Miracle-dz/UniFAR-FTUs huggingface dataset:
Assuring the future of prairie grouse: dogmas, demagogues, and getting outside the box

Abstract We discuss the necessity of a paradigm shift among managers toward dealing with the recovery and management of prairie grouse (Tympanuchus spp). To assure the future of these species, we will need to test dogmatic assumptions about grouse and their management and challenge the demagogues who insist on perpetuating untested “principles. ” Tolerance for descriptive and qualitative studies is needed. Additionally, managers will need to remove themselves from the box and embrace landowners, theoretical biologists, economists, human-dimensions researchers, marketing and advertising specialists, and many other professionals outside the normal sphere of wildlife management. There is crucial need for a willingness to devise, test, and apply innovative ideas that are not normally considered in the management of grouse species, especially applying management to large areas within ecosystems. A comprehensive plan is needed to guide rangewide prairie grouse management. Planned management systems are needed to provide operational guidance in implementing species plans.
Life-history and ecology of sharks at Aldabra Atoll, Indian Ocean

Ten species of shark belonging to three families were recorded from Aldabra Atoll. Carcharhinus melanopterus and acutidens were the most abundant species in the lagoon, while Carcharhinus albimarginatus was the most common shark outside the reef. Twelve hundred sharks of six species were tagged and individual recapture rates varied from 15 to 34% . Some specimens of C. melanopterus were caught up to seven times. All five species for which recapture data were available are restricted in their movements at Aldabra. C. melanopterus in particular is very localized, normally remaining in an area of a few square kilometres. Length increment data obtained from tagging demonstrated a slow growth rate for C. melanopterus, averaging 3.5 cm a-1, with no detectable difference between the growth rates of small and large individuals. Limited data for juvenile Negaprion and C. albimarginatus indicated average growth rates of 12.5 and 8.8 cm a-1 respectively. Population densities calculated for several areas in the lagoon varied from 19 to 198 C. melanopterus per square kilometre. It is suggested that C. melanopterus may be foodlimited at Aldabra owing to the intensity of intra- and inter-species competition. C. melanopterus and Negaprion have restricted and almost identical reproductive cycles at Aldabra. C. melanopterus females mature at 110 cm total length and breed every second year giving birth to about four pups after a 10-11 month gestation period. Stomach contents of the more abundant species indicate that fish are the most important item in the diet, except for Nebrius concolor which feeds principally on octopus.
An effective method for extraction and polymerase chain reaction (PCR) amplification of DNA from formalin preserved tissue samples of snow leopard

Formalin-preserved biological samples obtained from endangered species are valuable in assessing genetic diversity. To make use of snow leopard samples preserved in formalin over a period of two to seven years, we optimized the method of extracting DNA from these samples. We used (a) phenol chloroform : isoamyl alcohol, (b) the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Germany), (c) the Qiagen DNeasy Blood and Tissue Kit after treating the samples with NaOH for three days and (d) the Qiagen DNeasy Blood and Tissue Kit after treating the samples with phosphate buffered saline (PBS) for three days. The usefulness of the extracted DNA was assessed on the basis of mitochondrial (150 to 550 bp) and nuclear (95 to 229 bp) markers. There was no PCR amplification with the first two methods. The PCR amplification with the NaOH and PBS treatment had a success rate of 30 to 100% for both mitochondrial and nuclear markers. The PBS method is the best method for extraction of DNA from formalin-preserved samples of longer period (two to seven years) because of higher success rate in amplifying mitochondrial gene of ca. 550 bp (60%) than the NaOH method (28%). The overall amplification of microsatellite markers in such samples was also higher in samples treated with PBS (43 to 100%) than NaOH (0 to 100%). The PCR products obtained were confirmed through DNA sequencing to be of snow leopard origin. The optimized protocol will enable genetic studies to be conducted on tissue samples of other species that have been preserved in formalin. The protocol will be particularly useful for species that are elusive and from which it is difficult to collect fresh tissue samples.
Les Molopina hypogés des Pyrénées avec la description d'une nouvelle espèce de Zariquieya Jeannel, 1924 d'Espagne (Insecta, Coleoptera, Carabidae, Pterostichini)

