Miracle-dz/UniFAR-FTUs huggingface dataset:
One Real-Time Fluorescent Loop-Mediated Isothermal Ampliﬁcation Combined with Propidium Monoazide for Detection of Viable Vibrio Parahaemolyticus in Seafood

Vibrio parahaemolyticus is one of the crucial foodborne pathogens in the world. At present, the rapid detection methods for V. parahaemolyticus cannot distinguish between dead and viable cells and false positive results may occur. In this study, one rapid and accurate method that combines Propidium Monoazide (PMA) with real-time fluorescent loop-mediated isothermal ampli? cation (LAMP) using SYTO-16 dye was developed to detect viable cells of V. parahaemolyticus. LAMP amplification was performed on specific primers designed for toxR gene of V. parahaemolyticus and the concentration of PMA and the maximum concentration of dead cells were optimized. The results showed that the concentration of PMA was 10 ÂµM and PMA could efficiently treat dead cells up to 4.5A—105 CFU/mL. The detection sensitivity of real-time fluorescent PMA-LAMP were 4.5A—100 CFU/mL and PMA-qPCR were 4.5A—101 CFU/mL. In addition, the correlation coefficients (R2) is 0.9992, indicating that SYTO-16 dyed real-time fluorescent PMA-LAMP assay can be used for quantification with high sensitivity. This method exhibits high specificity and sensitivity, can be used as an effective tool for rapid detection of V. parahaemolyticus and a scientific basis to follow the effect of the pathogen infection on growth of cultured seafood.
A Comparison of Neural Networks and Model Updating Methods for Damage Localization

In this paper a comparison between classical Model Updating methods and Neuronal Network methods for damage localization is presented. Both methods are based in modal parameters and have been applied to the same experimental problem. The main objective of this research is to establish the comparatives qualities of each method. Model Updating is a consolidated method for damage detection, but it is a long process that requires a considerable computational and experimental cost. Artificial Neuronal Networks (ANN) methods are faster and consequently they require less computational cost if the neural network is properly chosen and trained. A laboratory modal test of a beam supported in four points has been developed in order to apply Finite Element Model Update and damage detection. In a first step Model Update has been made by means of Iterative Methods. In a second step a small damage is introduced to the beam and damage localization is applied with both Iterative and Neural Network methods. The full process of numerical model update is developed. Guyan reduction and the Independence Effective method have been used to select the best transducers position. Correlation, validation and adaptation of experimental and numerical data techniques have been used. The adaptation techniques used are: Guyan reduction, Dynamic reduction, Improved Reduction System (IRS) and the SEREP reduction. The correlation techniques are: Modal Assurance Criterion (MAC), Coordinate Modal Assurance Criterion (COMAC) and Modal Assurance Criterion Modified (MACMO). Also parameterization, damage localization and sensibility analyses have been done before the final updating. Different Iterative methods based in penalty functions have been applied depending of the number of experimental data and the number of parameters to update. The ANNs have been trained with the results obtained in numerical simulations by Finite Element Method. These numerical simulations have been done introducing damage with different localization in the beam. Ones the ANN is trained, it has been evaluated as a tool to predict the position of the damage with the natural frequencies Paper 49
The complete chloroplast genome of Pinus squamata (Pinaceae), a critically endangered species in China

Abstract The complete chloroplast (cp) genome of Pinus squamata, a critically endangered species in China, was reported in this study. The cp genome is 118,300 bp in length and has four regions: 65,298 bp of large single copy (LSC) region and 52,098 bp of small single copy (SSC) region separated by 452 bp of highly reduced inverted repeat (IR) regions. This cp genome with GC content of 38.8% contains 107 unique genes (73 protein-coding genes, 30 tRNA genes, and four rRNA genes). Phylogenetic analysis based on the complete cp genomes indicates that P. squamata is closer to P. gerardiana than P. bungeana.
Multicellular tumor spheroids- an effective in vitro model for understanding drug resistance in head and neck cancer

