Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting Vessel Structure From 3D Image Data

This thesis is focused on extracting the structure of vessels from 3D cardiac images. In many biomedical applications it is important to segment the vessels preserving their anatomicallycorrect topological structure. That is, the final result should form a tree. There are many technical challenges when solving this image analysis problem: noise, outliers, partial volume. In particular, standard segmentation methods are known to have problems with extracting thin structures and with enforcing topological constraints. All these issues explain why vessel segmentation remains an unsolved problem despite years of research. Our new efforts combine recent advances in optimization-based methods for image analysis with the state-of-the-art vessel filtering techniques. We apply multiple vessel enhancement filters to the raw 3D data in order to reduce the rings artifacts as well as the noise. After that, we tested two different methods for extracting the structure of vessels centrelines. First, we use data thinning technique inspired by Canny edge detector. Second, we apply recent optimization-based line fitting algorithm to represent the structure of the centrelines as a piecewise smooth collection of line intervals. Finally, we enforce a tree structure using a minimum spanning tree algorithm.
Robust Bipedal Locomotion Based on a Hierarchical Control Structure

Summary To improve biped locomotion’s robustness to internal and external disturbances, this study proposes a hierarchical structure with three control levels. At the high level, a foothold sequence is generated so that the Center of Mass (CoM) trajectory tracks a planned path. The planning procedure is simplified by selecting the midpoint between two consecutive Center of Pressure (CoP) points as the feature point. At the middle level, a novel robust hybrid controller is devised to drive perturbed system states back to the nominal trajectory within finite cycles without chattering. The novelty lies in that the hybrid controller is not subject to linear CoM dynamic constraints. The hybrid controller consists of two sub-controllers: an oscillation controller and a smoothing controller. For the oscillation controller, the desired CoM height is specified as a sine-shaped function, avoiding a new attractive limit cycle. However, this controller results in the inevitable chattering because of discontinuities. A smoothing controller provides continuous properties and thus can inhibit the chattering problem, but has a smaller region of attraction compared with the oscillation controller. A hybrid controller merges the two controllers for a smooth transition. At the low level, the desired CoM motion is defined as tasks and embedded in a whole body operational space (WBOS) controller to compute the joint torques analytically. The novelty of the low-level controller lies in that within the WBOS framework, CoM motion is not subject to fixed CoM dynamics and thus can be generalized.
Salmonella Serovar Kentucky Flagella is Required for Broiler Skin Adhesion and Caco-2 1 Cell Invasion

Non-typhoidal Salmonella are the main source of pathogenic bacterial contamination in the 25 poultry industry. Recently, Salmonella enterica serovar Kentucky has been recognized as the 26 most prominent serovar on carcasses in poultry processing plants. Previous studies showed that 27 flagella are one of the main factors that contribute to bacterial attachment to broiler skin. 28 However, the precise role of flagella and mechanism of attachment are unknown. There are two 29 different flagella subunits ( fliC and fljB ) expressed alternatively in Salmonella enterica serovars 30 using phase variation. Here, by making deletions in genes encoding flagella structural subunits 31 ( flgK, fliC , and fljB ), and flagellar motor ( motA ), we were able to differentiate the role of flagella 32 and its rotary motion in colonization of broiler skin and cellular attachment. Utilizing a broiler 33 skin assay, we demonstrated that the presence of FliC is necessary for attachment to broiler skin. 34 Expression of the alternative flagella subunit FljB enables Salmonella motility, but this subunit is 35 unable to mediate tight attachment. Deletion of the flgK gene prevents proper flagella assembly, 36 making Salmonella significantly less adherent to broiler skin compared to wild type. S . Kentucky 37 with deletions in all three structural genes fliC , fljB , and flgK , as well as a flagellar motor mutant 38 ( motA ), exhibited less adhesion and invasion of Caco-2 cells, while a fljB mutant was as adherent 39 and invasive as the wild type strain. 43 broiler skin. this subunit comparisons for assay on a 217 generalized randomized four for comparison of the 218 percentage of associated bacterial count between mutants and wild type strain. A p ≤ 0.05 was 219 statistically significant.
Antitumor Activity and Minimal Toxicity of Concentrated Thymidine Infused in Nude Mice1

