Miracle-dz/UniFAR-FTUs huggingface dataset:
Extinction, colonization, and metapopulations: environmental tracking by rare species

Extinction and metapopulation theories emphasize that stochastic fluctuations in local populations cause extinction and that local extinctions generate empty habitat patches that are then available for recolonization. Metapopulation persistence depends on the balance of extinction and colonization in a static environment. For many rare and declining species, I argue (1) that extinction is usually the deterministic consequence of the local environment becoming unsuitable (through habitat loss or modification, introduction of a predator, etc.); (2) that the local environment usually remains unsuitable following local extinction, so extinctions only rarely generate empty patches of suitable habitat; and (3) that colonization usually follows improvement of the local environment for a particular species (or long-distance transfer by humans). Thus, persistence depends predominantly on whether organisms are able to track the shifting spatial mosaic of suitable environmental conditions or on maintainance of good conditions locally. Las teorias sobre extincion y metapoblaciones enfatizan que fluctuaciones estocasticas en poblaciones locales causan la extincion y que la extincion total genera parches de habitat vacios que estan entonces disponibles para la recolonizacion. En un ambiente estatico, la persistencia de la metapoblacion depende del balance entre extinciones y colonizaciones. Yo sostengo que para muchas especies raras y en declinacion, (i) usualmente la extincion es una consecuencia deterministica de un ambiente local que se hace inadecuado (e.g., pedida o modificacion del habitat, introduccion de un predador, etc.); (ii) usualmente, el ambiente local permanece inadecuado luego de la extincion local, por consiguiente, solo raramente, extinciones locales generan parches vacios de habitats adecuados; y (iii) usualmente la colonizacion viene despues de la mejora de las condiciones ambientales para una especie en particular (o la transferencia a larga distancia por humanos). Por consiguiente, la persistencia depende predominantemente de que los organismos puedan adaptarse al mosaico espacial cambiante de las condiciones ambientales o de que se mantengan buenas condiciones locales.
CULTIVATION‐INDEPENDENT SPECIES IDENTIFICATION OF DINOBRYON SPECIES (CHRYSOPHYCEAE) BY MEANS OF MULTIPLEX SINGLE‐CELL PCR 1

With the discovery of a high molecular diversity of protists, a discrepancy between morphological and molecular species richness estimates became apparent. Solving the current concerns requires a comparative analysis of different sequences combined with morphological analyses of single cells originating from preserved field samples. We refined a single‐cell PCR (SC‐PCR) protocol for analyzing cells from field samples preserved with Lugol’s iodine solution. We linked microscopic screening with multiplex PCR targeting the SSU rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), and the mitochondrial cytochrome oxidase 1 (CO1) in a single PCR reaction. Using this method, we investigated the intraspecific molecular variation in Dinobryon populations originating from two lakes in the Salzkammergut area of Austria. All investigated genetic markers showed two separated clusters within the investigated populations of Dinobryon divergens O. E. Imhof, indicating a reproductive isolation of the two coexisting populations. Based on these findings, we describe a lineage, which is morphologically similar to D. divergens but, based on the molecular data, is reproductively isolated.
Modelling the time-temperature relationship in cold injury and effect of high temperature interruptions on survival in a chill-sensitive collembolan.

1. Temperature- and time-dependent mortalities were studied and modelled in insects exposed in regimes with constant and alternating temperatures. In these experiments, freezing was not a cause of death. 2. Survival rates at a range of constant low temperatures (– 5 to + 1 °C) and for different exposure periods (1–14 days) were measured in the summer acclimated springtail Orchesella cincta. 3. Daily interruptions of the cold exposure with short intervals at high temperature reduced mortality or slowed the increase of mortality. This effect was stronger at higher temperature (19 vs 5 and 12 °C) and increased with the duration of the interruption (0·25–2 h). 4. The injury was reversible when the cold exposure was limited to 2 days. 5. Survival in desiccated animals (14% water loss) was reduced. 6. It is suggested that the mortality of summer acclimated springtails is caused by a complex metabolic disorder and membrane changes at low temperatures.
The effects of thermal and light exposure on the development of broiler chicken leg musculature

