Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying compartments in presence–absence matrices and bipartite networks: insights into modularity measures

The identification of compartments (i.e. clusters of overlapping species ranges across an environmental gradient) is an important methodological challenge for biogeographical studies. Recent developments in network theory offer promising perspectives on this issue using the measurement of modularity. A presence–absence matrix is modular if particular subgroups of species are mainly linked to particular subgroups of sites. Modularity is still rarely considered in biogeographical studies. Here, I compare different modularity indices to investigate which is the most appropriate for studying presence–absence matrices and similar types of networks, such as bipartite networks.
Molecular characterisation of the bacterial communities in cabbage aphid (Brevicoryne brassicae) and their associated fitness effects

xv 1. General Introduction 1-35 1.1 Aphids as Successful Crop Pests. 1-8 1.1.1 The cabbage aphid. 1-2 1.1.2 Aphid damage to crops. 3-5 1.1.3 The life cycle of aphids. 6-7 1.1. 4 Factors controlling aphid population dynamics. 7-8 1.2 Parasitoid Biology and Their Role as Aphid Natural Enemies. 8-15 1.2. 1 Parasitoid life history. 8-10 1.2. 2 Parasitoids as biological control agents of aphids. 10-12 1.2. 3 Abiotic and biotic factors influencing the aphid–parasitoid interaction. 13-15 1.3 The Symbiotic Bacteria of Aphids. 15-33 1.3. 1 Symbiosis in aphids and other insects. 15-17 1.3. 1.1 The primary symbiont of aphids Buchnera aphidicola. 18-20 1.3. 1.2 The secondary symbionts of aphids. 20-21 1.3. 2 Co-diversification of primary symbiotic bacteria with aphids. 22-23 1.3. 3 Transmission patterns of secondary symbiotic bacteria in aphids. 23-24 1.3. 4 Serratia symbiotica, thermal tolerance and the primary symbiosis. 25-26 1.3. 5 Secondary symbionts and the aphid–plant interaction. 26-29 1.3. 6.1 Secondary symbionts and resistance to parasitism. 30-31
Molecular Characterization of a Diverse Maize Inbred Line Collection and its Potential Utilization for Stress Tolerance Improvement

A diverse collection of 359 advanced maize (Zea mays L.) inbred lines from the International Maize and Wheat Improvement Center (CIMMYT) and International Institute for Tropical Agriculture (IITA) breeding programs for drought, low N, soil acidity (SA), and pest and disease resistance was genotyped using 1260 single nucleotide polymorphism (SNP) markers. Model-based population partition, neighbor-joining (NJ) clustering, and principal component analysis (PCA) based on the genotypic data were employed to classify the lines into subgroups. A subgroup largely consisting of lines developed from La Posta Sequia (LPS) consistently separated from other lines when using different methods based on both SNP and SNP haplotype data. Lines related by pedigree tended to cluster together. Nine main subsets of lines were determined based on pedigree information, environmental adaptation, and breeding scheme. Analysis of molecular variance (AMOVA) revealed that variation within these subsets was much higher than that among subsets. Genetic diversity and linkage disequilibrium (LD) level were tested in the whole panel and within each subset. The potential of the panel for association mapping was tested using 999 SNP markers with minor allelic frequency (MAF) ≥ 0.05 and phenotypic data (grain yield [GY], ears per plant [EPP], and anthesis to silking interval [ASI]). Results show the panel is ideal for association mapping where type I error can be controlled using a mixed linear model (Q + K). Use of pedigree, heterotic group, and ecological adaptation information together with molecular characterization of this panel presents a valuable genetic resource for stress tolerance breeding in maize.
Historical trends in productivity of 120 Pacific pink, chum, and sockeye salmon stocks reconstructed by using a Kalman filter

