Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Algorithms for Complex Systems with Applications to Non-linear Oscillators and Genome Assembly

Title of dissertation: NETWORK ALGORITHMS FOR COMPLEX SYSTEMS WITH APPLICATIONS TO NON-LINEAR OSCILLATORS AND GENOME ASSEMBLY Karl R. B. Schmitt, Doctor of Philosophy, 2013 Dissertation directed by: Assistant Professor Michelle Girvan Department of Physics & Dr. Aleksey Zimin Institute for Physical Science and Technology Network and complex system models are useful for studying a wide range of phenomena, from disease spread to traffic flow. Because of the broad applicability of the framework it is important to develop effective simulations and algorithms for complex networks. This dissertation presents contributions to two applied problems in this area First, we study an electro-optical, nonlinear, and time-delayed feedback loop commonly used in applications that require a broad range of chaotic behavior. For this system we detail a discrete-time simulation model, exploring the model’s synchronization behavior under specific coupling conditions. Expanding upon already published results that investigated changes in feedback strength, we explore how both time-delay and nonlinear sensitivity impact synchronization. We also relax the requirement of strictly identical systems components to study how synchronization regions are affected when coupled systems have non-identical components (parameters). Last, we allow wider variance in coupling strengths, including unique strengths to each system, to identify a rich synchronization region not previously seen. In our second application, we take a complex networks approach to improving genome assembly algorithms. One key part of sequencing a genome is solving the orientation problem. The orientation problem is finding the relative orientations for each data fragment generated during sequencing. By viewing the genomic data as a network we can apply standard analysis techniques for community finding and utilize the significantly modular structure of the data. This structure informs development and application of two new heuristics based on (A) genetic algorithms and (B) hierarchical clustering for solving the orientation problem. Genetic algorithms allow us to preserve some internal structure while quickly exploring a large solution space. We present studies using a multi-scale genetic algorithm to solve the orientation problem. We show that this approach can be used in conjunction with currently used methods to identify a better solution to the orientation problem. Our hierarchical algorithm further utilizes the modular structure of the data. By progressively solving and merging sub-problems together we pick optimal ‘local’ solutions while allowing more global corrections to occur later. Our results show significant improvements over current techniques for both generated data and real assembly data. NETWORK ALGORITHMS FOR COMPLEX SYSTEMS WITH APPLICATIONS TO NON-LINEAR OSCILLATORS AND GENOME ASSEMBLY
Stability of Cleft maxilla in Le Fort I Maxillary advancement

Context: Le Fort 1 maxillary osteotomy in operated patients of cleft lip and cleft palate (CLCP). Aims: To study stability of Le Fort 1 maxillary osteotomy in operated patients of CLCP by two-dimensional evaluation using cephalometric analysis. Settings and Design: Prospective study conducted at Army Dental Centre (Research and Referral) from May 2009-May 2012. Materials and Methods: Subjects included nine consecutively operated patients of CLCP with maxillary hypoplasia. Maxillary advancement by Le Fort 1 maxillary step osteotomy was performed. There were four males and five females with an age range of 16-18 years and follow-up range was 12-36 months. Presurgical and postsurgical changes were compared using cephalometrics for orthognathic surgery (COGS) system to determine stability of maxillary movement and quantify amount of relapse at 15 days and 12 months. Statistical Analysis: Student's t-test. Results: Mean linear horizontal advancement achieved along nasion (N) to anterior nasal spine (ANS) with reference to true vertical plane at 15 days and 12 months was 5.17 and 3.91 mm, respectively. The mean relapse in anteroposterior dimension was 21.63%. The mean vertical displacement observed along nasion and ANS with reference to true horizontal plane at 15 days and 12 months was 5.21 mm and 3.2, respectively with a resultant relapse of 41.54%. Conclusions: Based on clinical and COGS analysis, it is evident that Le Fort 1 advancement in operated cases of CLCP has inherent potential for relapse.
Studies with 4-14C-lynestrenol in normal and lactating women.

