Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting species vulnerability with minimal data to support rapid risk assessment of fishing impacts on biodiversity

Summary 1. Large-bodied species are especially vulnerable to fishing in mixed fisheries. Their effective conservation requires predictions of sensitivity and exposure to fishing mortality, but such predictions are hard to make when the population dynamics of most of these species have not been described. 2. We present a method for assessing sensitivity and conservation management reference points using widely available life-history data. The method allows the sensitivity of all fish species in a community to be assessed in relation to conservation- and yield-based fishery reference points. 3. Knowledge of sensitivity is used to (i) rank species by sensitivity, (ii) conduct a risk assessment to identify species potentially vulnerable to current fishing pressure and (iii) examine potential trade-offs between fishery catches and the conservation status of sensitive species. 4. The method is applied to the Celtic Sea bottom-dwelling fish community. For the species present, conservation threshold fishing mortalities ranged from 0·05 per year for the most sensitive large elasmobranchs to over 1 per year for small teleosts. The assessment predicts that current levels of fishing mortality may place all the elasmobranchs and over a quarter of the teleosts below conservation reference points. 5. Depending on the relative mortality rates affecting commercially targeted species and species of conservation concern, up to 65% of the potential yield-per-recruit of commercially important species may have to be forgone to reduce fishing mortality below conservation limit reference points for the most sensitive species. 6. Synthesis and applications. The method presented provides a clear objective procedure to construct ranked species sensitivity lists that can inform management, monitoring and research. The Celtic Sea case study demonstrated that limiting fishing pressure on key commercial stocks to meet fisheries production targets may be insufficient to guarantee the persistence of more sensitive species. Management actions that effectively decouple the mortality rates on commercial species and ‘conservation’ species are likely to be required to make progress in relation to conservation objectives. The method would support rapid assessment of sensitivity to fishing in many regions around the world as only taxonomic lists and estimates of body size are required.
Statistical Assessment of the Age–Length Key

Since 1934 when Fridriksson originated the age–length key, it has been widely used by fisheries biologists to estimate age distributions of populations. In recent years, there has been a general recognition that often the key has little value, or even worse, gives biased results. The analysis presented here indicates why the age–length key is so susceptible to bias. More importantly, a criterion is presented for determining whether the age–length key should be used in a particular situation. If the key is to be used, results from examples indicate that random age subsamples (i.e. the number of specimens aged from each length category proportional to the number in each length category) are superior to fixed age subsamples (i.e. a constant number of specimens aged from each length category). Generally, small increases in the age sample will likely increase the accuracy of an age-distribution determination more effectively than relatively large increases in the length sample.
Genetic engineering, ecosystem change, and agriculture: an update

Genetically modified organisms (GMOs), alternatively called biotech crops, dominate soybean and cotton production and are rapidly increasing their fraction of market share for maize and rice in the U.S. Engineered canola is important in Canada, soybeans are dominant in Argentina and Brazil, and cotton is prominent in China and India. Adoption is much slower elsewhere, in large part due to concerns for potential ecosystem effects that may occur through development of weedy plants, by selection of herbicide resistant weeds and by effects of insecticidal proteins on nontarget insects. The precautionary principle is invoked by critics concerned that one must know in advance the effects of GMOs before releasing them. Alteration of weed species composition of agricultural fields is well documented to occur under herbicide selection pressure. Gene flow to wild relatives of crop plants can be shown under herbicide selection, and one instance (sunflower) is provided for insect resistance transfer leading to increased seed production by a weedy relative. Detailed stewardship programs have been developed by seed producers to minimize risks of gene flow. Although herbicides and insecticides are known to have major effects on agroecosystems, the ecosystem impacts of GMOs per se, thus far appear to be small. Key words: gene-flow, herbicide-resistant weeds, genetically engineered crops, Bt maize, Roundup Ready soybeans
The dose-response of weekly resistance training volume on skeletal muscle adaptations in trained males