To avoid infusing large volumes of fluid while treating patients with the standard thymidine solution (30 g/liter), it may be pos sible to administer this drug in more concentrated form. At 25Â°C, thymidine is saturating at a concentration of 52 g/liter of 0.6% NaCI solution, and the thymidine concentration at saturation increases with temperature. Nude mice were infused at 29Â°C with thymidine (60 or 72 g/liter) in cycles consisting of 4 to 5 days infusion followed by 9 days rest. Therapeutically effective doses of concentrated thymidine did not cause significant mor tality in mice, and weight loss attributable to treatment was small and reversible. Significant growth inhibition of CA 1 human melanoma heterotransplants was observed after 3 treatment cycles. After 4 or 5 cycles, tumor responses were obtained in 7 mice (6 complete responses) of 12 inoculated with this tumor. These results show that concentrated thymidine solutions are highly effective against human tumor heterotransplants in nude mice and suggest that clinical use of concentrated thymidine may allow practical administration of maximum tolerated doses of this drug.
BIOFORTIFICATION IN MACROBRACHIUM ROSENBERGII USING CRUDE EXTRACTS FROM CURCUMA LONGA : ASSESSMENT VIA GROWTH AND BIOCHEMICAL INDICES.

The all-round nutritional status of aquaculture candidate can be augured by the application of medicinal herbs. In the present work nutritional status of freshwater prawn, Macrobrachium rosenbergii was assessed subsequent to certain concentrations of Curcuma longa oral supplementation. Terminations were affected on 30 th and 60 th days for experimental analysis of growth, feed utilization were done. Biochemical parameters such as protein, glycogen and lipid of muscle, gill and gut tissues were assessed as follows at 30 th and 60 th days of the experimental period. From the experiments it can be concluded that the Curcuma longa (25 mg/kg of feed) with daily administration has better growth promotion and feed utilization efficacy in M.rosenbergii.
Adaptive evaluation of different coat colour of Morada Nova sheep in an equatorial semiarid region

: Present paper is aimed to show thermoregulatory responses of locally adapted sheep with different coat colors, in an equatorial semiarid region. There were used four groups according to the coat color: (1) dark red animals, (2) intermediate red, (3) light red, and (4) white coated animals. Animals were measured for rectal temperature (RT), skin surface temperature (ST), respiratory rate (RR), heat loss by respiratory evaporation (RE), heat exchange by convection (HC) and radiation (HR), from 1100 to 1400 hour, after the animals had stayed in a pen exposed to the sun. Results showed that all groups maintained homeothermy. The RR was higher in the animals of groups 1 to 3, which also showed higher values for ST when compared to the white coated animals. Sensible heat exchange mechanisms were not important for heat loss and HR was a significant source of heat gain by animals from the environment. Groups 1, 2 and 3 used RR in a more intense way compared to group 4. It was concluded that Morada Nova sheep has good adaptability to the semiarid environment, regardless of the coat color.
CYLD and the NEMO zinc finger regulate tumor necrosis factor signaling and early embryogenesis

Results: Cylindromatosis (CYLD) findings in patients with immune deficiency disorders. ABSTRACT NEMO and CYLD are intracellular proteins that regulate the NF-kappa B signaling pathway. Although mice with either CYLD deficiency or an alteration in the zinc finger domain of NEMO (K392R) are born healthy, we found that the combination of these two gene defects in double mutant (DM) mice is early embryonic lethal but can be rescued by the absence of TNF receptor 1 (TNFR1). Notably, NEMO was not recruited into the TNFR1 complex of double mutant (DM) cells, and consequently NF-kappa B induction by TNF was severely impaired and DM cells were sensitized to TNF-http://www.jbc. org/cgi/doi/10.1074/jbc.M115. 658096 show that mice that harbor a NEMO K392R mutation and are deficient in CYLD experience early embryonic lethality. Further genetic deletion of TNFR1 rescues embryonic development, demonstrating that the inability of DM cells to signal properly in response to TNF results in attenuated NF-kappa B activity and cell death. In double mutant cells, we found both linear and K63-linked polyubiquitin chains on RIP in the TNFR1 complex. However, in DM cells this complex was devoid of NEMO K392R, suggesting that interaction between the NEMO
Recent Advances in Control and Verification for Hybrid Systems Generalised L 2 -gain of switched non-linear systems

