Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural Network Architecture for Database Augmentation Using Shared Features

The popularity of learning from data with machine learning and neural networks has lead to the creation of many new datasets for almost every problem domain. However, even within a single domain, these datasets are often collected with disparate features, sampled from different sub-populations, and recorded at different time points. Even with the plethora of individual datasets, large data science projects can be difficult as it is often not trivial to merge these smaller datasets. Inherent challenges in some domains such as medicine also makes it very difficult to create large single source datasets or multi-source datasets with identical features. Instead of trying to merge these non-matching datasets directly, we propose a neural network architecture that can provide data augmentation using features common between these datasets. Our results show that this style of data augmentation can work for both image and tabular data.
Below‐Canopy distribution of photosynthetically active radiation and its relation to seedling growth in a boreal Pinus sylvestris stand

A simulation model was used to predict the spatial distribution of direct and diffuse photosynthetically active radiation below a heterogenous canopy of a Pinus sylvestris stand in eastern Finland. Seedling growth was related to both measured and predicted radiation. The model predicted rather well the overall pattern of radiation distribution beneath the canopy. All the growth parameters of Pinus sylvestris seedlings (height, current height increment and mean height increment) correlated positively with the amount of both measured and predicted radiation. The correlation between seedling growth and irradiance was better for predicted diffuse radiation than for total radiation. This was probably because diffuse radiation, being symmetrically distributed around trees, correlates more strongly than direct radiation with other factors affecting seedling growth.
Development of aptamer based targeted reversibly attenuated probes

vi CHAPTER 1. GENERAL INTRODUCTION 1 DISSERTATION ORGANIZATION 1 BACKGROUND 2 RESEARCH AIMS AND SIGNIFICANCE 4 CHAPTER 2. LITERATURE REVIEW 8 SELEX 8 APTAMERS 18 PRINCIPLES OF TRAP DESIGN 21 ALLOSTERIC NUCLEIC ACID MOLECULES 24 SELECTION IN VIVO 35 APTAMER APPLICATIONS 38 DETECTION AND IMAGING OF RNA IN LIVING CELLS 50 BRIEF REVIEW OF RNA SECONDARY STRUCTURE PREDICTION 56 TABLES AND FIGURES 60 CHAPTER 3. ALLOSTERIC APTAMERS; TARGETED REVERSIBLY ATTENUATED PROBES (TRAPS) 71 ABSTRACT 7
The evolution, ecology, and restoration of anadromy in rainbow trout/steelhead Oncorhynchus mykiss

Evolution can occur on ecologically relevant timescales, creating the potential for a bidirectional link between evolution and ecology. For example, migrating species provide important pulses of resources to recipient ecosystems, but are increasingly subject to intense selection due to ongoing global change. If heritable variation underlies migration, then contemporary evolution may increase non-migratory life histories, thereby increasing population persistence, but at the expense of important ecological processes. I examine contemporary evolution and its consequences of migration in an economically and ecologically important species, the resident and migratory ecotypes of the species Oncorhynchus mykiss. In Chapter 2, I show that a stream barrier has driven the evolutionary loss of the migratory ecotype in only ∼25 generations. I estimated the genetic contribution to variation in traits underlying the expression of migration and show that in the above-barrier population there has been a 30% decrease in expression of the migratory ecotype relative to the below-barrier population of origin. In Chapter 3, I examine the ecological consequences of this contemporary evolution. I show that the density decreases associated with loss of anadromy consistently had a greater effect on mesocosm ecosystems than the per-capita effects of the ecotypes. In Chapter 4, I use an analytical model to explore whether a population of O. mykiss would evolve toward greater residency in response to increased costs of migration. I find that evolution can rescue isolated populations; populations that persist are those that evolve in response to the changing selection regime on timescales that prevent population extinction. However, when conditions are restored to the pre-disturbance state, the rate of recovery of the migratory ecotype was unpredictable and generally slower than its loss. Finally, in Chapter 5 I review pathways for restoring the migratory ecotype, and how restoration of a life history may differ from restoring a species. Effective restoration of this life history will entail understanding the ecological and genetic mechanisms underpinning the expression of migratory behavior. Together, these chapters highlight that migratory barriers can drive contemporary evolution of the non-migratory ecotype that increases population persistence, but decreases their ecological impacts. More generally, this research highlights the importance of incorporating evolutionary perspectives in management, conservation, and restoration.
An introduction to behavioural ecology

