Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential role of spiny dogfish in gray and harbor seal diets in the Gulf of Maine

Harbor seal Phoca vitulina and gray seal Halichoerus grypus populations have in creased by 28.7% (1997−2001) and 8.6% (1999−present), respectively, in the Gulf of Maine. Here, we investigated what seals are eating and how their diet influences the food web in the Gulf of Maine. There is suggestion, but little evidence, that seals are eating spiny dogfish Squalus acanthias, currently an abundant species (standing stock biomass = 235 000 t) in the Gulf of Maine and surrounding areas. We used an Ecopath food web model to explore the potential of dogfish being a primary food source for seals and how this may be impacting the ecosystem. We explored various plausible diets for seals and the implications for other non-prey species in the ecosystem. In addition, white sharks Carcharodon carcharias have increased in abundance regionally, and shark predation on seals is documented in the southern Gulf of Maine. We therefore also explored top-down impacts of white shark predation on seals and lower trophic level fish species. Our results suggest that (1) dogfish could be contributing to the recovery of seal populations by providing an alternative prey base, (2) there is a tipping point between 10 and 20% of dogfish in seal diet that elicits a linearly increasing trend in seal biomass over time, and (3) seals as prey will have a continued impact on the projected increase in white shark biomass. This work advances our understanding of top-down control and may help to inform fisheries and resource management.
Influence of High Tunnel and Field Conditions on Strawberry Growth and Development

Plant growth, yield, and fruit quality of two strawberries (Fragaria ×ananassa Duch.)-'Chandler' and 'Sweet Charlie'-grown under high tunnels (HTs) were compared with that of field plants during 2002-03 and 2003-04 growing seasons. Plug plants were planted in mid-October 2002 and mid-September 2003 on raised beds covered with black polyethylene mulch. Microclimate of the HTs protected strawberry crowns from winter damage and advanced fruit production 5 weeks earlier than that of plants grown under field conditions. From December to February, average minimum and maximum crown temperatures under the HTs were 5 and 12 °C warmer than those of the field crowns, respectively. The earliest HT fruit were harvested on 7 Apr. 2003 and 11 Mar. 2004. Yield and fruit quality under the HTs were superior to that of field-grown plants. HT plants, especially 'Sweet Charlie', bloomed earlier than did field plants, but 'Chandler' produced higher yield than 'Sweet Charlie' late in the season. Larger fruit with higher soluble solids concentration (SSC) were produced inside the HTs than outside. HT 'Sweet Charlie' fruit were sweeter than 'Chandler' fruit, but 'Chandler' produced larger fruit. Larger leaf area, greater number of leaves and shoot biomass, more branch-crowns, and fewer runners were developed under HTs than field conditions. Total leaf area, leaf production, total shoot biomass, and number of branch-crowns of HT 'Chandler' were greater than HT 'Sweet Charlie'. Results of this study indicate that strawberry plants under HTs were not only precocious, but also produced higher yields and superior quality to that of field plants. HT conditions suppressed runner growth, but enhanced branch-crown development.
Deoxyspergualin delays xenograft rejection in the guinea pig‐to‐C6‐deficient rat heart transplantation model

Abstract This study aimed to investigate the effects of 15‐deoxyspergu‐alin (DSG), tacrolimus (FK 506) and cyclosporin A (CyA), alone or in combination, on delayed xenograft rejection (DXR). We used the guinea‐pig‐to‐C6‐deficient(C6‐)‐PVG‐rat heart transplantation model, since in this strain combination, hyperacute rejection is avoided. In C6‐ control rats, the guinea pig xenografts survived for 39.2 ± 6.3 h (mean ± SD). Splenectomy alone resulted in a xenograft survival of 71.8±7.8 h, but the addition of CyA or FK 506 did not further improve graft survival (73.6 ±3.0 h and 72.0±17.6 h, respectively). In contrast, DSG treatment increased graft survival to a mean of 99.8±9.2 h. When CyA or FK 506 was combined with DSG, no additional effects were observed (105±24.3 h and 95.1±5.6 h, respectively). DSG alone or in combination with FK 506 or CyA resulted in a significant reduction in the serum IgM levels and reduced the deposits of IgM and IgG in rejected grafts. However, all xenografts were still heavily infiltrated by EDI + macrophages, regardless of the treatment used. Thus, DSG treatment resulted in moderate prolongation of xenograft survival in C6‐ rats. The effect seems to be related to suppression of xenoreactive antibody production. To prolong xenograft survival further, strategies that inhibit macrophage infiltration seem required.
Naupliar Stages of Hemicyclops japonicus (Copepoda: Poecilostomatoida) Reared in the Laboratory

