Miracle-dz/UniFAR-FTUs huggingface dataset:
A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping

Alternative splicing plays an important role in eukaryotic gene expression by producing diverse proteins from a single gene. Predicting how genes are transcribed is of great biological interest. To this end, massively parallel whole transcriptome sequencing, often referred to as RNA-Seq, is becoming widely used and is revolutionizing the cataloging isoforms using a vast number of short mRNA fragments called reads. Conventional RNA-Seq analysis methods typically align reads onto a reference genome (mapping) in order to capture the form of isoforms that each gene yields and how much of every isoform is expressed from an RNA-Seq dataset. However, a considerable number of reads cannot be mapped uniquely. Those so-called multireads that are mapped onto multiple locations due to short read length and analogous sequences inflate the uncertainty as to how genes are transcribed. This causes inaccurate gene expression estimations and leads to incorrect isoform prediction. To cope with this problem, we propose a method for isoform prediction by iterative mapping. The positions from which multireads originate can be estimated based on the information of expression levels, whereas quantification of isoform-level expression requires accurate mapping. These procedures are mutually dependent, and therefore remapping reads is essential. By iterating this cycle, our method estimates gene expression levels more precisely and hence improves predictions of alternative splicing. Our method simultaneously estimates isoform-level expressions by computing how many reads originate from each candidate isoform using an EM algorithm within a gene. To validate the effectiveness of the proposed method, we compared its performance with conventional methods using an RNA-Seq dataset derived from a human brain. The proposed method had a precision of 66.7% and outperformed conventional methods in terms of the isoform detection rate.
Molecular mechanisms of germ cell specification and migration in Xenopus laevis

Vegetal localization of mRNA during Xenopus oogenesis is critical for future germ layers formation, embryonic patterning and germ line development. In frogs, a number of germ cells specific transcripts were identified, but functional role of majority of these mRNAs remains unknown. In this work, we aimed in isolation and functional characterization of two novel vegetally localizing and germ line specific transcripts XGRIP2.1 and xKIF13B. Our gain- and loss-of-function data suggest an important role for XGRIP2.1 is PGC positioning along the anteroposterior axis of Xenopus embryos, whereas XKIF13B is involved in the establishing of germ cell polarity and proper directional migration of PGCs. In scopes of the XGRIP2.1 part of the project, we identified a minimal localization element necessary and sufficient for XGRIP2.1 mRNA translocation to the vegetal pole of an oocyte. Analysis of the protein binding profile of this fragment revealed striking similarities with two other germ plasm/ germ cell specific mRNAs. Another part of the work was devoted to establishing the in vivo imaging of germ cell migration in the context of the entire embryo and in culture as well as to the assignment of the proper positioning of PGCs along the anteroposterior axis of tailbud stage embryos, which was not described earlier.
Plant-animal interactions : an evolutionary approach

Part I: Introduction1. Species Interactions and the Evolution of Biodiversity. (Peter W. Price)2. The History of Associations between Plants and Animals. (Conrad C. Labandeira)Part II: Mostly Antagonisms3. Plant-Insect Interactions in Terrestrial Ecosystems. (Sharon Y. Strauss and Arthur R. Zangerl)4. Mammalian Herbivory in Terrestrial Environments. (Kjell Danell and Roger Bergstrom)5. Granivory. (Philip E. Hulme and Craig W. Benkman)Part III: Mostly Mutualisms6. Pollination by Animals. (Olle Pellmyr)7. Seed Dispersal by Vertebrates. (Carlos M. Herrera)Part IV: Synthesis8. Ant-Plant Interactions. (Andrew J. Beattie and Lesley Hughes)9. Plant-Animal Interactions: Future Directions. (John N. Thompson)Appendix: Supplementary Information for Chapter 2
Economic impacts of labelling thresholds for the adventitious presence of genetically engineered organisms in conventional and organic seed

