Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Variation in Macro-Moth Abundance and Species Richness in a Lowland Fijian Forest1

Abstract: In this study we investigated temporal patterns in activity of adult macro-moths in Colo-i-Suva mixed lowland tropical forest on Fiji's largest island, Viti Levu. Moths were collected for 2 or 3 nights per month over a 12-month period using a mercury-vapor light as an attractant and collecting moths that had settled onto a white sheet for 4 hr after dusk. In total 1,397 specimens were captured, belonging to 116 species in 10 families. There were no significant relationships between total abundance and species richness with any of the climatic factors measured: average minimum and maximum daily temperature, average daily rainfall, and relative humidity. There were no obvious trends in total abundance and species richness over the 12-month monitoring period, although multivariate analysis suggested that moth assemblages in the wet and dry seasons were distinct in terms of their composition. These differences appear to be caused by some of the more-common species exhibiting clear peaks in abundance at certain times of the year, whereas other less-common species were restricted to only dry-season or only wet-season samples. We believe that this study is the first to obtain detailed information on flight periods of adult macro-moths in Fiji. Further research is required to ascertain whether patterns we have observed at this location repeat themselves in subsequent years, and to compare seasonal patterns of moths in other forests, other habitats, and other Fijian islands.
Etude des intéractions entre Sesbania rostrata, Hirschmanniella oryzae et les rendements du riz

Sesbania rostrata Brem. , est une legumineuse tropicale annuelle que l’on trouve en Afrique de l’Ouest durant la saison des pluies dans les sols hydromorphes (Berhaut, 1976). L’aptitude de cette legumineuse a noduler a la fois sur les tiges et sur les racines lui confere des potentialites fixatrices d’azote exceptionnelles. Utilisee comme engrais vert en precedent cultural du riz inonde, S. rostrata permet des augmentations de rendement du riz tres importantes (Rinaudo, Dreyfus & Dommergues, 1983; Rinaudo & Moudiongui, 1985). Les etudes effectuees par Germani, Reversat et Luc (1983) ont suggere que les augmentations de rendement observees pourraient etre egalement dues a un effet piege )) de S. rostrata vis-a-vis d‘Hirschmanniella oryzae (Van Breda de Haan), nematode pathogene du riz inonde tres frequent au Senegal (Fortuner, 1975). On a recemment mis en evidence que cet G effet piege )) etait d’une nature particuliere (Pariselle, 1987). En effet au lieu de conduire a la mort des animaux infestants, comme dans le cas des juveniles de Meloidogyne spp. sur l’arachide (Netscher, 1975), l’effet piege de S. rostrata vis-a-vis d’H. oryzae, semble consister en une simple retention. Les animaux pieges survivent et peuvent etre liberes ulterieurement, notamment a l’occasion de la decomposition des racines. Toutefois tant que le mecanisme de cette retention n’aura pas ete elucide (mecanique ou chimique), on continuera a employer provisoirement l’expression (( effet piege D. L’objet de la presente etude est d’evaluer l’importance relative de (( l’effet engrais vert )> et de (( l’effet piege B sur la productivite du riz. Materiels et methodes
Molecular phylogeny of the fern family Blechnaceae (Polypodiales) with a revised genus‐level treatment

Blechnaceae, a leptosporangiate fern family nested within eupolypods II, comprises 200–250 species, typically divided among seven to nine genera. Despite recent molecular studies of the family, it still lacks a modern taxonomic update based on broad sampling from the two centres of diversity—the Neotropics and Australasia/Oceania. To test generic circumscriptions, we have assembled the broadest dataset thus far, from three plastid regions (rbcL, rps4‐trnS, trnL‐trnF) and with taxonomic sampling focused on both major diversity centres. Our sampling includes 156 taxa and 178 newly generated sequences. We recognize three subfamilies, each corresponding to a highly supported clade across all analyses (maximum parsimony, Bayesian inference and maximum likelihood). The genera Salpichlaena, Stenochlaena and Telmatoblechnum are monophyletic, while Blechnum is polyphyletic, because Brainea, Doodia and Sadleria all nest within it. We outline and explain a plan to resolve the polyphyly of Blechnum by recognizing additional, monophyletic, segregate genera.
Constructional morphology, origin, and evolution of the gastropod operculum

