Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct observation of fishing effort, catch, and discard rates of charter boats targeting reef fishes in the northern Gulf of Mexico

The views and opinions expressed or implied in this article are those of the author (or authors) and do not necessarily reflect the position of the National Marine Fisheries Service, NOAA. Abstract—Fishing activities on charter boats that targeted reef fishes were documented by observers in 2012 and 2013 to examine the effect of fishing season (open versus closed) for red snapper (Lutjanus campechanus) on fishing effort, catch, and discard variables. During 54 trips of charter boats with observers, 38 species of fishes were identified; 32 trips were taken during red snapper open seasons and 22 trips were taken during closed seasons. The majority of the catch and discards comprised lutjanids but also included small demersal reef fishes, highly migratory pelagic fishes, and elasmobranchs. Boat captains targeted artificial reefs at depths <40 m with red snapper abundances that were higher and species diversity that was lower during open seasons than the abundances and diversity found at deeper natural reefs that were fished during closed seasons. On closed-season trips, distance from shore, number of sites fished, and time fished per site were greater, whereas the number of fishermen was significantly lower than the number on open-season trips. The number, size, and proportion of red snapper caught were significantly greater during open-season trips than during closed seasons, but the number of red snapper discards was not significantly different between seasons. This study supports the use of onboard observer programs for the collection of accurate and reliable catch, effort, and discard data regarding the recreational for-hire sector, and for identifying changes in fishing strategies and behavior between closed and open seasons for the red snapper fishery in the northern Gulf of Mexico. Fisheries bycatch and discards affect marine ecosystems worldwide, constituting as much as 25% of the annual global catch (Alverson et al., 1994; Kelleher, 2005; Matsuoka, 2008). The ethical issue of wasted marine resources, as well as the negative impacts that discards can have on fishes and ecosystems, warrants efforts to minimize discards and mitigate their effects (FAO, 1995; Kennelly and Broadhurst, 2002; MSFCMA 2007; NMFS, 2011). To that end, initiatives to minimize bycatch and discards have been fostered by the United Nations, European Union, and United States (FAO, 1995; European Commission1; Hermes2). Under U.S.
The Use of Prickly Pear Cactus as Nesting Cover by Northern Bobwhites

Years of research on the nesting ecology of the northern bobwhile (Colinus virginianus) have documented the use of bunchgrasses as common nesting cover. However, in the Rolling Plains of Texas, recent studies indicate a relatively high use of prickly pear cactus (Opuntia spp.) as suitable nesting cover. To explain this previously unreported use of prickly pear, we evaluated 2 hypotheses: (1) the limited-bunchgrass, and (2) nest-protection hypotheses. We speculated that bobwhites nested in prickly pear cactus because of low availability of bunchgrasses and/or structural protection against predators. We radioinarked 218 bobwhites during spring and summer of 1997 and 1998 on 4 sites in Shackelford County, Texas, USA. Bobwhites nested in prickly pear despite adequate bunchgrass cover (>600 potential nesting sites/ha). Of 81 nests located, 12% were in shrubs (e.g., catclaw [Acacia greggii]), 30% were in prickly pear, and 58% were in bunchgrass. Nest success did not differ among nesting substrates (X 2 = 2.1, df= 2, P= 0.35) but was dependent on the degree of protection provided by the nesting substrate (X 2 = 16, df= 2, P= 0.001). However, successful nests also had a higher density of bunchgrasses in the surrounding arca than unsuccessful nests (P = 0.001). Our data partially supported the nest-protection hypothesis and did not support the limited-bunchgrass hypothesis.
Parkia paya (Leguminosae: Mimosoideae), a New Species from Swamp Forest and Notes on Variation in Parkia speciosa sensu lato in Malesia