Modified incubation factors affect skeletal musculature development of broiler chickens during embryonic and postnatal periods of development. These changes appear to have great influence on the proliferation of myoblasts and muscle growth after hatching. In this study, the histomorphological and -morphometric parameters of broiler chicken leg musculature, after thermal and light treatments during embryogenesis, were examined. The applied treatments included thermal manipulation (exposure of fertilized eggs to increased temperature), light manipulation (exposure of fertilized eggs to monochromatic green light) and simultaneous thermal and light manipulations. Following the specific parameters that were observed, it was determined that in the late postnatal period of development, treated groups have a larger diameter and smaller nucleocytoplasmic ratio of muscle cells compared to those of the control group, in which fertilized eggs were incubated at a constant temperature of 37.8°C, without light. Diameter was increased by 4.20%, 3.77% and 4.55% on day 42 after hatching in thermal, light and combined thermal and light treated groups, respectively, compared to the control. The nucleocytoplasmic ratio was increased by 37.5% on day 42 after hatching in the control group compared to all treated groups. The volume density of the muscle connective tissue was approximately at the same level between the groups. It can be concluded that thermal and light treatments stimulate the proliferation of myoblasts and enhance development and growth of leg muscles in broiler chickens. [Projekat Ministarstva nauke Republike Srbije, br. TR 31033i br. OI173009]
The cuticular structure of the 495-Myr-old type species of the fossil worm Palaeoscolex, P. piscatorum (?Priapulida)

Abstract Latex impressions of the cuticle of a compression fossil of the ? priapulidPalaeoscolex piscatorum, from the Lower Ordovician of Shropshire, demonstrate a complex ornamentation of sclerites similar to isolated material, e.g.Hadimopanellaand phosphatized arrays. Each ‘segment’ is defined by an intercalary zone and bears two rows of sub-circular plates with prominent nodes on the upper surface. The intercalary zone bears two narrow grooves and a series of platelets, similar to but smaller than the plates. The remainder of each segment is occupied by microplates.Palaeoscolex piscatorumis fairly similar to a number of other species, includingGamoscolex herodesandMilaculum elongatum. Present evidence suggests the palaeoscolecidans are priapulid worms (or near relatives). Their abundance, combined with records from Burgess Shale-like occurrences, suggest priapulids were a major component of many Lower Palaeozoic benthic communities.
Mycobiota in needles of Abies alba with and without symptoms of Herpotrichia needle browning

Summary The ascomycete Nematostoma parasiticum (syn.: Herpotrichia parasitica) is commonly perceived as the causal agent of the so-called Herpotrichia needle browning in silver fir (Abies alba). However, its fruitbodies are rarely present on symptomatic needles, which are also colonized by many presumably saprotrophic fungi. We compared the internal colonization of healthy and symptomatic needles on two sites in Poland. In addition, the endophytic mycobiota in needles of various age was recorded on two other sites without disease symptoms. Fungi were isolated from 95.6% of the dead needles and from 62.9% of the living needles on symptomatic trees, whereas on healthy trees, only 45.0% of the needles were colonized internally. Colonization frequency increased with needle age. From a total of 2017 isolates, 116 fungal taxa were identified. Frequency of many species was influenced by needle type. Anthostomella formosa, Gloeosporidiella sp. , Hypoxylon fragiforme, Xylaria hypoxylon and X. polymorpha were the most common fungi isolated from living needles. In symptomless living needles, fungi occurred significantly more often in the basal than in the apical parts. In dead needles, the most common fungi were Alternaria alternata, Paraconiothyrium sporulosum, Fusarium sp. , Mollisia cinerea, Rhizoctonia sp. , Rhizosphaera oudemansii, Thysanophora penicillioides, Xylaria hypoxylon and X. polymorpha. Rhizoctonia sp. was the most frequently isolated fungus in dead needles (23.4%) but occurred rarely also in living needles (0.3–1.1%). The supposed pathogen N. parasiticum was detected only sporadically (at most in 0.6% of the needles). Our findings demonstrate the need for understanding the role of Rhizoctonia sp. in Herpotrichia needle browning disease aetiology.
Período de descanso, valor nutritivo e desempenho animal em pastagem de Panicum maximum cv. Mombaça sob lotação intermitente