Temporal trends in productivity of Pacific salmon (Oncorhynchus spp.) stocks are important to detect in a timely and reliable manner to permit appropriate management responses. However, detecting such trends is difficult because observation error and natural variability in survival rates tend to obscure underlying trends. A Kalman filter estimation procedure has previously been shown to be effective in such situations. We used it on a Ricker spawner–recruit model to reconstruct indices of annual productivity (recruits per spawner (R/S) at low spawner abundance) based on historical data for 120 stocks of pink (Oncorhynchus gorbuscha), chum (Oncorhynchus keta), and sockeye (Oncorhynchus nerka) salmon. These stocks were from Washington, British Columbia, and Alaska. The resulting estimated temporal trends in productivity show large changes (on average 60%–70% differences in R/S and average ratios of highest to lowest R/S between 5.4 and 7.9 for the three species). Such changes suggest that salmon stock asses.
EFFECTS OF CITRIC ACID ON GROWTH PERFORMANCE AND NUTRIENT RETENTION OF BROILER CHICKEN FED DIETS HAVING TWO LEVELS OF NON-PHYTATE PHOSPHORUS AND RICE BRAN

Citric acid has been reported to increase utilization efficiency of dietary phytate-bound phosphorus and protein. Objective of this study was to determine the effects of citric acid on growth performance and nutrient retention of broiler chickens fed diets having two levels of non-phytate phosphorus and rice bran. Giving a completely randomize design in 2 × 2 × 2 factorial arrangement, 144 broiler chicks in 48 pens received one of the eight experimental diets containing two levels of dietary rice bran (20% or 30%), citric acid (0% or 2%) and non-phytate phosphorus (0.25% or 0.35%) ad libitum from day 21 to 42. Retention of nitrogen, phosphorus, mineral and dry matter was determined using a total collection trial. Feed intake, weight gain, feed conversion ratio and weights of feather, liver, gizzard and pancreas were not significantly (P>0.05) affected by the levels of dietary rice bran, citric acid, or non-phytate phosphorus levels. Retention of nitrogen, phosphorus or dry matter were not significantly affected (P>0.05) by the levels of dietary rice bran, citric acid, non-phytate phosphorus or their interactions. 2% citric acid improved the retention of mineral with 30% rice bran compared to diets with 20% of rice bran. There was no significant difference (P>0.05) in tibia ash when diet contained 20% or 30% rice bran. A significantly (P<0.05) higher tibia ash content was observed when diets had 2% of citric acid with 0.35% of non-phytate phosphorus. It is concluded that 30% rice bran had no adverse effects on growth performance of broiler chicken from day 21 to 42. 2% citric acid produces no beneficial effects at dietary rice bran levels of 20 or 30% or non-phytate phosphorus levels of 0.25 or 0.35%.
A partial review of the European Magelonidae (Annelida: Polychaeta): Magelona mirabilis redefined and M. johnstoni sp. nov. distinguished

The identification of magelonids with mucronate chaetae on chaetiger 9 has long been confused. Until 1977 all corresponding European specimens were erroneously referred to Magelona papillicornis; a Brazilian species. Since then, but without any detailed study, the name M. mirabilis (originally given to a species from Scotland) has been widely employed. However, in recent years, it has become clear that two morphologically similar species coexist in European waters. Magelona mirabilis is redescribed and a neotype designated, and M. johnstoni sp. nov. is formally distinguished. Following re-examination of the other five species present in the region, a dichotomous key and a synoptic table of characters is provided for all seven European species.
Sustaining Leadership

E DUCATIONAL CHANGE is rarely easy, always hard to justify, and almost impossible to sustain. Educational change that enhances deep learning among students is particularly problematic, and sustaining such change over time has presented severe challenges for education reformers. Discussions of the sustainability of educational change try to address these challenges, but they often trivialize the idea of sustainability by equating it with maintainability — with how to make change last. Here we develop deeper meanings of “sustainability” and examine the extent to which efforts to sustain change are in tune with the ecological origins of the concept.
Reports ON PLAGUE INVESTIGATIONS IN INDIA

THE Advisory Committee, appointed by the Secretary ofState for India, the Royal Society and the Lister Insti-. tute, acting in conjunction, to inquire into some of the problems concerning plague, has now presented a further report, which, like the first, is published as a special number of the Tournal of Hygiene. ' An analysis of the first report was published in the BRITISH MEDICAL JOURNAL of October 20th, 1906, p. 1045 et seq. The members of the Commission are:
Tackling experimental colisepticaemia in broiler chickens using phytobiotic essential oils and antibiotic alone or in combination

