Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of random range truncations on patterns of evolution in the fossil record

Both fossil preservation and sampling methods affect perceived patterns of biotic diversity. Artificial range truncations, for example, may lead to incongruences between apparent- and actual-diversity curves. Thus, a catastrophic extinction event may appear gradual. Recent advances in biostratigraphic-gap analysis provide models for the distribution of gap lengths between fossil occurrence horizons and provide methods to place confidence intervals on local taxon ranges and remove the biases caused by artificial range truncations. Confidence intervals for a set of local taxon ranges may then be evaluated collectively to test a hypothesis of co-extinction/co-emigration or co-origination/co-immigration. In the case of terminal Cretaceous ammonites from Seymour Island, range-chart data are compatible with an abrupt extinction event, although the test statistic is not minimized at the stratigraphic horizon that was suggested by Macellari (1986).
Seed transmissibility of viruses in winter squash landraces collected from the Black Sea region of Turkey.

Sevik M.A., Balkaya A. (2015): Seed transmissibility of viruses in winter squash landraces collected from the Black Sea region of Turkey. Plant Protect. Sci., 51: 195–199. The presence of seed-borne viruses in winter squash landraces in the Black Sea region of Turkey were detected. The seed samples of landraces were tested by ELISA for Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV), Squash mosaic virus (SqMV), Tobacco ring spot virus (TRSV), and Cucumber green mottle mosaic virus (CGMMV). Based on the ELISA results, 11.3% of the samples were infected with the viruses; ELISA, CMV was found at the rate of 5.1% in the winter squash samples, while incidence of ZYMV was determined as 6.2%. Moreover, none of the plants germinated from seeds were found to be infected with SqMV, TRSV, and CGMMV. This is for the first time that seed-borne viruses of winter squash landraces have been identified in the Black Sea region of Turkey.
Ecology and fate of butterflyfishes, Chaetodon spp., in the temperate, western north Atlantic

Three of seven Chaetodon species in the western North Atlantic are reported from temperate waters, quite unlike most other chaetodontids which are only found at tropical and subtropical latitudes. This study describes the ecology of these species at temperate latitudes and tests the hypothesis that these individuals are expatriates that die from hypothermal conditions at the onset of winter. We collected fish with dip nets and bottom traps during 4 yrs, 1990-1993, in a New Jersey estuary. The most abundant species, C. ocellatus, arrived as pelagic juveniles (or tholichthys stage) as early as July and at sizes of 17-22 mm total length. It settled as small as 18 mm, grew about 0.1-0.2 mm d -1 , and reached a maximum size of 77 mm (n = 388). All sizes appeared to be young-of-the-year fish, based on modal progression of lengths from July to November. Eighteen of 52 (35%) marked C. ocellatus were recaptured, generally within 10 m of their release point, indicating good short-term survival and high site fidelity. Individuals were collected during early November in four consecutive years, at temperatures as low as 12°C, but not in winter months. In the laboratory, C. ocellatus stopped feeding at about 12°C and did not survive temperatures of about 10°C or less. Chaetodon capistratus was present in 3 of 4 yrs, but the total number collected (n = 28) precluded detailed examination. Despite earlier reports of C. striatus in this region, we did not observe this species. Overall, Chaetodon species in our study area were much more abundant than previously reported, and they grew and survived well for several months in estuarine conditions. Nonetheless, the evidence did not suggest they were capable of emigrating during autumn nor surviving the ambient winter temperatures, so they become expatriates that will not survive through their first winter.
The first record of Tinodes antonioi Botosaneanu & Taticchi-Viganò, 1974 (Insecta, Trichoptera) in Croatia with DNA barcoding and ecological data and notice of biodiversity and distribution of the genus Tinodes in Croatia

1Department of Biology (Laboratory for Entomology), Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000 Zagreb, Croatia 2Croatian Natural History Museum, Demetrova 1, 10 000 Zagreb, Croatia 3Marina Tartaglie 2, 10 000, Zagreb, Croatia 4Grožnjanska 18, 10 000 Zagreb, Croatia 5Elektroprojekt, d.d. , Civil and Architectural Engineering Department, Alexandera von Humboldta 4, 10 000 Zagreb, Croatia 6S. Toraigyrov State University in Pavlodar, Kazakhstan 7Tuk Bjelopoljski 14, Plitvička jezera, 53230, Korenica, Croatia
Chemical composition and nutritional characteristics of safou of Cameroon, the Congo-Brazzaville, the Congo-Kinshasa and Gabon