Introduction Natural Selection, Ecology And Behaviour Testing Hypotheses In Behavioural Ecology Economic Decisions And The Individual Predator Versus Prey: Evolutionary Arms Races Competing For Resources Living In Groups Fighting And Assessment Sexual Conflict And Sexual Selection Parental Care And Mating Systems Alternative Breeding Strategies On Selfishness And Altruism Co-Operation And Helping In Birds, Mammals, And Fish Co-Operation And Altruism In The Social Insects The Design Of Signals: Ecology And Evolution Conclusion
Alfalfa protein concentrate in milk replacer formulas for dairy calves

Alfalfa protein concentrate (APC) was evaluated as a partial substitute for milk protein in milk replacer for calves. Milk replacer formulations (21% crude protein, 12% fat and equal in supplemental vitamins, minerals and antibiotics) contained all milk protein (A), 30% of the crude protein from APC (B), and 60% of the crude protein from APC (C). The three replacers were fed to calves (5 calves per treatment) 3-5 days of age for 6 weeks. No calf starter or hay were fed. Average daily gains (g), time scouring per calf and fecal scores on a scale of 1, (normal) to 4 (fluid) of calves on replacers A, B, C were 291, 272, 241 grams; 3.6, 3.6, 5 days and 1.48, 1.68, 1.83. The scores for appetite, calf demeanor and dehydration were close to 1 for the three treatments as rated on a scale 1(good) to 4 (poor). Total feed costs/Kg weight gain of calves were $2.80, $1.89 and $1.36 for replacers A, B and C respectively. It was concluded that APC could supply a major portion of the protein in milk replacers for calves after 3 weeks of age.
Rooting characteristics and turfgrass quality of three bermudagrass cultivars and a zoysiagrass

Abstract Warm season turfgrasses are increasingly used throughout the transitional areas of Mediterranean countries due to their low water requirements. A two-year field study was carried out in north-eastern Italy to evaluate the turf canopy quality and root system architecture of three seeded bermudagrass cultivars (La Paloma, Princess-77 and Yukon), and a zoysiagrass (Companion) under non-irrigated conditions. Plots (1.6×4.5 m) were established in July 2005 and arranged in a randomized complete block with three replicates. Visual quality ratings were assessed weekly from April to November in 2006 and 2007. Soil cores were collected at depths of 0–3, 3–8, 8–15, 15–25 and 25–40 cm in August 2006, January 2007, May 2007 and September 2007 to measure main rooting characteristics: root length density (RLD), root mass density (RMD) and root diameter. Companion zoysiagrass had higher canopy quality than bermudagrass cultivars in early spring and in the late growing season, while it displayed poorest quality from June to October. Among the bermudagrass cultivars, Yukon showed the highest quality in both years. Differences in RLD among grasses appeared to be related to seasonal changes in air temperature and precipitation. In August 2006 Companion zoysiagrass averaged 3.5–4.4 cm cm−3 less RLD than bermudagrass cultivars La Paloma and Princess-77. Visual turf quality was positively correlated to the RLD and RMD in the 25–40 cm soil layer, whereas no correlations were found with root diameters nor any parameter collected in the upper soil layers. Deep-rooting cultivars may have an advantage in deficit soil moisture periods resulting in higher quality turf throughout the year.
Long‐term population trends in three grassland insect groups: a comparative analysis of 1951 and 2009

Development of farming practices has caused drastic changes in European agricultural landscapes during the past 50 years. As a consequence of these changes, insect diversity is widely expected to decline. We performed a comparative analysis with long‐term data of three insect groups: Auchenorrhyncha, Heteroptera and Orthoptera. In 2009, we revisited nine grassland sites in northern Germany that were originally sampled in 1951 using the same techniques and during a similar time frame. We found that the insect community exhibited no consistent trends between years. Species richness of Auchenorrhyncha and Heteroptera increased on plot level as well as on landscape level but remained unchanged for Orthoptera. Abundance of Auchenorrhyncha and Orthoptera significantly decreased, while Heteroptera increased. There is a strong trend towards homogeneity in community composition for Heteroptera and a weak one for Auchenorrhyncha. The frequency and abundance of species preferring disturbed and/or eutrophic habitats increased, whereas the number of species preferring low‐productive habitats declined. This trend is especially pronounced in Auchenorrhyncha. Generalistic species were more abundant in relative proportions as well as in absolute numbers. We hypothesize that these trends arise from alterations of Central European landscapes because of agricultural intensification over the last several decades.
Woody Species Variations in Biomass Allocation, Photosynthetic WUE and Carbon

