Miracle-dz/UniFAR-FTUs huggingface dataset:
Why less complexity produces better forecasts: an independent data evaluation of kelp habitat models

Understanding how species are distributed in the environment is increasingly important for natural resource management, particularly for keystone and habitat forming species, and those of conservation concern. Habitat suitability models are fundamental to developing this understanding; however their use in management continues to be limited due to often-vague model objectives and inadequate evaluation methods. Along the Northeast Pacific coast, canopy kelps (Macrocystis pyrifera and Nereocystis luetkeana) provide biogenic habitat and considerable primary production to nearshore ecosystems. We investigated the distribution of these species by examining a series of increasingly complex habitat suitability models ranging from process-based models based on species' ecology to complex Generalised Additive Models applied to purpose-collected survey data. Seeking limits on model complexity, we explored the relationship between model complexity and forecast skill, measured using both cross-validation and independent data evaluation. Our analysis confirmed the importance of predictors used in models of coastal kelp distributions developed elsewhere (i.e., depth, bottom type, bottom slope, and exposure); it also identified additional important factors including salinity, and interactions between exposure and salinity, and slope and tidal energy. Comparative results showed that cross-validation can lead to over-fitting, while independent data evaluation clearly identified the appropriate model complexity for generating habitat forecasts. Our results also illustrate that, depending on the evaluation data, predictions from simpler models can out-perform those from more complex models. Collectively, the insights from evaluating multiple models with multiple data sets contribute to the holistic assessment of model forecast skill. The continued development of methods and metrics for evaluating model forecasts with independent data, and the explicit consideration of model objectives and assumptions, promise to increase the utility of model forecasts to decision makers.
KrigHedge: GP Surrogates for Delta Hedging

We investigate a machine learning approach to option Greeks approximation based on Gaussian process (GP) surrogates. The method takes in noisily observed option prices, fits a nonparametric input-output map and then analytically differentiates the latter to obtain the various price sensitivities. Our motivation is to compute Greeks in cases where direct computation is expensive, such as in local volatility models, or can only ever be done approximately. We provide a detailed analysis of numerous aspects of GP surrogates, including choice of kernel family, simulation design, choice of trend function and impact of noise. We further discuss the application to Delta hedging, including a new Lemma that relates quality of the Delta approximation to discrete-time hedging loss. Results are illustrated with two extensive case studies that consider estimation of Delta, Theta and Gamma and benchmark approximation quality and uncertainty quantification using a variety of statistical metrics. Among our key take-aways are the recommendation to use Matern kernels, the benefit of including virtual training points to capture boundary conditions, and the significant loss of fidelity when training on stock-path-based datasets.
Biometrical and morphological analyses of Macrobrachium olfersii (Wiegmann, 1836) (Crustacea, Decapoda, Palaemonidae) embryos exposed to UVA and UVB radiation

Macrobrachium olfersii (Wiegmann, 1836) is a prawn that lives in shallow and transparent freshwater in Southern Brazil. Aquatic organisms that inhabit these systems can be exposed to incident UV radiation. Many studies have demonstrated the effects of ultraviolet (UV) radiation on the development, survival rate, morphological abnormalities, and impairments in swimming behavior in crustaceans. However, fewer studies have elucidated how the embryos of crustaceans respond to the exposure of UV radiation. Thus, the aim of this study was to evaluate whether UVA and UVB affect biometrical and morphological parameters of eggs and embryos of M. olfersii. Embryos were divided into two groups: Group I, composed of embryonic day 7 (E7) to E10 and Group II, composed of E11 to E14. Both groups were irradiated with 60 min UVA and 30 min UVB. Non-irradiated embryos at the same orcid.org/0000-0002-4407-5018 orcid.org/0000-0002-3635-0526 orcid.org/0000-0002-7489-6597 original arTiCle This article is part of the special series offered by the Brazilian Crustacean Society in honor to Ludwig Buckup in recognition of his dedication and contributions to the development of Carcinology CORRESPONDING AUTHOR Yara Maria Rauh Müller yara.rauh@ufsc.br SUBMITTED 4 October 2017 ACCEPTED 29 March 2018 PUBLISHED 21 June 2018 Guest Editors Alessandra Angélica de Pádua Bueno and Sandro Santos DOI 10.1590/2358-2936e2018013 orcid.org/0000-0002-6213-4077 orcid.org/0000-0002-9052-1808 orcid.org/0000-0002-4192-6809 orcid.org/0000-0003-1031-0566
Altitudinal filtering of large-tree species explains above-ground biomass variation in an Atlantic Central African rain forest