325 fruits harvested from 33 trees located in different countries in Central Africa : Cameroon, the Congo-Brazzaville, the Congo-Kinshasa and Gabon, have been submitted to a morphological and physico-chemical study in view of their characterization and evaluation of their nutritional interest. They are fruits of medium size about 6-7 cm long by 3-4 cm wide and weighing 40-50 g for a pulp thickness of about 0.6 cm. The variation range of moisture, oil, protein and ashes content is respectively : 55-60%, 10-14%, 3-4%. All these mineral elements: P, Na, K, Ca, Mg, Fe, Cu, Zn, Mn, are contained with contents worthy of interest. The major constituents of oil extracted from the pulp are palmitic (41-48%), oleic (20-27%) and linoleic (21-29%) acids. The content in alpha linoleic acid in all cases is less than 2%. The ratio ((% of polyunsaturated fatty acids) /(% of saturated fatty acids)) is about 0.6 whereas that of (% of linoleic acid) / (% of saturated fatty acids) varies for different countries from 15 to 22. The results of this work reinforce the nutritional interest of safou pulp.
The Periphyton Community of a Second Order Subalpine Stream Following Salmon Carcass Decomposition

An abstract of the thesis of Jonathan Michael Honea for the Master of Arts in Biology presented May 23, 1997. Title: The Periphyton Community of a Second Order Subalpine Stream Following Salmon Carcass Decomposition: a potential facilitator of the energy flow from adult to juvenile salmonids. To protect and manage Pacific Northwest salmonid stocks, sound management programs must be developed that incorporate knowledge of the ecological processes critical to their survival. One such process is the nutrient dynamic in headwater spawning streams. It is essential that we understand the trophic relationships among the spawners, the I to 3 year-old juveniles, the invertebrates, and the primary producers in these streams. The hypothesis that I tested is that photoautotrophic production increases due to the decomposition of salmon carcasses. Increased primary production would stimulate the production of invertebrates which are an important food resource of juvenile salmonid species. The hypothesis was tested by comparing periphyton communities sampled from upstream reference sites with those sampled from sites within and downstream of a onemile reach of Still Creek, a stream within the Zigzag Ranger District of the Mount Hood National Forest, in which approximately 300 coho (Oncorhynchus kisutch) carcasses were distributed. Comparisons were based on the numbers of each diatom species observed and periphyton biomass measured as chlorophyll a concentration and mass of organic matter lost on ignition. To more accurately characterize the response of the periphyton community, base-line data were collected before enrichment ascertaining the initial degree of nutrient limitation and measuring the variation within and among sample sites prior to site modification. Nutrient concentration and physical characteristics of the water were also monitored. The data collected indicate that the periphyton communities at each site were similar before carcass enrichment. After enrichment, treatment sites showed an increase m periphyton biomass. No change in species composition was observed from reference to treatment sites during the enrichment. Some suggestions are made for improving the experimental design to better characterize the response of the periphyton community to salmon carcass decomposition, such as increasing sample size, adding more "before treatment" sample times, and adding a second treatment stream. THE PERIPHYTON COMMUNITY OF A SECOND ORDER SUBALPINE STREAM FOLLOWING SALMON CARCASS DECOMPOSITION: A POTENTIAL FACILITATOR OF THE ENERGY FLOW FROM ADULT TO JUVENILE SALMONIDS by JONATHAN MICHAEL HONEA A thesis submitted in partial fulfillment of the requirements for the degree of MASTER OF ARTS Ill BIOLOGY Portland State University 1997
Effects of Grain Sorghum (Sorghum bicolor) Herbicides on Charcoal Rot Fungus