4-14C-Lynestrenol was administered either orally or by intravenous injection to women using Lyndiol (5 mg lynestrenol plus 150 mcg mestranol) to determine the plasma levels of radioactivity and excretion of radioactivity in milk and urine. 6 of the subjects were normal lactating women and 3 had been hospitalized for minor surgery. In order to study the effect of the pharmaceutical form in oral administration the radioactive progestagen was given either as the pure compound in the form of a gelatin capsule or as a tablet containing all the ingredients usually present in the Lyndiol tablets. The clearance rate of radioactivity from the blood was very low. A half-life in the order of 40 hours was estimated for labelled lynestrenol and metabolites. 54-65% of the radioactivity was excreted in the urine within 4-5 days after oral administration of the 14C-lynestrenol containing tablet. Much smaller amounts about 15% of the dose were excreted after oral administration of the 14C-lynestrenol taken in a capsule. After intravenous administration 45-56% of the administered radioactivity was recovered in the urine excreted within 4 days after injection. After oral administration of a 14C-lynestrenol containing tablet to 3 lactating women . 022 . 028 and . 088% of the administered radioactivity was excreted in the milk collected during the first 5 days after administration. Results indicate that resorption may be considerably influenced by the pharmaceutical form of the orally administered compound. (Authors modified)
Human Kallikrein-related Peptidase 14 (KLK14) Is a New Activator Component of the KLK Proteolytic Cascade

Human kallikrein-related peptidases (KLKs) are a family of 15 serine proteases mainly known for their biomarker utility in various neoplastic and non-neoplastic diseases. Despite significant progress in understanding their clinical application, little is known about the activation mechanism(s) of this important family of enzymes. Emerging evidence indicates that KLKs are activated in a stepwise manner, which is a characteristic of proteolytic cascades. Thus far, KLK cascades have been implicated in semen liquefaction and skin desquamation. Many members of the KLK family have been reported to be active in seminal plasma and/or skin, suggesting their involvement in common proteolytic cascades. KLK14, in particular, is highly active and has recently been proposed as one of the key trypsin-like proteases involved in skin desquamation. This study aims to elucidate a probable cascade-mediated role of KLK14 by 1) examining KLK14-mediated cleavage of a heptapeptide library encompassing activation sites of the 15 KLKs and 2) verifying activation of certain candidate downstream targets of KLK14 (i.e. pro-KLK1, -KLK3, and -KLK11). Heptapeptides encompassing activation motifs of KLK2, -3, -5, and -11 were cleaved with a high (≥85%) cleavage efficiency. Activation of these candidates was confirmed using full-length recombinant proteins. Pro-KLK11, -KLK3, and -KLK1 were rapidly activated in a concentration-dependent manner. Pro-KLK3 regulation was bidirectional because activation was followed by inactivation via internal cleavage of active KLK3. We are proposing a putative cascade model, operating through multiple KLKs. Identification of novel members of such proteolytic cascades will aid in further defining mechanisms involved in seminal/skin homeostasis.
Expression of Interleukin-1β, Tumor Necrosis Factor Alpha, and Interleukin-6 in Human Peripheral Blood Leukocytes Exposed to Human Granulocytic Ehrlichiosis Agent or Recombinant Major Surface Protein P44

