Miracle-dz/UniFAR-FTUs huggingface dataset:
The Paracladistic Approach to Phylogenetic Taxonomy

ABSTRACT The inclusion of some paraphyletic groups in a temporally and taxonomically comprehensive phylogenetic classification is inevitable because cladistic methodology is incapable of excluding the possibility that a structurally (i.e., based on the branching pattern of a given cladogram) monophyletic group contains the ancestor of another group, i.e., that it is historically paraphyletic. Paracladistics is proposed as a pragmatic synthesis of phylogenetic and evolutionary taxonomy in which true monophyly is distinguished from structural monophyly with historical paraphyly, some structurally paraphyletic groups are retained in the interest of nomenclatorial continuity and stability, and both unranked and suprageneric ranked taxon names are defined phylogenetically. Ancestral groups are structurally paraphyletic or structurally monophyletic but historically paraphyletic sets of species that are believed to contain the ancestor for the most recent common ancestor of a descendent group. Historical paraphyly is determined by considering evidence of nesting in cladistic analyses, timing of first appearances in the fossil record, polarity in character evolution, and taxa that are morphologically intermediate between groups of species. The decision to name an ancestral group is based on the same criteria as the decision to name a clade. Ancestral groups are defined in the same manner as clades, except that their descendent group(s) are designated as external specifiers. Recognizing that two supposedly monophyletic, cladistically defined sister taxa can represent ancestral and descendent groups has implications for inferring their times of origination. To illustrate the advantages of the paracladistic approach to phylogenetic taxonomy, alternative paracladistic and phylogenetic classifications of the crown group families of Nuculanoidea (Mollusca, Bivalvia) are presented.
Lichen Inventory of the Canton of Geneva, Switzerland — Large Biodiversity for a Small Canton

Abstract: Vust, M. , Clerc, P., Habashi, C. & Mermilliod, J.-C. 2015. Lichen inventory of the canton of Geneva, Switzerland — large biodiversity for a small canton. — Herzogia 28: 153–184. This paper presents a lichen inventory of the Canton of Geneva, Switzerland, based on field, herbarium and literature data. A total of 614 taxa occurred in the studied area, which represents an increase of 253 taxa (+70%) recorded for the canton. The main reason for such a huge increase in the number of taxa is that the present inventory is the first comprehensive floristic study conducted in the canton since 1862. Out of the 614 identified taxa, 18 species are recorded for the first time in Switzerland. A further 66 species mentioned for the area from the literature or herbarium specimens have been excluded. The species list includes information on the years of the oldest and the most recent collection and the respective collectors.
Chemical characteristics of dissolved organic matter in an oligotrophic subtropical wetland/estuarine

Fluorescence properties of whole water samples and molecular characteristics of ultrafiltrated dissolved organic matter (UDOM ≫ 1,000 D) such as lignin phenol and neutral sugar compositions and 13C nuclear magnetic resonance (NMR) spectra were determined along a freshwater to marine gradient in Everglades National Park. Furthermore, UDOM samples were categorized by hierarchical cluster analysis based on their pyrolysis gas chromatography/mass spectrometry products. Fluorescence properties suggest that autochthonous DOM leached/exuded from biomass is quantitatively important in this system. 13C NMR spectra showed that UDOM from the oligotrophic Taylor Slough (TS) and Florida Bay (FB) ecosystems has low aromatic C (13% ± 3% for TS; 2% ± 2% for FB) and very high O‐alkyl C (54% ± 4% for TS; 75% ± 4% for FB) concentrations. High O‐alkyl C concentrations in FB suggest seagrass/phytoplankton communities as dominant sources of UDOM. The amount of neutral sugars was not appreciably different between the TS and FB sites (115 ± 12 mg C g C>−1 UDOM) but their concentrations suggest a low level of diagenesis and high production rates of this material in this oligotrophic environment. Total yield of lignin phenols (vanillyl + syringyl phenols) in TS was low (0.20–0.39 mg 100 mg C>−1 UDOM) compared with other riverine environments and even lower in FB (0.04–0.07 mg 100 mg C−1 UDOM) and could be a result of photodegradation and/or dilution by other utochthonous DOM. The high O‐alkyl and low aromatic nature of this UDOM suggests significant biogenic inputs (as compared with soils) and limited bioavailability in this ecosystem.
Investigating global invasion routes of the harlequin ladybird (Harmonia axyridis) using mtDNA.