ABSTRACT All 6 naupliar stages of Hemicyclops japonicus (Copepoda: Poecilostomatoida) are described on the basis of specimens reared in the laboratory. The appendages that are directly related to feeding, such as the coxa and basis of the second antenna and mandible, reach their final state of armature by the fourth naupliar stage. The second maxilla, maxilliped, and legs 1 and 2 first appear at the sixth naupliar stage. Marked differences are noted between the naupliar stages of H. japonicus and H. adhaerens, described previously. Both species exhibit the typical characters of a feeding nauplius.
FORAGE DIGESTIBILITY AND DIET OF DEER ON SOUTHERN UPLAND RANGE

Four white-tailed deer ( Odocoileus virginisnus) were shot from a mixed pinhardwood habi- tat in east Texas at each of six consecutive 10-week intervals. Browse items made up at least 19 percent of the diet in all seasons. Forbs were important dietary constituents in May, mushrooms in July, and acorns in autumn. Acetic acid:propionic acid ratios in rumen liquor samples were wider in the spring after a poor mast year (4:1) than during other seasons (2:1). More gas (S ml gas per gram of solids per hour) was produced in controlled fennentations of rumino-reticular (R-R) contents of deer feeding on acorns than on othejr dietary items. In in vitro digestion trials, composited mixed browse, mixed forbs, mixed grasses, and loblolly pine (Pinus taedu) samples were generally highest in nutrient quality during spring. Grasses and forbs were significantly less digestible rhen mature than when imnlature. Forbs were digested better than were browse or pine tissues. Dead leaves were poorly digested. Green grasses selected during the winter were as digestible as those growing during spring and summer. For- ages most refractory to microbial fermentation had higher lignin:acid-detergent fiber (ADF) ratios than other foodstuffs.
New stalked and sessile cirripedes from the Eocene Mo Clay, northwest Jutland (Denmark)

ABSTRACT New taxa of thoracican cirripedes are recorded from the Eocene Mo Clay of northwest Jutland, Denmark, namely Stipilepas molerensis Carriol n. gen., n. sp. , a scalpelliform gooseneck barnacle, and Plesiobrachylepas jutlandica Carriol n. gen., n. sp. , a brachylepadomorph sessile form. This material is of importance in that the former not only represents the first extinct example of the tribe Ashinkailepadini, it also is the second fossil neolepadine, while the latter adds to the diversity of the family Brachylepadidae, which previously embraced only three genera. The geological context of these taxa is outlined and their phylogenetic interest discussed.
Analysis of Hybridization Between Crotaphytus wislizenii and Crotaphytus silus (Sauria: Iguanidae) in California

Crotaphytus silus and C. wislizenii are considered distinct species on the basis of morphological, biological, ecological and behavioral differences. The two species are essentially allopatric, C. silus occurring in the San Joaquin Valley region of California, C. wislizenii having a widespread distribution in the western North American deserts. A population of presumed hybrid origin occurs in a narrow ecotone between the California steppe and Great Basin pinyon-juniper woodland. The hybrid genotype seems best suited for the ecotonal environment, and neither parental species was found within the ecotone. Interbreeding is occurring principally between C. silus and the hybrid population, and there is phenotypic evidence for back-crossing but recombinants are apparently being selected against outside the ecotone. C. wislizenii occurs as localized, disjunct populations in pinyon-juniper woodland adjacent to the ecotone and does not appear to be in contact with the hybrid population.
NON-DESTRUCTIVE MEASUREMENT OF ACIDITY, SOLUBLE SOLIDS, AND FIRMNESS OF JONAGOLD APPLES USING NIR-SPECTROSCOPY