The level of the labelling threshold will have profound impacts on the future of farming with respect to the possibility of co-existence and consumer choice: co-existence costs for farmers and the entire food chain will be influenced by the level of seed purity. A labelling threshold above 'zero' would allow contamination with GE organisms to become permanently entrenched at the seed level, threatening existing EU food markets that rely on segregation, traceability and transparency. It would increase costs for maintaining co-existence and also bring about financial losses for farms and processors. Consumer choice would be narrowed, and in some market segments even completely eliminated. To some extent the tasks of the risk manager would be impacted as well.
Field calculation in single- and multilayer coaxial cylindrical shells of infinite length by using a coupled T- Omega and boundary element method

A method is presented for the calculation of the electromagnetic field in systems of single-layer or multilayer coaxial cylindrical shells of infinite length excited by an oscillating current source arbitrarily oriented inside the first shell. The electric vector potential T and the magnetic scalar potential Omega are used for the evaluation of the quantities of the problem. The Helmholtz equations for T and Omega are transformed into integral equations by the use of the Green's function method. Applying the boundary element method, three systems of simultaneous equations have to be solved to give the sought field quantity. >
Over weight, obesity and metabolic syndrome in a semi urban adolescent population in Uyo, Nigeria

Background: Overweight and Obesity are becoming increasingly common in developing countries with the attendant health risks associated with these conditions including Metabolic syndrome. The aim of this study was to find out the prevalence of overweight, obesity and metabolic syndrome in a population of adolescents living in a semi urban area and the relationship between the weights of these children and the various components of the metabolic syndrome. Materials and Methods: One hundred and fifty-five adolescents aged 10-17 years were selected via a multistage random sampling technique. Sociodemographic data were obtained using a structured questionnaire and anthropometric indices were measured using standard tools. Overweight and obesity were defined based on the International Obesity Task Force criteria while metabolic syndrome was defined using the International Diabetes Foundation criteria. Blood samples were taken for Fasting blood sugar, serum Triglycerides and High-density lipoprotein cholesterol. Results: The prevalence of overweight, obesity and metabolic syndrome were 1.94%, 0%, and 1.94% respectively. Weight showed a significant positive correlation with the study participants’ waist circumference, systolic and diastolic blood pressures but not with serum triglyceride, high density lipoprotein cholesterol and fasting blood glucose levels. Abdominal obesity and hyperglycaemia werealso significantly associated with Metabolic syndrome. Conclusion: The prevalence of overweight, obesity and metabolic syndrome was very low in the population studied however, weight demonstrated a significant positive correlation with some components of the metabolic syndrome.
Genetic diversity analysis on Brassica campestris L. from Guizhou Province in China.

RAPD markers were used to analyze the genetic diversity of 65 Brassica Campestri L.from Guizhou Province.16 primers were selected from 78 random primers by their PCR amplification quality and efficiency in revealing polymorphic fragments in rapeseed.Among the 153 amplified fragments,137 were polymorphic between the studied varieties.The average number of polymorphism bands revealed by each primer was 8.6. The size of these band arrange from 150 to 1800 bp.A dendrogram with 65 varieties of Brassica Campestri L.from Guizhou province was constructed by UPMGA method.The genetic distance of 65 Brassica Campestri L is from 0.1431 to 0.9904,and genetic identity is from 0.3714 to 0.8667. The genetic distance between Fengang-Huayoucai(2) and Majiang-Huayoucai(2) was the smallest(0.1431) and the genetic similarity was the highest(0.8667). The results indicated that a high genetic diversity was present among the 65 Brassica Campestri L.from Guizhou province and this was in a good accordance with their geographic distribution.
Colonisation and diversification in invertebrates : looking within species on islands to connect pattern and process