ABSTRACT Hypogean Molopina of Pyrenees with the description of a new species of Zariquieya Jeannel, 1924 from Spain (Coleoptera, Carabidae, Pterostichini). A second blind species of the genus Zariquieya Jeannel, 1924, Z. boumortensis n. sp. , is described from the southern slope of central Spanish Pyrenees (Lleida, Spain). Morphological structure of the new species, especially male and female genitalia as well as the external morphology suggests that this carabid beetle should be included in the genus Zariquieya, created for a single species endemic of eastern Spanish Pyrenees. The new species is morphologically distinct from Z. troglodytes Jeannel, 1924 by numerous characters like maxillary palpus glabrous, pronotum more transverse, frontal impressions lighter, and elytra with flat disk without strong lateral and apical declivity. A key for identification of Pyrenean Molopina is given, and ecology and biogeographical considerations are detailed, including distribution map of Pyrenean hypogean Molopina.
Detection of regime shifts in multi‐species communities: the Bay of Quinte phytoplankton example

1. Human activities have led to ecological regime shifts, first revealed at the community level in ecosystems. A regime shift in a biological community is a sudden change in the relative contributions of several taxa, resulting in a post‐shift state that remains stable over the long term with a structure that is outside the boundaries of the ‘normal’ pre‐shift variability. Most methods for regime shift detection are based on univariate statistics (e.g. commercial fish catch data, sea surface temperature anomalies). Multivariate methods suitable for identifying change in multi‐species communities can be used to identify regime shifts in communities.
Editorial

Outlook on AGRICULTURE Vol 37, No 1, 2008 World Cancer Research International’s latest report on diet and health once again sheds suspicion on meat as a safe component of a healthy diet, though it is careful not to attribute anything directly to meat. The report, Food, Nutrition, Physical Activity and the Prevention of Cancer: a Global Perspective, was released in October 2007. In order of importance it recommends people to:
Clostridium tertium Infection in a Moluccan Cockatoo (Cacatua moluccensis) with Megacolon

A 4-year-old Moluccan cockatoo (Cacatua moluccensis) was examined because of lethargy and a necrotic wound on the lateral base of the tail. Over the previous 2 years, the bird had chronic diarrhea and was treated with long-term antibiotics. A contrast radiographic study demonstrated slow gastrointestinal transit time and a large filling defect in the caudal abdomen. Clostridium tertium, a bacterium rarely found in psittacine birds, was isolated on bacterial culture of a fecal sample. Despite wound debridement and parenteral antibiotic treatment, the bird died. At necropsy, the colon was severely dilated. Histopathologic examination revealed diffuse, severe lym- phoplasmacytic inflammation of the colon and massive ulceration and bacterial colonization of the
Genetic Revolutions in Relation to Speciation Phenomena: The Founding of New Populations

As a dynamic process of genetic change, evolution manifests itself in two ways: It produces adaptive characters, and it produces species. To recognize that evolution has occurred by studying these products does not satisfy interested population geneticists. They see their science as providing an opportunity to contribute information that permits us to describe how the process of descent with genetic change occurs in populations of sexually reproducing, crossfertilizing organisms.
BIOGEOGRAPHY OF CLADOPHOROPSIS MEMBRANACEA (CHLOROPHYTA) BASED ON COMPARISONS OF NUCLEAR rDNA ITS SEQUENCES 1

Nucleotides were compared at 988 sites, spanning both internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal DNA, among 17 isolates of the green alga Cladophoropsis membranacea (Hofman Bang ex C. Agardh) Boergesen and two isolates of Struvea anastomosans (Harvey) Piccone and Grunow. Collections were made from Bonaire, Curaçao, St. Croix, the Canary Islands, the Cape Verde Islands, Mauritania, Syria, the Red Sea, Okinawa, and Hawaii. Two nucleotide substitutions were found between the sequenced coding regions of C. membranacea and S. anastomosans. Of the 720 nucleotides compared in ITS1 and ITS2, an average of 6.7% sequence divergence was found within C. membranacea and 17.4% between C. membranacea and S. anastomosans. Sequences were analyzed using maximum parsimony. Phylogenetic hypotheses were compared with the biogeographic hypothesis of an east‐west Tethyan vicariance. Results of the study allow the identification of widely dispersed biogeographic populations, the identification of an underlying Tethyan imprint, and support for the hypothesis that dispersal has occurred between the Caribbean and the tropical eastern Atlantic. These results demonstrate the usefulness of ITS sequences at the sub‐specific level in C. membranacea.
NEW PERSPECTIVES ON LIPID DIGESTION AND METABOLISM IN RUMINANTS

