Miracle-dz/UniFAR-FTUs huggingface dataset:
Architectures hybrides auto-assemblées à base de systèmes polyconjugués et de nanocristaux de semi-conducteurs pour le photovoltaïque plastique

Cette these a eu pour objectif l’elaboration de materiaux hybrides auto-assembles a base de poly(3-hexylthiophene) et de nanocristaux de CdSe en vue d’applications en cellules photovoltaiques. Pour cela, des groupements de reconnaissance moleculaire complementaires ont ete introduits lateralement a la chaine principale du polymere et a la surface de nanocristaux. Ainsi des groupements diaminopyrimidine ont ete introduits par post-fonctionnalisation d’un copolymere de poly(3-hexylthiophene-co-3-bromohexylthiophene) et des groupements thymine ont ete introduits a la surface des nanocristaux par reaction d’echange de ligand avec le 1-(6-mercapto-hexyl)thymine. Les solubilites respectives du polymere et des nanocristaux rendent leur mise en œuvre par melange de solutions difficile. Un protocole « one pot » a ete developpe, mais cette voie reste peu satisfaisante du point de vue du controle de la composition de l’hybride et de la mise en œuvre pour des dispositifs photovoltaiques. Finalement, la technique du depot couche par couche permet de s’affranchir des problemes de solubilites tout en controlant precisement le processus de depot. Quelques parametres experimentaux du depot couche par couche ont ete explores pour identifier leurs influences sur les depots. Les films obtenus ont ensuite ete caracterises par des techniques de microscopie et diffraction des rayons X, revelant une structure interpenetree plutot que multicouche. Le comportement electrochimique de ces films a egalement ete etudie par cyclovoltammetrie et spectroelectrochimie UV-vis-PIR. Des cellules solaires ont ete realisees avec ces hybrides et elles ont ete testees sous eclairement. Les caracteristiques I=f(V) obtenues revelent qu’un effet photovoltaique a bien lieu dans ces materiaux.
Usage of Detoxification Enzyme Glutathione-S-Transferases over Galleria mellonella L. (Lepidoptera: Pyralidae) as Biomarkers of Insecticide Resistance

Insecticides are preferred because of their easy applicability in combating pest insects and their short-term results. Insecticides used over dose and unconsciously in agricultural areas cause ecological damage. Also; the use of over dose insecticides in agricultural areas has led to the development of insect resistance. Since the resistance mechanism developed is genetic, it is transmitted to later fertilizers. For this reason, it is important to apply the insecticides in the restricted areas and in the optimal amount. Insects increase their detoxification capacities to protected themselves from insecticides. Detoxification mechanisms are based on the breakdown of insecticides before reaching the target area. The most important detoxification enzyme in insects are Glutathion-S-Transferases (GST). GST enzyme in insects has a role in protection of cellular membranes against oxidative degradation as well as detoxification mechanism. Galleria mellonella may be used as a model organism for understanding the insecticide resistance mechanism.
Cropping practices influence incidence of herbicide resistance in annual ryegrass (Lolium rigidum) in Australia

Herbicide resistance is a common occurrence in southern Australia. The evolution of herbicide resistance is influenced by the selection pressure placed on the weed species controlled by that herbicide. Results from resistance screening of ~4500 annual ryegrass (Lolium rigidum Gaud.) samples were entered in a GIS database, together with several agricultural parameters used in the Australian Bureau of Statistics Agricultural Surveys. This allowed a study of the associations between mode of action of resistance, geographic distribution of resistance across southern Australia, and farming practices employed in particular regions. Cultivation was negatively associated with resistances in acetyl-CoA carboxylase (ACCase)-inhibiting cyclohexanedione and acetolactate synthase (ALS)-inhibiting herbicides. Higher proportions of wheat sown were associated with higher incidences of resistance. ACCase-inhibiting aryloxyphenoxypropionate and cyclohexanedione and ALS-inhibiting resistances were higher in those shires where soils were predominantly acidic. This study demonstrates the association between farm practice and the evolution of herbicide resistance. The analysis provides reinforcement to the principle of rotating chemical modes of action with non-chemical weed control measures to minimise the risk of herbicide resistance evolution in any farming system.
Noise reduction of ECG signals through genetic optimized wavelet threshold filtering