How species originate and how communities of species assemble are among the most intriguing questions in biology, and colonisation is a key element to understand them. Using two island scenarios and applying molecular tools, this thesis looks within species to investigate the themes of colonisation (both island colonisation and European continental recolonisation) and diversification processes in invertebrates. The aim was to address three gaps in our understanding about island colonisation, speciation and the assembly of biota. In the Canary Islands, an oceanic island system, the gaps addressed were: (i) the possibility that genomic admixture among multiple founding lineages has featured in the diversification of a very species rich coleopteran genus; and (ii) the lack of information regarding the colonisation history and dynamics of the small arthropod soil dwelling fauna. In Great Britain, a continental island system, the gap addressed was the under-explored possibility that the UK was not completely defaunated during glaciations, then recolonised from external sources, but that a more complex pattern, involving persistence within small cryptic refugia, may have featured in the history of its invertebrate soil dwelling fauna. I reveal two instances of shared mtDNA variation among weevil species from different Canarian islands for which I was able to dismiss explanations of incomplete lineage sorting and reveal a history of colonisation and speciation involving genetic admixture (first gap). I characterise Collembola evolutionary diversity within Tenerife and the distribution of lineage colonisation times, and reveal this fauna to be represented by a mosaic of very old lineages and a large number of very recently arrived lineages (second gap). Finally, I reveal signatures of survival and persistence of the Collembola fauna through the last Pleistocene glaciation in Great Britain (third gap). How these results fit into a broader evolutionary and conservation context as well as future directions are discussed.
Herbicidas alternativos no controle de Bidens pilosa e Euphorbia heterophylla resistentes a inibidores de ALS na cultura do algodão

The presence of Bidens pilosa and Euphorbia heterophylla resistant to ALS inhibitors is a problem to weed management in cotton crop, due to the fact that few alternatives broadleaf selective herbicides area available. In order to supply this information gap, four experiments were established in greenhouse conditions with the objective of evaluating herbicides applied in post-emergence conditions, recommended either for conventional and transgenic cotton (resistant to glyphosate and amonio-glufosinate) for controlling these resistant biotypes. The experimental design was entirely randomized with four replications and 21 herbicides treatments, besides a check without herbicide application. Two experiments were conducted per species, where the first one corresponded to herbicides application in stages of two to four leaves, and the second in the stage of four to six. It was evaluated the percentage of control at 7 and 28 days after herbicide application. Amonio-glufosinate and glyphosate applied isolated or in combinations with other herbicides were effective in controlling B. pilosa independently of the growth stage. The two biotypes demonstrated to be highly resistant to ALS inhibitor herbicides. E. heterophylla showed greater sensitivity to herbicide amonio-glufosinate herbicide and glyphosate in early stages applications. Glyphosate stood out as a satisfactory alternative for controlling E. heterophylla . For this biotype, synergistic effect was verified for associations between amonio-glufosinate and pyrithiobac-sodium.
2P optogenetics : simulation and modeling for optimized thermal dissipation and current integration

Depuis maintenant quinze ans, l’optogenetique a bouleverse la recherche en neurosciences en permettant de controler les circuits neuronaux. Le developpement recent de plusieurs approches d’illumination, combinees a de nouvelles proteines photosensibles, les opsines, ont permis d’ouvrir une voie vers le controle neuronale avec la precision de la cellule unique. L’ambition nouvelle d’utiliser ces approches afin d’activer des dizaines, centaines, milliers de cellules in vivo a souleve de nombreuses questions, notamment concernant les possibles degâts photoinduits et l’optimisation du choix du couple illumination/opsine. Lors de mon doctorat, j’ai concu une simulation verifiee experimentalement qui permet de calculer, dans toutes les conditions actuelles d’illumination, quel sera l’echauffement au sein du tissus cerebral du a l’absorption de la lumiere par le cerveau. Parallelement, j’ai parametre a partir de donnees experimentales des modeles de dynamique des populations, a partir d’enregistrements d’electrophysiologie, qui permettent de simuler les courants intracellulaires observes lors de ces photostimulations, pour trois proteines differentes. Ces modeles permettront les chercheurs d’optimiser leurs protocoles d’illumination afin de garantir l’echauffement le plus faible possible dans l’echantillon, tout en favorisant des dynamiques de photocourant adaptees aux besoins experimentaux.
Influence of Rootstocks on Changing the Pattern of Phenolic Compounds in Thompson Seedless Grapes and Its Relationship to the Incidence of Powdery Mildew