Abstract: Patterns in above-ground biomass of tropical forests over short altitudinal gradients are poorly known. The aim of this study was to investigate the variation of above-ground biomass with altitude in old-growth forests and determine the importance of changes in floristic composition as a cause of this variation. We used a dataset from 15 1-ha permanent plots established from lowland (200 m asl) to submontane forests (900 m asl) in the Ngovayang Massif, south-western Cameroon. We analysed variation over altitude in two specific functional traits, the potential maximum tree height and the wood density. Forest above-ground biomass decreased from 500–600 Mg ha−1 in lowland plots to around 260 Mg ha−1 at the highest altitudes. The contribution to above-ground biomass of large-tree species (dbh ≥ 70 cm) decreased with altitude, while the contribution of smaller trees was constant. Contribution of the Fabaceae subfamily Caesalpinioideae decreased with altitude, while those of Clusiaceae, Phyllanthaceae and Burseraceae increased. While potential maximum tree height significantly decreased, wood specific gravity displayed no trend along the gradient. Finally, the decrease in above-ground biomass along the short altitudinal gradient can be at least partially explained by a shift in species composition, with large-tree species being filtered out at the highest altitudes. These results suggest that global change could lead to significant shifts in the properties of montane forests over time.
The Antimicrobial resistance and investigation of Yersinia ruckeri from rainbow trout (Oncorhynchus mykiss) farms in the Eastern Black Sea Region

OZET Bu calismada, Dogu Karadeniz Bolgesi’nde kulturu yapilan gokkusagi alabaligi ( Oncorhynchus mykiss ) ciftliklerinde hastalikli baliklardan izole edilen Yersinia ruckeri 'nin varligi arastirilmistir. Hastalik semptomlari gosteren baliklarin dalak ve bobreklerinden saglanan orneklerin cogaltim besi yerlerine ekimleri yapilmistir. Ornekler 20±2oC’de 48 saat sureyle inkubasyona birakilmistir. Inkube edilen bakteri izolatlarinda hareket muayenesi, katalaz, oksidaz ve OF besi yerinde oksidatif/fermentasyon testleri yapilmistir. Bu test sonuclarina gore API 20E test kiti kullanilarak suslar biyokimyasal olarak tanimlanmistir. Kaynatma DNA ornekleri kullanilarak Y. ruckeri izolatlari polimeraz zincir reaksiyonu (PZR) ile dogrulanmistir. Ayrica, Y. ruckeri Tip 1 antikoru ile yapilan aglutinasyon testine gore serotip O1 oldugu belirlenmistir. Antibiyotik hassasiyet testleri yapilmistir. Y. ruckeri izolatlarin % 97.5'i ampisilin'e ve % 62.8'i oksitetrasiklin'e karsi direncli oldugu gosterilmistir. Bu calismayla bolgemizdeki kontamine balik ciftlikleri tespit edilmistir.
Lichens of the family Teloschistaceae in Dagestan, an eastern part of the Caucasian biodiversity hot-spot

Abstract: Teloschistaceae, one of the largest families of lichenized fungi, has its known Eurasian diversity hot-spots in the Mediterranean basin and in arid continental territories. The Caucasus is a natural boundary between these territories and the diversity of Teloschistaceae is therefore expected to be high in this region. We studied the easternmost part of the Caucasus, Dagestan, a region neglected by lichenologists in the past, but with recent lichenological activity. We provide here a checklist of 85 species of Teloschistaceae, 39 of them new to Dagestan from our field work in 2015, and four species new to Russia (Athallia nesodes, "Caloplaca" emilii, "Caloplaca" xerica and Gyalolechia epiphyta). This total is higher than the numbers known from some well-surveyed Central European countries, but lower than numbers reported from Mediterranean countries. It suggests a rather high diversity of Teloschistaceae in Dagestan, although the absence of well-developed maritime and Mediterranean habitats (which are usually rich in species of Teloschistaceae) precludes an even higher diversity.
Trait Correlates of Climatic Niche Tracking in British Birds