The Electrocardiogram (ECG) is a valuable signal recording the heart's electrical activity. The filtering quality of ECG signals directly affects the medical diagnosis. Since wavelet analysis can provide both time and frequency information, many nonlinear thresholding methods based on wavelet transform denoising have been applied to the noise reduction of ECG signals. However, most of these threshold shrinkage functions cannot adapt to different signals due to the fixed transition curve of threshold. Therefore, a novel genetic optimized wavelet thresholding approach (GOWT) is proposed in this paper. A quadratic curve thresholding function (QCTF) was devised to realize the smooth connection of threshold points. Moreover, in terms of the root mean square error and the filtering smoothness, a new genetic algorithm was devised to automatically search the optimal parameters of QCFT for different noisy signals. Finally, the GOWT was evaluated and compared with hard thresholding and soft thresholding by means of MIT-BIH arrhythmia database ECG records. The filtering results indicate that the GOWT can realize smooth threshold transition, avoiding the oscillation at the cutoff threshold point caused by the hard thresholding and the wavelet coefficient bias brought by the soft thresholding. Its adaptability to various signals has been strengthened by the genetic algorithm. The GOWT can find a trade-off between the smoothness and distortion of signal filtering, generating the desirable noise-free signal for feature extraction.
Modelling mitochondrial epilepsy in vitro : conceptualisation, mechanisms, and therapeutic implications

iii Acknowledgments . vii Table of contents . xi List of figures . xvi List of tables . xxi List of abbreviations . xxii Chapter 1 General introduction . 1 1.1 Mitochondria . 3 1.2 Mitochondrial ATP production . 5 1.3 Mitochondrial supercomplexes . 7 1.4 Mitochondrial DNA . 8 1.5 Mitochondria, metabolism, and the brain: the blood-brain barrier . 10 1.6 Neurons . 11 1.6. 1 Excitatory neurotransmission . 13 1.6. 2 Inhibitory neurotransmission . 18 1.7 Astrocytes . 23 1.7. 1 Astrogliosis . 26 1.7. 2 Manipulation of astrocytic function . 29 1.8 Energy metabolism in the brain . 31 1.8. 1 Overview of glucose metabolism . 31 1.8. 2 Glycolysis . 33 1.8. 3 TCA cycle (Krebs cycle) . 36 1.8. 4 Fatty acid metabolism . 37 1.8. 5 Ketogenesis . 38 1.8. 6 Glutamate-glutamine cycle . 41 1.8. 7 Astrocyte-neuron lactate shuttle hypothesis . 43 1.9 Mitochondrial disease . 44 1.10 Mitochondrial epilepsy. 48 1.11 Animal models of mitochondrial epilepsy . 50 1.12 In vitro brain slice electrophysiology . 51 1.13 Temporal lobe and hippocampus in epilepsy . 55 1.14 Pharmacological treatment of epilepsy . 58 1.15 Non-pharmacological treatment of epilepsy . 60 1.15. 1 Ketogenic diet . 60
Glycolysis upregulation is neuroprotective as a compensatory mechanism in ALS