The total phenolic content and individual groups of phenols, such as flavonones, flavonoids, and flavon-3-ols, were estimated in the leaves and berries of Thompson Seedless grapes grafted onto different rootstocks and own-rooted vines during 3 stages of berry development. The leaves at all the stages of sampling contained more total phenol and individual phenolic groups than berries. The reduction in phenolic content was gradual in leaves from the first to third stage of sampling, but it was drastic in berries. Thompson Seedless grafted onto Dog ridge, 110 R, and 1103 P rootstocks had the highest phenolic content and individual phenolic groups in the third stage of sampling and the least on Thompson Seedless grafted onto 99 R, St. George rootstocks, and onto own-rooted vines. The number of bunches infested with powdery mildew was the highest on own-rooted vines, and on those grafted onto St. George and 99 R. A significant negative correlation was observed between the number of bunches infected by powdery mildew and phenolic content.
The Using Incentives to Control Deforestation in the Andes- Amazon: insights from Field Study of Opportunity Costs

This paper uses a property-level dataset of socio-economic and physical information from more than 500 properties in three Andean countries to estimate supply curves of land for conservation via incentive programs. We also evaluate the expected impact of a basic incentive payments program and several proposed improvements in design. We find that the distribution and magnitude of opportunity costs present two challenges. First, a large percentage of the landscape will remain forested in the medium term independent of any incentive. Second, landowners likely place a value on land they plan to clear that significantly exceeds the payment offered by existing incentive programs. We find significant potential to reduce the cost of avoiding deforestation through 1) focusing operations on regions with higher deforestation rates, 2) targeting regions and actors who clear for less profitable activities, and 3) excluding from contracts those areas that are less likely to be cleared.
Ca2+ signaling in porcine myometrial cells: Ca2+ channels, intracellular Ca2+ stores and guanine nucleotide-binding protein-coupled receptors

Introduction 91 92 iii Metiiods 94 Results 95 Discussion 105 Acknowledgments 112 References 11 2 CHAPTER VI OXYTOCIN-INDUCED A BIPHASIC INCREASE IN [CA'^], IN 117 PORCINE MYOMETRIAL CELLS FROM PREPARTUM SOWS: PARTICIPATION OF PERTUSSIS-SENSITIVE G-PROTEIN, INOSITOL-1,4,5-TRISPHOSPHATESENSITIVE CA^-" STORE AND VOLTAGE-DEPENDENT CA'^" CHANNELS Abstract 11 7 Introduction 118 Materials and Methods 11 9 Results 122 Discussion 137 Acknowledgements 141 References 14111 7 Introduction 118 Materials and Methods 11 9 Results 122 Discussion 137 Acknowledgements 141 References 141 CHAPTER VII SIGNALING MECHANISMS ON Oj-ADRENERGIC RECEPTOR146 MEDIATED CA^"' INFLUX AND RELEASE IN PORCINE MYOMETRIAL CELLS Abstract 146 Introduction 147 Experimental Procedures 148 Results 150 Discussion 165 Acknowledgments 172 References 172146 Introduction 147 Experimental Procedures 148 Results 150 Discussion 165 Acknowledgments 172 References 172 CHAPTER Vlil GENERAL DISCUSSION 175 L-type and T-type Voltage-dependent Ca^"^ Channels 175 IP3and Caffeine-sensitive intracellular Ca^^ Stores 177 Modulation of L-type Ca^^ Currents by G Protein-coupled Receptors 179 Voltage-independent Ca^"^ Channels 181 iv Modulation of Ca^^ by G protein-coupled Receptors 182 G protein: Signal Organizer 183 Physiological Implications of Oj-adrenergic receptors 184 CHAPTER IX GENERAL CONCLUSIONS 187 LITERATURE CITED 191 ACKNOWLEDGEMENTS 210
Investigating the mechanical & structural properties of human cells using atomic force & confocal microscopy.