ABSTRACT Human granulocytic ehrlichiosis (HGE) is an emerging febrile systemic disease caused by the HGE agent, an obligatory intracellular bacterium of granulocytes. The pathogenicity- and immunity-related mechanisms of HGE are unknown. In this study, several cytokines generated in human peripheral blood leukocytes (PBLs) incubated with the HGE agent or a recombinant 44-kDa major surface protein (rP44) of the HGE agent were examined by reverse transcription-PCR and a capture enzyme-linked immunosorbent assay. The HGE agent induced expression of interleukin-1β (IL-1β), tumor necrosis factor alpha (TNF-α), and IL-6 mRNAs and proteins in PBLs in a dose-dependent manner to levels as high as those resulting from Escherichia colilipopolysaccharide stimulation. The kinetics of induction of these three cytokines in PBLs by rP44 and by the HGE agent were similar. Proteinase K treatment of the HGE agent or rP44 eliminated the ability to induce these three cytokines. Induction of these cytokine mRNAs was not dependent on superoxide generation. These results suggest that P44 proteins have a major role in inducing the production of proinflammatory cytokines by PBLs. Expression of IL-8, IL-10, gamma interferon, transforming growth factor β, and IL-2 mRNAs in response to the HGE agent was not remarkable. Among PBLs, neutrophils and lymphocytes expressed IL-1β mRNA but not TNF-α or IL-6 mRNA in response to the HGE agent, whereas monocytes expressed all three of these cytokine mRNAs. These observations suggest that induction of proinflammatory-cytokine gene expression by the major outer membrane protein of the HGE agent in monocytes, which are not the primary host cells of the HGE agent, contributes to HGE pathogenesis and immunomodulation.
Postnatal development of CO2‐O2 interaction in the rat carotid body in vitro.

1. The effect of PCO2 upon the discharge response to changes in PO2 (between ca 450 and 30 mmHg) was observed in adult (> 5 weeks old) and neonatal (5‐7 days old) rat carotid body chemoreceptors using an in vitro, superfused preparation. 2. In both adult and neonatal rats, regression analysis revealed that increasing PCO2 was without effect upon the shape of the PO2‐response curves (P > 0.30), but did cause an upward shift in the position of the curves, as indicated by a significant increase in the baseline chemoreceptor discharge during hyperoxia (0.22 +/‐ 0.02% maximum discharge per mmHg PCO2, P < 0.001, and 0.25 +/‐ 0.07% maximum discharge per mmHg PCO2, P < 0.005, respectively). However, whilst increasing PCO2 caused a significant rightward shift of the response curves in adults (0.75 +/‐ 0.23 mmHg PO2 per mmHg PCO2; P < 0.005), it was without effect in neonates (0.21 +/‐ 0.22 mmHg PO2 per mmHg PCO2; P > 0.200). Thus increasing levels of hypoxia increased CO2 chemosensitivity in adult but not in neonatal rats as shown by multiple regression analysis of the CO2‐response curves which revealed a significant interaction between PCO2 and PO2 for adult (P < 0.010) but not for neonatal (P > 0.150) rats. 3. We suggest that the previously reported maturation of peripheral chemoreceptor hypoxic sensitivity (resetting) may be due to the postnatal emergence of a significant degree of interaction between PCO2 and PO2 at the level of the peripheral chemoreceptor and/or its afferent innervation.
Cavity-backed wideband magneto-electric antenna for through-the-wall imaging radar applications

A wideband magneto-electric antenna is proposed for through-the-wall imaging radar (TWIR) applications in the frequency range 1.5-2.5 GHz. A rectangular cavity is introduced to improve the total gain and the front-to-back ratio (FBR) of the antenna. The through-the-wall imaging (TTWI) performance of the proposed antenna aimed to detect stationary targets has been investigated and compared with a conventional Vivaldi antenna. The results obtained by numerical simulations and processed by the back projection (BP) algorithm show that, compared with the Vivaldi antenna, the proposed antenna can not only detect the desired target, but also eliminate the effect of the undesired back objects, making it a promising candidate for TWIRs.
"Neuroendocrine" differentiation in hepatocellular carcinomas (HCCs): immunohistochemical reactivity is related to distinct tumor cell types, but not to tumor grade.