Gastropod opercula are classified here on a new morphogenetic basis, which distinguishes three main types: (1) flexiclaudent spiral (mostly multispiral) operculum, the shape of which does not coincide with that of the aperture, (2) rigiclaudent spiral (usually paucispiral) operculum, the shape of which fits that of the aperture, and (3) rigiclaudent concentric operculum, also aperture-fitting. The first type fits by flexing into the aperture and is secreted when the soft parts are partly or wholly extended (i.e., when the operculum is not in a closed position). The other two types do not flex upon retraction (except at the very margin) and grow when the operculum closes over the aperture, with or without rotation. A study of opercular types at the family level confirms the systematic and evolutionary significance of opercula. Types 1 and 2 are the only ones present in archaeogastropods, Type 1 being predominant. Opercula (if present) in Neritopsina are always rigiclaudent. Within Caenogastropoda, Type 2 predominates; the only flexiclaudent spiral opercula are found in certain basal cerithioidean families. Concentric opercula are predominant in higher neotaenioglossans and exclusive in neogastropods. Except for one family, opercula in Heterostropha are always rigiclaudent spiral. Morphological, systematic, and histological criteria point to the flexiclaudent spiral operculum as the ancestral form. This leads us to propose the “periostracum shaving” model in prosobranchs to account for the origin of this kind of operculum. According to this model, in the earliest trochospiral gastropods the periostracum ceased to serve a shell-formation function at the band of overlap between whorls (the parietal band). The periostracal band was then extruded from the shell to constitute an incipient operculum, taking on the appearance of a spiral strip coiling opposite to the shell. The parietal segment of the periostracal groove migrated toward the epipodium and became independent from the rest of the mantle. The concomitant development of an opercular disc allowed the successive turns of periostracal strip to seal together. In this way, a spiral operculum emerged, coiling counterclockwise without matching the aperture shape. During the course of prosobranch evolution, rigiclaudent spiral opercula emerged several times from the ancestral flexiclaudent type, although they were always restricted to apertures with a spiral-shaped outer (labral) edge. Such opercula enlarged the range of shell morphologies for which the operculum constituted an efficient protective barrier to include those of neritoidean or naticoidean type. The onset of calcification in opercula took place with the rigiclaudent type. Concentric opercula also evolved independently from rigiclaudent spiral opercula in several gastropod groups, thus further broadening the spectrum of apertures and, hence, of shell morphologies using opercula for protection. From the standpoint of adaptation, the concentric type was probably the only one available to neogastropods having long and wide siphonal canals.
Is the mobility of stream insects related to their diet

The relationship between mobility and diet in eight common stream insects was investigated in a New Zealand mountain stream. Propensity to drift, distance drifted (return rate to the streambed) and propensity to colonize patches of stony substrata were used as measures of mobility, while diet was assessed by gut contents analysis. The eight insect species formed two well-defined groups on the basis of diet; leaf-eaters (shredders) with homogeneous diets, and grazer-collectors with more heterogeneous gut contents dominated by elements of epilithon and fine particulate detritus. With the exception of the cased caddisfly Olinga feredayi, shredders (two trichopterans, a plecopteran and a scirtid beetle) had a high propensity to drift, settled from the drift slowly, and were strong colonizers of substrate patches. In contrast, grazer-collectors (two ephemeropterans and a plecopteran) exhibited a much lower propensity to drift, returned to the streambed rapidly and colonized stony patches less readily. Despite being very similar in size, body form and mouthpart morphology, the two stoneflies had very different diets and mobility characteristics. By comparison, the two mayflies differed strongly in body form and general behaviour (crawler v swimmer) but had very similar diets and levels of mobility. We propose that the contrasting mobilities of the two groups of insects reflect differences in the distribution (patchiness) of their main foods (leaf detritus and epilithon) on the streambed.
Community organization of avian malaria parasites in lowland Amazonia: Prevalence, diversity, and specialization in a local assemblage