In this study the potential of visible and near infrared spectroscopy (380-1650 nm) as a non-destructive measurement technique for measuring quality characteristics of Jonagold apples is evaluated. A relation has been established between the reflectance spectra recorded with a bifurcated optical fibre and fruit parameters such as the pH, the soluble solids content, the stiffness factor and other texture parameters such as the elastic modulus of the flesh. The data were analyzed with multivariate calibration techniques such as principal component analysis (PCA), principal component regression (PCR) and partial least squares analysis (PLS). The impact of the data preprocessing on the prediction performance has also been investigated. The prediction models indicate a good to excellent prediction performance. The best pH model has a standard error of prediction (SEP) of 0.068 and a correlation between predicted and measured values (r) of 0.93. The proposed model for the stiffness factor has a SEP of 2.49 and an r-value of 0.90. For the soluble solids content model a SEP of 0.61 and an r-value of 0.82 is obtained. It has been shown that the pH model has a physico-chemical background. The prediction performance of the model for the elastic modulus, however, was not yet satisfactory (SEP = 0.26, r = 0.75).
Letter to the Editor

In an ex vivo porcine working heart model perfused with plasma of each of the human ABO blood groups, we have shown that human plasma of groups A or O were associated with pig heart survivals that were 10 to 30 times less than those achieved when plasma of groups B or AB were perfused [1]. Blood group B gave the best survival. We provided evidence that suggested that the antiB antibody in plasma of groups A and O may be augmenting rejection, as the B antigen and Gala1,3Gal (Gal) antigen are similar in structure. As we blood typed the pigs (and found them to be A+ or A)), and ensured that factors such as the levels of anti-Gal antibody and complement were similar in the groups, we concluded that the differences in graft survival could only be related to the ABO blood group of the human plasma. We have subsequently done in vitro hemagglutination assays using porcine red blood cells (pRBC) to study the interactions of the human anti-A, anti-B, and anti-aGal antibodies. A 3% suspension of pRBC was used in 96 well round bottom plates for the assays. Human anti-A antibody was purchased from Dominion Biologicals, human Anti-B antibody was purchased from Calbiochem and heat-inactivated pooled human AB plasma (does not have anti-A or anti-B antibody) was used as a source of human antiaGal antibody. A serial dilution was done with the various antibodies and the pRBC were then added and left for 90 min at room temperature. The wells were then scored for hemagglutination (4 being very strong and 0 being none). The antibodies were tested alone first to determine if they hemagglutinated pig RBC (Fig. 1). We then used a high concentration of anti-aGal antibody (that gave 4+ hemagglutination) and titrated the concentration of either anti-A or anti-B antibody to determine if there was any inhibitory effect of anti-A (Fig. 2) or anti-B (Fig. 3 – top) on anti-aGal antibody. We then used a low concentration of anti-aGal antibody and titrated the anti-B antibody (Fig. 3 – bottom) to see if anti-B antibody augmented the binding of anti-aGal antibody. Figure 1 demonstrates that all three antibodies do bind pRBC with anti-A binding least well. Figure 2 and the top portion of Fig. 3 show that anti-A and anti-B both inhibit the binding of antiaGal antibody (though anti-B does not inhibit very strongly). Figure 3 bottom portion shows that anti-B antibody does not significantly augment hemagglutination when present with anti-aGal antibody.
The Consequences of Predation and Competition upon the Demography of Gambusia manni (Pisces: Poeciliidae)