Fat is an important energy component in the diet of ruminants and over the last decade fat supplementation has become a common practice to increase the energy density of the diet for high producing dairy cows. Recent advances have renewed the interest in dietary fats and lipid metabolism. One development is improved analytical procedures which have revealed the complex pattern of fatty acids that are produced in the rumen and incorporated into ruminant meat and milk fat. The old adage “what you eat is what you get” is clearly incorrect in the case of dietary lipids and ruminant animals, and this is of special importance given recent efforts to include lipid metabolism in dynamic models of ruminant digestion. Following absorption, a major fate of fatty acids is their oxidation for energy. However, a second recent development is the recognition that specific fatty acids produced in the rumen also play a critical role as signaling molecules involved in the expression of specific genes and the regulation of metabolic processes. Finally, recent discoveries in the functional foods area indicate that specific fatty acids produced in the rumen may have beneficial effects on human health, and there is a keen interest in the possibility of designing natural food products with enhanced levels of these fatty acids.
Activation of Interferon-γ Inducing Factor Mediated by Interleukin-1β Converting Enzyme

The interleukin-1β (IL-1β) converting enzyme (ICE) processes the inactive IL-1β precursor to the proinflammatory cytokine. ICE was also shown to cleave the precursor of interferon-γ inducing factor (IGIF) at the authentic processing site with high efficiency, thereby activating IGIF and facilitating its export. Lipopolysaccharide-activated ICE-deficient (ICE−/−) Kupffer cells synthesized the IGIF precursor but failed to process it into the active form. Interferon-γ and IGIF were diminished in the sera of ICE−/− mice exposed to Propionibacterium acnes and lipopolysaccharide. The lack of multiple proinflammatory cytokines in ICE−/− mice may account for their protection from septic shock.
The impact of Bacillus thuringiensis technology on the occurrence of fumonisins and other mycotoxins in maize

In many developing countries, maize is both a staple food crop and a widely-used animal feed. However, adventitious colonisation or damage caused by insect pests allows fungi to penetrate the vegetative parts of the plant and the kernels, the latter resulting in mycotoxin contamination. Maize seeds contaminated with fumonisins and other mycotoxins pose a serious threat to both humans and livestock. However, numerous studies have reported a significant reduction in pest damage, disease symptoms and fumonisin levels in maize hybrids expressing the Bacillus thuringiensis (Bt) gene cry1Ab, particularly in areas where the European corn borer is prevalent. When other pests are also present, the cry1Ab gene alone offers insufficient protection, and combinations of insecticidal genes are required to reduce damage to plants caused by insects. The combination of Cry1Ab protein with other Cry proteins (such as Cry1F) or Vip proteins has reduced the incidence of pests and, indirectly, mycotoxin levels. Maize hybrids .
Influence of Graded Levels of Organic Zinc on Growth Performance and Carcass Traits of Broilers

Abstract This study investigated the effect of graded levels of organic Zn (Bioplex Zn) on growth performance and carcass traits of broilers fed diets containing organic Se (Sel-Plex). Dietary treatments consisted of adding 0, 15, 30, 45, or 60 ppm organic Zn to a basal diet containing 60 ppm Zn from an inorganic source. Feed and water were provided ad libitum. Body weight, feed intake, feed conversion, and carcass traits were evaluated. Carcass evaluation was also performed on the last day of the experimental period. Body weight, feed intake, feed conversion, and weights of individual meat cuts were not statistically influenced by increasing organic Zn levels in the diet. However, a significant increase in skin tearing strength was observed in response to increasing levels of dietary organic Zn. Zinc plays a role in epithelial cell layers and collagen synthesis, thus affecting susceptibility of skin to tearing. These data indicated that organic Zn does not affect growth performance of broilers but increases resistance of skin to tearing, therefore improving carcass quality.
A microbiological and morphological study of blocked biliary stents