One of the hallmarks of cancer, is the ability of cancer cells to develop resistance to therapy. Therefore, developing effective in vitro strategies for the identification of drug resistant cancers remains with paramount importance for treatment success. A way cancer cells achieve drug resistance is through expression of efflux pumps that actively pump drugs out of the cells. To date, several studies have investigated the potential of using multicellular tumor spheroids (MCSs) for multidrug resistance (MDR) profile; however, a unified system that uses MCSs to differentiate between MDR and non-MDR cells does not exist. Using MCSs obtained from patient derived cell lines of head and neck squamous cell cancer that often develops resistance to therapy, we have exploited the drug efflux pump overexpression and function of MDR cancer cells for the identification, characterization and profiling of multidrug resistance. To achieve this aim, we employed an integrated approach combining clinical drug response and cell cytotoxicity screening, monitoring real-time drug uptake, and assessing transporter activity using flow cytometry in the presence and absence of their specific inhibitors. In the present study, using a novel strategy involving the assessment of cell cytotoxicity, MDR response, real time drug efflux capability, and reactive oxygen species (ROS) activity, we obtain drug resistance profiles of patient-derived MCSs treated with clinically used chemotherapeutic agents, while simultaneously demonstrating that monolayer two-dimensional cultures of the same set of cells cannot be used reliably for this purpose. Our strategy can be clinically applicable for the profiling of drug resistance in pre-treated post diagnosed cancer cells with unknown resistance profiles, which consequentially can indicate benefit from downstream therapy.
The Effects of Restriction Pressures on the Acute Responses to Blood Flow Restriction Exercise

Purpose No current guidelines or recommendations exist informing the selection of restriction pressure during blood flow restriction exercise (BFRE). Moreover, the effects of specific relative restriction pressures on the acute muscle, metabolic and cardiopulmonary responses to BFRE are unclear. The purpose of this study was to characterize these acute responses at different levels of restriction pressure. Methods Participants (n = 10) completed rhythmic isometric knee extension exercise across five experimental trials in a balanced randomized order. Three were BFRE trials {B-40 [restriction pressure set to 40% LOP (total limb occlusion pressure)]; B-60 (60% LOP); and B-80 (80% LOP)} with a workload equivalent to 20% maximal voluntary force (MVC), one was non-BFRE at 20% MVC (LL) and one was non-BFRE at 80% MVC (HL). Measurements recorded were torque, muscle activity via electromyography (EMG), tissue oxygenation via near infrared spectroscopy, whole body oxygen consumption, blood lactate and heart rate. Results For the LL and B-40 trials, most measures remained constant. However, for the B-60 and B-80 trials, significant fatigue was demonstrated by a reduction in MVC torque across the trial (p < 0.05). Blood lactate increased from baseline in HL, B-60, and B-80 (p < 0.05). Submaximal EMG was greater in B-60 and B-80 than LL, but lower compared with HL (p < 0.05). Tissue oxygenation decreased in HL, B-40, B-60, and B-80 (p < 0.05), which was lower in the B-80 trial compared to all other trials (p < 0.01). Whole body oxygen consumption was not different between the BFRE trials (p > 0.05). Conclusion We demonstrate graded/progressive acute responses with increasing applied pressure during BFRE, from which we speculate that an effective minimum “threshold” around 60% LOP may be necessary for BFRE to be effective with training. While these data provide some insight on the possible mechanisms by which BFRE develops skeletal muscle size and strength when undertaken chronically across a training program, the outcomes of chronic training programs using different levels of applied restriction pressures remain to be tested. Overall, the present study recommends 60–80% LOP as a suitable “minimum” BFRE pressure.
Four chemoreceptors govern bidirectional pH taxis in Bacillus subtilis

We investigated pH taxis in Bacillus subtilis. This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We found that four chemoreceptors are involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid and base-sensing chemoreceptors, we identified four critical amino-acid residues – Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB – involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria. IMPORTANCE Many bacteria can sense the pH in their environment and then use this information to direct their movement towards more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis. This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid and base sensing chemoreceptors. By analyzing the response of these chimeric receptors, we were able to identify four critical amino-acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.
Landscape and within-field factors affecting the damages of the brassica pod midge (Dasineura brassicae) in Swedish winter oilseed rape cultivation

The brassica pod midge (Dasineura brassicae) has been a serious upcoming problem in Swedish oilseed cultivation during recent years. This small dipteran utilized pods damaged by its facilitator, the cabbage seed weevil (Ceutorynchus obstrictus), to be able to oviposit. The larvae of D. brassicae feed on the inner pod wall, causing the pod to split prematurely and releasing its seeds, which causes yield loss for the farmer. In this study, we investigate how landscape and within-field factors such as previous years percentage of oilseed rape in the landscape, landscape complexity, distance to previous years oilseed rape field, abundance of C. obstrictus and chemical treatments affect the damages caused by D. brasssicae. This was done on 19 locations in Skane, the southernmost province of Sweden. Yellow pan traps and yellow sticky traps were used to monitor the C. obstrictus populations. Information on chemical treatments were gathered by contacting the farmers. The landscape parameters where assessed using geographical information systems and data from the Swedish Board of Agriculture and the Swedish Environmental Protection Agency. Our results showed a positive correlation between abundance of C. obstrictus and damages caused by D. brassicae. Both abundance of C. obstrictus and damage from D. brassicae showed a positive correlation with an increasing landscape complexity at a small distance (1000m), C. obstritcus also showed a positive correlation at larger distances (2000-4000m). However, no correlation was found between an increasing percentage of previously cultivated winter oilseed rape and the damages from D. brassicae or abundance of C. obstrictus. Some regions within the province showed a significantly higher amount of damage than others; these provinces generally contained a more complex landscape compared to the ones where surveys had shown less damage. Stepwise multiple regression models with the within-field and landscape factors as independent variables showed that previous year’s percentage of oilseed rape had a positive impact on the damages caused by D. brassicae during the entire season. In the late pod set, the abundance of C. obstrictus also had a positive impact on the damages caused by D. brassicae. However, the chemical treatment did not seem to affect the damages caused by D. brassicae in late pod set in any way.
Is Kasuri Methi Genetically Different from other Methi (Fenugreek) Varieties

