Miracle-dz/UniFAR-FTUs huggingface dataset:
Potentiel toxique et structure génétique de populations de Microcystis en lien avec les différentes phases de son cycle de vie

L‟eutrophisation croissante des ecosystemes aquatiques favorise le developpement des cyanobacteries, parmi lesquelles Microcystis est la plus representee dans les regions temperees. La capacite de Microcystis a produire une puissante hepatotoxine, la microcystine, est a l‟origine de diverses perturbations ecologiques, et de nombreuses nuisances sanitaires. La comprehension des facteurs determinant la toxicite des efflorescences de Microcystis constitue, de fait, un enjeu majeur des recherches actuelles. Dans ce contexte, l‟objectif premier de ce travail de these etait d‟etudier la variabilite temporelle et l‟implication potentielle de la toxicite de Microcystis a l‟echelle de son cycle de developpement annuel. Pour cela, il etait necessaire de considerer, en particulier, les parties les moins connues du cycle de developpement : la phase de survie benthique, et les transitions entre les phases benthique et planctonique, via les processus de recrutement et de sedimentation. Nous avons alors etudie le potentiel toxique des populations de Microcystis grâce a des approches complementaires menees a differentes echelles spatio-temporelles, en considerant a la fois les genes impliques dans la synthese de microcystines, leur transcription et les concentrations en microcystines. Cette etude s‟est appuyee, en parallele, sur la caracterisation de la structure genetique des populations de Microcystis dans les compartiments benthique et planctonique. La prise en compte systematique de la phase de vie benthique a tout d‟abord permis d‟ameliorer nos connaissances sur cette phase du cycle de developpement de Microcystis. Ainsi, Microcystis peut survivre plusieurs annees en profondeur dans les sediments, sans que les populations ne perdent leur potentiel toxique, ou que leur structure genetique soit alteree. En revanche, en surface des sediments, le potentiel toxique et la structure genetique des populations sont variables, de maniere similaire a ce qui peut etre observe dans la colonne d‟eau. Enfin, ces travaux ont egalement mis en evidence l‟influence des phases de transition entre l‟eau et les sediments dans la variabilite du potentiel toxique et de la structure genetique des populations de Microcystis. Les processus de recrutement benthique et de sedimentation occasionnent, en effet, une selection genetique, qui, bien que paraissant independante du potentiel toxique des genotypes, peut grandement affecter le potentiel toxique des sous-populations benthiques et planctoniques de Microcystis.
Structural studies of RNA localisation signals

Asymmetric localisation of cytoplasmic mRNA in the cell appears in a variety of organisms and is important for establishment of spatially differential expression of genes. Localised transcripts typically contain codes (localisation signals), expressed within cis-acting elements that specify subcellular targeting. These signals are recognised by a complex of adaptor and motor proteins that move along the cytoskeleton. Cis-acting elements usually present in the 3'-UTRs of localising transcripts. Different signals do not appear to share either primary or secondary structures that are distinct from non-localising transcripts. Although secondary structure is important, the structural basis of the elements that contribute to the specificity of the localising transcripts is poorly understood. The presented thesis examines the basis of selective RNA transport, by studying the shortest signal known to drive localisation in Drosophila Melanogaster, a 44 nucleotides sequence on the 3' UTR of the fs(1)K10 transcript. This signal is necessary and sufficient for its localisation during embryo development and has a structure of stem loop with two unpaired bases ("bulges"). The components that are important for signal activity are analysed by studying the effect of specific mutations on localisation in the embryo and on the corresponding structure of the RNA. Using NMR structure solution, the importance of the two bulges is demonstrated in wild type and mutated signals and a new structural element of an unusual B-form-like double-stranded RNA helix is revealed. This unusual helix form subsequently been shown to be crucial for the localisation of the K10 transcript. These features might be important as representatives of a general structure that characterise a common group of localising transcripts.
Restoration and management of wildflower-rich machair for the conservation of bumblebees

ii List of Figures xii Declaration xvi 1 General introduction 1 1.1 The decline of bumblebees 1 1.2 Agricultural intensification 2 1.2.1 Habitat loss and fragmentation 3 1.2. 2 The negative impact of herbicides and fertilisers 6 1.2. 3 Grassland management 7 1.2. 4 Bumblebee conservation within agricultural landscapes 11 1.3 The great yellow bumblebee, Bombus distinguendus 13 1.3. 1 Machair – The Last Stronghold 15 1.3. 2 Machair management and restoration: The future of great yellow bumblebee conservation? 20 1.4 Aim and structure of the thesis 20 2 A comparative analysis of the foraging behaviour of the rare and declining bumblebee Bombus distinguendus 22 2.1 Abstract 22
Biochemical markers for the detection and classification of Aspergillus