Water is one of the most limiting environmental factors for successful rehabilitation in Mongolia. In this study, variations in biomass allocation, water use effi ciency (WUE) and carbon isotope composition of fi ve woody species (Caragana arborescens Lam., Hippophae rhamnoides L., Larix sibirica Ledeb., Pinus sylvestris L. and Ulmus pumila L.) seedlings were investigated in an open fi eld nursery. There are diverse responses of species under drought conditions. Hardwood species, U. pumila, showed the lowest photosynthetic WUE and carbon isotope composition among fi ve species but demonstrated superior morphological response in terms of root weight ratio (0.49±0.02) and root biomass allocation compared to other species (p Key words: Caragana arborescens, carbon isotope discrimination, drought tolerance, fi eld nursery, Hippophae rhamnoides, Larix sibirica, photosynthesis, Pinus sylvestris, root weight ratio, Ulmus pumila, water deficit
Tri-trophic interactions and the minimal effect of larval microsite and plant attributes on parasitism of Sphenella fascigera (Diptera: Tephritidae)

Parasitoid insects are important natural biocontrols of insect herbivores. How parasitoids choose particular hosts among many larvae on different plants is not fully understood. Our study system was the coastal plant Senecio lautus and its tephritid herbivore Sphenella fascigera parasitised by an undescribed parasitoid wasp Pteromalus sp. We located S. fascigera larvae in the field and reared pupae to investigate factors that might promote variation in parasitism: host larval location on the plant (stem gall versus flower head), plant density and quality, host larval density, and presence of other insect herbivores. The overall rate of parasitism of S. fascigera was 25%. There was no significant effect of larval location, or any other recorded variable, upon parasitism. One explanation could be the evolution of an efficient search strategy by Pteromalus sp. Future research on whether S. fascigera larvae on congeneric plants experience different rates of parasitism could contribute to understanding the larger web of interactions involving these species.
Integrating Hebbian and homeostatic plasticity: the current state of the field and future research directions

We summarize here the results presented and subsequent discussion from the meeting on Integrating Hebbian and Homeostatic Plasticity at the Royal Society in April 2016. We first outline the major themes and results presented at the meeting. We next provide a synopsis of the outstanding questions that emerged from the discussion at the end of the meeting and finally suggest potential directions of research that we believe are most promising to develop an understanding of how these two forms of plasticity interact to facilitate functional changes in the brain. This article is part of the themed issue ‘Integrating Hebbian and homeostatic plasticity’.
Phylogeny of the Aphnaeinae: myrmecophilous African butterflies with carnivorous and herbivorous life histories

The Aphnaeinae (Lepidoptera: Lycaenidae) are a largely African subfamily of 278 described species that exhibit extraordinary life‐history variation. The larvae of these butterflies typically form mutualistic associations with ants, and feed on a wide variety of plants, including 23 families in 19 orders. However, at least one species in each of 9 of the 17 genera is aphytophagous, parasitically feeding on the eggs, brood or regurgitations of ants. This diversity in diet and type of symbiotic association makes the phylogenetic relations of the Aphnaeinae of particular interest. A phylogenetic hypothesis for the Aphnaeinae was inferred from 4.4 kb covering the mitochondrial marker COI and five nuclear markers (wg, H3, CAD, GAPDH and EF1α) for each of 79 ingroup taxa representing 15 of the 17 currently recognized genera, as well as three outgroup taxa. Maximum Parsimony, Maximum Likelihood and Bayesian Inference analyses all support Heath's systematic revision of the clade based on morphological characters. Ancestral range inference suggests an African origin for the subfamily with a single dispersal into Asia. The common ancestor of the aphnaeines likely associated with myrmicine ants in the genus Crematogaster and plants of the order Fabales.
Symposium: Use of Pheromones in Tropical Crops: Grandlure: Use in Boll Weevil Control and Eradication Programs in the United States