Out of all available varieties of fenugreek (methi), kasuri methi is different in phenotypic characteristics, flavour, leaf sizes, fragrance and seed size also. Scientific name of Kasuri methi is Trigonella corniculata. It has sickle shaped pods, contains 10 to 20 small hard yellowish brown round seeds with about 3 mm size. Dry leaves of kasuri methi are rich in protein, iron and vitamin A and widely used as spice and herb in food preparation (Gurjar 2005).
Improving the utility of topic models: an uncut gem does not sparkle

This thesis concerns a type of statistical model known as topic model. Topic modelling learns abstract “topics” in a collection of documents, and by “topic” we mean an idea, theme or subject. For example we may have an article that discusses space exploration, or a book about crime. Space exploration and crime, these two subjects, are the “topics” that we are talking about. As one imagine, topic modelling has a direct application in digital libraries, as it automates the learning and categorisation of topics in books and articles. The merit of topic modelling, however, is that its machinery is not limited to processing just words but symbols in general. As such, topic modelling has seen applications in other areas outside text processing such as biomedical research for inferring protein families. Most applications, however, are small scale and experimental and much of the impact is still contained in academic research. The overarching theme of the thesis is thus to improve the utility of topic modelling. We achieve this in two ways: (1) by improving a few aspects of topic modelling to make it more accessible and usable by users; and (2) by proposing novel applications of topic modelling to real-world problems. In the first step, we look into improving the preprocessing methodology of documents that serves as the creation of input for topic models. We also experiment extensively to improve the visualisation of topics—one of the main output of topic models—to increase its usability for human users. In the second step, we apply topic
Explant type and hormone regime influences somatic embryogenesis and regeneration of cassava

Cassava (Manihot esculenta Crantz) is a tropical root crop that serves as a food staple and a vital income source to resource deprived farmers in the tropics. Despite its importance, cassava production and consumption is faced by a myriad of biotic/abiotic constraints. Genetic transformation which can be applied to mitigate these challenges however has as a prerequisite the availability of robust regeneration systems. This study evaluated the effect of explant type and hormone regime on somatic embryogenesis and regeneration of Kenyan cassava cultivars. The embryogenic competence of immature leaf lobe and stem explants of three cassava cultivars was determined by culturing them in MS medium supplemented with picloram (4, 6, 8 and 10 mg/l). The optimum media composition for embryo maturation, germination and plant recovery was assessed by culturing embryos in media supplemented with varying concentrations of 6-Benzylaminopurine (BAP), α–Naphthalene acetic acid (NAA) and Gibberellic acid (GA3). Somatic embryo formation frequencies in leaf explants were significantly higher (P≤0.05) than in stem explants. Embryo formation rates were found to increase with increasing concentrations of picloram. Cultivar 08/080 gave the least response to embryogenesis while embryogenesis rates for cultivar 08/274 were similar to the control cultivar TMS 60444. Maturation and plant recovery rates differed significantly with regard to the ratios of BAP, NAA and GA3 in the maturation media. The optimal medium for embryo germination and plant recovery was supplemented with 1 mg/l BAP, 0.02 mg/l NAA and 1.5 mg/l GA3. This optimized regeneration protocol can be coupled with mutation breeding or genetic transformation to improve the cassava germplasm. Key words: Cassava, explant, regeneration, somatic embryogenesis, plant growth regulator.
Measuring and Modelling the Emergence of Order in the Mouse Retinocollicular Projection