Summary This study was designed to compare the efficacy of a phytobiotic containing a mixture of essential oils of Oreganum aetheroleum and an antibiotic containing ciprofloxacin as an active principle for the treatment of experimental Escherichia coli ( E. coli ) infection in broiler chickens. Two - hundred - day - old broiler chickens were divided into 5 equal groups. The 1st group was neither challenged nor treated, but groups 2, 3, 4 and 5 were challenged with E. coli . The 2nd group was challenged with E. coli only, while the 3rd, 4th and 5th group were treated with phytobiotic, ciprofloxacin and phytobiotic and ciprofloxacin combinations, respectively. Results confirmed significant (P<0.05) improvement of productive performance parameters, reduction in signs, mortalities, post mortem lesions and bacterial re-isolation, enhancement in cell mediated and humoral immune responses, reduction in levels of liver and kidney function tests and increase in the total protein and globulin levels in challenged chickens treated with either essential oils or ciprofloxacin compared to challenged non treated chickens. Moreover, best significant (P<0.05) results in all measured parameters were detected in the group treated with the combination in comparison with those exposed to single treatments. In conclusion, a mixture of essential oils of
Biogeographic studies on the spittlebug Philaenus signatus Melichar, 1896 species group (Hemiptera: Aphrophoridae) with the description of two new allopatric species.

Etudes sur la biogeographie du groupe d'especes Philaenus signalas Melichar 1896 (Hemiptera: Aphrophoridae) et description de deux nouvelles especes allopatriques. - De nombreux specimens appartenant au genre Philaenus et originaires de toute la region mediterraneenne ont ete mesures apres separation des sexes, et les genitalia des mâles disseques pour examen. Le groupe P. signatus comprend trois especes bien caracterisees par la structure des genitalia et bien separees du point de vue geographique, dont deux nouvelles especes qui sont decrites ci-apres. La distribution de P. signatus recouvre la peninsule balkanique, la partie nord de la Mediterranee orientale et l'Anatolie. P. italosignus, n. sp. est present uniquement dans la moitie sud de la peninsule italique, y compris la Sicile. P. maghresignus, n.sp. se trouve en Espagne du sud et en Afrique du nord-ouest. La repartition de toutes les especes connues du genre Philaenus et leurs caracteres d'identification sont regroupees sur une carte et une figure ci-incluses. Quelques notes sur l' espece P tarifa decrite comme nouvelle dans une autre publication, completent ce-travail.
Spectrum of Morphological Changes in Tuberculous Lymphadenitis

The results of our study showed that in early lesions there is suppuration and caseation necrosis. As immunity increases first ill defined (in exuadative lesions) and then well defined granulomas are formed. Neutrophils as nuclear dust are present in early lesion and they are absent in late lesion when granulomas are well defined. Lymphocytes are maximum in late granulomas phase and in intense caseous phases they are absent. Plasma cells are present with well defined granulomas.
Effect of Potassium, Magnesium, and Calcium Deficiencies on Nitrogen Constituents and Chloroplast Components in Citrus Leaves

ADDITIONAL INDEX WORDS. amino acids, Citrus volkameriana, leaf chlorosis, nitrate reductase, proline, RuBPcase ABSTRACT. The chlorotic appearance of mineral-deficient citrus leaves presumably reflects degradative changes in chloroplast components, most of which have nitrogen as a principal constituent. To examine this assumption the size of some major nitrogen pools, the SDS-PAGE pattern of soluble and chloroplast membranal proteins, and the activities of nitrate reductase and ribulose bisphosphate carboxylase (RuBPcase) were determined in leaves of rough-lemon ( Citrus volkameriana Ten. & Pasq) plants grown hydroponically for 3 to 10 months under K, Mg, and Ca deficiencies. Plants grown under minerally deficient conditions produced less biomass. Leaves developing under K, Mg, and Ca-deficient conditions had significantly reduced concentrations of the respective elements. Chlorophyll levels of the chlorotic Mg and Ca-deficient leaves were lower than those of control leaves but chlorophyll a/b ratios were not markedly different. Calcium deficiency caused significant decreases in total nitrogen, nitrates, and the free amino acid pool. Proline which is the major component of the free amino acid pool decreased by 82.5%. Calcium-deficient leaves had significantly lower nitrate reductase and RuBPcase activities. The level of RuBPcase holoenzyme and its subunits were also reduced. Protein levels of K, Mg, and Ca-deficient leaves were not significantly altered. The SDS-PAGE patterns of soluble and chloroplast membranal proteins did not reveal major qualitative changes. In conclusion, the data do not demonstrate a general close link between chlorosis of minerally deficient citrus leaves and nitrogen metabolism. Calcium deficiency seems to specifically interfere with early stages of nitrogen assimilation and free amino acid accumulation but the metabolic integrity of the leaf is apparently maintained even under severe nutritional stress conditions.
Apoptosis: Current therapeutic approach in retinitis pigmentosa