Purpose: Previous literature is unclear on the dose response relationship between resistance training (RT) volume and skeletal muscle adaptations when weekly sets exceed 10-12. The present study compared the effects of various weekly RT volume on skeletal muscle thickness and strength in young RT trained males over 6 weeks. Methods: RT trained young (aged 18-21) males (n=21) were randomly allocated to a low (LOW, n=7) moderate (MOD,n=7) or high (HIGH,n=7) group. Participants undertook RT of the biceps over a 6- week period. LOW performed 1 RT session per week consisting of 9 sets (9 weekly sets), MOD performed 2 RT sessions per week consisting of 9 sets (18 weekly sets), HIGH performed 2 RT sessions per week consisting of 14 and 13 sets (27 weekly sets). All participants consumed 40g whey protein post RT session, whilst recording dietary intake and external RT volume throughout the 6-week period. Pre and Post training period assessments of muscle thickness (MT; Ultrasound), isometric maximal voluntary contraction and one repetition maximum strength was completed by all groups. Data was analysed using a mixed design ANOVA to examine within and between group pre-post changes. Results: MT significantly increased pre-post in LOW (9.3 ± 5.5%, p<.001) and MOD (14.3 ± 10.4%, p<.001) but not in HIGH (5.59 ± 4.0%, p=.054). All groups experienced significant increases in 1RM strength but no significant increase in isometric strength. There were no significant differences between groups for MT, 1RM and isometric strength. Conclusion: The findings of this study suggest that moderate and high weekly RT volumes, performed twice per week, provide minimal further benefit to skeletal muscle adaptations over lower weekly RT volumes performed once per week for 6 weeks.
Screening and Isolation of Pectinase producing Bacteria from Various Regions in Bangalore

This work has been undertaken for the Screening and isolation of Pectinase producing strains of Bacteria were carried out from Ten soil samples, collected from dump yards of vegetable wastes various regions of Bangalore and used to screen for Pectinase production by using pectinase screening agar medium (PSAM). In the present study, an attempt was made to isolate efficient Pectinase producing bacteria from diverse regions of Bangalore. Different isolates were screened for possessing the ability to produce Pectinase. About 6 bacterial isolates were found to be promising to produce Pectinase. The organisms were tested for various biochemical tests, which leads to their identification as Bacillus licheniformis, Bacillus cerus, and Staphylococcus aureus.
Opinion building on a socio-scientific issue: the case of genetically modified plants

This paper presents results from a study with the following research questions: (a) are pupils' opinions on genetically modified organisms (GMOs) influenced by biology teaching; and (b) what is important for the opinion pupils hold and how does knowledge work together with other parameters such as values? 64 pupils in an upper secondary school answered questionnaires, in which they expressed opinions and gave arguments on applications of GMOs, before and after biology courses. The pupils' knowledge of genetics and GMOs was also investigated. Eleven pupils were then in-terviewed to examine their reasoning in more depth. More pupils were positive about genetically modified tomatoes after the courses. Males were more positive than females. No correlation was found between knowledge of basic genetics and opinion. Most of the pupils could express arguments for and against the applications but they built their personal opinion on different arguments. An important concern was potential risks. Depending on risk judgement and/or how they trusted scientists, the pupils came to different conclusions. Few had any idea of how the different applications are risk assessed or how scientists work. Other important factors for decision-making were the purpose of the application, the time perspective and feelings.
Badger Meles meles setts–architecture, internal environment and function

Badger setts vary considerably in size, ranging from simple single-entrance burrows to complex tunnel systems hundreds of metres long with multiple entrances and underground chambers. Data from 19 excavated setts show that main setts are larger than other setts in terms of area and volume, and contain more chambers, nests and latrines; but setts of different sizes and types are built according to the same basic architectural principles. Little is known about the environmental conditions within setts, other than that temperature and humidity are constant in parts of a sett that are at least 7 m from the nearest entrance. Setts are used for breeding and as sleeping places and refuges, but a question remains as to the functional value of large setts. It is suggested that large main setts allow members of a social group to avoid one another underground, especially when breeding. Little is known about the use of other types of sett.
Understory species interactions in mature boreal mixedwood forests