It was assessed the nutritive value of hand plucked forage samples collected along the grazing period and the animal performance on Mombacagrass pasture under intermittent stocking with three rest periods (RP). The RPs were defined by the time required for the expansion of 2.5, 3.5, and 4.5 new leaves per tiller, after six days grazing period. The experimental area was divided into five paddocks for the 2.5 new leaves RP and six paddocks for the 3.5 and 4.5 new leaves RPs. Five crossbreed (Holstein x Zebu) steers were randomly assigned to each treatment (RP) as tester animals; put and taken steers were used to assure residual leaf area index of about 2.0, by the end of each grazing period. A NPK fertilization of 100; 25 and 100 kg/ha of N, P2O5 and K2O, respectively, divided into two applications, was broadcasted on each paddock at the beginning and middle of the experimental period. The following evaluations were performed: chemical composition and in vitro dry matter digestibility of hand plucked forage samples, forage intake and live weight gain of tester animals. The rest period had less effect on forage nutritive value than the grazing period; still, the rest period affected steer live weight gains. The longest RP resulted in low animal performance (433 g/steer ´ day) and yield (363 kg BW/ha); on the other hand, the shortest RP favored high animal performance (704 g/steer ´ day) and yield (546 kg BW/ha). It is concluded that rest period of Panicum maximum cv. Mombaca should not exceed the time for the expansion of 2.5 new leaves per tiller, which varied from 24 to 41 days over the experimental period.
Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov.

T. Nakayama, S. Suda, M. Kawachi, and I. Inouye. 2007. Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov. Phycologia 46: 680–697. DOI: 10.2216/04-25.1 A new species of Nephroselmis, Nephroselmis anterostigmatica, is described from coastal waters of the Palau Islands and the southern part of Japan. The long flagellum was stretched out at angle to the cell and showed a characteristic sigmoid line. A cup-shaped yellowish green chloroplast with two narrow sinuses included a pyrenoid with tubular invaginations of thylakoids. In contrast to other species of Nephroselmis, the eyespot was located at the anterior side of the cell. The transitional region of the flagellum possessed a single transitional plate and a stellate structure. The cell body was covered by two types of square scales (windmill/Maltese cross scales absent), small stellate scales and two types of large spiny scales. The flagellar surface was covered by inner square and outer rod-shaped scales, and ornamented with T- and Pl-hairs. Tip hairs are absent. Nephroselmis anterostigmatica is superficially similar to Nephroselmis pyriformis (N. Carter) Ettl, but a detailed comparison of morphological characters, such as chloroplast shape, position of eyespot, composition of hair scales, presence or absence of the two types of small square scales and the large spiny scales, reveals clear differences between the two species. The molecular phylogenetic analysis on the basis of small subunit ribosomal DNA (SSU rDNA) sequences showed that N. anterostigmatica was not closely related to N. pyriformis, but was allied to Nephroselmis astigmatica Inouye & Pienaar. Comparisons of the hair scales and SSU rDNA sequences confirm that the identity of strain CCMP717 is N. pyriformis, and Pseudoscourfieldia marina (Throndsen) Manton has flagella ornamented with a different type of hair scales. The morphological evolution within the genus Nephroselmis is discussed and the order Nephroselmidales is proposed.
Polyphyly across oceans: a molecular phylogeny of the Chromodorididae (Mollusca, Nudibranchia)

