Miracle-dz/UniFAR-FTUs huggingface dataset:
An evaluation of survey methods for monitoring swift fox abundance

Swift foxes (Vulpes velox) were historically distributed across the shortgrass and mixed-grass prairie regions of North America. Today, the swift fox is found in small, isolated populations in the southern and western margins of its historic range. Although methods for censusing wild canids exist, an evaluation of survey techniques for monitoring trends in the abundance of swift foxes has not been conducted. We conducted a 2-year study evaluating 6 survey methods and their ability to accurately monitor changes in swift fox density (independently determined from radiocollared foxes). The study was conducted on the United States Army Pinon Canyon Maneuver Site, southeastern Colorado, from January 1997 to December 1998. We evaluated catch-per-unit-effort (trapping surveys), mark-recapture estimates, scent-post surveys, spotlight counts, scat deposition rate surveys, and an activity index. All surveys were conducted along 5 10-km transects during 3 seasons annually. All methods, except spotlight counts, were reliable and consistent for detecting swift fox presence across the 5 survey transects. Regression analyses indicated that the correlation between swift fox density and survey method varied among methods and seasons, with mark-recapture estimates being the highest predictor (r=0.711), followed by scat deposition surveys (r=0.697), scent-post surveys (r=0.608), spotlight surveys (r=0.420), trapping surveys (r=0.326), and the activity index (r=0.067). Stepwise regression analysis of all survey methods indicated that the combination of mark-recapture estimates and scent-station indices was the highest predictor of swift fox density (r=0.853). The combination of these 2 surveys would be economical and reliable for monitoring swift fox population trends. The combination of scent-station indices and scat deposition surveys was almost as reliable (r=0.829) but was far less costly than surveys involving mark-recapture estimates. A combination of more surveys did little to increase the level of prediction. Survey costs varied due to differing requirements of labor and equipment.
Effect of drought on photosynthesis in Trifolium repens: maintenance of photosystem II efficiency and of measured photosynthesis

White clover plants (Trifolium repens L.; cv. Crau) were grown from seedlings in controlled conditions and then subjected to an edaphic drought by withholding watering. A strong reduction of leaf gas exchange due to stomatal closure in the early state of water deficit (1 to −1.2 MPa) was observed. Chlorophyll a measurements demonstrated that the photochemistry of PSII, the light driven electron transport and enzymatic reactions requiring ATP and NADPH in chloroplasts were not affected by plant water status. Moreover, oxygen evolution showed that the capacity of the photosynthetic apparatus was not altered by the stress
Long‐term response of temperate canopy trees to removal of browsing from an invasive arboreal herbivore in New Zealand

Defoliation of forest tree canopies by herbivores and other agents, leading to tree mortality and reduced productivity, threatens the ecological stability of forests globally. This study shows that long-term control of a mammalian arboreal folivore (brushtail possums; Trichosurus vulpecula Phalangeridae) reduces crown dieback and increases foliage cover in browsing-damaged canopy trees. We monitored indices of possum density, possum browsing, tree foliage cover and crown dieback for 20 years following initiation of possum control in 1994 that repeatedly reduced possum densities to near zero every 5–6 years and kept the population below 35% of pre-control levels over the entire period. Observable possum browsing was recorded on 20–49% of individuals of three palatable tree species at the time of first control. Those percentages fell to zero after control and never exceeded 2–10% for individual species over the next 19 years. We recorded significant increases in foliage cover attributable to recovery from defoliation by possums for all three species during the first 10 years. Large increases in foliage cover occurred on individuals that were heavily browsed in 1994 (mean increases: 36–89%), but mean population increases were modest (3–19%) because only 10–19% of trees were initially heavily browsed. Twenty-year mortality rates were similar for plants with, or without, initial possum browsing, indicating no residual impact of pre-control browsing on tree mortality. Times for full recovery of crown foliage cover varied from 10 years for the youngest trees and faster growing species to more than 20 years for mature individuals of the slowest growing species.
Clonotypic analysis of the fetal B cell repertoire: evidence for an early and predominant expression of idiotypes associated with the VH 36-60 family.