The genus Aspergillus includes a diverse group of filamentous fungi that are widely distributed in nature, commonly found in soil. The Aspergilli include species that can be beneficial or detrimental to humans, so detection and accurate identification of these organisms can be very important. Morphology and genetic sequence analysis are well established methods for classifying and identifying fungi, but morphology remains a widely used technique that generally works well for Aspergilli. However, some organisms may be misidentified due to atypical morphology and some hidden (cryptic) species may not be recognized as different from named species based on readily observable traits. In this study, reference strains of different Aspergillus species, Penicillium chrysogenum, Candida albicans, and Cryptococcus neoformans were characterized using LC/MS and GC/MS biochemical profiling techniques in order to find specific small molecules, peptides or biochemical profiles that can be used in addition to established methods to detect and classify Aspergilli to the species level. Subsequently, analytical methods developed for characterizing the reference strains were applied, along with morphology and PCR, to characterize and identify several laboratory and field isolates. Some unique compounds and biochemical patterns did emerge from small molecule profiling that could be used for classifying Aspergilli, but protein profiling by LC/MS/MS was a much more effective approach. Tandem mass spectra from LC/MS/MS of tryptic peptides from fungal proteins were searched against protein databases and matched to theoretical spectra derived from those databases. Many of the amino acid sequences detected were taxonomically diagnostic for classifying Aspergillus species. Protein profiling also provided a great deal of additional biochemical information on the test organisms by identifying the predominant enzymes and structural proteins present under different experimental conditions and may find broader application for identifying and studying other organisms.
Early Effector T Cells Producing Significant IFN-γ Develop into Memory1

Currently, transition of T cells from effector to memory is believed to occur as a consequence of exposure to residual suboptimal Ag found in lymphoid tissues at the waning end of the effector phase and microbial clearance. This led to the interpretation that memory arises from slightly activated late effectors producing reduced amounts of IFN-γ. In this study, we show that CD4 T cells from the early stage of the effector phase in which both the Ag and activation are optimal also transit to memory. Moreover, early effector T cells that have undergone four divisions expressed significant IL-7R, produced IFN-γ, and yielded rapid and robust memory responses. Cells that divided three times that had marginal IL-7R expression and no IFN-γ raised base level homeostatic memory, whereas those that have undergone only two divisions and produced IFN-γ yielded conditioned memory despite low IL-7R expression. Thus, highly activated early effectors generated under short exposure to optimal Ag in vivo develop into memory, and such transition is dependent on a significant production of the cell’s signature cytokine, IFN-γ.
Sex differences between serum uric acid levels and cardiovascular outcomes in patients with coronary artery disease after stent implantation

Background The relationship between elevated serum uric acid (SUA) levels and cardiovascular outcomes after stent implantation remains uncertain. This study sought to evaluate the impact of SUA on 12-month cardiovascular outcomes after stent implantation. Methods We performed a retrospective study of patients who successfully underwent stent implantation and enrolled 3,222 patients with coronary artery disease (CAD) from a single center. SUA levels were measured before stent implantation. The patients were divided into six groups (<4, 4–4.9, 5–5.9, 6–6.9, 7–7.9 and ≥ 8 mg/dL) at SUA intervals of 1.0 mg/dL. The incidence of cardiovascular outcomes in the six groups was monitored for 1 year after stent implantation and the hazard ratios were estimated. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) for cardiovascular outcomes were estimated using a Cox proportional hazard regression analysis. The primary endpoint was all-cause death. The secondary endpoint was a composite of all-cause death, myocardial infarction, target vessel revascularization, stent thrombosis and stroke. The follow-up duration was 12 months. Results Over the 12-month follow-up period, there were 101 all-cause deaths and 218 MACCE. After adjustment for several parameters, the group with SUA levels of more than or equal to 8 mg/dL had significantly higher hazard ratios in the incidence of all-cause death or MACCE. The group with <4.0 mg/dL had significantly higher hazard ratios in all-cause death only in male patients. In contrast, there were no significant differences observed for cardiovascular outcomes in female patients. Conclusions Our study identified a U-shaped association between SUA levels and cardiovascular outcomes during 12-month follow-up for males, but not for females. Further studies are warranted to clarify the sex differences between SUA levels and clinical outcomes.
Use of ichthyoplankton ecology to evaluate ecosystem changes: a case study in a large, semi-enclosed Australian bay