Although species invasions have important ecological and economical consequences, there is still much we do not understand about why only certain species become successful invaders, and what impacts they have on other species. Molecular techniques can be used to gain vital information on invasion dynamics, so as part of an ongoing study, we have used mitochondrial DNA sequence data to investigate the global invasion of Harmonia axyridis, and particularly the characteristics of the founding population(s). This will also complement data currently being gathered on microsatellite genotype and endosymbiont presence to provide a powerful dataset for understanding the invasion history of this species, and, more broadly, to attempt to determine what factors might make an invasive species successful.
Cd2+ affects the growth, hierarchical structure and peptide composition of the biosilica of the freshwater diatom Nitzschia palea (Kützing) W. Smith

Biosilica from diatoms is formed at ambient conditions under the control of biological and physicochemical processes. The changes in growth and biosilica formation through uptake of different concentrations of Cd2+ by the diatom Nitzschia palea (Kützing) W. Smith was investigated, correlating Cd2+ effects to changes in the biosilica nanostructure and the relative content of the encapsulated biomolecules. Diatom growth rates at different Cd2+ concentrations (as 1, 2, 3, 4, and 5 × 10−1 mg L−1 CdCl2) were studied in order to determine the concentrations at which sublethal effects were visible, allowing the harvest of sufficient diatom cells for further experiments. We found a clear correlation between the Cd2+ concentrations and both the nanostructure of the biosilica and content of encapsulated peptides. Cd2+ induced biosilica deformation was assessed by scanning electron microscopy and attenuated total reflectance‐Fourier Transformed Infrared Spectroscopy (FTIR), revealing that micromorphological changes in frustule features (striae, costae, pores) and nanostructural modifications (structure of the silica and conformation of the encapsulated peptides) occurred at applied Cd2+ concentrations of 2 and 3 × 10−1 mg L−1. In particular the FTIR contribution of peptides decreased at elevated Cd2+ concentrations, whereas shifts in wave number of several relevant organic bonds as C = O stretching (1765 cm−1) and possibly hydrated sulfate (1160, 1110 and 980 cm−1) were assigned. Additional analysis of the amide I band showed a relative increase in β‐sheet structure (1680–1620 cm−1) when Cd2+ concentration increased. Cadmium uptake clearly affected the molecular ordering of the biosilica in Nitzschia palea, most probably by interfering in biological or physicochemical processes involved in diatom biosilicification.
Getting Good Results from Survey Research: Part III

dedicated to getting good results from survey research. In this series, good results is a stenographic term used to define surveys that yield accurate and meaningful information that decision makers can use with confidence when conducting program evaluation and policy assessment studies. From a research perspective, a survey earns a decision maker’s confidence when it achieves “high marks” for population validity (provides a representative sample), measurement validity (provides a well-designed questionnaire), and conclusion validity (yields an accurate data analysis and report preparation strategy). More detailed information on these validity requirements was presented in the initial article in this series (McNamara, 2004a). The second article in this series was used to recommend a basic reference library that practitioners could use to understand all that is involved in the design, implementation, and evaluation of a survey. This reference library (McNamara, 2004b) was constructed to address these six knowledge domains: (1) theory of survey research, (2) practice of survey research, (3) sampling plans, (4) questionnaire design, (5) data analysis and report preparation, and (6) evaluation of published surveys.
Interactive effects of plant growth–promoting rhizobacteria and organic fertilization on P nutrition of Zea mays L. and Brassica napus L.