Determining the mechanisms by which B cells develop that culminates in the generation of a diverse repertoire is critical to our understanding of how the immune response is regulated. The B cell specificity repertoire appears to be developmentally acquired in a predetermined, temporally ordered fashion. Thus, in the Balb/c mouse, the ontogenetic appearance of functional B cells specific for various hapten probes occurs in the order of dinitrophenol (DNP), fluorescein (Fl), and phosphorylcholine (PC). In addition, when the influenza virus hemagglutinin molecule was used as an antigen probe, similar conclusions were drawn regarding a patterned acquisition of the specificity repertoire. More recently, we have used a fetal organ culture system to show that hapten-responsive B cells appear in the same predictable, temporal order in vitro. The importance of these studies was that the effects of environmental influences were minimized in the absence of circulation and cell migration, and therefore the results indicated that the patterned emergence of the specificity repertoire observed was largely the result of genetic regulatory processes. Recent molecular findings may relate to such genetic regulatory processes. The VH genes in Balb/c mice have been grouped into eight families based on sequence homology, and have been mapped relative to the constant region genes. Yancopoulos et al. and Perlmutter et al. have shown that the VH gene segments closest to the JH cluster, the VH1B 7183 family, are preferentially utilized in transformed fetal pre-B cell lines and in fetal B cell hybridomas. This led to the hypothesis that the developmental control of the expression of VH gene segments is related to chromosomal organization. A logical extension of these findings is that the programmed appearance of particular clonotypes in ontogeny may be explained, in part, by the preferential use of particular VH gene segments. However, to what extent the transformed B cell lines represent members of the functional expressed repertoire could not be evaluated. In the studies described herein, the fetal organ culture system was used to assess the early expressed repertoire at the clonotypic level using idiotypic analysis. Anti-DNP secreting clones were derived from fetal organ cultures and tested for the presence of two idiotypes, 36 and MOPC 460 (460). The 36 idiotype is a predominant DNP clonotype of the neonatal repertoire, while the 460 idiotype is a major cross-reactive idiotype of the adult DNP response. (ABSTRACT TRUNCATED AT 400 WORDS)
Transcription Factors and Transcriptional Regulation

I. INTRODUCTION Particular aspects of Caenorhabditis elegans biology — embryonic development, sex determination, muscle and nerve biology, and so on — are considered in other chapters in this volume. This chapter focuses on a theme common to many of these chapters, namely, transcription factors and the regulation of genes transcribed by RNA polymerase II. A recent compendium of human gene sequences (Adams et al. 1995) suggests that 7–8% of all genes code for transcription factors. If the same gene distribution applies to the approximately 13,000 genes in the C. elegans genome, then C. elegans must have 1000 such factors. C. elegans sequence databases contain many examples of classes of proteins that are known to control transcription in other organisms, and the genome sequencing project will soon provide a complete inventory. The task will then be to identify the genes that all of these factors regulate. The first section of the present chapter summarizes information on the basal transcription machinery in C. elegans. The second section describes the most important properties of known transcription factors in C. elegans. The final section summarizes studies that have begun to unravel the transcriptional control of particular genes by analyzing their promoters. II. THE BASAL TRANSCRIPTION MACHINERY Although several features of C. elegans transcription are unusual (e.g., trans -splicing and the arrangement of genes in operons), the basic transcriptional machinery is likely to be highly similar, both structurally and functionally, to that found in other eukaryotes. For example, RNA polymerase II from C. elegans behaves much like.
Endocytosis in Dictyostelium discoideum amoebae: Inhibition by cyclohexlmide and other inhibitors of protein synthesis