Intensive night sampling was conducted fortnightly in 1995/96 to investigate the ichthyoplankton assemblage of Port Phillip Bay. Results are compared with those from a similar survey in 1983/84, and are used to ascertain whether major changes have occurred in the composition and abundance of fish eggs and larvae, and whether these are related to ecosystem changes in the bay between 1969 and 1995. The 17 157 larvae caught during this study belonged to 60 taxa from 32 teleost fish families, with Gobiidae (54.2%), Engraulidae (16.7%), Clinidae (10.0%) and Odacidae (5.9%) dominating the catches. Larval concentrations peaked only in summer, in contrast to summer and winter in 1983/84. Larvae from 13 families recorded in 1995/96 did not occur in 1983/84, including Gobiesocidae (9 spp.) and Odacidae (3 spp.). Larvae absent in 1995/96 but present in 1983/84 included Acanthopegasus lancifer (Pegasidae) and taxa from another seven families. Neoodax balteatus larvae ranked fourth in 1995/96 but were absent in 1983/84, while Engraulis australis eggs and Gymnapistes marmoratus larvae were comparatively fewer in 1995/96. We suggest that some of the main differences between the two surveys may be attributable to major ecosystem changes in the bay, particularly the introduction and establishment of exotic marine species.
Perubahan Histopatologi Hati Mencit (Mus musculus) yang Diberikan Ekstrak Daun Ashitaba (Angelica keiskei)

Penelitian ini bertujuan untuk mengetahui perubahan histopatologi hati mencit (Musmusculus) yang diberikan ekstrak daun Ashitaba (Angelica keiskei). Penelitian inimenggunakan 25 ekor mencit jantan yang dibagi secara acak sederhana menjadi 5 grup.Grup A sebagai kontrol diberikan aquades, dan grup B, C, D, dan E masing-masingdiberikan 125 mg, 250 mg, 500 mg dan 1000 mg extrak Ashitaba secara oral. Pemberianekstrak etanol daun Ashitaba dilakukan setiap hari selama 21 hari. Pada hari ke 22 semuamencit dinekropsi dan hati diambil untuk diproses pembuatan preaparat dengan metodeembedding blocking dengan paraffin serta pewarnaan hematoxylin eosin (HE). Pemeriksaanperubahan histopatologi dilakukan berdasarkan adanya degenerasi melemak dan nekrosis.Hasil penelitian menunjukkan adanya nekrosis dan degenerasi yang ringan pada semuagrup perlakuan. Hasil analisis statistik dengan metode Kruskal Wallis menunjukkan hasilyang tidak berbeda diantara grup perlakuan. Penelitian ini membuktikan ekstrak daunAshitaba (Angelica keiskei) antara dosis 125 mg sampai 1.000 mg tidak menimbulkan efektoksik pada hati mencit.
Advances in the oral microbiota and rapid detection of oral infectious diseases

Several studies have shown that the dysregulation of the oral microbiota plays a crucial role in human health conditions, such as dental caries, periodontal disease, oral cancer, other oral infectious diseases, cardiovascular diseases, diabetes, bacteremia, and low birth weight. The use of traditional detection methods in conjunction with rapidly advancing molecular techniques in the diagnosis of harmful oral microorganisms has expanded our understanding of the diversity, location, and function of the microbiota associated with health and disease. This review aimed to highlight the latest knowledge in this field, including microbial colonization; the most modern detection methods; and interactions in disease progression. The next decade may achieve the rapid diagnosis and precise treatment of harmful oral microorganisms.
Sodium/(calcium + potassium) exchanger NCKX4 optimizes KLK4 activity in the enamel matrix microenvironment to regulate ECM modeling