Parkia paya H. C. Hopkins is described as new from Borneo and Sumatra. It is a tree, primarily from swamp forest, with opposite, bipinnate leaves and opposite peduncles. The leaflets are almost oblong and the capitula have a well-developed staminodial fringe at anthesis. Some of the material now placed in this species was previously considered intermediate between P sumatrana and P singularis subsp. borneensis. Geographical variation in the pods of Parkia speciosa sensu lato, or petai, is discussed.
Evolutionary demography of a bruchid beetle. I: Quantitative genetical analysis of the female life history

The quantitative genetical technique can provide a qualitative and a quantitative measure of trade-offs between characters in a genetically polymorphic population. Quantitative genetical analysis of the life history of female Callosobruchus maculatus (F.) shows that egg to adult development rate is genetically negatively correlated with both adult longevity and fecundity, while the last two traits are positively correlated. These results are consistent with the existence of trade-offs between development rate, adult longevity and fecundity, constraining the animal's evolutionary options in the culture environment. The trade-offs come about because of effects of adult body weight. Heavier genotypes take longer to mature, but then enjoy increased fecundity and live longer. Key-words: Callosobruch us maculatus, cost of reproduction, development rate, fecundity, life-history theory, methodology, trade-offs
Habitat Use by Northeastern Forest Rodents

Activity of three rodent species was measured on tracking stations in 10 different sampling areas within a northeastern deciduous forest throughout the summer of 1974. Total activity was measured as the number of crossings of the stations (903 Peromyscus maniculatus, 186 Clethrionomys gapperi and 9996 Napaeozapus insignis) and was compared with measures of habitat structure. Habitat separation between the rodents was detected by discriminant function analysis. Habitat use differed among the three rodents. Napaeozapus insignis used coniferous areas with heavy ground cover. Clethrionomys gapperi used areas with little ground cover and heavy mid-story cover. Peromyscus maniculatus used areas with heavy ground and mid-story cover. Habitat use changed and separation increased through the summer. Habitat separation between these rodents is insufficient to account for species coexistence. This contradicts previous predictions and observations in southeastern forests. Separation on some other resource axis is necessary for the coexistence of these three rodents.
Clostridium thermocellum Cel5L - Cloning and Characterization of a New, Thermostable GH5 Cellulase

Aims: Clostridium thermoc ellum is a thermophilic, anaerobic bacterium that ferments cellulose and produces ethanol. While many of the predicted cellulases have been characterized from C. thermocellum , characte rization of additional members is still needed to unravel the function of these enzymes. Study Design : This report describes the first cloning, expression, characterization, and evaluation in cellulose degradation of Clostridium thermocellum Cel5L as well as its relationship to other cellulases. Results: Cel5L, a 526 amin o acid protein that shows low homology to other cellulases of C. thermocellum , possesses both endo and exo activity on  - glucan, carboxymethylcellulose, and cellooligosaccharides; the enzyme does not hydrolyze xylan, xyloglucan or glucomannan. When
Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.
Erster Nachweis von Chalara fraxinea T. KOWALSKI sp. nov. in Deutschland – ein Verursacher neuartiger Schäden an Eschen