: In this study, a generalised L 2 -gain property for switched systems is presented by using multiple storage functions. The new notion describes the non-uniform gain property for switched systems characterised by a positive function of the state. For interconnected switched systems, a small-gain theorem using generalised L 2 -gain is obtained, which generalises the well known small-gain theorem. Moreover, if each subsystem of a switched system does not admit a generalised L 2 -gain, by choosing an appropriate switching law, the overall system can be made to satisfy a generalised L 2 -gain condition. Furthermore, the authors propose an invariance principle for switched non-linear systems based on which sufficient conditions for attractivity with respect to a set are given for switched systems with the generalised L 2 -gain property. Finally, two examples are provided to illustrate the effectiveness of the main results.
Ontogeny of the Maize Shoot Apical Meristem

The maize ( Zea mays ) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAMontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic profiling before and after SAM initiation indicates that organogenesis precedes stem cell maintenance in maize; analyses of the first three lateral organs elaborated from maize embryos provides insight into their homology and to the identity of the single maize cotyledon. Compared with the newly initiated SAM, the mature SAM is enriched for transcripts that function in transcriptional regulation, hormonal signaling, and transport. Comparisons of shoot meristems initiating juvenile leaves, adult leaves, and husk leaves illustrate differences in phase-specific (juvenile versus adult) and meristem-specific (SAM versus lateral meristem) transcript accumulation during maize shoot development. This study provides insight into the molecular genetics of SAMinitiation and function in maize. The maize ( Zea mays ) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAM ontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic pro ﬁ ling before and after SAM initiation indicates that organogenesis precedes stem cell maintenance in maize; analyses of the ﬁ rst three lateral organs elaborated from maize embryos provides insight into their homology and to the identity of the single maize cotyledon. Compared with the newly initiated SAM, the mature SAM is enriched for transcripts that function in transcriptional regulation, hormonal signaling, and transport. Comparisons of shoot meristems initiating juvenile leaves, adult leaves, and husk leaves illustrate differences in phase-speci ﬁ c (juvenile versus adult) and meristem-speci ﬁ c (SAM versus lateral meristem) transcript accumulation during maize shoot development. This study provides insight into the molecular genetics of SAM initiation and function in maize.
The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes in a Sea of Repeats

Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of (cid:2) 80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that (cid:2) 20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.
PARTIAL PURIFICATION AND CHARACTERIZATION OF NEWLY EXPRESSED GUAIACOL PEROXIDASE FROM DEHYDRATED SEEDLINGS OF HORSE GRAM ( Macrotyloma Uniflorum ) TISSUE CULTURE

Accumulation of reactive oxygen species (ROS) is a predominant behavior in the most plants when subjected to any abiotic stresses. Seedlings of horse gram tissue culture stressed by dehydration responded by expression of a new isoform of guaiacol peroxidase (GPOX) comparison with unstressed seedlings. This new GPOX was purified by passing the ammonium sulfate fraction of extract through 7-12 % gradient resolving gel of PAGE at 4 °C. A small part of the gel was cut and subjected to activity staining of peroxedase. By aligning the stained and unstained gels, the portion of unstained gel corresponding to the enzyme band have been excised. The enzyme was recovered by electro-eluting technique using Tris buffer, pH 6.8 for 45 min, and partially characterized. The purified GPOX has approximately 43 kD molecular mass; it was stable at low pH and it was maximally active at pH 6. The enzyme was more sensitive to high temperature, and its optimum temperature was at room temperature. Kinetic constants were determined, K m values was 15 mM and 0.6 mM of for guaiacol and H 2 O 2 respectively while V max was 582.9 U/mg for guaiacol and 122.5 U/mg for H 2 O 2 . The K m values indicate that the enzyme is highly specific to hydrogen peroxide and showed higher substrate affinity than previously reported GPOXs. This fact suggest that the new isoform of GPOX which expressed during dehydration stress is as part of the defense system in the plant which may enhance scavenging of ROS and assist the stressed plant to keep survive.
The Anti-inflammatory Properties of Cocoa Flavanols