Laboratory and greenhouse studies examined effects of atrazine, alachlor, and metolachlor on growth and colonization of grain sorghum roots by Macrophomina phaseolina, causal fungus for charcoal rot disease. In laboratory studies, all three herbicides reduced fungal colony diameter and increased production of microsclerotia. Alachlor and metolachlor reduced germination of fungal microsclerotia. Atrazine did not affect microsclerotia germination, but lessened the effects of alachlor and metolachlor on germination when applied in combination. In greenhouse studies, atrazine reduced numbers of M. phaseolina microsclerotia recovered from soil after 8 wk, and this resulted in reduced colonization of roots by this fungus at harvest. Colonization of grain sorghum roots by M. phaseolina was not affected by alachlor or metolachlor. Grain sorghum growth was reduced by atrazine at all intervals and by alachlor and metolachlor at harvest, despite use of seed safened with cyometrinil.
The Importance of the Insulin-like Growth Factor Signaling Pathway in Lung Cancer and the Potential of its Components as Therapeutic Targets

THE IMPORTANCE OF THE INSULIN-LIKE GROWTH FACTOR SIGNALING PATHWAY IN LUNG CANCER AND THE POTENTIAL OF ITS COMPONENTS AS THERAPEUTIC Sarah Elizabeth Franks Advisor: University of Guelph, 2015 Dr. Roger Moorehead Lung cancer is the leading cause of cancer-related mortalities worldwide. Despite the introduction of new therapeutics, there has been very little improvement in survival for patients with advanced stage disease. The insulin-like growth factor (IGF) system is frequently activated in lung cancer and the type I insulin-like growth factor receptor (IGFIR) has emerged as a potential therapeutic target. However, clinical trials to date have had limited success and it is clear that a more thorough understanding of the IGF-system is required to improve clinical efficacy in targeting this pathway. Here we show that treatment with a dual inhibitor that targets the IGF-IR and the insulin receptor decreased proliferation and survival of lung cancer cells, which was mediated by inhibition of Akt signaling. Furthermore, use of the dual inhibitor enhanced the effects of low doses of platinum therapeutics in lung cancer cells. Akt is an important mediator of IGF-IR signaling and is currently under investigation as a therapeutic target in its own right. Akt exists as three isoforms (Akt1-3), which were previously thought to be largely redundant in activity; however, recent evidence indicates that they have unique functions. In order to investigate the specific roles of Akt isoforms in lung tumorigenesis our lab used a previously developed tissue-specific, inducible transgenic mouse model of lung cancer. In these mice, IGF-IR overexpression in type II alveolar cells is sufficient to induce the formation of nodular adenomas and adenocarcinomas. By combining these transgenic mice with isoform specific Akt knockout mice, we were able to determine if the lack of a single Akt isoform was sufficient to disrupt lung tumorigenesis. Akt1 deficiency was sufficient to decrease IGF-IR-mediated lung tumor development resulting in fewer surface tumors and a lower tumor burden but having no influence in tumor histology. In contrast, Akt2 deficient mice had an increase in tumor burden as well as a change in tumor histology. These mice had diffuse tumor tissue throughout their lungs as tumors did not maintain nodular growth. Therefore, Akt isoforms have unique roles in IGF-IR mediated lung tumorigenesis, which should be reflected in the design and implementation of Akt-targeting
THE ROLE OF MUTUALISTS IN PLANT RESPONSE TO PATHOGEN INFECTION

Under climate change, alterations to precipitation and temperature reg imes are expected to impact ecosystem structure and function. These impacts may be dete rmined by feedbacks between plants and associated microbes, including both endophytic fungal symbionts and viral pathogens. To test the role of biotic and abiotic factors in shapi g virus prevalence in a managed grassland, we experimentally manipulated air tempe ature and precipitation, and after one growing season, evaluated four co-occurring gr ass species for infection by three species of barley and cereal yellow dwarf viruses (B/CYDVs). For one dominant grass species, tall fescue, we also manipula ted fungal endophyte infection status, and tracked changes in viral prevalence over an additiona l two growing seasons for a total of three growing seasons. Plant species identi ty played a strong role in determining virus prevalence; Kentucky bluegrass and dallisg rass were more frequently infected than either tall fescue (endophyte-infected or nd phyte-free) or Indian goosegrass. Both elevated temperature and elevated precipitation als o had strong impacts on virus prevalence, but these effects varied among years and interacte d with fungal endophyte symbiosis for tall fescue. In plots receiving additional precipi tation in 2011, endophyte infection increased virus prevalence in tall fescue. Also in 2011, but
Antennation and sexual performance of male digger wasps Sphex ingens Smith (Hymenoptera: Sphecidae)