Growing evidence indicates that species respond idiosyncratically when exposed to the same changes in climate. As a result, understanding the potential influence of biological traits on species’ distributional responses is a research priority. Yet, empirical support for hypothesised influences of traits on climate change responses remains equivocal. In this paper, we developed a novel approach to determine whether biological traits predict the degree of climatic niche tracking of British breeding birds in response to recent climate change. First, we quantified how well predicted positive and negative changes in probability of presence from climate-based species distribution models agreed with observed local gains and losses in species’ occupancy – our measure of climatic niche tracking. Second, we examined whether the degree of climatic niche tracking could be predicted by species’ ecological and life-history traits, as well as phylogenetic relationships. Overall, British breeding birds displayed a low degree of climatic niche tracking over the period of our study, though this varied substantially among species. Models incorporating traits and phylogeny explained a low proportion of the variation in climatic niche tracking. Nevertheless, we did find statistical evidence that species with lower lifespans tracked their climatic niches more closely, whilst species with a mixed diet displayed a lower degree of climatic niche tracking. We present here a tractable approach for quantifying the degree to which observed local range gains and losses can be related to climate redistribution and apply it to British breeding birds. Although we do not find strong evidence that traits predict the degree of climatic niche tracking, we discuss why this is likely to be a consequence of the features of our study system rather than the approach itself. We believe this approach may prove to be useful as datasets of temporal changes in species distributions become increasingly available.
Molecular Simulations of Protein-Induced Membrane Remodeling

Membranes organize much of the cell and host a great deal of molecular machinery required to integrate signals from the outside, regulate the surrounding matrix, change shape, move, and grow. Understanding how a dense forest of proteins, sugars, and biomarkers modulates the shape of the cell is necessary to produce more detailed, accurate predictions of cell behavior, particularly in the studies of cell signaling processes that lead to oncogenesis. In this dissertation, I will present a series of molecular models which, when combined with continuum models and both in vitro and in vivo experiments, describe the molecular basis for membrane morphology changes. In particular, we investigate the mechanisms by which proteins assemble on a bilayer undergoing thermal fluctuations. This work serves to quantify and explain a series of biophysical experiments in molecular detail, and contributes to the development of multiscale models for predicting cell fate. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering First Advisor Ravi Radhakrishnan
Slow flow of granular aggregates: the deformation of sediments beneath glaciers

Shear deformation of sediments is widespread beneath glaciers. Sediment rheology and the structure of the subglacial drainage system control the deformational behaviour of sediments and the way in which they play a role in determining the dynamics of glaciers, the magnitude of subglacial erosion, the nature of till deposition and many geotechnical properties of glacial sediments which are of concern to engineers. It is suggested that a power law relating shear strain rate, shear stress and effective stress is the most useful general description of their continuum behaviour. Evidence is reviewed from laboratory and field experiments, from the structural properties of tills and from the large–scale patterns of till deposition by former ice sheets to suggest the principal modes of rheological behaviour for tills of different granulometries and to speculate on the interparticle processes which determine them.
Study of polychlorinated biphenyls (PCBs) in soil samples from Al-Ahdab oil field in Waset region/Iraq

Abstract Levels of twelve Polychlorinated biphenyls (PCBs) were studied in soil samples collected from the vicinity of the Ahdab oil field in Kut area/Iraq. All the samples were extracted, cleaned up and analyzed using GC/MS for dioxin-like PCBs. The total concentration of PCBs ranged between 38 μg/kg (site 16) and 980 μg/kg (site 15) with a total mean concentration of 270 μg/kg. Pentachlorobiphenyls were the predominant PCB congeners, accounting for 57.6% of the total PCB concentration found in the soil samples. The toxicity equivalents (TEQ PCBs) in all the soil samples were found in the range of 0.01–35.66 μg TEQ/kg which is 400-fold higher than other studies. Sixteen of the 24 studied soil samples show a carcinogenity higher than the allowable concentration of 5 μg WHO-TEQ/kg.
The correlation between shape of the nose and the underlying hard tissue structures in adults: (cephalometric study)