Seit mehreren Jahren werden in Deutschland und einigen angrenzenden europaischen Landern zunehmend Schaden an Eschen ( Fraxinus spp.) im Wald- und Flurgeholz sowie in Baumschulen festgestellt. Dabei sind sowohl Jungpflanzen als auch altere Baume auf verschiedenen Standorten betroffen. Die Symptomatik ausert sich vorwiegend in Welkeerscheinungen, vorzeitigem Blattfall und einem auffalligen Wipfeltriebsterben in Verbindung mit Rindennekrosen ohne Schleimfluss. Unterhalb der absterbenden oder abgestorbenen Rinde nimmt der Holzkorper mitunter eine schwache, vom Jahrringverlauf unabhangige Verbraunung an. Der Krankheitsprozess ist haufig chronisch und kann bei jungen Baumen auch letal verlaufen. Die Ursachen werden mehrheitlich in abiotisch pradisponierenden (Trockenheit, Frost, wechselnde Winterwitterung) und biotisch verstarkenden (Schwacheparasiten) Schadfaktoren gesehen. Unklarheit besteht uber die Bedeutung der nachgewiesenen Pilzarten. In Deutschland wurde neben einer Reihe bereits langer bekannter Schaderreger nunmehr erstmalig der kurzlich beschriebene Hyphomycet Chalara fraxinea T. KOWALSKI sp. nov. aus dem Xylem erkrankter Eschen isoliert, welcher z. B. in Polen und Schweden als primarer Verursacher der Schaden angesehen wird. Stichworter: Fraxinus excelsior, F. angustifolia, Chalara fraxinea sp. nov., Eschentriebsterben, Rindennekrosen, Welke, vorzeitiger Blattfall First record of Chalara fraxinea T. KOWALSKI sp. nov. in Germany – a new agent of ash decline Since a few years damages on ashes ( Fraxinus spp.) have been increasingly recorded in forests, landscapes and nurseries in Germany and some other European countries. Both young plants as well as older trees with different site conditions are involved. The symptoms mostly show wilting; premature leaf-shedding and a noteworthy decline of shoots in connection with non exudating bark necroses. Under dying or dead bark the wood sometimes gets a brownish colour what does not follow the annual rings. The pathogenesis is often chronic and can be lethal. The causes of the decline are seen by abiotic predisposition (drought, frost and changing winter conditions) and biotic increasing factors (fungi), although the significance of the recorded fungi is still uncertain. In Germany, apart from several other species, the recently described hyphomycete Chalara fraxinea T. KOWALSKI sp. nov. was now isolated from woody tissue for the first time. The fungus seems to be a conspicuous cause of the new ash decline in Poland and Sweden. Keywords: Fraxinus excelsior, F. angustifolia, Chalara fraxinea sp. nov., ash decline, bark necroses, wilting, premature leaf-shedding
The role of p21-activated kinases in melanoma progression

Tumour metastasis initially requires invasion through the basement membrane and tissue migration towards the vascular system. During these stages cancer cells are thought to use actin rich protrusions called invadopodia to facilitate matrix and basement membrane degradation. p21-activated kinases (PAKs), a family of six serine/threonine protein kinases, have been linked to cell invasion and are found to be amplified/overexpressed in a wide variety of human invasive cancer cell lines and tissue. PAK1 localises in invadopodia, and PAK4 in podosomes (a closely related structure). This study looks at the role of these two PAK isoforms in invadopodia formation and cellular invasion in melanoma. In this study a significant increase in the level of PAK1 and PAK4 expression in melanoma cell lines was demonstrated and both proteins were expressed in cell strains derived from patient samples. PAK1 overexpression correlated with melanoma cell line invasive potential, while both PAK1 and PAK4 overexpression occurred in cell lines and cell strains that formed invadopodia. Depletion of PAK1 and/or PAK4 expression resulted in a significant decrease in invasive capacity in melanoma cell lines and in an in vivo zebrafish invasion assay. Protein depletion experiments point to differential roles for PAK1 and PAK4 during the invadopodia lifecycle. The data suggest that PAK1 promotes the formation of this protrusion while PAK4 is more important for the maturation and matrix degradation activity of invadopodia. This is the first time that PAK4 has been shown to be involved in invadopodia activity. Furthermore, this study has identified a signalling pathway, unique to PAK4, which suggests that this protein inhibits the function of PDZ-RhoGEF to promote the formation and degradation of invadopodia. In conclusion, the data obtained from this study indicate that PAK1 and PAK4 play an important role in invadopodia activity and cellular invasion in melanoma. Distinct functions for each of these PAK isoforms in the invadopodia lifecycle has been established, with the identification of a novel PAK4 pathway involving the localised inhibition of PDZ-RhoGEF. PAK1 and PAK4 therefore present interesting therapeutic targets for the prevention/reduction of metastatic melanoma progression.
Why We Should Stop Trying to Measure the Cost of Reproduction Correctly