Biliary stent blockage represents the main limitation of the use of such devices in relieving obstructive jaundice due to a variety of malignant and benign conditions. Microbiological and morphological analysis of the occluding sludge present on the inner surface of 30 biliary stents was performed to evaluate the different components of such material and the effect of the antibiotic treatment on the biofilm formation. A highly organized biofilm, constituted by microbial cells embedded in an amorphous matrix together with crystallized bile salts, was observed Enterococcus spp . represented the most common isolate from both occluded and non-occluded stents. The antibiotic therapy, while selecting for multi-resistant bacteria and fungi, might possibly delay the biofilm formation. Key words: biliary stents, microbial colonization, biofilm.
Molecular Mechanisms of Glucocorticoid Action

Key words Abstract Glucocorticoids are steroid hormones synthesized and secreted by the adrenal cortex. They regulate a variety of physiologic functions and play an important role in maintaining basal and stress-related homeostasis. The actions of these hormones are mediated by the glucocorticoid receptor (GR). The human glucocorticoid receptor (hGR) gene is located on chromosome 5; its activity is regulated by at least three different promoters, which account for tissue-specific expression. The molecular structure of hGR is similar to that of other steroid receptors, and is comprised of three functional domains. Mechanisms of hGR action are now well established.
Atypical Acorns Appear to Allow Seed Escape After Apical Notching by Squirrels

Abstract Atypical acorn traits, such as multiseeded acorns, have frequently been reported in oaks (Genus: Quercus), yet there is disagreement over whether such traits are advantageous or selectively neutral. Squirrel embryo-excision behavior is one factor that has not previously been considered in discussions of these traits. Several tree squirrels are known to remove acorn embryos before caching them by notching acorns apically using their incisors. We hypothesized that atypical acorns could potentially be advantageous in environments where such embryo excision occurs. To test this, we conducted germination tests on whole acorns, squirrel-notched acorns and artificially-notched acorns for Quercus alba trees that produced either single-seeded or atypical acorns. Atypical acorns included both multiseeded acorns and acorns with non-apical embryos. Atypical acorns appear to confer a survival advantage following either squirrel or artificial notching. Trees producing such acorns had higher successful acorn germination following notching when compared to trees that produced only single-seeded acorns. For acorns that had been either notched by squirrels in the field or artificially-notched apically in the lab, only acorns from trees producing atypical acorns successfully produced shoots with plumules. These acorns were planted and developed into healthy single seedlings. We review the literature for reports of atypical acorn traits, specifically multiseeded acorns, and find that this trait has been reported for 14 species of oaks, across both oak subgenera in temperate and tropical regions. We argue that atypical acorns are advantageous for oaks, allowing escape from both insect and mammalian seed predators.
A Novel Modified Endosperm Texture in a Mutant High-Protein Digestibility/High-Lysine Grain Sorghum (Sorghum bicolor (L.) Moench)

ABSTRACT Development of high-protein digestibility (HPD)/high-lysine (hl) sorghum mutant germplasm with good grain quality (i.e., hard endosperm texture) has been a major research objective at Purdue University. Progress toward achieving this objective, however, has been slow due to challenges posed by a combination of genetic and environmental factors. In this article, we report on the identification of a sorghum grain phenotype with a unique modified endosperm texture that has near-normal hardness and possesses superior nutritional quality traits of high digestibility and enhanced lysine content. These modified endosperm lines were identified among F6 families developed from crosses between hard endosperm, normal nutritional quality sorghum lines, and improved HPD/hl sorghum mutant P721Q-derived lines. A novel vitreous endosperm formation originated in the central portion of the kernel endosperm with opaque portions appearing both centrally and peripherally surrounding the vitreous portion. Kernels exhi.
A role for PKCθ in outside‐in αIIbβ3 signaling