Results: There was a correlation between skeletal and nasal parameters. The Facial hight, anteroposterior and vertical position of the maxilla and mandible were correlated with the nose shape and length. In skeletal class I patients NMA, NLA were negatively correlated with the SNA, SNB (r = 0.60, P < 0.05), (r = 0.52, P<0. 05). A positive correlate between B angle with NMA, Nbone Lenght (r= 0.55, P<0.05, r= 0.52, P < 0.05 respectivly) negative correlated with Cconv. (r= 0.47, P<0.05), positive correlation was found between SN-Go Me and NMA, NboneL (r = 0.54, P < 0.05, ) (r = 0.54, P<0.05). In skeletal class II a negative correlated between SPP
Validation of Molecular Markers Linked to Fusarium Wilt Resistance in Chickpea Genotypes

Chickpea (Cicer arietinum L.) is third most important legume crop called as poor men's meat due to good source of protein. However, the productivity of chickpea is limited due to fungal disease wilt, caused by Fusarium oxysporum f. sp. ciceris. The resistance breeding aimed to developed disease resistance variety and Marker Assisted Selection can gear up conventional breeding approaches. The present research work was appointed for validation of different markers viz., CS-27, UBC-170, CS-27A, OP-U17-1, UBC-825, TA-59, TA-96 and TR-19 previously reported to be linked to wilt disease either susceptibility or resistance in chickpea. Among susceptibility linked markers CS-27700 and UBC-8251200 validated for all susceptible genotypes, whereas CS-27A700 was not validated only in susceptible genotypes, GG-4 while OP-U17-11014 was not validated in GG-4. The resistance linked markers UBC-170500 was validated in all resistant genotypes. The markers TA-59258 and TA-96265 did not give specific amplicon in resistance genotypes GG-1, GG-2 and annigeri, GG-1, respectively while TR-19227 did not amplify specific product in resistance genotypes annigeri, GG-1 and GG-2. Out of eight markers studied, three markers CS-27700, UBC-8251200 and UBC-170500 were validated in fifteen diverse chickpea genotypes and found to be consistence for marker assisted characterization. These markers could be utilized in future for maker assisted breeding for wilt resistance in chickpea.
A formulation of neem cake seeded with Bacillus sp. provides control over tomato Fusarium crown and root rot

ABSTRACT Fusarium crown and root rot (FCRR) caused by the fungus Fusarium oxysporum f. sp. radicis-lycopersici is a damaging soil-borne disease of tomato. A plant growth rhizobacterium, Bacillus sp. strain HN09 isolated from neem tree rhizosphere soil, was shown to inhibit the growth, germination and development of normal morphology of the FCRR pathogen. A substantial level of disease control was achieved in greenhouse trials by soil supplementation with a preparation of neem cake seeded with HN09. Dry sterilisation of neem cake before fermentation gained comparable disease control effect as those in the unsterilised treatment, whereas moist sterilisation treatment decreased the effect significantly. This bioformulation also led to significantly raised activities in tomato genes encoding pathogenesis-related proteins, hence providing an effective alternative for the control of FCRR, reducing the need for chemical fungicide and fertilisers that impact the environment.
Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement

DNA sequences show that the traditional genus Micromphale appears to be polyphyletic. Nuclear ribosomal LSU and ITS DNA sequences place Micromphale sect. Perforantia Singer (typus sect. M. perforans) within Gymnopus, comprising a clade sister to a mixture of traditional Gymnopus taxa including G. fusipes (typus generis) plus traditional Marasmius sect. Androsacei. This study enlarges sect. Perforantia and shows that sect. Perforantia is a clade separate from those including Micromphale sect. Micromphale and sect. Rhizomorphigena. A new subsection Pinophili is proposed to include new species G. pinophilus and G. ponderosae. Eleven taxa are accepted at species rank, of which nine are proposed as new, mostly morpho-taxa.
for the Pathogenesis of Infectious and Differentiating Dendritic Cells: Implications Functional Phenotype of Locally Airway Epithelial Cells Regulate the

