rice bran groups and the control group. In Experiment 3, 10 experimental diets and 1 control diet were each fed to two groups of 6 hens each in individual battery cages. The diets contained 73.8 to 91.0% of rice bran. Nine diets represented a factorial design with three protein levels (14.3, 15.2, and 16.1%) and three metabolizable energy levels (2450, 2650, and 2850 kcal/kg). The other diet contained 12.5% protein and 2350 kcal/kg. There were no significant differences in egg production, egg weight, Haugh units, or shell deformation between hens fed the rice bran diets and hens fed the control diet.
A deterministic model to study the importance of density-dependence for regulation and the outcome of intra-specific competition in populations of sparse plants

SUMMARY The importance of density-dependence is addressed by discussing the results of a simple deterministic model for plant populations. The model takes into account that plants, once germinated, do not move. It is shown that density-dependence can keep sparse populations sparse. Also, it is shown that density-dependence, even if it affects only a minority of the individuals, can determine the outcome of competition. The effect of density-dependence on selection for a specific seed size and generation time are discussed.
Differential isotopic enrichment and half-life among tissues in Japanese temperate bass (Lateolabrax japonicus) juveniles: implications for analyzing migration

As a first step for field applications of stable isotope techniques to investigate the migration of Japanese temperate bass (Lateolabrax japonicus) (Perciformes) juveniles, we conducted a diet switch experiment and fitted an exponential model to changes in stable carbon (δ 13 C) and nitrogen (δ 15 N) isotope ratios for muscle, fin, and liver. The trophic enrichment values were ranked liver < muscle < fin for δ 13 C (range -0.80‰ to +3.66‰) and liver < fin < muscle for δ 15 N (+0.59‰ to +3.12‰). The half-life values were similar for muscle and fin for both δ 13 C and δ 15 N (19.3-25.7 days), while those for liver were 5.3 days for δ 13 C and 14.4 days for δ 15 N. Both the δ 13 C and δ 15 N values of muscle reached the asymptotic value after a threefold body weight increase, reflecting the diet after the switch. These results suggest that fin is a useful substitute for muscle in field applications of stable isotope techniques and that liver, with a shorter half-life, has the potential to provide more recent information about migration.
Effects of Climate Variability on Interannual Variation in Parasites, Pathologies, and Physiological Attributes of Bivalves from the U.S. East, Gulf, and West Coasts

We analyzed weighted prevalence of various parasites and pathologies for 1995 to 2006 along with a set of physiological variables to determine the degree of concordancy in their interannual variations over 500-km stretches of coastline using data from the National Oceanic and Atmospheric Administration's (NOAA's) National Status and Trends “Mussel Watch” Program. The variables examined in mytilid mussels fell into three groups based on the temporal patterns observed: ceroid bodies, taxon richness, digestive tubule atrophy, and major pathologies varied concordantly along the Northeast and West Coasts. For reproductive stage, sex ratio, and gill ciliates, concordant temporal trends were limited to the northeast coast. Gregarines, found only in West coast mussels, behaved similarly to those variables falling into the first group. A final group, trematode metacercariae and sporocysts, tissue pathologies, and the prokaryotes, was characterized by limited concordancy. For oysters, a similar triplet of groups wa.
Female-Biased Helping in a Cooperatively Breeding Bird: Female Benefits or Male Costs?

There is often a sex bias in helping effort in cooperatively breeding species with both male and female helpers, and yet this phenomenon is still poorly understood. Although sex-biased helping is often assumed to be correlated with sex-specific benefits, sex-specific costs could also be responsible for sex-biased helping. Cooperatively breeding brown jays (Cyanocorax morio) in Monteverde, Costa Rica have helpers of both sexes and dispersal is male-biased, a rare reversal of the female-biased dispersal pattern often seen in birds. We quantified helper contributions to nestling care and analyzed whether there was sex-biased helping and if so, whether it was correlated with known benefits derived via helping. Brown jay helpers provided over 70% of all nestling feedings, but they did not appear to decrease the workload of breeders across the range of observed group sizes. Female helpers fed nestlings and engaged in vigilance at significantly higher levels than male helpers. Nonetheless, female helpers did not appear to gain direct benefits, either through current reproduction or group augmentation, or indirect fitness benefits from helping during the nestling stage. While it is possible that females could be accruing subtle future direct benefits such as breeding experience or alliance formation from helping, future studies should focus on whether the observed sex bias in helping is because males decrease their care relative to females in order to pursue extra-territorial forays. Explanations for sex-biased helping in cooperative breeders are proving to be as varied as those proposed for helping behavior in general, suggesting that it will often be necessary to quantify a wide range of benefits and costs when seeking explanations for sex-biased helping.
Barley- versus protein-supplemented corn-based diets for feedlot cattle evaluated using the NRC and CNCPS beef models