Amyotrophic Lateral Sclerosis (ALS), is a fatal neurodegenerative disorder, with TDP-43 inclusions as a major pathological hallmark. Using a Drosophila model of TDP-43 proteinopathy we found significant alterations in glucose metabolism including increased pyruvate, suggesting that modulating glycolysis may be neuroprotective. Indeed, a high sugar diet improves locomotor and lifespan defects caused by TDP-43 proteinopathy in motor neurons or glia, but not muscle, suggesting that metabolic dysregulation occurs in the nervous system. Overexpressing human glucose transporter GLUT-3 in motor neurons mitigates TDP-43 dependent defects in synaptic vesicle recycling and improves locomotion. Furthermore, PFK mRNA, a key indicator of glycolysis, is upregulated in flies and patient derived iPSC motor neurons with TDP-43 pathology. Surprisingly, PFK overexpression rescues TDP-43 induced locomotor deficits. These findings from multiple ALS models show that mechanistically, glycolysis is upregulated in degenerating motor neurons as a compensatory mechanism and suggest that increased glucose availability is protective.
Hidden diversity in European bees: Andrena amieti sp. n., a new Alpine bee species related to Andrena bicolor (Fabricius, 1775) (Hymenoptera, Apoidea, Andrenidae)

We revise the Alpine bee taxa related to Andrenabicolor (Fabricius, 1775), including A.montana Warncke, 1973 and A.allosa Warncke, 1975, the status of which has remained contentious. Phylogenetic analyses of one mitochondrial gene and one nuclear gene, as well as morphological examination reveal the presence of four Alpine species in this complex, one of which is new to science, A.amietisp. n. This new species is widely distributed in the Alps from southern France throughout Switzerland, northern Italy and southern Germany to Austria; a single record is known from the Apennines. The type locality is located within the Unesco World Heritage site “Swiss Alps Jungfrau-Aletsch”. Two widely divergent mitochondrial lineages are found in sympatry in A.amietisp. n. ; the status of these lineages, which together form a paraphyletic unit from which A.allosa arose, is briefly discussed. We show that A.allosa, A.amietisp. n. and A.montana are polylectic but that each species exhibits a distinct spectrum of pollen hosts: the univoltine A.allosa shows affinities for pollen of the early-blooming Alpine plant genus Crocus. A.amietisp. n. is bivoltine and, as in A.bicolor, the summer generation exhibits a distinct preference for Campanulaceae, while the spring generation is widely polylectic. A.montana has a single generation in the summer and forages on a diversity of flowers such as Campanulaceae, Cistaceae and Caryophyllaceae. An identification key is presented for central European members of the subgenus Euandrena Hedicke, 1932. Lastly, the new Alpine species appears to represent the tip of the iceberg of substantial cryptic diversity in southern European Andrena (Euandrena): A.croatica Friese, 1887 is resurrected from synonymy with A.bicolor and treated as a valid species (stat. rev.), A.pileata Warncke, 1875, described as a subspecies of A.allosa, is elevated to species rank (stat. n.), and three additional unclear taxa are briefly described.
Complete mitogenome of a Baltic Sea specimen of the non-indigenous polychaete Marenzelleria neglecta

Abstract We sequenced the complete mitogenome of Marenzelleria neglecta, a non-indigenous polychaete of the Baltic Sea originating from North America. This is the first complete mitogenome made available for the family Spionidae. The genome is 15,339 bp with a gene order identical to the generic order of the Pleistoannelida. The multigene maximum likelihood phylogeny, based on all protein-coding genes, weakly resolved the position of M. neglecta, as it tended to asssociate it with species representing the basal lineage of Annelids. This result underlines the need for more mitogenomes of Spionidae in order to improve the accuracy of their phylogeny.
Identification of regulatory genes through global gene expression analysis of a Helicobacter pylori co-culture system

Helicobacter pylori is a gram-negative bacterium that establishes life-long infections by inducing immunoregulatory responses. We have developed a novel ex vivo H. pylori co-culture system to identify new regulatory genes based on expression kinetics overlapping with that of genes with known regulatory functions. Using this novel experimental platform, in combination with global transcriptomic analysis, we have identified five lead candidates, validated them using mouse models of H. pylori infection and in vitro co-cultures under pro-inflammatory conditions. Plexin domain containing 2 (Plxdc2) was selected as the top lead immunoregulatory target. Gene silencing and ligand-induced activation studies confirmed its predicted regulatory function. Our integrated bioinformatics analyses and experimental validation platform has enabled the discovery of new immunoregulatory genes. This pipeline can be used for the identification of genes with therapeutic applications for treating infectious, inflammatory, and autoimmune diseases.
Investigation of zooplankton fauna in water wells of Kuyubeli village (Adana, Turkey) with the first record of the genus Speocyclops Kiefer, 1937 (Copepoda, Cyclopoida, Cyclopidae) for Turkish inland waters