ABSTRACT Antennation can play several roles in hymenopteran copulation, mainly in wasps. The digger wasp Sphex ingens Smith has a very peculiar sexual behaviour, in which forced copulation is a striking element. However, communication through antennation during the pre-copulation and copulation phases and the relationship between the sexual performance of males and the final result of copulation require further clarification. The sexual behaviour of wild populations of S. ingens was filmed during the breeding season in a site between the beaches Meros and Aventureiro, Ilha Grande, southeastern Brazil. We assessed antennation behaviour, courtship duration, sexual performance, and genital clasping. Only successful males had the genital clasping assessed. Evidence found so far points out that the successful males showed better sexual performance – that is, they antennated more in a shorter courtship duration. Also, genital clasping in successful males did not depend on antennation, courtship duration, or sexual performance. Our results shed light on some aspects of the sexual behaviour of wasps, as they explain part of the sexual selection mechanisms adopted by the species.
Large and medium-sized mammals of the Humaitá Forest Reserve, southwestern Amazonia, state of Acre, Brazil

Large and medium-sized mammals are essential to forest ecosystems as they are responsible for prey population control, seed dispersal and predation. A mammal survey was conducted in the Humaita Forest Reserve (HFR), a 20 km² forest fragment located in the southeastern part of the state. The survey was carried out using census transects, camera traps, and occasional records such as bones and footprints. In all, 27 species of large to medium-sized mammals were recorded for the RFH, representing 48% of those expected for the region. Dasyprocta fuliginosa , Pecari tajacu and Didelphis marsupialis were the species with the highest number of records with camera traps. The occurrence of two species of cats ( Leopardus pardalis and Puma concolor ) and three endangered species ( Callimico goeldii , Myrmecophaga tridactyla and Priodontes maximus ) are important records for the RFH. The results may aid future research on the ecology, biogeography and conservation of mammals in the region.
Atherosclerosis : Vascular biology

Atherosclerosis, a disease of the large arteries, is the primary cause of heart disease and stroke. In . westernized societies, it is the underlying cause of about 50% of all deaths. Epidemiological studies have revealed several important environmental and genetic risk factors associated with atherosclerosis. Progress in defining the cellular and molecular interactions involved, however, has been hindered by the disease's aetiological complexity. Over the past decade, the availability of new investigative tools, including genetically modified mouse models of disease, has resulted in a clearer understanding of the molecular mechanisms that connect altered cholesterol metabolism and other risk factors to the development of atherosclerotic plaque. It is now clear that atherosclerosis is not simply an inevitable degenerative consequence of ageing, but rather a chronic inflammatory condition that can be converted into an acute clinical event by plaque rupture and thrombosis.
Distribución Espacial de la Flora Vascular, La Humedad y el pH en un Turbal de Esfagno (Sphagnum Magellanicum Brid.), Magallanes, Chile. Spatial Distribution of the Vascular Flora, Moisture and pH in a Sphagnum Bog (Sphagnum Magellanicum Brid.), Magallane

Se presenta un estudio exploratorio instantaneo de la distribucion espacial de variables floristicas como la composicion y riqueza de especies, y variables ambientales como la humedad y el pH del sustrato en un turbal de esfagno (Sphagnum magellanicum Brid.) localizado en una pendiente de 10 grados aproximadamente. Los resultados sugieren la existencia de un gradiente ambiental y floristico en este turbal de esfagno inclinado.
IMPACT OF LEISHMANIA DONOVANI INFECTION ON EARLY EVENTS IN HAEMATOPOIESIS