The Chromodorididae is a large and colourful family of nudibranch sea slugs distributed across the world's oceans. Most diversity is centred in the Indo‐Pacific, but several genera are present in multiple ocean basins, or across regions separated by biogeographical barriers. The monophyly of these widespread genera had not been tested previously. We used 18S rDNA, 16S rDNA and COI sequence data to generate a molecular phylogeny for this group. We recovered evidence of paraphyly or polyphyly in all of the widespread genera examined (Hypselodoris, Mexichromis, Chromodoris and Glossodoris). East Atlantic Hypselodoris and west Atlantic + east Pacific Mexichromis species were more closely related to each other than they were to their Indo‐Pacific congeners. The addition of Southern Ocean species of Digidentis demonstrated an interesting alternative to this relationship, becoming the sister group for the east Atlantic Hypselodoris on the basis of 16S and 18S data, but not COI data. Sister group relationships were recovered for most monotypic or enigmatic genera. Ardeadoris is linked to Glossodoris, as is Diversidoris; Pectenodoris is sister to the Indo‐Pacific Mexichromis clade, and Verconia is the sister to Noumea haliclona. Controversy surrounding the placement of the three most basal genera was only partially resolved. Using Actinocyclus to root the mitochondrial trees, Cadlinella was the unsupported sister to the Chromodorididae (excluding Cadlina), and Tyrinna occupied a relatively basal position, although this also did not receive significant statistical support. Adding nuclear 18S data gave support for Cadlina as the sister group to the rest of the Chromodorididae s.s. Otherwise, like previous molecular studies, mitochondrial genes supported an alternative position for Cadlina (with other dorid genera).
Some medicinal plants counteract alterations of neuroendocrine stress response system, oxidative and nitrosative stress caused by repeated restraint in rats

Stress affects neuroendocrine stress response system, oxidative and nitrosative stress. Some reports claim that antioxidants and antistressors could attenuate these alterations. This study was realized to investigate antistress and antioxidant effects of Hypericum perforatum, Melissa officinalis, Valeriana officinalis and Passiflora incarnata extracts on repeated restraint (RS) in rats. Thirty-six rats were equally divided into six groups: A (control), B (only RS treated), C (H. perforatum + RS treated), D (M. officinalis + RS treated), E (V. officinalis + RS treated), F (P. incarnata + RS treated). Cortisol, lipid peroxidation, protein oxidation and nitric oxide (NO) levels escalated dramatically in group B compared to control, whereas almost all of them diminished remarkably again in groups C, D, E and F. Besides slight alterations of reduced glutathione content and glutathione-s-transferase, catalase activities were recorded between groups. Among vitamins only depletion of vitamin E was significant in Group B comparing to control. Interestingly administration of each plant extract led to increments of vitamins A and E even when compared to control. The results revealed that the aforementioned plant extracts has remarkable potentials to counteract repeated RS caused alterations of cortisol as well as oxidative and nitrosative stress biomarkers probably through their antistress, antioxidant and free radical defusing effects. Key words: Some medicinal plants, neuroendocrine stress response system, oxidative stress, nitrosative stress, restraint stress antioxidant.
Exogenous Cytokinin Induces ''Out of Season'' Flowering in Protea cv. Carnival

The cytokinin concentration in the xylem sap of Protea L. cv. Carnival (Protea compacta R. Br. · Protea neriifolia R. Br.) shoots was determined at regular intervals from 11 weeks before until 10 weeks after spring budbreak. Cytokinin levels were high during the early phases of spring shoot growth. Benzyladenine (BA) at 50, 250, or 500 mg L was applied to entire shoots on 22 Feb., 12 Apr., and 22 May 2001 (fall in the southern hemisphere) or only to terminal buds on 22 May 2001 at 500 mg L. Most of the terminal buds sprouted and initiated an inflorescence when BA application at 500 mg L in May was directed only to terminal buds, whereas lower flowering percentages (0%-35%) were achieved when the entire shoot was treated. After whole shoots were treated with BA in Apr. 2001, between 5% and 45% floral reversion was observed. High flowering percentages of 87% to 93% were recorded when BA was applied at 500 mg L to the terminal bud in the dormant state or up to the stage when sprouting buds reached the green point development stage. Later applications were less effective, inducing 42% to 43% inflorescence initiation. The flowering time of BA-induced inflorescences was advanced by more than 2 months compared with flowers that initiated naturally on the spring flush.
The use of dendrochronological material from buildings to get information about past spruce budworm outbreaks