We have analyzed neuroendocrine differentiation (ND) in hepatocellular carcinomas (HCCs) of fifty patients. It turned out that ND is frequent in HCCs, and that it is not restricted to fibrolamellar hepatocellular carcinoma (FL-HCC). Multiexpression is seen in a quarter of the cases, and marker coexpression may occur within the same tumor cell. ND predominates in trabecular and mixed HCCs, but does not appear to be related to grade. Most positive cases showed a hepatocyte-like cell morphology, frequently associated with bile formation. It thus appears that the HCC cell type most likely to show ND is a hepatocyte-like one, i.e. differentiated cell, frequently polarized and producing bile, rather than a small and poorly-differentiated cell. Possible pathogenic mechanisms leading to ND in HCCs are briefly discussed.
Comparative evaluation of the antimicrobial activity of natural extracts of Morinda citrifolia, papain and aloe vera (all in gel formulation), 2% chlorhexidine gel and calcium hydroxide, against Enterococcus faecalis: An in vitro study

Aim: A comparative evaluation of the antimicrobial activity of natural extracts of Morinda citrifolia, papain, and aloe vera (all in gel formulations), 2% chlorhexidine gel and calcium hydroxide, against Enterococcus faecalis—an in vitro study. Materials and Methods: The antimicrobial efficacy was assessed in vitro using dentin shavings collected at 2 depths of 200 and 400 μm. The total colony forming units at the end of 1, 3, and 5 days were assessed. Results: The overall percentage inhibition of bacterial growth (200 and 400 μm depth) was 100% with chlorhexidine gel. This was followed by M. citrifolia gel (86.02%), which showed better antimicrobial efficacy as compared with aloe vera gel (78.9%), papain gel (67.3%), and calcium hydroxide (64.3%). There was no statistical difference between data at 200 and 400 μm depth. Conclusion: Chlorhexidine gel showed the maximum antimicrobial activity against E. faecalis, whereas calcium hydroxide showed the least. Among the natural intracanal medicaments, M. citrifolia gel consistently exhibited good inhibition up to the 5th day followed by aloe vera gel and papain gel.
Soyhulls as an alternative feed for lactating dairy cows: a review.

Dairy producers use soyhulls, a byproduct of soybean processing, to replace either grain or forage in diets of lactating dairy cows. In view of the nutritional and economical value of soyhulls it is anticipated that this practice will continue to increase in popularity among nutritionists and producers of ruminant animals. This paper reviews information regarding the nutritional value of soyhulls and the effects of feeding this alternative feed on ruminal fermentation, nutrient digestion and utilization, and performance of dairy cows. Soyhulls can replace corn grain to supply about 30% of the dry matter (DM) in high-grain diets without negatively affecting either the fermentation or digestion of nutrients in the gastrointestinal tract or the performance of dairy cows. Additionally, data suggest that soyhulls might successfully replace forage to supply < or = 25% of the DM in diets of dairy cows when the supply of effective fiber, which includes a chemical and a physical component, remains adequate after including the hulls. However, caution should be exercised when data from different studies are extrapolated to practical situations because the response to feeding soyhulls appears to be largely affected by the type of carbohydrate being replaced by soyhulls; the amount, type, and physical form of the dietary forage; and the incidence of either negative or positive associative effects before and after the addition of soyhulls to the original diet. Unfortunately, the paucity of data from experiments in which soyhulls constituted more than 25 to 30% of the dietary DM restricts the ability to identify the maximum amount of soyhulls that can be used in diets of dairy cows. Information from studies in which > or = 25 to 30% of dietary DM supplied as either cereal grains or forages are replaced with soyhulls is needed to better understand and predict the production of dairy cows fed diets containing the hulls. This knowledge is essential for maximizing the use of soyhulls in diets for dairy cows.
Chronic Stress Triggers Social Aversion via Glucocorticoid Receptor in Dopaminoceptive Neurons