– PCR and DNA sequencing were used to screen for haemosporidian parasites (Haemoproteus and Plasmodium) in 2488 individual birds from 104 species and 22 families, primarily understory suboscine passerines, in a lowland Amazonian forest in Ecuador. Putative evolutionary lineages of haemosporidia were identified using the mtDNA gene cytochrome b (cyt b). Sampling was conducted over nine years and in two 1-ha plots with different levels of moisture, allowing us to assess annual variation in haemosporidian prevalence and whether prevalence is greater in the plot containing more Svensson-Coelho, L. Maria E. , 2012, UMSL, p. 8 water, which suggests it offers more suitable vector habitats. Additionally, among-species variation in prevalence was investigated and relationships between traits of hosts and prevalence of haemosporidia were analyzed in a comparative analysis. Finally, host specificity of each recovered parasite lineage was estimated and multiple indices, incorporating varying details of information, were compared. Prevalence of haemosporidia was 21.7% when years and study sites were combined and ranged from 5.6% to 91.2% among well-sampled host species. There was significant variation in prevalence among years, ranging from 14.5% in 2006 to 33.2% in 2009. There was some support for that haemosporidian prevalence increases with the level of sexual dimorphism and decreases with foraging height of a host species. Sixty-five unique cyt b haplotypes were identified, some of which were considered variation within the same evolutionary lineage. In total, 45 putative evolutionary lineages were defined based on 363 identified parasites. Fourteen haplotypes were identical to haplotypes found elsewhere, sometimes on different continents. Host specificity varied greatly among parasite lineages, and we found that an index initially developed for community phylogenetics, the standardized effect size of the weighted mean pairwise distance (SESMPD), did not correlate with sample size. This makes it useful in statistical analyses in which host specificity is considered a dependent variable, in that there is no need to control for variable sampling effort.
Combined use of dietary probiotic and acidifier for the production of antibiotic free broiler

The effect of feeding probiotic (Bio-Top; Bacillus subtilis and Bacillus licheniformis), acidifier (Sal-Stop), antibiotic growth promoter (AGP) or probiotic plus acidifier was investigated in commercial broiler. A total of four hundred Cobb 500 day-old straight run chicks were randomly distributed to 5 different dietary groups having 4 replications each. The number of birds in each replication was 20. The five dietary groups were as control (basal diet; BD), BD containing AGP at a level of 20g/100kg, BD containing probiotic at a level of 200g/100kg, BD containing acidifier at a level of 200g/100kg; and BD containing an equal amount of probiotic plus acidifier (200g/100kg). Broilers that received either probiotic, acidifier or a mixture of probiotic and acidifier (1:1) exhibited higher body weight gain, lower feed conversion ratio (FCR) and higher costeffectiveness compared with the broilers fed on control diet (P<0.05). However, feeding of diet containing both probiotic and acidifier resulted in the highest growth rate and net profit in all dietary regimens. Broilers fed on probiotic and acidifier in a mixture had FCR similar to other treatment groups. This study indicated that the diet containing probiotic-acidifier mixture seems to be more cost-effective in promoting growth performance of broilers, as an alternative to the AGP, as compared to the use of probiotic or acidifier alone in the diet Res. Agric. , Livest. Fish.3(1): 127-137, April 2016
Reproductive rates of the Red-backed Shrike (Lanius collurio) (Aves: Laniidae) in the Sofia region western Bulgaria

The nesting success of the Red-backed Shrike (Lanius collurio) was determined on the basis of 55 nests during eight consecutive years (1995-2002) from three localities in the Sofia Region, Western Bulgaria. The Mayfield'sexposure-day method was used, the egg stage was on an average 13.7 days and the nesting stage - 12 days. The established overall probability of survival was 0.309, i.e. 30.9 %. The mean clutch size was 5.43 (′ 0.78 SD, range 3-7), and the replacement clutches were significantly smaller than the first clutches. The hatching success was 50.7 %, and the fledging success - 90.3 %. A total of 56.4 % of all nests was lost, of which 67.7 % were due to predation and 32.3% to inclement weather or human interference.
Regulation of the hunting season as a tool for adaptive harvest management — first results for pink-footed geese Anser brachyrhynchus