Summary. Fibrinogen binding to platelets triggers αIIbβ3‐dependent outside‐in signals that promote actin rearrangements and cell spreading. Studies with chemical inhibitors or activators have implicated protein kinase C (PKC) in αIIbβ3 function. However, the role of individual PKC isoforms is poorly understood. Biochemical and genetic approaches were used to determine whether PKCθ is involved in αIIbβ3 signaling. PKCθ was constitutively associated with αIIbβ3 in human and murine platelets. Fibrinogen binding to αIIbβ3 stimulated the association of PKCθ with tyrosine kinases Btk and Syk, and tyrosine phosphorylation of PKCθ, Btk and the actin regulator, Wiskott‐Aldrich syndrome protein (WASP). Mouse platelets deficient in PKCθ or Btk failed to spread on fibrinogen. Furthermore, PKCθ was required for phosphorylation of WASP‐interacting protein on Ser‐488, an event that has been linked to WASP activation of the Arp2/3 complex and actin polymerization in lymphocytes. Neither PKCθ nor Btk were required for agonist‐induced inside‐out signaling and fibrinogen binding to αIIbβ3. Thus, PKCθ is a newly identified, essential member of a dynamic outside‐in signaling complex that includes Btk and that couples αIIbβ3 to the actin cytoskeleton.
BEETLE FOLIVORY INCREASES RESOURCE AVAILABILITY AND ALTERS PLANT INVASION IN MONOCULTURES OF GOLDENROD

One way that insect herbivores can influence plant community structure is by altering the ambient availability of resources required by plants. To examine the im- portance of this mechanism, I tested the following three hypotheses in a field experiment in 1990: (H1) Folivory by the leaf beetle Trirhabda canadensis (Coleoptera: Chrysomelidae) increases availability of light, water, and N in monocultures of goldenrod (Solidago mis- souriensis). This hypothesis was partially supported. Folivory by Trirhabda reduced leaf, root, and total biomass of goldenrod and increased light penetration, soil water content, and soil nitrate concentration. However, Trirhabda grazing did not affect overall soil N availability. (H2) The invasion of goldenrod monocultures by other plant species and the response of goldenrod to folivory reflects an increased availability of resources in mono- cultures grazed by Trirhabda. This hypothesis was supported. Folivory by Trirhabda raised the probability that a species would invade the experimental monocultures and increased the species richness of the invading plant assemblage. Relative growth rate of goldenrod and production of aboveground biomass by invaders were higher in monocultures grazed by Trirhabda than in ungrazed ones. Prostrate and creeping forbs increased in relative abundance following folivory by Trirhabda. (H3) Reduced N uptake by goldenrod or in- creased N mineralization accompanies increased N availability in grazed monocultures. This hypothesis was also supported. Net N mineralization and nitrification were higher in monocultures grazed by Trirhabda than in ungrazed monocultures. Folivory by Trirhabda larvae reduced N uptake by goldenrod, but that of adults did not. The impact of herbivores upon plant communities may be effected through increased availability of important plant resources.
Compliance vs. constraints: A theory of rebel targeting in civil war

This article offers a theory of rebel targeting in civil war. Rebels face two logics of targeting: the logic of compliance in areas where they are fighting for territory, and the logic of legitimacy in areas where they remain clandestine. The first boosts civilian targeting because rebels use it as a way to discipline local populations. The second moderates it because unqualified civilian killings could prompt rebels’ supporters to turn against the group and easily help bring down its clandestine structures. In order to avoid this backlash, rebels focus on attacking ‘legitimate’ targets such as security forces and authorities. This supporters’ constraint is mitigated when the state heavily represses the rebels’ constituency – which increases supporters’ appetite for indiscriminate retaliation – and when the rebels can rely on independent funding – which reduces rebels’ dependence on supporters’ help. I test the argument with detailed information about rebel presence and political violence in Peru from 1980 to 1995. The results support that civilian victimization is driven by rebel strength, since the more control the rebels hold, the more civilians are targeted. Thus, when Shining Path was forced to operate clandestinely on a permanent basis, it carried out more actions against hard targets, so as to remain a legitimate force within its urban support base.