We explored interactions among plant growth forms in the understory of mature boreal mixedwood forests in western Canada by investigating the competitive influence of erect shrubs on herbs (forbs and grasses). We established 10 pairs of plots; all erect shrubs were removed in one plot of each pair (removals) and left intact in the other plot (controls). Two years later, we harvested all aboveground biomass of the herbaceous layer (herb biomass: this included graminoids, forbs, trailing shrubs, and species with a woody base but not woody stems) from the 20 plots. We tested for significant differences in understory species biomass and composition between control and removal plots and examined the influence of 25 environmental factors on species composition of the herbaceous layer. Competition intensity was measured by the natural logarithm of response ratio (ln RR) index based on herb biomass. After erect shrub removal, there was a significant increase in herb biomass, mostly due to an increase of the most .
The Effects of Stress Related Genes on Carcass Traits and Meat Quality in Pigs

The current study was conducted to investigate the relationship between stress related gene and meat quality in pigs. A total number of 212 three-way cross bred (Landrace-YorkshirexDuroc) and 38 Duroc were sampled from the Korean pig industry to determine genotype frequency of porcine stress syndrome (PSS) and heat shock protein 70 kDa (HSP70) genes and their relationship with carcass traits and longissimus meat quality. Screen of HSP70 was performed by the single strand conformation polymorphism (SSCP) technique. Based on the analysis of restriction fragment length polymorphism (RFLP) in ryanodine receptor 1 (RYR1) gene, genetic disorder of PSS was related to a mutation at 18, 168 t h (C to T) of exon 17. There was no significant difference in ultimate meat pH and backfat thickness between HSP70 Kl-AA type and -BB type in pure Duroc breed. In Landrace-YorkshirexDuroc (L-YxD) cross bred pig, our results indicated that HSP70 derivate type in Duroc had a limited effect on backfat thickness, but L-YxD type had a noticeable linkage with HSP70 K1-AA and K3-AB. This tendency was also observed in hot carcass weight where HSP70 Kl-AA and K3-AB resulted in heavier weight with 86.3 kg compared to HSP70 Kl-AB and K3-BB of 74.3 kg. Results imply that stress related HSP70 genotype has a potential association with backfat thickness and carcass weight.
Complement receptor 1 gene polymorphisms in Tunisian patients with systemic lupus erythematosus

Complement receptor 1 (CR1) is a membrane protein mediating the transport of immune complexes (ICs) to phagocytes, and at least two polymorphisms on the CR1 gene are related to erythrocyte surface density of CR1 molecules, in turn related to the rate of IC clearance from circulation. The aim of the study was to explore whether the polymorphic sites of CR1 gene in exon 22 (His 1208 Arg), and exon 33 (Pro 1827 Arg), leading to amino acid change in the protein sequence are associated with systemic lupus erythematosus (SLE) susceptibility. To investigate this association, genomic DNA of 62 SLE patients and 76 healthy blood donors were genotyped by PCR-RFLP and direct sequencing. The CR1 analysis showed no significant association of the CR1 functional polymorphisms with SLE. However, the C/G genotype in Pro 1827 Arg polymorphism was significantly associated to nephritis and to the presence of cryoglobulins/ ICs compared to C/C and G/G genotypes (OR: 3.68, 95% confidence interval [CI], 1.028 - 13.2; p = 0.038 and OR: 16.6, 95% confidence interval [CI], 3.92 - 31.1; p=0.0002, respectively). This study indicates that the analysed polymorphisms of the CR1 gene do not appear to be primarily involved in the susceptibility of SLE. Nevertheless the Pro 1827 Arg polymorphism could constitute a risk factor of gravity of the disease. Key words: Complement receptor 1, polymorphism, systemic lupus erythematosus, nephritis, cryoglobulins, immune complexes.
Choosing the Safest Route: Frog Orientation in an Agricultural Landscape