Krumholz (1963) proposed that predation and competition affected the survivorship and fertility schedules of Gambusia manni at Bimini, Bahamas. He showed that in predator exposed populations the sex ratio was lower, no senile individuals were present, the number of offspring per brood was higher and that in males there was a definite shift in the size at maturity. He was unable to explain the shift in the size at maturity by use of the predation and competition hypothesis. New information on the forces affecting maturity in the poeciliid fishes (Borowsky, 1973) is used to demonstrate that this unexplained demographic variable can be plausibly explained by the predation-competition hypothesis. I demonstrate that the size at maturity is functionally related to the presence of an adult male and that maturation is delayed until a juvenile exceeds the adult male in size.
Declines in populations of woodland caribou

We summarize the demography of woodland caribou (Rangifer tarandus caribou) inhabiting 6 ranges in northeast Alberta, Canada, from 1993 to 2002. Among ranges, mean annual survival of radiomarked adult females averaged 0.88 (range: 0.86-0.93). Predation by wolves (Canis lupus) and other predators was implicated as the most common cause of death for adult caribou in northeast Alberta. Pregnancy rates (90-100%) and calf production (75-95%) were relatively high in all caribou ranges; however, mean annual recruitment was near or below 20 calves per 100 cows in most ranges (x = 17.1, range = 11.4-22.7). Caribou populations in 3 ranges have declined at average rates exceeding those that would lead to a 50% decline from initial population size over 3 generations; another population is declining at half this rate. Populations of caribou in 2 ranges appear to be stable, declining marginally since inception of our study. The current distribution, intensity, amount, and type of human activity in and near caribou ranges is likely compromising the integrity of caribou habitat. Treatment of declines will require new land-use guidelines that promote caribou conservation.
Understanding the importance of taxonomic sampling for large-scale phylogenetic analyses by simulating evolutionary processes under complex models

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Much of the previous work examining the impact of taxon sampling on phylogenetic accuracy has focused on the effects of random taxon sampling or directed taxon addition/removal. Therefore, the effect of realistic, nonrandom taxon sampling strategies on the accuracy of large-scale phylogenetic reconstruction is not well understood. Typically, broad systematic studies of diverse clades select species according to current classification to span the diversity within the group of interest. I simulated phylogenies under a realistic model of cladogenesis and used these trees to generate sequence data. Using these simulations, I vi explored the effect of taxonomy-based taxon sampling on the accuracy of maximum likelihood reconstruction. The results demonstrate that taxonomy-based sampling has a stronger, negative, effect on phylogenetic accuracy than random taxon sampling. Therefore, it is recommended that systematists conducting phylogenetic analyses of diverse clades concentrate on improving sampling density within their group of interest by selecting multiple representatives from each taxonomic level. Phylogenetic tree imbalance is often used to make inferences about macroevolutionary processes that generate patterns of tree shape. However these patterns may be obscured by non-biological factors that can bias tree shape. Using published trees inferred from biological data and trees simulated under a realistic branching model; I investigated the affect of random taxon omission on phylogenetic tree imbalance. My results indicate that incomplete taxon sampling in the presence of variable rates of speciation and extinction may be sufficient to explain much of the imbalance observed in empirical phylogenies. Previous research has indicated that some methods of phylogenetic inference can produce biased tree topologies and shapes. Using simulated model tree topologies and sequence data, I investigated the non-biological factors that lead to biases in phylogenetic tree imbalance. Based on my results, I concluded that phylogenetic noise is the primary cause of tree shape bias. Methods that account for unobserved substitutions, such as maximum likelihood, can overcome the systematic bias toward imbalanced topologies. Figure 2.1: The relationship between weighted mean imbalance and node size for four sets of trees simulated under a range of variance parameters . Figure 3.2: The nodal imbalance for the combined collection of empirical trees and the collection of trees simulated under varying rates of speciation and
Effect of Population Size on Brood Production, Worker Survival and Honey Gain in Colonies of Honeybees