Visceral leishmaniasis (VL) in humans and in animal models is associated with, among other factors, parasite persistence in the bone marrow (BM) and significant changes in haematological function. However, the mechanisms underlying haematologic dysregulation are largely unknown. Using a panel of stem cell markers, we characterized murine haematopoietic stem and precursor cells in the BM over the course of L. donovani-infection in C57BL/6 (B6) mice. In steady-state, the majority of LT-HSCs (Long-term haematopoietic stem cells) (LSK CD150+ CD34- CD48- cells) were found in a quiescent state, representing cells with the highest degree of reconstitution potential. In contrast, during chronic infection, most LT-HSCs were found to have progressed to cell-cycle and this correlated with a reduced potential to engraft into syngeneic recipients. The loss of quiescent LT-HSCs was associated with expansion of cells displaying a phenotype attributed to early, and uncommitted progenitors. However this increase in uncommitted progenitors did not result in an increase in effective haematopoiesis, but rather chronically infected mice displayed signs of anaemia and thrombocytopenia. The loss of quiescent HSCs and other alterations in the haematopoietic compartment were absent in infected RAG2 KO mice, but adoptive transfer of CD4+ T cells restored this phenotype. In subsequent experiments, we transferred IFNγ-deficient CD4+ T cells into RAG KO recipients and established that this pro-inflammatory cytokines was pivotal for the depletion of the reservoir of LT-HSCs in quiescence, as well as for the establishment of anaemia and thrombocytopenia. Subsequently, using mixed BM chimeras, we established that IFNγ signalling and TNF signalling pathways converge to induce an expansion of BM T cells, suggesting that both cytokines are required to drive the development of CD4+ T cells with the potential to cause alterations in haematopoiesis and haematological dysfunction in the periphery. These data suggest new avenues for clinical research into the pathogenesis of VL and have relevance for the development of new therapeutic strategies and clinical follow-up.
Effect of pre-sowing hydration on germination, emergence and early seedling growth of bambara groundnut (Vigna subterranea L. Verdc)

Experiments were conducted under controlled-environment conditions to investigate the influence of pre-sowing hydration on germination, emergence and seedling growth of three landraces of bambara groundnut. A study on the imbibition time course of landraces DodR, LunT and DipC indicated a triphasic pattern of water uptake leading to germination. DodR began imbibition earlier than the other two landraces while LunT showed delayed water uptake, recording an initial weight increase between 8-12 h compared with 0-4 h for the other landraces. Pre-sowing hydration for different durations improved rates and final percentage germination, emergence and seedling growth of bambara groundnut. The optimal soaking time for bambara groundnut was landrace-dependent.
ROLES OF BUFFERING CAPACITY AND PENTOSE PHOSPHATE PATHWAY ACTIVITY IN THE GAS GLAND OF THE GULF TOADFISH OPSANUS BETA

The teleost gas gland is truly remarkable in its abilities to secrete gases into the swim bladder of physoclistous fish. The physiological and metabolic adaptations of this tissue have been elegantly summarized in a recent review article by Pelster and Scheid (1992). There are two key contributors to the function of the gland. First, a specialized metabolism of the swim bladder, involving copious and simultaneous production of lactate and CO2 from anaerobic glycolysis and the pentose phosphate pathway (also known as the hexose monophosphate shunt), respectively, contributes to gas exchange through pH and salting-out effects on the oxygen-carrying capacity of the blood. Second, a countercurrent multiplier system (i.e. a rete mirabile) enables gas tensions to be elevated further by back diffusion. Several features of metabolism and acid-base physiology remain unclear. First, despite the remarkable ability of this tissue to produce acid, it is not clear if or how intracellular pH (pHi) is regulated. Since ultimately the blood must be acidified, one would predict that the pHi of the tissue would be well regulated via high rates of membrane exchange of protons and/or high tissue buffering capacity. Second, although the functioning of the pentose phosphate pathway has been strongly inferred from measurements of enzyme activities (Bostrom et al. 1972; Pelster and Scheid, 1991), and from measurements of enhanced rates of CO2 excretion relative to the rates of oxygen uptake (Pelster et al. 1989), direct evidence for the existence of the shunt is lacking. Lastly, although the pentose phosphate pathway is expected to produce CO2, and thus contribute to the acidification of blood entering the gland, the pathway may have a different primary, or perhaps a dual, role, namely to maintain high tissue levels of NADPH for protection against oxygen radical damage to cells (Pelster and Scheid, 1992). The composition of the gas stored in the swim bladder can approach pure oxygen in some species, so it is not surprising that the teleost gas gland contains substantial levels of the enzymes catalase, superoxide dismutase and glutathione peroxidase, which scavenge deleterious radicals of oxygen and related harmful compounds (Morris and Albright, 1984). Noteworthy is glutathione peroxidase, which requires a constant supply of NADPH (presumably from the shunt) to maintain glutathione in a reduced state. Reduced glutathione is then used in a variety of oxygen radical detoxification mechanisms. If the pentose phosphate pathway has a role in oxygen detoxification, one would predict that flux rates through the pathway would increase with increased oxygen levels.