Abstract Orientation is a key component to successful movements between habitats. We hypothesized that barren agricultural landscapes hinder the ability of frogs to orient and move between habitats. Specifically, we predicted that when presented with a choice between a short route through a hostile environment and a longer but safer route, individuals would select the one that entails the least risk. During a field experiment, we translocated 104 Edible Frogs (Rana klepton esculenta) into a recently harrowed field according to two treatments: the distance to their pond of origin (5–70 m) and the distance to a wooded hedgerow (10–60 m). The frogs' ability to orient toward the pond decreased with pond distance and increased with distance to the hedgerow, but we did not detect interactive effects. In addition, frogs were more successful in orienting toward the pond under high wind conditions. We have shown that both the configuration of the landscape and weather variables influence the movement behavior of amphibians in agricultural settings, and these may have important implications for population persistence.
Role of Antioxidative System in Paraquat Resistance of Tall Fleabane (Conyza sumatrensis)

Abstract In order to explore the physiological mechanism of paraquat resistance in tall fleabane, a widespread weed in Taiwan where resistance to this herbicide has been observed since 1980, the role of the antioxidative system was assessed. The susceptible (S) and resistant (R) biotypes of tall fleabane were distinguished clearly by the relative distribution frequency of injury index caused by 78 µM paraquat. Although malondialdehyde, an indicator for peroxidation damage to the plant, in the the R-biotype was not changed, in the S-biotype malondialdehyde increased within 2 h after treatment of 50 µM paraquat. Analysis of several antioxidants and pertinent enzymes revealed that ascorbate peroxidase activity was decreased by paraquat treatment in the S-biotype; and a lower basal level of ascorbate was present in the S-biotype as well. The maintenance of a high ratio of reduced glutathione to total glutathione, coupled with a pronounced and rapid increase of glutathione reductase (GR) activity in the the R-biotype, suggests that an active reduced glutathione/oxidized glutathione (GSH/GSSG) cycle is critical to paraquat resistance of tall fleabane. The decisive contribution of a functional GSH/GSSG cycle to paraquat resistance through an enhancement of GR activity in this weed was further confirmed by an experiment of exogenous application of ascorbate.
Targeting TNF-Alpha to Elucidate and Ameliorate Neuroinflammation in Neurodegenerative Diseases

Inflammatory signals generated within the brain and peripheral nervous system direct diverse biological processes. Key amongst the inflammatory molecules is tumor necrosis factor-alpha (TNF-α), a potent pro-inflammatory cytokine that, via binding to its associated receptors, is considered to be a master regulator of cellular cascades that control a number of diverse processes coupled to cell viability, gene expression, synaptic integrity and ion homeostasis. Whereas a self-limiting neuroinflammatory response generally results in the resolution of an intrinsically or extrinsically triggered insult by the elimination of toxic material or injured tissue to restore brain homeostasis and function, in the event of an unregulated reaction, where the immune response persists, inappropriate chronic neuroinflammation can ensue. Uncontrolled neuroinflammatory activity can induce cellular dysfunction and demise, and lead to a selfpropagating cascade of harmful pathogenic events. Such chronic neuroinflammation is a typical feature across a range of debilitating common neurodegenerative diseases, epitomized by Alzheimers disease, Parkinsons disease and amyotrophic lateral sclerosis, in which TNF-α expression appears to be upregulated and may represent a valuable target for intervention. Elaboration of the protective homeostasis signaling cascades from the harmful pathogenic ones that likely drive disease onset and progression could aid in the clinical translation of approaches to lower brain and peripheral nervous system TNF-α levels, and amelioration of inappropriate neuroinflammation.
PLANKTON COMMUNITIES OF ARTIFICIAL LAKES CREATED ON IRISH CUTAWAY PEATLANDS

Abstract:Lake creation represents a major post-harvesting land-use option for industrial cutaway peatlands in Ireland, yet little is currently understood about the ecology of cutaway water-bodies, particularly at the microbiota level. The current paper describes for the first time the littoral zooplankton community in three contrasting artificial cutaway lakes and one natural bog lake. The study lakes, which were sampled on five occasions in 2003, contrasted strongly in their physico-chemical characteristics, nutrient states and trophic classifications. These trends reflected variations between sites in sediment types, water supply sources and catchment land uses. In the absence of fish, invertebrate predation by cyclopoid copepods (Tropocyclops prasinus) and cladocerans (Polyphemus pediculus) appeared to play an elevated role in structuring the zooplankton communities in the study lakes, in terms of abundance, species composition and size structure.
Review of the Family Brachypsectridae (Coleoptera: Elateroidea)