The organic matter supply can promote the dispersal and activity of applied plant growth–promoting rhizobacteria (PGPR), but the complementary effect of organic fertilization and PGPR application on the turnover of P is scarcely known. The effects of the application of two PGPR strains (Pseudomonas fluorescens strain DR54 and Enterobacter radicincitans sp. nov. strain DSM 16656) alone and in combination with organic fertilization (cattle manure and biowaste compost) on growth and P uptake of maize (Zea mays L.) and oilseed rape (Brassica napus L.) were investigated under semi–field conditions. Furthermore, P pools and phosphatase activities in soil and the arbuscular mycorrhizal–fungi colonization of maize roots were examined. The organic-fertilizer amendments increased the growth and P uptake of both plant species and the soil P pools. The application of the E. radicincitans strain increased P uptake of oilseed rape when no organic fertilizer was added. Furthermore, the application of both bacterial strains increased the activities of phosphatases under both plant species. Here, the effect of the PGPR application even exceeded the effect of organic fertilization. The magnitude of this effect varied between the different fertilizing treatments and between the two bacterial strains. Phosphatase activities were increased to the greatest extent after application of P. fluorescens in the unfertilized soil. Under rape increases of 52% for acid phosphatase activities (ACP), 103% for alkaline phosphatase activities (ALP), and 133% for phosphodiesterase (PDE) were observed therewith. In the unfertilized soil, the application of P. fluorescens also resulted in a strong increase of the arbuscular mycorrhizal colonization of maize. We conclude that application of PGPR can promote the P mobilization and supply of crops in P-deficient soils, however, in combination with organic fertilization these effects might be masked by a general improved P supply of the crops. Interactive effects of applied bacterial strains and organic fertilization depend on the sort of organic fertilizer and crop species used.
Enhanced production of pullulan by two strains of A. pullulans with different concentrations of soybean oil in sucrose solution in batch fermentations

Aureobasidium pullulans is a microorganism that produces pullulan (homopolysaccharide) extracellularly through a fermentation process with sugars (maltose, d-xylose, sucrose and starch) as its carbon source. Pullulan is a linear polysaccharide of D-glycopyranose containing (1 ®4)-a and (1 ® 6)-a linkages at a 2:1 ratio, is highly soluble in water and has various applications in the food, packaging, film and pharmaceutical industries. Lipids, primarily oils, having antifoaming properties as well as nutritional particularities, are considered an essential additional carbon source for the growth of microorganisms, especially fungi. These nutrient sources are very important for the maintenance of microorganism cells. In fact, these positive effects are only achieved when the right source is added at both the right time and the right dosage into the broth of the fermentation process. In this research on pullulan production with the strains NRRL Y-6220 and NRRL Y-2311-1, it was found that the latter strain achieved better results for undesirable pigment formation, pullulan titer, time of maximum production (96 hours) and biomass yields than strain NRRL Y-6220, which also showed suitable results for biomass yields and cell morphology. However, the dark pigmentation of the strain NRRL Y-6220, formed through the process, makes its application unacceptable for foods and pharmaceuticals. Strain NRRL Y-2311-1 was shown to be a promising potential industrial microorganism, whose applications should be studied more in depth.
Yield performance of oyster mushroom (Pleurotus ostreatus) on different substrates

An experiment was conducted at Mushroom Lab of Horticulture Centre under Department of Agricultural Extension (DAE), Khairtala, Jessore to determine the performance of different substrates on the yield of oyster mushroom ( Pleurotus ostreatus ). Sugarcane bagasse, sawdust, and coconut coir individually and their combinations were used as substrates. The experiment was laid out in Completely Randomized Design (CRD) with five replications. Data were taken from 1st and 2nd flush of different growth and yield attributes of mushroom. The maximum number of effective fruiting bodies was obtained from sawdust (40) and the lowest number (31.6) from combination of sawdust and coconut coir (1:1). In the 1st flush, the maximum weight of individual fruiting body was observed in coconut coir and minimum in sawdust. The highest biological (186.06 g) and economic yield (180.64 g) were obtained from coconut coir and the lowest from sugarcane bagasse. The maximum and minimum harvest index was found in 1st flush at coconut coir and combination of sawdust and sugarcane bagasse (1:1), respectively. Most yield attributes were found higher in coconut coir. Economic yield was positively correlated to number of effective fruiting bodies, pileus diameter, and biological yield. DOI: http://dx.doi. org/10.3329/bjar.v38i4. 18946 Bangladesh J. Agril. Res. 38(4): 613-623, December 2013
Does an early aversive experience to humans modify antipredator behaviour in adult Rock partridges?