Apoptosis is a genetically programmed mechanism of cell death in which the cell activates a specific set of instructions that lead to the deconstruction of the cell from within. Retinitis pigmentosa (RP) represents a group of hereditary retinal degenerations principally characterized by progressive rod-dominant photoreceptor degeneration in the initial stage and eventual cone photoreceptor degeneration in later stages. RP has been known to be initiated by photoreceptor apoptosis as a final common pathway at the cellular level, irrespective of gene mutations, and apoptosis can thus be considered as a therapeutic target. The goal of this review is to discuss the rationale behind the recent suggestions that calcium channel blockers may be useful in the treatment of retinitis pigmentosa. The National Center for Biotechnology Information (NCBI) at the US National Library of Medicine (NLM) was searched using the terms “Calcium channel blockers in retinitis pigmentosa”. It is time to conduct a randomized controlled trial to provide direct evidence of the effectiveness of specific type calcium channel blockers in lowering progression of RP. New intervention as calcium channel blockers usage to prevent retinitis pigmentosa progression remains an important strategy to limit the morbidity of this significant health problem. Key words: Apoptosis, retinitis pigmentosa, photoreceptors degeneration, calcium channel blockers, therapeutic effect.
Record of egg parasitoid in Erinnyis alope (Drury, 1773) (Lepidoptera: Sphingidae) in Brazilian cassava crops

Abstract: Parasitoids of genus Trichogramma (Hymenoptera: Trichogrammatidae) are one of the most studied groups of insects in the world because they function as biological control agents when the pest is still in the early developmental stages, eliminating it before the injury shows up. Therefore, it was investigated the occurrence of egg parasitoids of Erinnyis spp. collected during a technical visit at cassava plantations located in Fazenda Jucara, Murici, Alagoas. Samples were transported to the Centro de Ciencias Agrarias, Universidade Federal de Alagoas (CECA, UFAL) in Rio Largo, AL, for observations. Caterpillars hatched from non-parasitized eggs were reared until adult emergence, when they were killed and mounted. Parasitoids that emerged from parasitized eggs were placed inside plastic microtubes with 70% alcohol. Both hosts and parasitoids were sent for identification to the Laboratory of Taxonomy, at the Departamento de Entomologia e Acarologia, ESALQ, USP, Piracicaba, SP, where the specimens were preserved in the Institution’s Museum. From the samples, Erinnyis alope (Drury, 1773) (Lepidoptera: Sphingidae) and Trichogramma marandobai Brun, Moraes & Soares, 1986 (Hymenoptera: Trichogrammatidae) were collected from cassava plantations, at Alagoas State. This is the first record of occurrence of E. alope in the State and its parasitism by T. marandobai in Brazil. Key words: Alope Sphinx Moth, Euphorbiaceae, Manihot esculenta, Trichogramma
Physiological limitation of phytoplankton photosynthesis in the eastern equatorial Pacific determined from variability in the quantum yield of fluorescence

On a transect study in the eastern equatorial Pacific, from the high-nutrient, low-chlorophyll tropical waters to the oligotrophic subtropical waters, we determined the variability in the maximum change in the quantum yield of chlorophyll fluorescence (A&,) by means of a fast repetition rate fluorometer. A& is a quantitative measure of photochemical energy conversion efficiency in photosystem 2, the variability of which is determined by the functional organization of the photosynthetic apparatus. The results revealed that A&,, was relatively low throughout the nutrient-rich equatorial waters, providing unequivocal evidence for physiological limitation of photochemical energy conversion efficiency in the natural phytoplankton populations. Shipboard enrichment studies showed that A&, increased following addition of nanomolar concentrations of inorganic iron as well as aerosol dust added at similar iron concentrations. This response reflects an iron-induced repair of photosystem 2 function in the enclosed bottle community. Low A&, at the top of the Equatorial Undercurrent indicated that the amount of iron upwelled to the surface was insufficient . t,o repair photosystem 2 function. Our results strongly suggest that iron availability limits photochemrcal energy conversion efficiency and is the principal mechanism controlling rates of photosynthesis and growth in the nutrient-rich equatorial Pacific.
Saami reindeer herders cooperate with social group members and genetic kin