Zooplankton samples were collected from water wells in Kuyubeli village (Kozan, Adana, Turkey). A total of 24 zooplanktonic species were identified, including 13 rotifers, 9 copepods, and 2 cladocerans. The genus Speocyclops was reported for the first time from Turkish inland waters.
An Integrative DNA Sequencing Panel To Assess Mismatch Repair Deficiency

Detecting mismatch repair (MMR) deficiency requires serial testing of both germline and tumour DNA using several assays to determine the underlying mechanism of MMR gene disruption. We have created an integrated targeted panel (MultiMMR) that tests for multiple sources of genome variation from a single aliquot of tumour or normal DNA. We have profiled 11 genes related to MMR deficiency or hereditary cancer syndromes on 82 individuals. For each sample, we performed hybrid capture of a single DNA sequencing library constructed using methylated adapters for parallel bisulfite and conventional sequence analysis. MultiMMR recapitulated clinical testing in 22/24 cases and was able to explain the mechanism of MMR loss in an additional 28 patients. This study has shown the utility of integrated mutation, copy number, and methylation profiling to detect hereditary and somatic causes of MMR deficiency. MultiMMR amalgamates the current step-wise and complex clinical testing workflow into a
Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics

Circadian rhythms are generated by interlocked transcriptional-translational negative feed-back loops (TTFLs), the molecular process implemented within a cell. The contributions, weighting and balancing between the multiple feedback loops remain debated. Dissociated, free-running dynamics in the expression of distinct clock genes has been described in recent experimental studies that applied various perturbations such as slice preparations, light pulses, jet-lag, and culture medium exchange. In this paper, we provide evidence that this “presumably transient” dissociation of circadian gene expression oscillations may occur at the single-cell level. Conceptual and detailed mechanistic mathematical modeling suggests that such dissociation is due to a weak interaction between multiple feedback loops present within a single cell. The dissociable loops provide insights into underlying mechanisms and general design principles of the molecular circadian clock.
The Effects of European Debt Crisis on Turkey’s Exports

The crisis that arose in Greece at the last quarter of 2009 affected the countries that have heavily government debt like Spain, Portugal, Italy and Ireland as soon as 2008 Global Financial Crisis originating from USA Mortgage Markets affect European Union (EU) countries under heavily debt burden. The effects of that crisis in the short run are demand shrinking and decrease in export. Turkey, which has important economic relations with EU countries in the last fifty years, is the primary country that can be negatively affected from demand shrinking in Europe. Turkey that indirectly experience 2008 global financial crisis because of the decrease in export volume in Europe also seem fatefully affected in this crisis. This article aims to determine the effects of the crisis to Turkey’s export ampirically in the EU countries that have the lion’s share in the Turkey’s export markets. As well, it is trying to explain whether this crisis affects over-all Europe or not.
Using Educational Social Networking Sites in Higher Education: Edmodo through the Lenses of Undergraduate Students