Enamel development is a process in which extracellular matrix models from a soft proteinaceous matrix to the most mineralized tissue in vertebrates. Patients with mutant NCKX4, a gene encoding a K+-dependent Na+/Ca2+—exchanger, develop a hypomineralized and hypomature enamel. How NCKX4 regulates enamel protein removal to achieve an almost protein-free enamel is unknown. We characterized the upregulation pattern of Nckx4 in the progressively differentiating enamel-forming ameloblasts by qPCR, and as well as confirmed NCKX4 protein to primarily localize at the apical surface of wild-type ruffle-ended maturation ameloblasts by immunostaining of the continuously growing mouse incisors, posing the entire developmental trajectory of enamel. In contrast to the normal mature enamel, where ECM proteins are hydrolyzed and removed, we found significant protein retention in the maturation stage of Nckx4 −/− mouse enamel. The Nckx4 −/− enamel held less Ca2+ and K+ but more Na+ than the Nckx4 +/+ enamel did, as measured by EDX. The alternating acidic and neutral pH zones at the surface of mineralizing Nckx4 +/+ enamel were replaced by a largely neutral pH matrix in the Nckx4 −/− enamel. In situ zymography revealed a reduced kallikrein-related peptidase 4 (KLK4) activity in the Nckx4 −/− enamel. We showed that KLK4 took on 90% of proteinase activity in the maturation stage of normal enamel, and that recombinant KLK4 as well as native mouse enamel KLK4 both performed less effectively in a buffer with increased [Na+] and pH, conditions found in the Nckx4 −/− developing enamel. This study, for the first time to our knowledge, provides evidence demonstrating the impaired in situ KLK4 activity in Nckx4 −/− enamel and suggests a novel function of NCKX4 in facilitating KLK4-mediated hydrolysis and removal of ECM proteins, warranting the completion of enamel matrix modeling.
Management of respiratory tract exacerbations in people with cystic fibrosis: Focus on imaging

Respiratory tract exacerbations play a crucial role in progressive lung damage of people with cystic fibrosis, representing a major determinant in the loss of functional lung tissue, quality of life and patient survival. Detection and monitoring of respiratory tract exacerbations are challenging for clinicians, since under- and over-treatment convey several risks for the patient. Although various diagnostic and monitoring tools are available, their implementation is hampered by the current definition of respiratory tract exacerbation, which lacks objective “cut-offs” for clinical and lung function parameters. In particular, the latter shows a large variability, making the current 10% change in spirometry outcomes an unreliable threshold to detect exacerbation. Moreover, spirometry cannot be reliably performed in preschool children and new emerging tools, such as the forced oscillation technique, are still complementary and need more validation. Therefore, lung imaging is a key in providing respiratory tract exacerbation-related structural and functional information. However, imaging encompasses several diagnostic options, each with different advantages and limitations; for instance, conventional chest radiography, the most used radiological technique, may lack sensitivity and specificity in respiratory tract exacerbations diagnosis. Other methods, including computed tomography, positron emission tomography and magnetic resonance imaging, are limited by either radiation safety issues or the need for anesthesia in uncooperative patients. Finally, lung ultrasound has been proposed as a safe bedside option but it is highly operator-dependent and there is no strong evidence of its possible use during respiratory tract exacerbation. This review summarizes the clinical challenges of respiratory tract exacerbations in patients with cystic fibrosis with a special focus on imaging. Firstly, the definition of respiratory tract exacerbation is examined, while diagnostic and monitoring tools are briefly described to set the scene. This is followed by advantages and disadvantages of each imaging technique, concluding with a diagnostic imaging algorithm for disease monitoring during respiratory tract exacerbation in the cystic fibrosis patient.
Study of risk of malignancy index scoring system in the preoperative evaluation of patients with ovarian tumor and its correlation with histopathological examination