One factor critical to the success of a captive-bred animal in nature is its antipredator behaviour, which is often either inadequate or almost absent under intensive rearing conditions. In this study we evaluated the effects of an early stressful experience (i.e. a rough visual and acoustical contact with humans) on the antipredatory reactions of adult Rock partridges. During the 1st week after hatching, one group of Rock partridges was exposed to repeated human intrusions into its aviary, and another undisturbed group served as control. Five months later, we observed that the escape reaction to an approaching human was elicited at greater distances in the experimental group than in the control one. On the other hand, the repeated disturbance by a human did not affect the reactions to raptor and fox dummies, which were however appropriate to the predator. In the Rock partridge the effect of this early aversive interaction was thus stimulus-specific, increasing defensive response only to the predator they experienced, although avoidance behaviour was not generalized to further common predators of these game-birds. This study stresses the importance, in farm reared birds, of the early experience of specific aversive stimuli to develop longterm appropriate responses to predators, and thus to increase the probability of survival after release in nature.
Morphological variation in Norops capito (PETERS, 1863), a wide-spread species in southeastern Mexico and Central America

Pholidosis, morphometrics, and hemipenis morphology of the Central American anole Norops capito (PETERS, 1863) are described. Head scalation and hemipenis illustrations and a distribution map are provided. No individual or geographic variation is evident in hemipenis morphology among the material studied. There is no evidence for cryptic species among the various populations of Norops capito.
Plant microarray for gene expression profiling and their application

Microarray can parallel quantification of large numbers of genes and promises to provide detailed insight into cellular processes involved in the regulation of gene expression. In plants, microarray for gene expression profiling should provide an important way for understanding of gene functions and signaling networks that operate plants growth and development, respond to biotic and abiotic stresses, important agronomic characters. This review focuses on the application of microarray for gene expression profiling in plants. Moreover, development and application of tobacco microarray is also summarized. This review will provide useful information for better application of plant microarray in studies of gene function and regulation mechanism.
Differential Responses of Anabaena Variabilis and Nostoc Linckia to Salt Stress and Their Role in Improvement the Growth Conditions of Some Salt Stressed Plant Seedlings

Two Species of cyanobacteria: namely, Anabaena variabilis and Nostoc linckia were isolated from Baltem and Sedi-Salem (saline-sodic soils), respectively (Kafr El-Sheikh Governorate, Egypt). A. variabilis was able to grow in salinity level between 4-6 g L -1 NaCl; above 6 g L -1 NaCl the growth rate was relatively constant till 10 g L -1 NaCl. Over 10 g L -1 NaCl, the growth rate declined. Results indicated that A. variabilis was able to utilize NaCl between 1-10 g L-1. On the other hand, N. linckia had a wide range of salinity tolerance. Whereas, the growth rate increased gradually from 1- 4 g L -1 NaCl and more than 4 till 20 g L-1 NaCl the pattern of growth was nearly stable. N. linckia was able to withstand a wide range of salinity but it had no good ability to utilize NaCl. The results indicated that the addition of A. variabilis led to significant increase of shoot and root length as well as, significant decrease of proline content of bean, zea and barley seedlings grown in saline environment, respectively. Also, the presence of alga caused a significant increase in chlorophyll a content of zea seedlings as well as, the germination percentage of barley seedlings in as compared to control ones. N.linckia caused a significant decreasing in proline content of bean, zea and barley seedlings, while, it caused an increasing of both chlorophyll a content of zea and shoot length of barley seedlings as compared with control.
Neuroblastoma Cell Lines