In the formation of retinotopic maps both experimental and theoretical work implicate guidance molecules and patterned neuronal activity. A common view is that molecular cues define and activity cues refine mappings. Important insights have come from studies of the retinocollicular projection in transgenic mice, in which cues have been modified either in isolation or in combination. Mostly these have generated descriptions of endpoint mappings. The dynamics of map formation remain under-explored experimentally and computationally. We have quantified changes in the ordering of the mouse retinocollicular projection with age after making local collicular injections of fluorescent microspheres. Contour analysis shows that, at birth (P0), cells from over 80% of the retina converge on a given collicular locus; this percentage falls gradually to P4 then rapidly approaches adult values by P12. Paired injections reveal how the segregation of labelled cells depends both on injection site separation and relative orientation and also age. At P0, large anterior-posterior separations failed to produce segregated label: segregation improved with a similar timecourse to convergence to reach near adult-values by P12. An implementation of a combined activity-molecular model captures these segregation dynamics. The developmental dynamics were then studied in the nAChR-β2−/− mouse, which has altered patterns of retinal activity in the first postnatal week that results in a more diffuse adult retinal projection. Surprisingly, both measures of map refinement (convergence and segregation) remain largely constant and imprecise in the first postnatal week – only subsequently does the projection begin to refine. Substituting nAChR-β2−/− activity patterns for wild-type patterns [5] into the model failed to capture the biology: refinement was initially faster. By reducing the relative importance of the gradients’ contribution to the model energy (to 15% of normal) we were able to mimic the delayed refinement observed in vivo. Our model therefore predicts the altered activity patterns may affect readout of guidance cues.
Uncovering Staphylococcus aureus genes with roles in pathogenicity by silkworm infection model

The regulatory network of virulence factors production by Staphylococcus aureus, an opportunistic pathogen, is incompletely understood, and the functions of many uncharacterized genes in its genome remain to be uncovered. We screened 380 function unassigned genes disrupted mutants of the community-acquired methicillin-resistant S. aureus USA300 for pathogenicity using silkworms and identified 11 strains with reduced silkworm killing ability. Nine out of the 11 strains displayed reduced virulence in the mouse model as evidenced by reduced colony-forming units in organs of the infected mice. Three of the identified gene-disrupted mutants had reduced hemolytic activity, one among the three also had reduced proteolytic activity and pigment production. These results suggest that silkworm model could identify the genes required for virulence in the mouse model. The newly identified genes involved in virulence in this study facilitates the further understanding of the pathogenicity of S. aureus. Importance We performed a large scale screening of mutants of Staphylococcus aureus with disruption in function unassigned genes using silkworm infection model and identified eleven genes required for full virulence in silkworm. Nine of the eleven genes were involved in virulence in mice and were previously not known to aggravate virulence of S. aureus. The results suggest that silkworm model is suitable for quantitative measurement of virulence, which is shared between silkworms and mammals.
The complete mitogenome of the granular torrent frog, Amolops granulosus (Anura: Ranidae)

Abstract We obtained the complete mitochondrial genome of Amolops granulosus, which was 17,785 bp in length and it contained the 37 typical mitochondrial genes: 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and 1 control region (CR). The hotspot of gene arrangement was ranged as ‘W-gap-OL-gap-A-N-gap-C-Y’ which consisted with most published Amolops mitogenomes. Our phylogenetic results suggested the gene arrangement of ‘WANCY’ region can facilitate to distinguish the Amolops species as an efficient genetic marker.
Inflammatory agents partially explain changes in cortical thickness and surface area related to body mass index in adolescence

Excessive body mass index (BMI) has been linked to a low-grade chronic inflammation state. Unhealthy BMI has also been related to neuroanatomical changes in adults. However, research in adolescents is relatively limited and has produced conflicting results. This study aims to address the relationship between BMI and adolescents’ brain structure as well as to test the role that inflammatory adipose-related agents might have over this putative link. We studied structural MRI and serum levels of interleukin-6, tumor necrosis factor alpha (TNF-α), C-reactive protein and fibrinogen in 65 adolescents (aged 12-21 years). Relationships between BMI, cortical thickness and surface area were tested with a vertex-wise analyzes. Subsequently, we used backward multiple linear regression models to explore the influence of all inflammatory parameters in each brain-altered area. We found a negative relationship between cortical thickness and BMI in the left lateral occipital cortex (LOC), the left fusiform gyrus and the right precentral gyrus as well as a positive relationship between surface area and BMI in the left rostral middle frontal gyrus and the right superior frontal gyrus. In addition, we found that higher fibrinogen serum concentrations were related to thinning within the left LOC (β = −0.45, p < 0.001) and the left fusiform gyrus (β = −0.33, p = 0.035), while higher serum levels of TNF-α were associated to a greater surface area in the right superior frontal gyrus (β = 0.32, p = 0.045). These results suggest that adolescents’ body mass increases are related with brain abnormalities in areas that could play a relevant role in some aspects of feeding behavior. Likewise, we have evidenced that these cortical changes were partially driven by inflammatory agents such as fibrinogen and TNF-α. 1.