Atopic asthma pathogenesis is driven by the combined effects of airway inﬂammation generated during responses to viral infections and aeroallergens, and both these pathways are regulated by dendritic cells (DC) that differentiate locally from monocytic precursors. These DCs normally exhibit a sentinel phenotype characterized by active Ag sampling but attenuated presentation capability, which limits the intensity of local expression of adaptive immunity. How this tight control of airway DC functions is normally maintained, and why it breaks down in some atopics leading to immunopathological changes in airway tissues, is unknown. We postulated that signals from adjacent airway epithelial cells (AEC) contribute to regulation of local differentiation of DC. We tested this in a coculture model containing both cell types in a GM-CSF-IL-4-enriched cytokine milieu characteristic of the atopic asthmatic airway mucosa. We demonstrate that contact with AEC during DC differentiation up-regulates expression of the function-associated markers MHC class II, CD40, CD80, TLR3, and TLR4 on DCs with concomitant up-regulation of Ag uptake/processing. Moreover, the AEC-conditioned DCs displayed increased LPS responsiveness evidenced by higher production of IL-12, IL-6, IL-10, and TNF- (cid:1) . The Th2 memory-activating properties of AEC-conditioned DCs were also selectively attenuated. Data from microarray and blocking experiments implicate AEC-derived type 1 IFNs and IL-6 in modulation of DC differentiation. Collectively, these ﬁndings suggest that resting AECs modulate local DC differentiation to optimize antimicrobial defenses in the airways and in the process down-modulate capacity for expression of potentially damaging Th2 immunity. The Journal of Immunology, 2009, 182: 72–83. FACSCalibur (BD Pharmingen) using CellQuest and FlowJo For identiﬁcation of surface MDDCs with biotinylated mAb against as a second-incu- bation postwashing with ﬂuorochrome (BD Appropriate isotype controls were always included.
Geographic Variation in Intraspecific Differentiation of a Marine Primary Producer

Author(s): Benes, Kylla Marie | Advisor(s): Bracken, Matthew E.S | Abstract: Steep environmental gradients offer the opportunity to study organismal adaptation to local conditions. Yet these local-scale gradients are often nested within latitudinal gradients, which could mediate neutral and selective processes on the local scale. I used a classic study system, a gradient in tidal elevation on temperate rocky shores, to test for geographic variation in intraspecific differentiation across tide heights in a marine primary producer. The seaweed Fucus vesiculosus is a foundation species on rocky shores throughout the temperate North Atlantic Ocean. In the Gulf of Maine in particular, F. vesiculosus occurs from the lower to upper intertidal zones along the entire coastline, spanning local and latitudinal gradients in abiotic and biotic stressors. I conducted a series of observations and experiments across the species’ intertidal distribution at sites along the Gulf of Maine coastline to: 1) identify patterns of genetic diversity and structure from tide height to regional scales, 2) test for inter-population differences in adaptation to tide height, and 3) determine if traits important to ecosystem-level processes were associated with local adaptation. Molecular studies using microsatellite markers showed genetic variation was significant across multiple sampling scales. Patterns of inbreeding (i.e., FIS) revealed spatial variation in isolation. Genetic differentiation (i.e., FST) was attributable to distance in between-site comparisons, but by environment in between-tide height comparisons. Reciprocal transplant experiments, between the upper and lower edges of the intertidal distribution of F. vesiculosus, were conducted at sites throughout the Gulf of Maine. Relative growth rates of F. vesiculosus showed adaptive phenotypic differentiation in the northeastern Gulf of Maine, countergradient variation in the central gulf, and environmentally-driven responses in the south. Importantly, observations of nutrient physiology demonstrated that nutrient uptake and allocation of tissue nitrogen towards growth were influenced by adaptation in the northeast and driven primarily by environment in the south. By combining molecular and physiological approaches, I have identified geographic variation in genetic and environmental constraints of organismal physiology and population-level processes. Given the important bottom-up role of seaweeds as providers of food and habitat, this variation could have important consequences for the associated rocky intertidal community.
Faunistic Study of Hover Flies (Diptera: Syrphidae) of Pakistan

Abstract The present study is based mainly on specimens of syrphid flies collected in Pakistan during country-wide surveys made from 2009 to 2014. These results are supplemented by known records of Syrphidae of Pakistan documented by various authorities earlier. These results yielded 71 species of 40 genera from Pakistan. Of these, 11 species viz., Paramixogaster contractus (Brunetti, 1923) Eoseristalis albibasis (Bigot, 1880), Mesembrius quadrivittatus (Wiedemann, 1819), Eumerus nepalensis Brunetti, 1908, Eumerus sexvittatus Brunetti, 1915, Psilota cyanea Hill, 1921, Volucella peleterii Macquart, 1834 Volucella ruficauda Brunetti, 1907, Chrysotoxum antiquum Walker, 1852, Syrphus vitripennis Meigen, 1822 and Xanthogramma pedissequum (Harris, 1776), are first records for Pakistan.