The grandlure-baited boll weevil trap is an essential component of most, if not all, boll weevil control programs. While there are other minor uses of grandlure, the major use is as an attractant for the boll weevil trap. The Southeastern Boll Weevil Eradication Program uses the grandlure-baited boll weevil trap to determine areawide distribution of boll weevils, field-by-field presence of boll weevils, where and when to apply insecticide treatments and suppress very low populations of boll weevils.
Effect of forest fragmentation on bird species richness in Papua New Guinea

Tropical forests worldwide are being fragmented at a rapid rate, causing a tremendous loss of biodiversity. Determining the impacts of forest disturbance and fragmentation on tropical biotas is therefore a central goal of conservation biology. We focused on bird communities in the interior (>100 m from forest edge) of forest fragments (300, 600, and 1200 ha) in the lowlands of Papua New Guinea and compared them with those in continuous forest. We surveyed bird communities using point counts, mist-netting, and random walks, and measured habitat and microclimate characteristics at each site. We also surveyed leaf-dwelling arthropods, butterflies, and ants, and obtained diet samples from birds to examine food availability and food preferences. We recorded significantly fewer bird species per point in the 300-ha forest fragment than in other study sites. Overall, we recorded 80, 84, and 88 species, respectively, in forest fragments, and 102 in continuous forest. Frugivores (especially large frugivores) and insectivores had lower species richness in forest fragments than continuous forest. Our results did not support the food scarcity hypothesis, that is, the decline of insectivorous birds in forest fragments is caused by an impoverished invertebrate prey base. We also found no significant differences among forest fragments and continuous forest in microclimates of forest interiors. Rather, we found that microhabitats preferred by sensitive birds (i.e., 30% of species with the strongest preferences for continuous forest) were less common in forest fragments (19%-31% of points) than in continuous forest (86% of points). Our results suggest that changes in microhabitats may make forest fragments unsuitable for sensitive species. However, limited dispersal capabilities could also make some species of birds less likely to disperse and occupy fragments. In addition, impoverished food resources, size of the forest fragment, or hunting pressure could contribute to the absence of large frugivorous birds in forest fragments. The forest fragments in our study, preserved as village-based protected areas, were not large enough to sustain the bird communities found in continuous forest. However, because these fragments still contained numerous bird species, preservation of such areas can be an important component of management strategies to conserve rainforests and birds in Papua New Guinea.
Crossroads: Interactive Music Systems Transforming Performance, Production and Listening

We discuss several state-of-the-art systems that propose new paradigms and user workﬂows for music composition, production, performance, and listening. We focus on a selection of systems that exploit recent advances in semantic and affective computing, music information retrieval (MIR) and semantic web, as well as insights from ﬁelds such as mobile computing and information visualisation. These systems offer the potential to provide transformative experiences for users, which is manifested in creativity, engagement, efﬁciency, discovery and affect.
Rôle des facteurs de transcription stat3 dans la réponse aux inhibiteurs de topoisomerase : Implication dans la résistance aux traitements de chimiothérapie

Les facteurs de transcription STAT3 sont actives dans de nombreuses tumeurs et leurs effets sur la proliferation et la survie suggeraient fortement que ces proteines puissent etre impliquees a la fois dans la transformation cellulaire et dans l'echappement aux traitements classiques de chimiotherapie. Nous nous sommes donc interesses aux differents aspects impliquant STAT3 dans la reponse de lignees cellulaires aux agents genotoxiques de chimiotherapie, et plus particulierement aux inhibiteurs de topoisomerase. Durant ces traitements, STAT3 interagit avec le represseur transcriptionnel Rb et l'inhibiteur du cycle cellulaire p21. Ces deux proteines inhibent son activite transcriptionnelle, notamment sur les genes c-myc et cdc25A, et permettent la mise en place de la senescence induite par les dommages de l'ADN et la catastrophe mitotique. Cependant, en presence d'une activite constitutive de STAT3 induite par l'oncogene v-src, STAT3 empeche l'activation de Rb et de p21, favorise la resistance des cellules aux inhibiteurs de topoisomerase II, et genere de l'instabilite genomique. Finalement, deux inhibiteurs de STAT3, le cetuximab, un anticorps monoclonal dirige contre l'EGFR, et un inhibiteur de la tyrosine kinase c-src, sensibilisent des cellules colorectales aux inhibiteurs de topoisomerase I. L'inhibition de STAT3 empeche l'activation du gene Eme1 qui induit l'expression d'une proteine de reparation de l'ADN. STAT3 est donc un facteur de resistance aux inhibiteurs de topoisomerase. Sa detection pourrait ainsi permettre de mieux predire la reponse des patients a ces inhibiteurs, et son inhibition, dans les tumeurs ou il est actif, pourrait permettre de les sensibiliser aux inhibiteurs de topoisomerase.
Chemistry and physiology of the vitamins