The Cost or Reproduction (CoR) is a basic assumption or most models or lire-history evolution. CoR's «correct» measurement, such that strictly genetic correlations between traits related to present versus future reproduction are evaluated, is not a valid test or the explanatory power or life-history models. If the genotype for an optimum effort is prevalent in a population, genetic variation for reproductive effort will be near zero. It follows that genetically based correlations will also be small, and artificial selection experiments will not reveal a genetic CoR. Similarly, no particular relationship between present and future reproductive output results from considering life-history traits to be «adaptively plastic» or using the «comparative approach» at inter-specific or higher taxonomic levels
Is really the “Local Datum” an Obsolete and Old-Fashioned Definition? The catalytic role of the velocity field for the modern geodetic reference frames: The Minimum Kinetic Energy Criterion

In the present paper we provide an alternative concept for the realization of an optimal reference frame which fits to the local geophysical features of a country or a region. The main idea is based on the implementation of the Minimum Kinetic Energy Criterion (MKEC). The MKEC can be materialized using exploiting 3D, 2D or even in 1D velocities, respectively. The alternative methodology is tested in a GNSS network of 151 stations located in Greece. The results point out that the MKEC criterion reduces more than 50% the initial velocity field and offers a serious advantage compared to the global or a regional Terrestrial Reference Frames (TRFs), respectively. We provide all the necessary mathematical equations for its successful application.
Evaluating community impacts of ocean acidification using qualitative network models

We applied Qualitative Network Models (QNMs) to evaluate the potential community effects of ocean acidification (OA) in a major shellfish-producing estuary (Willapa Bay, Washington). QNMs are well-suited to data-limited systems and only require information on the sign (+, −, 0) of the interactions between species. We examined qualitative predictions of community responses to 13 different OA scenarios that corresponded to 3 broad categories of hypothesized OA effects: (1) increased primary productivity, (2) reductions in bivalve populations, and (3) enhanced predation interactions between bivalves and their crab and gastropod predators. The cultivated bivalve Manila clam tended to respond negatively across scenarios, while primary producers (phytoplankton and eelgrasses) and Chinook salmon tended to respond positively. Tradeoffs between species were also assessed: Manila clam and Pacific oyster were predicted to decrease and increase, respectively, when direct OA effects were limited to eelgrasses and the reverse occurred when phytoplankton alone was stimulated by OA. We analyzed the QNMs to identify key linkages that influenced the sign outcome of community members and might therefore warrant future quantitative study. QNMs may be particularly relevant to researchers as a simple method for identifying conditions under which the sign response of species to OA, as inferred from single-species OA experiments, will likely hold in the wild. Given data limitations in most systems, QNMs are a practical alternative or complement to data-intensive quantitative ap proaches and may help accelerate our understanding of the community-wide effects of OA in marine systems.
Notes on the Local Distribution of Peromyscus leucopus and Zapus hudsonius

The factors influencing the local distribution of Peromyscus leucopus and Zapus hudsonius were studied in seven habitats (old field, hardwood swamp, coniferous swamp, bog mat, spruce burn, upland hardwood, and grass sedge marsh) in southern Michigan. The environmental factors considered were vegetation type, cover (fallen trees, brush, leaf litter), temperature, food, moisture, and interspecific competition. P. leucopus permanently inhabited only wooded habitats (those with trees or shrubs). There was no indication of an avoidance of herbaceous vegetation; there appeared to be a positive response to a tree-shrub type of vegetation. The reason for such a response was not determined. Among the forested areas, an oak-hickory upland was the most favorable habitat. A larger and more stable food supply (acorns and nuts) appeared to be the major factor responsible for the greater abundance of P. leucopus in this habitat. Temperature, moisture, cover, and interspecific competition were not important factors in the selection or avoidance of a particular habitat. Z. hudsonius was found only in moist situations and was slightly more abundant where there was standing water. Vegetation, temperature, cover, and interspecific competition were not important factors in its local distribution. During the course of a field study of the local distribution of microtine rodents and shrews in southern Michigan, data were obtained pertaining to the white-footed mouse. Peromyscus leuco pus, and the jumping mouse, Zapus hudsonius. Although the study was not designed primarily for these two species, there was sufficient variation in the habitats to determine the influences of certain factors. Since information concerning the local distribution of small mammals is relatively rare in the literature, it seems advisable to make these data available. The information presented in this paper has been extracted from a thesis presented in partial fulfillment of the degree of Doctor of Philosophy in the University of Michigan. DESCRIPTION OF THE STUDY AREA AND METHODS Study area. -All the work was done in the University of Michigan's Mud Lake Research Area in southern Michigan. Seven habitats (old field, hardwood swamp, bog mat, spruce-birch-larch swamp, spruce burn, oak-hickory upland, and marsh) within the area were selected for study. In addition, six transects were established to cross as many types of habitat as possible. The study areas and transects are described in detail elsewhere (Getz, 196ta, b). Methods. -Three methods of sampling the abundance of small mammals were utilized. (1) A rectangular study area consisting of 75 trap stations placed in a grid pattern with an interval of 12 meters
TERVERTICILLATE PENICILLIA: CHEMOTAXONOMY AND MYCOTOXIN PRODUCTION