Social Networking Sites (SNSs) such as Facebook, Google+, MySpace, have been used intensively and effortlessly by students currently. Thus, the use of such SNS paves the way for questioning how these sites can be effectively used in educational environments. Since the SNSs in educational environments are potentially used, Educational Social Networking Sites (ESNSs) in the market such as Edmodo, Ning, Elgg, which are innovative educational environments with social networking capabilities, have also been employed in education. The aim of this study is to determine why the undergraduate students use the Internet, SNSs and Edmodo which is an ESNS and to investigate their views about these tools. In this context, Edmodo was used within the scope of an undergraduate course. And in order to collect data about this experience, interviews with 15 students and a focus group interview with 7 students were performed. In analysis and interpretation of the data used, both uses and gratifications theory and diffusions of innovations theory were taken into consideration. As a result, it was found that the students expressed their likes about Edmodo’s features of assignment, quiz, poll and announcement / sharing. The study also reveals that the students also expressed their thoughts about the contributions of Edmodo to educational environments.
Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.
Interscapular and Perivascular Brown Adipose Tissue Respond Differently to a Short-Term High-Fat Diet

Brown adipose tissue (BAT) function may depend on its anatomical location and developmental origin. Interscapular BAT (iBAT) regulates acute macronutrient metabolism, whilst perivascular BAT (PVAT) regulates vascular function. Although phenotypically similar, whether these depots respond differently to acute nutrient excess is unclear. Given their distinct anatomical locations and developmental origins and we hypothesised that iBAT and PVAT would respond differently to brief period of nutrient excess. Sprague-Dawley rats aged 12 weeks (n=12) were fed either a standard (10% fat, n=6) or high fat diet (HFD: 45% fat, n=6) for 72h and housed at thermoneutrality. Following an assessment of whole body physiology, fat was collected from both depots for analysis of gene expression and the proteome. HFD consumption for 72h induced rapid weight gain (c. 2.6%) and reduced serum non-esterified fatty acids (NEFA) with no change in either total adipose or depot mass. In iBAT, an upregulation of genes involved in insulin signalling and lipid metabolism was accompanied by enrichment of lipid-related processes and functions, plus glucagon and peroxisome proliferator-activated receptor (PPAR) signalling pathways. In PVAT, HFD induced a pronounced down-regulation of multiple metabolic pathways which was accompanied with increased abundance of proteins involved in apoptosis (e.g., Hdgf and Ywaq) and toll-like receptor signalling (Ube2n). There was also an enrichment of DNA-related processes and functions (e.g., nucleosome assembly and histone exchange) and RNA degradation and cell adhesion pathways. In conclusion, we show that iBAT and PVAT elicit divergent responses to short-term nutrient excess highlighting early adaptations in these depots before changes in fat mass.
The Evaluation of Lidocaine-hydrochloride as Anaesthetic for the Transportation of Rhynchocypris steindachneri

The experimental transportation of Rhynchocypris steindachneri was carried out to study the effects of lidocaine-hydrochloride on water parameters. The dissolved oxygen, ventilation rate, ammonia nitrogen, and pH of control group, sham control group, and lidocaine-hydrochloride treated groups of 2,5 ppm, 5 ppm, 10 ppm and 20 ppm at time of 30 min, 60 min, 90 min, 120 min, 240 min and 360 min after elapsed from treatment were tested. During the experiment time it was found that lidocaine-hydrochloride treated groups were most effective, followed by sham control and control, in decreasing the oxygen consumption and the excretion of ammonia by the fish. There were lidocaine-hydrochloride dose-related decrease in oxygen consumption and the excretion of ammonia. Decreasing in pH value of lidocaine-hydrochloride groups and sham control group was much more higher than that of control group. These results reveal lidocaine-hydrochloride is effective as sedative for transportation mixture in R. steindachneri.
The Savvy Survey #5: The Process for Developing Survey Questions

A useful process for developing a high-quality questionnaire follows four steps. Brainstorm questions on a topic. Review the literature for concepts, questions, and indices. Collect ideas for questions and wording choices through focus groups or key informant interviews. And select questions linked to a program’s logic model. Each of these steps is discussed in this 3-page fact sheet written by Glenn D. Israel and Jessica L. Gouldthorpe and published by the UF Department of Agricultural Education and Communication, August 2013. http://edis.ifas. ufl.edu/pd065