This thesis describes the use of atomic force microscopy (AFM) and laser scanning confocal microscopy (LSM) to image and investigate the mechanical properties of two morphologically and functionally different human cell types, namely epithelial (NCI H727) and fibroblast (LL24) cells. Both the NCI H727 and LL24 cells were found to require different imaging parameters, in order to produce optimal images using the atomic force microscope. In contact mode, optimal loading forces ranged between 2 and 2.8x10 and 0.1 and 0.7x10 Newtons for LL24 and NCI H727 cells, respectively. In tapping mode, images of LL24 cells were obtained using cantilevers with a spring constant of at least 0.32 N/m, while NCI H727 cells required a greater spring constant of at least 0.58 N/m. To obtain tapping mode images, cantilevers needed to be tuned to oscillate above their fundamental resonant frequency in liquid. For NCIH 727 cells, contact mode imaging produced the clearest images. For LL24 cells, contact and tapping mode AFM produced images of comparable quality. A non-linear, extended Hertz model was developed and found to fit the AFM force data exceptionally well. When the apparent Young’s modulus (E) was plotted as a function of indentation, it was found that both the LL24 and NCI H727 cells exhibited a cell softening effect, which was followed by an increase in E. Overall, there was found to be considerable variation in the cell stiffness parameters (K1, K2 and Eb) for all populations of single and confluent LL24 and NCI H727 cells. Confluent LL24 cells were found to behave more uniformly in response to force compared with single LL24 cells. However, single NCI H727 cells were found to behave more uniformly than NCI H727 cells in a monolayer. The NCI H727 cells growing in a monolayer had considerably greater values of K1, K2 and Eb than the single NCI H727 cells. In contrast, the difference in K1, K2 and Eb for single LL24 cells versus LL24 cells grown to confluence did not differ considerably. When comparing the difference in the apparent stiffness between single LL24 cells and single NCI H727 cells, it was found that K1, K2 and Eb were considerably greater for the LL24 cells than the NCI H727 cells. Also, it was found that K1, K2 and Eb for the confluent LL24 cells were greater than for the NCI H727 cells grown in a monolayer. When increasing the strain rate during force-indentation measurements on single LL24 cells, the cells were found to display evidence of viscoeleastic behaviour. Interestingly, when prolonged force was applied to the surface of the LL24 cells, in some cases, the cells were found to exert a force back against the AFM cantilever. From investigation of the cytoskeleton using fluorescence microscopy, it was found that single LL24 cells contain actin stress fibres which decrease as cell density increases. Finally, it was found that the nuclear-membrane distance (distance between the cell nucleus and cell membrane) was greater in the NCI H727 cells compared with the LL24 cells, 1. 8μm versus 1. 5μm, respectively.
Determination of electro-energizing conditions for L-glutamic acid fermentation

The most effective electro-energizing fermentation (E-E F) conditions for l-glutamate (l-Glu) production by Brevibacterium flavum No. 2247 were determined. The adding of 0.01 mm neutral red at the beginning of cultivation was found most effective. A 1.5 V direct current was applied to the culture broth at 6~8 hr after inoculation in the cathode compartment, l-Glu was produced at 51.0 mg per ml, and this is about a 15 % increase in yield compared to the yield of the not electro-energizing (E-E) control (44.3 mg/ml).
Coronavirus Disease-2019 (COVID-19) and Cardiovascular Complications

Abstract The coronavirus disease 2019 (COVID-19) has become a global pandemic. It has been spread to more than 100 countries and more than 1 million patients have been confirmed. Although coronavirus causes severe respiratory infections in human, accumulating data have demonstrated cardiac complications and poor outcome in patients with coronavirus disease 2019. A large percent of patients have underlying cardiovascular disease and they are at a high risk of developing cardiac complications. We review the basics of the virus, the clinical manifestation, and the possible mechanisms of cardiac complications in patients with coronavirus disease 2019. Before the effective vaccine or medicine is available, supportive therapy and identifying patients who are at high risk of cardiac complications are important.
On the nature of the 35-day cycle in the X-ray binary Her X-1/HZ Her

Abstract The X-ray binary Her X-1 consists of an accreting neutron star and the optical companion HZ Her. The 35-day X-ray variability of this system is known since its discovery in 1972 by the UHURU satellite and is believed to be caused by forced precession of the warped accretion disk tilted to the orbital plane. We argue that the observed features of the optical variability of HZ Her can be explained by free precession of the neutron star with a period close to that of the forced disk precession. The model parameters include a) the intensity (power) of the stream of matter flowing out of the optical star; b) the X-ray luminosity of the neutron star; c) the optical flux of the accretion disk; d) the X-ray irradiation pattern on the donor star; e) the tilt of the inner and outer edge of the accretion disk. A possible synchronization mechanism based on the coupling between the neutron star free precession and the dynamical action of non-stationary gas streams is discussed shortly.