Cycloheximide, an inhibitor of protein synthesis, inhibited endocytosis pathways in the vegetative amoebae of the cellular slime mold Dictyostelium discoideum. Half-maximal inhibition of fluid-phase pinocytosis in nutrient medium or in buffer occurred at 0.08 mM or 0.35 mM cycloheximide, respectively. Other inhibitors of eucaryotic protein synthesis inhibited fluid-phase pinocytosis, with the following IC50 in nutrient medium: 0.15 mM anisomycin, ImM emetine, 0.25 mM puromycin. Kinetic studies showed that the inhibitory effects of cycloheximide occurred rapidly, with a half-time of less than 10 min, and were fully reversible upon removal of the drug. Both fluid-phase pinocytic influx and efflux were inhibited by cycloheximide, which furthermore prevented the vanadate-induced efflux of fluorescein-labeled dextran, the fluid-phase marker used in these experiments. The massive secretion of lysosomal enzymes: acid phosphatase, N-acetylhexosaminidase or α-mannosidase, which follows overloading of the endosomal compartment by sucrose, was also inhibited by cycloheximide. All these phenomena were unimpaired by cycloheximide in the cycloheximide-resistant (cycAl) mutant strain X6.
Inhibition of canine platelet aggregation by barbiturates.

: The ability of barbiturates to affect in vitro platelet aggregation of canine platelets was examined. Platelet-rich plasma was incubated with thiamylal, pentobarbital, and barbital for 10 minutes before the addition of the aggregating stimulus. All three barbiturates produced a concentration-related inhibition of platelet aggregation induced by adenosine diphosphate (ADP) and collagen. The inhibitory effect of the barbiturates could not be overcome by increasing the concentration of extracellular calcium. In contrast to ADP- and collagen-induced aggregation, no inhibitory effect was observed on aggregation initiated by A23187, 12-O-tetradecanoylphorbol-13-acetate, or phospholipase C. In further studies, the ADP-induced rise in free cytosolic calcium was blocked by the barbiturates. These findings suggest that barbiturates may interfere with the rise in internal calcium associated with agonist-receptor stimulation of platelets.
Factors affecting food provisioning of nestling Black-throated Blue Warblers

-Using video cameras at nests, we measured rates, quantities, and types of food delivered by male and female Black-throated Blue Warblers (Dendroica caerulescens) to nestlings of different ages and at different times of day and nesting season. Based on 89 1.5-2 h observation periods at 18 nests, all of which contained four young, we found that larval Lepidoptera comprised 60-87% of the estimated prey biomass brought to nestlings and that the female and male parents delivered approximately equal amounts of food over the nesting cycle. Food provisioning rates did not vary with time of day or with parental age, but did increase significantly with age of nestlings and decrease with time of season (early vs mid-summer). The lower rate and quantity of provisioning in mid-summer was reflected in significantly slower growth of nestlings in that part of the season, suggesting constraints on parental food provisioning, perhaps due to lower food availability. Received 27 Aug. 1995, accepted 2 Feb. 1996. Successful production of offspring is an essential component of individual fitness (Stearns 1992), as well as being crucial to the maintenance of population levels for most, if not all, bird species (Nolan 1978, Virolainen 1984, Sherry and Holmes 1992, Holmes, et al. 1992. Robinson et al. 1995). Although predation at the nest is probably the single most important factor affecting breeding success of most passerine birds (Ricklefs 1969, Holmes et al. 1992, Martin 1992a), parental care of nestlings can also be important (Kuitunen and Suhonen 1991). Parental care, which includes nest building, incubation, food provisioning, vigilance, and brooding, is not only energy-demanding but also potentially risky to the survival of the parents and their lifetime reproductive success (Curio 1988). Quantities of food delivered can influence nestling survival as evidenced by brood reduction due to starvation in many passerine birds (Magrath 1990) and in some cases by starvation of whole broods (Rodenhouse and Holmes 1992, Sherry and Holmes 1992). Also, nestlings that are not well fed may beg more, which could result in the attraction of predators, leading to higher nest losses (Skutch 1949, Martin 1992b). The patterns of food delivery to nestlings and the factors that affect them are, therefore, important for understanding population processes. Information about which factors influence food delivery patterns is also useful for designing sampling protocols for future studies of reproductive biology of particular species. In this study, we examined the rates and quantities of food delivered 'Dept. of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755. 2 Present address: Norfolk Academy, 1585 Wesleyan Drive, Norfolk, Virginia 23502.
Cytological, genetic and agronomic characterization of a barley reciprocal translocation