The history of the spruce budworm (Choristoneura fumiferana (Clem.)) outbreaks during the last three centuries has been reconstructed by analyzing material from churches. Wood samples were taken from eight churches within a 25-km radius of Chicoutimi, Quebec, Canada. The buildings were constructed between 1864 and 1924. Sampling was realized in the basement, under the roof (loft), and in the bell tower whenever possible. All the material from the basement has been identified as Thuja occidentalis L. (white cedar), with exception of Notre-Dame Church in Laterrire, where pine beams (Pinus sp.) were found. Pine and spruce species (Picea sp.) were found in the bell tower and under the roof in all churches. Chronologies were established for the three tree species: spruce covered the period from 1672 to 1954; white cedar, from 1616 to 1924; and pine, from 1771 to 1925. White cedar was used for a nonhost chronology. To demonstrate information about past spruce budworm outbreaks, only the results for the spruce samples have been presented. Spruce chronologies for the eight churches showed an average correlation of 0.54, with the highest correlation value (0.88) registered between Sainte-Anne and SacrO-Coeur churches. All these chronologies showed clear growth reduction periods caused by defoliation of the spruce budworm. The oldest spruce chronology (1672 to 1920) from the Chicoutimi Cathedral showed two clear defoliation periods during the 18th century, one from 1710 to 1716 and the other from 1754 to 1759. The 19th century was also marked by two defoliation periods: the first from 1811 to 1813 and the second from 1835 to 1841. These periods of spruce budworm outbreaks have also been observed in the wooden structures of the other churches. A third outbreak probably occurred in the 19th century from 1868 to 1878. It is visible in the samples taken from the Chicoutimi Cathedral and Saint-Cyriac.
Seroprevalence of COVID-19 in Niger State

Coronavirus Disease 2019 (COVID-19) Pandemic is ongoing, and to know how far the virus has spread in Niger State, Nigeria, a pilot study was carried out to determine the COVID-19 seroprevalence, patterns, dynamics, and risk factors in the state. A cross sectional study design and clustered-stratified-Random sampling strategy were used. COVID-19 IgG and IgM Rapid Test Kits (Colloidal gold immunochromatography lateral flow system) were used to determine the presence or absence of antibodies to SARS-CoV-2 in the blood of sampled participants across Niger State as from 26th June 2020 to 30th June 2020. The test kits were validated using the blood samples of some of the NCDC confirmed positive and negative COVID-19 cases in the State. COVID-19 IgG and IgM Test results were entered into the EPIINFO questionnaire administered simultaneously with each test. EPIINFO was then used for both the descriptive and inferential statistical analyses of the data generated. The seroprevalence of COVID-19 in Niger State was found to be 25.41% and 2.16% for the positive IgG and IgM respectively. Seroprevalence among age groups, gender and by occupation varied widely. A seroprevalence of 37.21% was recorded among health care workers in Niger State. Among age groups, COVID-19 seroprevalence was found to be in order of 30-41 years (33.33%) > 42-53 years (32.42%) > 54-65 years (30%) > 66 years and above (25%) > 6-17 years (19.20%) > 18-29 years (17.65%) > 5 years and below (6.66%). A seroprevalence of 27.18% was recorded for males and 23.17% for females in the state. COVID-19 asymptomatic rate in the state was found to be 46.81%. The risk analyses showed that the chances of infection are almost the same for both urban and rural dwellers in the state. However, health care workers and those that have had contact with person (s) that travelled out of Nigeria in the last six (6) months are twice ( 2 times) at risk of being infected with the virus. More than half (54.59%) of the participants in this study did not practice social distancing at any time since the pandemic started. Discussions about knowledge, practice and attitude of the participants are included. The observed Niger State COVID-19 seroprevalence means that the herd immunity for COVID-19 is yet to be achieved and the population is still susceptible for more infection and transmission of the virus. If the prevalence stays as reported here, the population will definitely need COVID-19 vaccines when they become available. Niger State should fully enforce the use of face/nose masks and observation of social/physical distancing in gatherings including religious gatherings in order to stop or slow the spread of the virus.