A study was conducted to evaluate the effects of supplementing a corn-based finishing diet [10.0% crude protein (CP), 6.2% degradable intake protein (DIP), dry matter basis, no protein supplementation] with DIP in the form of urea (13.0% CP, 9.1% DIP) or canola meal and urea (12.8% CP, 8.6% DIP) on dry matter intake (DMI) and average daily gain (ADG). Animal performances were compared with those obtained by feeding a barley-based diet (13.9% CP, 9.6% DIP). Crossbred beef steers (398 ± 28 kg) were allocated to 24 pens and six pens were assigned to each diet. There were no differences (P > 0.05) in DMI and ADG between cattle fed the barley diet and those fed the corn diets supplemented to provide a concentration of DIP similar to that supplied by the barley diet. However, ADG was 10% lower and DMI was 8% lower for cattle fed the corn diet with no protein supplementation (P < 0.05). The NRC and CNCPS models predicted the substantially lower gain of cattle fed the corn diet with no protein supplementation, bu.
Cryopreservation of Black Bengal buck semen: Effects of diluents and freezing on sperm motility and morphology

Semen from Black Bengal bucks was collected to establish a cooling protocol (to −196°C) for buck semen preservation, and to study the effect of freezing on sperm motility and morphology. Semen was diluted with diluents (Triladyl & Tris) and cryoprotectants, filled into straws, sealed, cooled (to 5°C) and equilibrated. After dilution, motility ranged from 75.00% to 76.67% and from 73.33% to 80.00% in Triladyl and Tris diluents, respectively. Motility of sperm after cooling to 5°C in Triladyl and Tris diluents ranged from 65.00% to 66.67% and from 63.33% to 70.00%, respectively. After equilibration in straws, the semen was subjected to a freezing protocol in a computer-controlled biofreezer CL-3000 (cooling at 10°C per minute, from 5°C to −80°C) and plunged into liquid nitrogen. Sperm motility of re-thawed semen varied from 38.33% to 43.33% and from 6.00% to−6.67% in Triladyl and Tris diluents, respectively. Sperm morphology of re-thawed semen was studied and head damage or cryoinjury was found in 2–3% of sperm in Triladyl diluents and 3–6% in Tris diluents. Whether the differences of sperm motility and head damage reflect fertility after artificial insemination is yet unknown and needs to be studied further.
Natural Selection and Mutation Rates in Mammals

Rates of fixation of amino acid substitutions were calculated for 13 amino acid positions of fibrinopeptides A and B. These positions were selected because they had sustained fixation of nonconservative amino acid substitutions and had sustained more fixations (6 or more) than those positions at which all substitutions fixed were conservative. We have used the average of these rates to estimate the average rate at which mutations would be fixed if all were selectively neutral. The percentage of mutations eliminated by selection after they have reached frequencies high enough for selection to act on them was estimated by comparing the potential rate at which mutations would be fixed if selectively neutral with an observed rate of fixation. It is estimated that at least 79% of mutations that become frequent enough to be affected by natural selection are eliminated. We assume that the probability of a mutation reaching a frequency at which selection affects it is independent of whether it is selectively advantageous, neutral, or deleterious. We conclude, therefore, that at least 79% of all mutations are deleterious. An estimate of the mutation rate can be derived from these data if all mutations at the 13 positions considered are selectively neutral. When allowances are made both for the number of cell divisions along the germ line leading from zygote to gamete and for the number of nucleotides that may be substituted, the estimated mutation rate is within an order of magnitude of mutation rates derived in other ways.