Cereals are the basis of global agriculture providing more than half of the human food consumption. In Spain, barley is the main crop in terms of growing area, mostly in the poorest agricultural areas. In semiarid areas crop productivity is not only limited by drought, but also by high temperatures at the end of the growth cycle. An increased use of ‘local’ germplasm could lead to the selection of varieties adapted to specific regional conditions. The use of a barley variety like ‘Albacete’, with its proven adaptation to semiarid conditions, can be an excellent option. It has been hypothesized that the high popularity of ‘Albacete’ with farmers particularly in semi-arid areas where barley is grown under rain fed conditions, may be due to the presence of a special form of chromosomal interchange, a reciprocal translocation. This thesis provides a cytological, genetic and agronomic characterization of this reciprocal translocation.
Haplotype-assisted genomic evaluations in Nordic Red Dairy Cattle

In admixed populations originating from different base breeds, such as the Nordic Red Dairy Cattle, identity by state of haplotypes instead of single nucleotide polymorphisms (SNP) is a better surrogate for identity by descent. Therefore, haplotypes are expected to be more useful in recovering genetic relationships among animals and linkage disequilibrium between markers and quantitative trait loci (QTL). The objective of this study was to improve the prediction accuracy in genomic evaluations by the use of haplotypes of short chromosomal segments. In the first step, around 38,000 SNPs from a 50K chip were simultaneously scanned for QTL signals with BayesB. Based on these results, the SNPs with the strongest QTL signals were then preselected and haplotype blocks were constructed around these. In the second step, we estimated the relative variances for the pre-selected haplotypes with BayesA. In the final step, mixed model equations of the evaluation model were solved to estimate haplotype effects. Here, a pre-defined proportion of the genetic variance was assigned to a pedigree-based animal effect and the rest to haplotypes. The accuracies of several combinations for the number and the length of haplotype blocks were assessed by calculation of genome-enhanced breeding values and validation test reliabilities (R 2 ). For three production traits (milk, protein, fat) and fertility, the highest R 2 observed were 0.48, 0.41, 0.42 and 0.33, respectively. For milk and protein, we observed an improvement over G-BLUP of 3 and 1 percentage points, respectively. For fat and fertility, the highest R 2 were the same as for GBLUP. Further analysis using only single SNPs instead of haplotype blocks yielded similar results. This may indicate a need to choose an alternative approach to pre-select haplotype blocks.
Insulin-like growth factor 1 and corticosteroid modulation of chondrocyte metabolic and mitogenic activities in interleukin 1-conditioned equine cartilage.

OBJECTIVE To evaluate potential stimulatory or matrix-sparing effects of insulin-like growth factor 1 (IGF-1), alone or in combination with a corticosteroid, in an interleukin 1 (IL-1)-induced model of cartilage degradation. SAMPLES Cartilage from the weightbearing surfaces of trochlea and condyles of clinically normal 2-year-old male horses. PROCEDURE Triamcinolone acetonide and IGF-1 effects were evaluated by assessing: matrix responses by sulfated glycosaminoglycan (GAG) assay and [35S]sulfated GAG synthesis; collagen content by hydroxyproline assay; and mitogenic response by [3H]thymidine incorporation into DNA and fluorometric assay of total DNA concentration. RESULTS Conditioning of cartilage explants with 10 ng of human recombinant IL-1 alpha increased degradation and decreased synthesis of matrix proteoglycans (PG), without affecting matrix collagen content. Human recombinant IGF-1 decreased PG loss and reversed the reduction of PG synthesis in cartilage explants conditioned with IL-1. Given alone, steroids decreased PG concentration and synthetic rate in normal cartilage. However, the previously diminished PG content, attributable to IL-1 conditioning, was not further exacerbated by steroid administration in IL-1-conditioned explants. Combined treatment of normal cartilage explants with IGF-1 and steroids resulted in PG preservation and increase in collagen content. Similar PG and collagen effects were not evident when treating IL-1-conditioned cartilage with IGF-1/steroid combinations. Decrease in chondrocyte proliferation was associated with steroid administration. Exposure to IGF and steroids prevented the decrease in mitogenesis that could lead to cellular loss, particularly in IL-1-conditioned explants. CONCLUSION Combination IGF-1 and steroid treatment of normal cartilage cultures indicated substantial ability to override the anabolic suppression associated with steroids alone. Potentially, administration of corticosteroids, followed by IGF-1, may act to decrease propagation of detrimental mediator release while allowing appreciation of the chondroenhancing effects of IGF-1. These beneficial effects were considerably reduced in IL-1-induced cartilage damage.
Low temperature spectroscopy of intact algae