: Signs of chronic or acute inﬂammation have been demonstrated in most cardiovascular diseases of multifactorial pathogenesis, including atherosclerosis and chronic heart failure. The triggers and mechanisms leading to inﬂammation may vary between clinical conditions but they share many common mediators, including speciﬁc patterns of eicosanoid and cytokine production. Certain cocoa-based products can be rich in a subclass of ﬂavonoids known as ﬂavanols, some of which have been found in model systems to possess potential anti-inﬂammatory activity relevant to cardiovascular health. Indeed, experimental evidence demonstrates that some cocoa-derived ﬂavanols can reduce the production and eﬀect of proinﬂammatory mediators either directly or by acting on signaling pathways. However, it should be noted that the evidence for any beneﬁcial eﬀects of cocoa ﬂavanols in providing a meaningful anti-inﬂammatory action has been gathered predominantly from in vitro experiments. Therefore, additional research in well-designed human clinical experiments, using cocoa properly characterized in terms of ﬂavanol content, would be a welcome addition to the evidence base to determine unambiguously if this beneﬁt does indeed exist. If so, then ﬂavanol-rich cocoa could be a potential candidate for the treatment, or possibly prevention, of the broad array of chronic diseases that are linked to dysfunctional inﬂammatory responses.
Differential Roles of Cardiomyocyte and Macrophage PPAR γ in Cardiac Fibrosis

AngII-induced cardiac fibrosis, 4) Macrophage PPAR γ activation prevents myocardial macrophage accumulation, and 5) PPAR γ ligands attenuate AngII-induced cardiac fibrosis by inhibiting myocardial macrophage infiltration. These observations have important implications for potential interventions to prevent cardiac fibrosis.
Characterization of a Pollen-Expressed Receptor-like Kinase Gene of Petunia inflata and the Activity of Its Encoded Kinase

From a pollen tube cDNA library of Petunia inflata, we isolated clones encoding a protein with structural features and biochemical properties characteristic of receptor-like kinases. It was designated PRKl for pollen receptor-like kinase 1. The cytoplasmic domain of PRKl is highly similar to the kinase domains of other plant receptor-like kinases and contains nearly all of the conserved amino acids for serine/threonine kinases. The extracellular domain of PRKl contains leucine-rich repeats as found in some other plant receptor-like kinases, but overall its sequence in this region does not share significant similarity. Characterization of a gene encoding PRKl revealed the presence of two introns. During pollen development, PRKl mRNA was first detected in anthers containing mostly binucleate microspores; it reached the highest level of mature pollen and remained ata high level in in vitro-germinated pollen tubes. The recombinant cytoplasmic domain of PRKl autophosphorylated on serine and tyrosine, suggesting that PRKl may be a dual-specificity kinase. Monospecific immune serum to the recombinant extracellular domain of PRKl detected a 69-kD protein in microsomal membranes of pollen and pollen tubes. The characteristics of PRKl suggest that it may play a role in signal transduction events during pollen development and/or pollination.
Fluctuations of maxima of discrete Gaussian free fields on a class of recurrent graphs

We provide conditions that ensure that the maximum of the Gaussian free field on a sequence of graphs fluctuates at the same order as the field at the point of maximal standard deviation; under these conditions, the expectation of the maximum is of the same order as the maximal standard deviation. In particular, on a sequence of such graphs the recentered maximum is not tight, similarly to the situation in $\mathbb{Z}$ but in contrast with the situation in $\mathbb{Z}^2$. We show that our conditions cover a large class of "fractal" graphs.
Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR

Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.
RNA m6A Modification Changes in Postmortem Nucleus Accumbens of Subjects with Alcohol Use Disorder: A Pilot Study

Background: The nucleus accumbens (NAc) is a key brain structure mediating the rewarding effect of alcohol and drug abuse. Chronic alcohol consumption may alter RNA methylome (or epitranscriptome) in the NAc, leading to altered gene expression and thus behavioral neuroadaptation to alcohol. Methods: This pilot study profiled the epitranscriptomes of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in postmortem NAc of three male Caucasian subjects with alcohol use disorder (AUD) and three matched male Caucasian control subjects using Arraystar’s m6A-mRNA&lncRNA Epitranscriptomic Microarray assay. Differentially methylated (DM) RNAs and the function of DM RNAs were analyzed by biostatistics and bioinformatics programs. Results: 26 mRNAs were hypermethylated and three mRNAs were hypomethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). Most of these 29 DM mRNAs are involved in immune-related pathways (e.g., IL-17 signaling). Moreover, four lncRNAs were hypermethylated and one lncRNA was hypomethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). Additionally, three miRNAs were hypermethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). Conclusions: This study revealed RNA methylomic changes in the NAc of AUD subjects, suggesting that chronic alcohol consumption may lead to AUD through epitranscriptomic RNA modifications. Our findings need to be replicated in a larger sample.