SummaryThe effect of population size on brood production, worker survival and gain or loss of honey was studied in colonies of honeybees (Apis mellifera) in Louisiana, USA. About 11 kg of bees were caged, stored for two days and subdivided into five populations numbering 2300, 4500, 9000, 17 000 and 35 000 bees. Each colony was started with a laying queen, no brood, and 230 bees per 1000 cm3 of hive space. The test ended 19 days after queen release, just before adult bees began to emerge. The test was conducted 10 times (two replicates being used in each of February, April, June, August and October). The two largest populations produced more honey per bee and in dearth times and winter consumed less honey per bee. Colonies of 4500 bees produced the most brood per bee; as population increased above that number brood production per bee decreased. However, during summer dearth, the colonies of 9000 bees produced the most brood per bee. Overall, the optimal colony size was 9000 bees; the rate of weight gain i.
Stocking rate effects on goats: A research observation.

Knowledge on the ecological effects of goat grazing on arid rangeland is far from complete, and specifically there is little scientific information on effects of heavy goat grazing on arid ecosystems. One objective of this study was to determine botanical composition of dairy-type goat diets on heavily (1.5 ha per goat) and lightly (15 ha per goat) grazed Chihuahuan desert range by fecal microhistological analysis. A second objective was to determine whether vegetation cover, some blood metabolites and mineral levels, as well as fertility of goats were sensitive to high grazing pressure. The lightly grazed site had more (P < 0.05) total foliage cover (38.6 vs 30.4%) than the overstocked pasture. Total shrubs in diets of goats was greater (86.4 vs 72.4 in the late-dry period, 78.6 vs 42.1 in late-wet period; P < 0.05) on the heavily stocked pasture than the lightly stocked pasture. Forbs in the diets were lower (P < 0.10) in the late-dry (11.4 vs 21.5%), early-wet (55.4 vs 64.0%) and late-wet period (15.0 vs 45.8%) on the heavily stocked pasture than the lightly stocked pasture. Substantially lower (P < 0.01) serum glucose, urea nitrogen, Zn and Mg concentration at the onset of the breeding period in goats on the heavily stocked pasture, compared to goats on the lightly grazed pasture resulted in a higher (P < 0.01) abortion rate (22 vs 12%) and consequently a lower (P < 0.05) kidding rate (42 vs 55%). We concluded that overstocking with goats greatly reduced shrub and grass cover. Also, decades of continuously high grazing pressure has forced goats to alter diet selection pattern by consuming more resinous, toxic, and coarse species. This switch was associated with a lower nutritional status, a negative daily weight gain, lower body condition score in the late-wet period, and lower fertility on heavily grazed range.
The use of pronase‐digested human leukocytes to improve specificity of the flow cytometric crossmatch

Abstract Two‐color fluorescence cytometry (FCXM) has recently been introduced to improve the detection of anti‐HLA antibodies that react to donor cells, especially in recipients receiving kidney allografts. Although this assay system is highly sensitive, it lacks specificity. Between 70% and 90% of potential kidney recipients with a positive FCXM would have been denied transplant if such an assay had been used alone to detect antidonor antibodies. Lack of specificity is principally due to normal or irrelevant IgG in aggregates or immune complexes binding to Fcy R receptors on lymphocytes including B cells and a significant subset of T cells. To circumvent this problem, we digested Fcy R receptors on lymphocytes with pronase. We present data demonstrating that pronase digestion of lymphocytes does not alter HLA antigenicity. In addition, pronased lymphocytes allow one to use either single‐ or two‐color FCXM. With single‐color FCXM, one can quantitate antibody reactivity to lymphocytes via a cursor (on the fluorescence histogram) that separates lymphocytes that do not bind to antibodies. We present data demonstrating that this modification renders FCXM highly sensitive and specific. In addition, one can discriminate between IgG and IgM antibodies that react to lymphocytes.