2 Historical Introduction Neuroblastoma accounts for approximately 9% of all childhood cancers, occurring once out of 8,000 live births. This results in an annual incidence of approximately 1 in 10 5 children less than 15 years of age worldwide (1). The median age at diagnosis is approximately 22 months with over one-third diagnosed at less than 1 year of age and over 88% diagnosed by the age of 5. Some studies indicate a bimodal age distribution with one peak at approximately 1 year and the second between 2 and 4 years (2). In children under 5 years of age, neuroblastoma usually presents in the abdominal region involving the sympathetic ganglia of the paraspinal region or the adrenal gland. In infants under a year of age there is a higher incidence of tumors in the thoracic region. In Stage I and II neuroblastoma where tumor is confined to the originating organ or surrounding tissue, the prognosis is quite favorable. However in Stage III and IV NB where tumor extends beyond the midline, is metastatic or involves bony lesions the prognosis for patients is quite poor. It is possible that early stage disease (Stage I,II, IVS) is a distinct entity from late stage (Stage III, IV) disease because their response rate to therapy and their molecular genetic and biologic characteristics are distinct. Of all human tumors Neuroblastomas have one of the highest rates of spontaneous tumor regression. This is primarily due to an unusual presentation of neuroblastoma called Stage IVS that occurs in infants under a year of age who present with widely disseminated disease that typically resolves with minimal therapy. Stage IVS tumors have intrigued scientists studying neuroblastoma who feel that an understanding of this disease entity will provide clues to the more devastating presentations of neuroblastoma. A report of familial NB which affected 4 of 5 siblings lead Knudson and Meadows to formulate a "Mutation Model for Neuroblastoma" in 1976 (3). This model proposed that all NB derive from a single cell that is transformed from a normal cell by two mutations; one that may arise prezygotically in the germline and the second that arises in a somatic cell of the target tissue. This "two-hit" model of tumor development was hypothesized to describe the genetics of retinoblastoma tumors (4) and subsequently was verified with the identification of Rb, the retinoblastoma tumor suppressor gene. While the probability of tumor occurrence would …
Disease Salience Effects on Desire for Affiliation With In-Group and Out-Group Members: Cognitive and Affective Mediators

This study tested the hypothesis that threats related to infectious diseases would make persons less willing to affiliate with out-groups and that feelings of disgust and beliefs about the out-group members would mediate this effect. To test this hypothesis, American participants of European descent were presented with either a disease threat or control threat. Then they were shown a photograph of someone of the same race or different race. Participants were asked to indicate whether they would avoid the target person and to state their emotional and cognitive responses to the person. As predicted, disease salience decreased the desire to affiliate with out-group members, and both feelings of disgust and beliefs about the infection risk posed by the target person mediated this relationship.
Unravelling the historical biogeography and diversification dynamics of a highly diverse conifer‐feeding aphid genus

Scenarios of aphid evolution suggest that adaptation to host plants plays a major role in aphid diversification. It is therefore commonly assumed that host association has also shaped the biogeographical patterns of aphids; particularly, it has been hypothesized that the intercontinental disjunctions observed in the Holarctic for many aphid groups resulted from the disappearance or migration of their hosts. We explored this hypothesis for the conifer‐feeding genus Cinara, one of the most diverse and widely distributed aphid genera in the Holarctic.
Valgine beetles : a preliminary review of the genera, with descriptions of two novelties

Heterovalgus popei (Java) and Tibiovalgus perplexus (Cameroun), new genera and species, are described and inserted in a key to the known genera of Valginae. A checklist of valgine genus-group names is given, including details about type-species, synonymies, number of species per genus, and occurrence in zoogeographical regions. For six old genus-group names type-species are designated.