Adjustment of hunting season length is often used to regulate harvest of waterbirds but the effects are disputed. We describe the first results of season length extension on the harvest of the pink-footed goose, which has been selected as the first test case of adaptive harvest management of waterbirds in Europe. In Denmark, the season (previously 1 September to 31 December) was extended to include January in 2014–2015 with the aim to increase the harvest and, in the longer term, reduce the population size. The total harvest in Denmark increased by 52% compared to previous years, and almost 50% of the Danish harvest was taken in the January extension. In the course of the hunting season, the proportion of adults in the bag increased. In this case, the outcomes from the first extension of season suggest that season length adjustment can be an effective tool to regulate harvest, though dependent on winter weather conditions and hunters' motivation for shooting geese.
Does environmental disturbance also influence within-stream beta diversity of macroinvertebrate assemblages in tropical streams?

ABSTRACT Riparian deforestation is a major threat to the ecological integrity of streams and aquatic biodiversity, influencing microhabitat availability and susceptibility to disturbances. Here we tested if riparian deforestation of tropical streams influenced beta diversity of macroinvertebrate assemblages, by comparing indices that weighted differentially rare and dominant taxa, and testing if nestedness in community composition increased in deforested streams. Within-stream beta diversity was higher in deforested than forested streams, mainly due to taxon loss and higher dominance. In disturbed streams, higher sedimentation in pool mesohabitats resulted in larger differences in community composition, whereas mesohabitats in forested streams were more stable.
Effects of Sulfur Dioxide and Polyvinylpolypyrrolidone on the Flavor Stability of Beer as Measured by Sensory and Chemical Analysis

A sensory panel was trained to articulate and quantify aged characters in ales and lagers. Key terms used to describe aging were hay/straw aroma, cardboard flavor, and apple/wine flavor. The panel was employed to detect the merits of adding sulfur dioxide (SO2) at levels that would be permissible without labeling in the United States. Although some benefit was observed, few of the differences were robust statistically. The observations made by the panel were compared with the observed impact of SO2 on total levels of carbonyl substances measured in the same beers. The reduction in carbonyls was similar irrespective of whether SO2 was added before or after accelerated aging regimes, whereas the limited benefits seen via sensory evaluation were only observed for sulfite addition prior to aging. It is inferred that the limited protective action of SO2 is as an antioxidant rather than as a binder of carbonyls through adduct formation. The taste panel was also used to demonstrate that the partial removal of polyphenols by polyvinylpolypyrrolidone was without any significant effect on the flavor stability of the beers studied.
Assessing Pathogens for Natural versus Laboratory Origins Using Genomic Data and Machine Learning

Pathogen genomic data is increasingly important in investigations of infectious disease outbreaks. The objective of this study is to develop methods for using large-scale genomic data to determine the type of the environment an outbreak pathogen came from. Specifically, this study focuses on assessing whether an outbreak strain came from a natural environment or experienced substantial laboratory culturing. The approach uses phylogenetic analyses and machine learning to identify DNA changes that are characteristic of laboratory culturing. The analysis methods include parallelized sequence read alignment, variant identification, phylogenetic tree construction, ancestral state reconstruction, semi-supervised classification, and random forests. These methods were applied to 902 Salmonella enterica serovar Typhimurium genomes from the NCBI Sequence Read Archive database. The analyses identified candidate signatures of laboratory culturing that are highly consistent with genes identified in published laboratory passage studies. In particular, the analysis identified mutations in rpoS, hfq, rfb genes, acrB, and rbsR as strong signatures of laboratory culturing. In leave-one-out cross-validation, the classifier had an area under the receiver operating characteristic (ROC) curve of 0.89 for strains from two laboratory reference sets collected in the 1940’s and 1980’s. The classifier was also used to assess laboratory culturing in foodborne and laboratory acquired outbreak strains closely related to laboratory reference strain serovar Typhimurium 14028. The classifier detected some evidence of laboratory culturing on the phylogeny branch leading to this clade, suggesting all of these strains may have a common ancestor that experienced laboratory culturing. Together, these results suggest that phylogenetic analysis and machine learning could be used to assess whether pathogens collected from patients are naturally occurring or have been extensively cultured in laboratories. The data analysis methods can be applied to any bacterial pathogen species, and could be adapted to assess viral pathogens and other types of source environments.
Compatibility of Nesidiocoris tenuis and Iphiseius degenerans with insecticides, miticides and fungicides used in tomato crops