BACKGROUND: The discrimination between benign and malignant ovarian tumor is important in considering an optimal plan for an appropriate surgical treatment. OBJECTIVE: To evaluate the ability of risk of malignancy index based on menopausal status, ultrasonographic score and serum level of CA125 to discriminate between benign and malignant ovarian tumor. MATERIAL AND METHODS: This is a prospective observational study of 100 patients of all age group who admitted with a diagnosis of ovarian tumor at Govt. R.S. R.M Lying in hospital, Chennai during the period of 2015 to 2016 . The sensitivity, specificity, positive predictive value and negative predictive value of different cut off values of RMI were calculated. Finally it was correlated with histopathological examination. RESULTS: By comparing the RMI with different cut off values, the RMI with cut off value 200 gave sensitivity 82.6%, specificity 94.8%, positive predictive value 82.6% and negative predictive value 94.8%. It was significantly better in predicting malignancy. CONCLUSION: The RMI is able to discriminate between benign and malignant ovarian tumors. The RMI with a cut off value 200 was the most reliable in predicting malignancy. It is a simple method that can be incorporated into clinical practice easily to enable the selection of patients for proper referral to tertiary care centre.
Selenium-enriched plant foods: Selenium accumulation, speciation, and health functionality

Selenium (Se) is an essential element for maintaining human health. The biological effects and toxicity of Se compounds in humans are related to their chemical forms and consumption doses. In general, organic Se species, including selenoamino acids such as selenomethionine (SeMet), selenocystine (SeCys2), and Se-methylselenocysteine (MSC), could provide greater bioactivities with less toxicity compared to those inorganics including selenite (Se IV) and selenate (Se VI). Plants are vital sources of organic Se because they can accumulate inorganic Se or metabolites and store them as organic Se forms. Therefore, Se-enriched plants could be applied as human food to reduce deficiency problems and deliver health benefits. This review describes the recent studies on the enrichment of Se-containing plants in particular Se accumulation and speciation, their functional properties related to human health, and future perspectives for developing Se-enriched foods. Generally, Se’s concentration and chemical forms in plants are determined by the accumulation ability of plant species. Brassica family and cereal grains have excessive accumulation capacity and store major organic Se compounds in their cells compared to other plants. The biological properties of Se-enriched plants, including antioxidant, anti-diabetes, and anticancer activities, have significantly presented in both in vitro cell culture models and in vivo animal assays. Comparatively, fewer human clinical trials are available. Scientific investigations on the functional health properties of Se-enriched edible plants in humans are essential to achieve in-depth information supporting the value of Se-enriched food to humans.
DeepAD: A deep learning application for predicting amyloid standardized uptake value ratio through PET for Alzheimer's prognosis

Introduction Amyloid deposition is a vital biomarker in the process of Alzheimer's diagnosis. 18F-florbetapir PET scans can provide valuable imaging data to determine cortical amyloid quantities. However, the process is labor and doctor intensive, requiring extremely specialized education and resources that may not be accessible to everyone, making the amyloid calculation process inefficient. Deep learning is a rising tool in Alzheimer's research which could be used to determine amyloid deposition. Materials and methods Using data from the Alzheimer's Disease Neuroimaging Initiative, we identified 2,980 patients with PET imaging, clinical, and genetic data. We tested various ResNet, EfficientNet, and RegNet convolutional neural networks and later combined the best performing model with Gradient Boosting Decision Tree algorithms to predict standardized uptake value ratio (SUVR) of amyloid in each patient session. We tried several configurations to find the best model tuning for regression-to-SUVR. Results We found that the RegNet X064 architecture combined with a grid search-tuned Gradient Boosting Decision Tree with 3 axial input slices and clinical and genetic data achieved the lowest loss. Using the mean-absolute-error metric, the loss converged to an MAE of 0.0441, equating to 96.4% accuracy across the 596-patient test set. Discussion We showed that this method is more consistent and accessible in comparison to human readers from previous studies, with lower margins of error and substantially faster calculation times. We implemented our deep learning model on to a web application named DeepAD which allows our diagnostic tool to be accessible. DeepAD could be used in hospitals and clinics with resource limitations for amyloid deposition and shows promise for more imaging tasks as well.