Abstract The monogeneric family Brachypsectridae is redescribed based on adults and larvae, and distribution, biology, and ideas on the phylogenetic relationships are summarized. Presently available data from both adults and larvae support previous conclusions that the family is a basal member of the Elateroidea. The four described species of Brachypsectra LeConte are reviewed. Brachypsectra moronei Branham sp. n. is described from the Dominican amber; larvae of Brachypsectra fulva LeConte, Brachypsectra lampyroides Blair, and an unnamed species from Australia are described; and keys are given to males of all described species and to known larvae. In addition, a lectotype and paratypes are designated for the six recognized syntypes of Brachypsectra lampyroides Blair, 1930.
Responses of Delphastus catalinae (Coleoptera: Coccinellidae), a Predator of Whiteflies (Hemiptera: Aleyrodidae), to Relative Humidity: Oviposition, Hatch, and Immature Survival

Abstract Delphastus catalinae (Horn) (Coleoptera: Coccinellidae) is a predator of whiteflies. It is tropical in origin. Whiteflies cause problems in agriculture in both humid and arid environments. A study was conducted to determine any effects of relative humidity on oviposition, hatching, and survival of immature D. catalinae. Comparative tests were conducted among relative humidities of 25, 35, 50, and 85% and between 10 and 85% RH. All tests were conducted at 26°C; hence, vapor pressure deficits ranged from 5.04 to 30.25 mb. The study was conducted using the B-biotype sweetpotato whitefly, Bemisia tabaci (Gennadius), as the host insect, which was reared on collard, Brassica oleracea ssp. acephala de Condolle. Egg hatch and survival to the adult stage were reduced at the lower relative humidities. At 85% RH, 99% of the eggs hatched and ≈90% of the beginning cohort survived to the adult stage. Conversely, ≈85% hatched and ≈60% survived to the adult stage at 25% RH, whereas 50% survived to the adult stage at 10% RH. Eggs required more time to develop at 10% RH (5.3 d) compared with 85% RH (4.1 d); a test was not set up to compare the developmental times for the larval and pupal stages. Weights of male and female D. catalinae were significantly reduced with a reduction in humidity. The results also suggest that density of immature D. catalinae, limited food supply, or both may affect survival and size of the ensuing adults. These results help in the understanding of the ecology of D. catalinae, and they indicate that extremes in ambient moisture can have an impact on the population of this predator.
Association of LXRA gene variants with carcass and meat quality traits in beef cattle

LXRA is an important regulator of genes involved in lipid, fatty acid and glucose metabolism in liver, and adipose tissue as well as in skeletal muscle. In this study, we discovered and evaluated the association of two SNPs (T1891C in intron 2, and A2377G in exon 3) in the bovine LXRA gene with carcass and meat quality traits in beef cattle. The T1891C SNP was significantly associated with carcass weight (CW), dressing percentage (DP), meat percent (MP) and loin muscle area (LMA) (P 0.05). These results suggested that T1891C SNP of the LXRA gene may be useful as a genetic marker for carcass and meat quality traits in beef cattle.
NOTES ON A LARGE DRAGONFLY AND BUTTERFLY MIGRATION IN NEW JERSEY

Abstract We report our observations of a large migratory flight of monarch butterflies (Danaus plexippus L.) and dragonflies (Anax junius Drury, Tramea lacerata Hagen) in central New Jersey and review what is currently known about these migratory movements in eastern North America. The migration followed the passage of Hurricane Floyd, one of the strongest coastal storms to cross New Jersey during the twentieth century. Our observations suggest that weather conditions associated with this storm may have signaled the onset of the migration we recorded.