I-Ascorbic acid from 2-keto-/gulonic acid or iu alkyl esters br bt.ating in the prese nce of no alka li salt of a weak acid ia anhydrous alcohol. /-Ascorbic acid from 2-keto-/gutonic acid by the action or glac ial acet iC acid a nd a mineral ac. -id . I-Ascor bic acid from di acetone-2keto -guloaic acid by acid t reatment . I-Ascorbic acid £com sor bose b y ca taly tic oxidation foll owed b)' acid treatme nt. I-Ascorbic acid from methyleneether derivatives or di bcaza l der ivatives of 2-keto-l -g ulonic acid b y treatmeut with concent rated HCI. Ascorbic acid fro m osones plus hrdrocyanic acid, t l.Je o! ione beinK prepared by oxida tion o f sugars with cupric ion in aqu eous orgau ic ncid solu tion . AscorUic acid by co nden sation o r mesoxalic acid e! »ter with l-threosc . AsCorbic acid from 1-sorbose 1,ia 2k:c t o-/-gulo nic acid or m e thylene ether dtrivativc t hereof. Ascorbic acid from 2-keto-l-gulooic aci.d est ers by alkali sa. μooi fi cation followed by lacton ization io a cid sol utj on. A~corbic acid from 2-ket o-J-g ulooic acid by aci d trea t me nt. Ascorbic acid £ram 2keto-l-gu1oaic acid or its derivatives which arc easily split with ac id s, b y aci d s in alcoholic solution . Ascorbic acid by heat ing 2-ketogulonic acid or its deri vati ves w hi ch are easjJ y split with acids. Ascorbic acid fr om 2k:cto-gu loaic acid by trea ti ng "ith alkali salts of weak acid s and converti n g the so~ formed a lk a li sa lts of ascorbic ucid b y means of strong acids into ascorbic acid . Ascorbic acid fro m 2· keto-l-gulom c acid o r der ivat ives which are hydro· ly :te<l easily by acid s, by lr~atm.eot with acids in the presence of a solvent in wbicb t he fo rmed ascorbic acid is insoluble. 590 PATB S T No. I D ATB I n t er m ediat e s for the Synthesis U . S . 2 ,140,480 Dec . 13, 1938 U. S . 2 ,039 ,929 M ay 6, t 936 B . 428,8 15 May 20 , 1935 B. 427 ,286 Apri l 18 , 1935 B . 435 ,9 71 Oct. 2, 1935 G. 699 ,877 N ov . 7 , 1940 G . 703,227 Mar . 4, 194 1 F. 780,0,5 5 April 18 , 1935 F. 45,774 Dec . 3, 1035 P ATENT IN DE X
Characteristics of random monoallelic gene expression during embryonic stem cell differentiation

Gene expression is not only tightly regulated during differentiation, forming the basis of lineage specification and cellular identity, but also flexible and stochastic, contributing to cellular heterogeneity within the organism. Monoallelic gene expression refers to the transcription of a gene from one of its two homologous alleles, and could potentially contribute to cellular diversity, although it has not been studied in a developmental context, nor characterised at the molecular level. An allele-specific RNA sequencing screen was performed in clonal populations of hybrid mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs) and identified 67 and 376 inheritable autosomal random monoallelically expressed genes respectively, a 5.6-fold increase upon differentiation. While DNA methylation and nuclear positioning did not play a role in maintaining monoallelic expression, specific histone modifications were differentially enriched between the two alleles and are thus likely involved in preserving the monoallelic state. Interestingly, transcript levels of 8% of the monoallelically expressed genes remained similar between monoallelic and biallelic NPC clones. These results support a model in which random monoallelic expression occurs stochastically during differentiation, and for some genes is compensated for by the cell to maintain the required transcriptional output of these genes. Therefore, monoallelic expression exemplifies the stochastic and plastic nature of gene expression in single cells during development.