Etude des spectres d'absorption, d'emission de fluorescence et d'excitation de fluorescence de plusieurs algues vertes a basse temperature. Les resultats montrent qu'il existe une grande similitude structurale et spectrale entre les complexes chlorophylles-proteines de ces diverses algues et ceux de plantes superieures. Quelques donnees complementaires concernent le transfert d'energie des differentes phycobiliproteines vers la chlorophylle a liee aux photosystemes I et II et les effets d'une preillumination sur le transfert d'energie
Fusion Protein

An isolated nucleic acid molecule selected from the group consisting of: vi. a nucleic acid molecule comprising a nucleotide sequence which is at least 85% identical to the nucleotide sequence of SEQ ID NO:1 or a complement thereof; vii. a nucleic acid molecule comprising a fragment of at least 1500 consecutive nucleotides of the nucleotide sequence of SEQ ID NO:1, or a complement thereof; viii. a nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence at least 85% identical to SEQ ID NO:2; ix. a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, wherein the fragment comprises at least 500 contiguous amino acids of SEQ ID NO: 2; and x. a nucleic acid molecule encoding a polypeptide containing a humanized immunoglobulin or parts of an immunoglubulin having binding specificity for CD133 a nucleic acid molecule which encodes a variant of a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising the entire SEQ ID NO: 1, or complement thereof under conditions of incubation at 45 DEG C in 6.0xSSC followed by washing in 0.2xSSC/0.1% SDS at 65 DEG C.
Morphological disparity of the postcranial skeleton in rodents and its implications for paleobiological inferences: the case of the extinct Theridomyidae (Rodentia, Mammalia)

Theridomyids were the most diverse and abundant rodents from the Late Eocene to Late Oligocene in Western Europe. As they lived in an archipelago, almost completely (Late Eocene) or partly (Oligocene) isolated from other continental areas, their evolution remained mainly insular, leading to an increase of evolutionary rates. If theridomyids are most often known from isolated teeth, partial postcranial material remains available. A few subcomplete skeletons of a ricochetal theridomyids (i.e. Issiodoromys) have already been studied, but their locomotor adaptations have unlikely been restricted to leaping habits, especially in the basal members of the group. The numerous isolated postcranial bones collected in the Paleogene Quercy localities and other Western European areas allow us describing for the first time the anatomy of the pivotal bones of the theridomyid locomotor apparatus, in order to approach their specificity and diversity. We also performed Factorial Discriminant Analyses (FDA) to evaluate theridomyid locomotory behaviour and body shape in comparison with extant taxa. Despite the limited number of taxa for which postcranial data are available, at least four different types of locomotion can be characterized: 1- the terrestrial quadrupedal (semi-fossorial? ) Suevosciurus, 2- the ricochetal Issiodoromys, 3- the putative arboreal Theridomys bonduelli, 4- the putative cursorial Blainvillimys.
Evolution of hole-nesting in birds: on balancing selection pressures

RESUMEN. -Una re-examinaci6n de los dos especimenes conocidos de Philydor hylobius, ambos provenientes del Cerro de la Neblina en el sur de Venezuela, indic6 que estos pertenecen a Automolus roraimae. El tipo de P. hylobius correponde a un adulto de A. roraimae con predominancia de pigmentacion rojiza (eritrismo), y el otro especimen es un juvenil tipico. Por lo tanto, Philydor hylobius Wetmore and Phelps es un sin6nimo junior de Automolus roraimae Hellmayr.