Nesidiocoris tenuis (Reuter) (Heteroptera Miridae) and Iphiseius degenerans (Berlese) (Acari Phytoseiidae) are omnivorous predators commonly used in IPM in Europe. The aim of this work was to assess the side effects of eight insecticides and miticides and four fungicides widely applied in IPM on each predator species. Lethal toxicity trials were performed on sprayed and unsprayed nymphs of N. tenuis and unsprayed females of I. degenerans when exposed to freshly dried residues of the pesticides used at the label doses. Sub-lethal effects (oviposition rate) were recorded on survived females of I. degenerans. As food, untreated eggs of Ephestia kuehniella Zeller (Lepidoptera Pyralidae) or pollen were offered to N. tenuis or I. degenerans individuals, respectively. The effects were monitored for a period up to 10 days after treatment. Exposure to imidacloprid and deltamethrin residues were harmful for the sprayed nymphs of N. tenuis but moderately and slightly harmful for the unsprayed ones, respectively. Fludioxonil + cyprodinil was classified as moderately harmful and abamectin, etoxazole, fosetyl-Al, pyraclostrobin + boscalid as slightly harmful, at both ways of exposure. Finally, pymetrozine, methoxyfenozide, spriromesifen, bifenazate and azoxystrobin were classified as harmless in both application scenarios. In the case of I. degenerans, imidacloprid, deltamethrin, abamectin, etoxazole and bifenazate were classified as harmful, spiromesifen, fosetyl-Al, pyraclostrobin + boscalid and fludioxonil + cyprodinil as slightly harmful and pymetrozine, methoxyfenozide and azoxystrobin were classified as harmless. The positive control (chlorpyrifos-methyl) caused 100% mortality 1 day after treatment and the negative control (distilled water) caused no mortality in both predators. Pymetrozine and methoxyfenozide did not cause any significant adverse effect on the number of eggs laid by I. degenerans females. Azoxystrobin caused a highly negative effect although it had no acute lethal effects. In the cases of deltamethrin and abamectin delayed mortality response of N. tenuis appeared indicating that the use of an extended observation period is useful for accurate evaluation of the pesticide side effects. Taken together, the current study’s outcomes advance more effective and sustainable approaches in the compatibility of pesticides and the use of these beneficial arthropods in IPM, clearly indicating that the side effects of fungicides should not be ignored.
Understanding non-helical nuclease resistant DNAs and their roles in TLR9 mediated cellular invasion

Just as seen in proteins, secondary structures of deoxyribonucleic acids (DNA) are highly dependent on primary structure, or base sequence. Unusual secondary structures found in the non-coding regions of DNA, such as quadruplexes, cruciforms or hairpins have been investigated for their role in gene expression, cancer development, and cell death. The structural and thermodynamic stabilities of these DNAs are of special interest in that they allow us a window into complex regulation mechanisms encoded from their primary base sequence. Recent differential scanning calorimetric (DSC) studies in our laboratory have revealed an unusually stable DNA hairpin (5’-dC-dG-dC-dG-dA-dA-dGdC-dG -3’) with a melting temperature of 890C. A more rigorous examination of hairpins with loop mutations has allowed us to investigate the thermodynamic contributions of key nucleotide functional groups that play a significant role in the thermal stability of the wild type hairpin. Utilization of nuclear magnetic resonance (NMR) techniques has allowed us to link the structural characteristics that may facilitate thermal stability. These results in total have helped to provide insight into the structural and energetic contributions of the loop sequence of this highly stable DNA hairpin. Introduction Hairpin structures, or stem loop structures, are formed from the base pairing of palindromic repeats separated by a short loop sequence. These structures can form in both single stranded DNA during processes such as replication or transcription, and in double stranded DNA as cruciforms. Due to their structure, hairpin DNAs have been known to play roles in genetic expression, replication, mutations, and has even become a large