A total of 4346 isolates of terverticillate Penicillium species was examined for production of my? cotoxins and other important secondary metabolites. Nearly all taxa and chemotypes (38 in all) produced one or more known mycotoxins consistently. Profiles of secondary metabolites were specific for each taxon, but several mycotoxins were produced by more than one species, suggesting a high degree of relatedness in the terverticillate penicillia. A high number of misidentified Penicillium isolates were reidentified, clarifying connections between taxa and profiles of mycotoxins and other secondary me? tabolites. Confirmed production of several mycotoxins in different taxa is reported for the first time. Penicillium chrysogenum, P. atramentosum, P. coprophilum, P. crustosum, P. expansum, P. glandicola var. glandicola and var. glaucovenetum, P. griseofulvum, P. hirsutum var. hirsutum, var. albocoremium, var. allii and var. hordei, and P. vulpinum are reported for the first time to be consistent producers of roquefortine C. Griseofulvin is reported from P. coprophilum. Tremorgen penitrem A was consistently produced by P. crustosum, P. glandicola var. glandicola and P. clavigerum. Terrestric acid is reported from P. hirsutum and its varieties, and P. crustosum. P. hirsutum var. hirsutum and P. solitum produce compactin. Penicillium mononematosum produces cyclopaldic acid and isochromantoxin. P. expansum was found to produce the mycotoxin chaetoglobosin C and P. atramentosum produces rugulovasine A. Several new varieties, chemotypes and combinations are proposed, based on profiles of secondary metabolites, morphology and physiological characters. Living ex type and authentic cultures of taxa believed to be synonyms of important species were examined and revised lists of synonyms are pre? sented.
Physiological and growth responses of young tomato seedlings to drip-irrigation containing two low doses of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum sp. nova

Summary Two different doses of an arbuscular mycorrhizal fungus (AMF; Glomus iranicum var. tenuihypharum sp. nova) were applied through a drip irrigation system to evaluate their effects on the physiological, nutritional, and agronomic performance of tomato plants. Trials were conducted in south-eastern Spain under controlled greenhouse conditions from September – December 2012. The high rate of AMF colonisation at both doses applied improved plant growth performance, leading to significant increases in leaf macro- (N, P, K, Ca and Mg) and micro- (Fe, Cu, Zn, Mn and B) nutrient concentrations. The AMF present in colonised plants not only exerted some control over the rate of transpiration (stomatal control), but also maintained a higher rate of net photosynthesis and hence improved the intrinsic water use efficiency (computed from the ratio of the rate of net photosynthesis:stomatal conductance). In addition, a close relationship was found between the respiratory activity of the AMF and the rate of net photosynthesis, leaf N, P, Fe, and K concentrations, and fruit yield (expressed as the product of the average number of fruit × the average fruit weight in each treatment). In summary, the application of AMF was effective at improving the performance (i.e., the growth, nutrition, and yield) of tomato plants cultivated under an intensive fertigation regime.