Defeat, Distress, and Glucocorticoids Understanding how individuals control emotions and cope with stressful events is a major clinical concern and of importance for the treatment of psychiatric illnesses (see the Perspective by McEwen). Barik et al. (p. 332) discovered that aggressive defeat stress in mice caused glucocortioid release and increased activity in the dopamine system. Deleting the glucocorticoid receptors in dopaminoceptive neurons completely prevented the social avoidance that usually follows aggressive defeat. How the combination of genetic factors and environmental stressors during adolescence determines adult behavior and how their disturbance results in neuropsychiatric disorders is poorly understood. Niwa et al. (p. 335) found that isolation stress during adolescence, which does not cause any long-lasting changes in wild-type mice, induced significant neurochemical and behavioral alterations in mutant mice expressing a dominant-negative variant of the disrupted in schizophrenia 1 gene under the control of the prion protein promoter. These deficits could be reversed by a glucocorticoid receptor antagonist. Aggressive defeat stress in mice causes glucocorticoid release and increased activity in the dopamine system. [Also see Perspective by McEwen] Repeated traumatic events induce long-lasting behavioral changes that are key to organism adaptation and that affect cognitive, emotional, and social behaviors. Rodents subjected to repeated instances of aggression develop enduring social aversion and increased anxiety. Such repeated aggressions trigger a stress response, resulting in glucocorticoid release and activation of the ascending dopamine (DA) system. We bred mice with selective inactivation of the gene encoding the glucocorticoid receptor (GR) along the DA pathway, and exposed them to repeated aggressions. GR in dopaminoceptive but not DA-releasing neurons specifically promoted social aversion as well as dopaminergic neurochemical and electrophysiological neuroadaptations. Anxiety and fear memories remained unaffected. Acute inhibition of the activity of DA-releasing neurons fully restored social interaction in socially defeated wild-type mice. Our data suggest a GR-dependent neuronal dichotomy for the regulation of emotional and social behaviors, and clearly implicate GR as a link between stress resiliency and dopaminergic tone.
Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA

ABSTRACT Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.
Green Synthesis of Antibacterial Zinc Oxide Nanoparticles Using Biopolymer Azadirachta indica Gum

The progress of green chemistry in the synthesis of nanoparticles with use of plants has engrossed a great attention nowadays due to its inexpensive, simple, non-toxic and environmentalfriendly nature. The present study has been undertaken to prepare Azadirachta indica gum stabilized ZnO nanoparticles with multifunctional properties. The prepared nanoparticles were characterized by FT-IR, XRD, FE-SEM and UV-Vis absorption studies. It was clear from XRD pattern that nanoparticles were crystallized in hexagonal wurtzite structure. The average size of the nanoparticles was found to be 30-60nm. The synthesized nanoparticles exhibited potent antibacterial activity against E. coli and S. aureus.
The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing

In Escherichia coli and some other γ‐Proteobacteria, the alternative σ factor RpoS functions as a regulator of the general stress response. The role of RpoS in Pseudomonas aeruginosa is not clear. Although P. aeruginosa RpoS contributes to the resistance to several environmental stresses, its role appears to be less pivotal than in E. coli. In P. aeruginosa, RpoS also regulates the production of several virulence factors and influences the expression of individual genes that are controlled by quorum sensing. Some quorum‐controlled genes are induced by RpoS, whereas others are repressed. To gain insights about RpoS function in P. aeruginosa and to understand better the regulation of quorum‐controlled genes, we used transcript profiling to define an RpoS regulon. We identified 772 genes regulated by RpoS in stationary but not in logarithmic growth phase (504 were induced and 268 were repressed), and we identified putative RpoS promoter sequence elements with similarity to the E. coli RpoS consensus in several of these genes. Many genes in the regulon, for example a set of chemotaxis genes, have assigned functions that are distinct from those in E. coli and are not obviously related to a stress response. Furthermore, RpoS affects the expression of more than 40% of all quorum‐controlled genes identified in our previous transcriptome analysis. This highlights the significance of RpoS as a global factor that controls quorum‐sensing gene expression at the onset of stationary phase. The transcription profiling results have allowed us to build a model that accommodates previous seemingly conflicting reports.