Cooperative behaviors evolve by ultimately increasing the inclusive fitness of performers as well as recipients of those behaviors. Such increases can occur via direct or indirect fitness benefits, theoretically explained by reciprocal altruism and kin selection, respectively. However, humans are known for cooperating with individuals who are not necessarily genetic relatives, which seemingly precludes kin selection as an explanation. Here, we aim to quantify the relative importance of kinship and social group membership as mediators of cooperative behavior. Using an experimental gift game, we test whether indigenous Saami reindeer herders in Norway give gifts to genetic relatives or to members of their cooperative herding group (the “siida”) or both. Membership of the same siida strongly increased the odds of gift giving. Kinship had a smaller, albeit positive, effect. Gifts were not preferentially given to younger family members, contrary to predictions relating to intergenerational resource transfers as a form of parental investment. These patterns suggest that social grouping can be at least as important as genetic factors in mediating cooperative behavior in this population. This is likely to reflect the importance of herding groups in day-to-day subsistence.
Population Biology of an Intertidal Dorid Nudibranch (Onchidoris muricata) in the Southern Gulf of Maine, U.S.A.: Changes in Phenology Due to an Invasive Prey?

Abstract. The invasion of the bryozoan Membranipora membranacea to the Gulf of Maine in 1987 eventually provided an additional prey resource to the dorid nudibranch Onchidoris muricata (Müller, 1776). The impact of this novel prey on the population and reproductive biology of O. muricata was investigated at an intertidal site in the southern Gulf of Maine from January 2005 to October 2009. Nudibranchs were found associated with a variety of bryozoans, with a seasonal shift from Electra pilosa (December to May) to M. membranacea (June to November). Juveniles (< 3 mm) were found in all months except May, June, and July and mature nudibranchs were present in all months. Copulating pairs were observed between lanuary and July and spawn masses were found between March and September on the undersides of rocks usually attached to the surface of bryozoans. The population structure and reproductive phenology of O. muricata at this intertidal site shows changes from historical reports. Whether adaptive change of this native predator to invasive prey species is occurring remains a possibility and emphasizes the need for long-term studies documenting native predators and invasive prey for possible changes in species interactions.
Long‐term pigment dynamics and diatom survival in dark sediment

In order to investigate survival of diatoms and long‐term pigment dynamics in dark sediment, we incubated samples of homogenized, sieved, tidal‐flat sediment for 1 yr in darkness. Microscopic observations revealed that some diatoms survived the full year in darkness and retained their pigments. Concentrations of the diatom‐specific phospholipid‐derived fatty acid (PLFA) 20:5ω3 indicate that these survivors represented only a small fraction of the original diatom community, probably no more than a few percent. Consequently, the effect of pigment retention in living diatoms on the overall pigment dynamics was negligible. The photosynthetic potential of the surviving diatoms was further investigated by re‐exposing the sediment to light in the presence of 13C‐bicarbonate. Rapid 13C fixation into algal PLFAs at a level similar to that in sediment freshly collected from the field indicates that surviving diatoms fully retained their photosynthetic capacity. Concentration dynamics of photosynthetic pigments generally reflected degradation of two different pools with clearly different loss rates. Losses during the first 1–2 months of the experiment (half lives of 6–22 d) reflected degradation of fresh algal material, while losses during the rest of the experiment reflected much slower degradation of more refractory pigment pools (half lives of ≥ 1 yr). Individual pigments showed distinctly different labilities, with losses ranging from 0% to 86% over the full year. The order of overall loss was fucoxanthin > chlorophyll c > chlorophyll a > diadinoxanthin > pheophorbide > pheophytin > diatoxanthin.