Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy

Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.
Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes

The spectroscopic and kinetic characterization of two intermediates from the H2O2 oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1–3 + guaiacol + H2O2 → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H2O2, resulting in only two types of kinetics that were developed during the first 0–4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N’-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, 1H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.
Determining Nitrate and Nitrite Content in Beverages, Fruits, Vegetables, and Stews Marketed in Arak, Iran

Background and Objectives. Presence of excessive nitrite and nitrate in foodstuff can have toxic and carcinogenic effects on humans. This study is aimed at measuring nitrate and nitrite in different foodstuffs available in Arak city market, Iran, in 2013. Methods. Totally 323 samples including stew (102 samples), beverage (116 samples), fruit (55 samples), and vegetables (50 samples) were randomly collected and analyzed according to official AOAC method 973 and ISO 6635 through spectrophotometric method. Results. Average concentration of nitrate and nitrite in the samples was 6.58–136.76, 1.52–38.22 mg kg−1 or liter, respectively. Presence of nitrate and nitrite was confirmed in all samples. High levels of nitrate and nitrite were observed in celery and ghormeh stew; and lower level of nitrate and nitrite was found in traditionally produced vinegar, verjuice, and tomato. Conclusions. It was found that the mean values for nitrite in investigated products were higher than ADI levels of WHO.
Consistency, Breakdown Robustness, and Algorithms for Robust Improper Maximum Likelihood Clustering

The robust improper maximum likelihood estimator (RIMLE) is a new method for robust multivariate clustering finding approximately Gaussian clusters. It maximizes a pseudo-likelihood defined by adding a component with improper constant density for accommodating outliers to a Gaussian mixture. A special case of the RIMLE is MLE for multivariate finite Gaussian mixture models. In this paper we treat existence, consistency, and breakdown theory for the RIMLE comprehensively. RIMLE's existence is proved under non-smooth covariance matrix constraints. It is shown that these can be implemented via a computationally feasible Expectation-Conditional Maximization algorithm.
Regimen-related toxicity in patients undergoing bone marrow transplantation.

Bone marrow transplantation is associated with significant morbidity and mortality, some of which is due to high-dose chemoradiotherapy. In order to quantitate toxicity that was felt to be due to the preparative regimen (termed regimen-related toxicity [RRT]), a system was developed in which toxicities were graded from 0 (none) to 4 (fatal). One hundred ninety-five patients who underwent marrow transplantation for leukemia were studied retrospectively to determine whether toxicities that were clinically felt to be due to the preparative regimen were influenced by other factors such as disease status, graft-versus-host disease (GVHD) prophylaxis, and allogenicity. All patients developed grade I toxicity in at least one organ, and 30 developed grades III-IV (life-threatening or fatal) RRT. RRT was more common in relapsed patients v remission patients (P = .04), in those receiving 15.75 Gy total body irradiation (TBI) v 12.0 Gy TBI (P = .028), and in those receiving allogeneic marrow v autologous marrow (P = .0029). Autologous marrow recipients did not develop grades III-IV toxicity in this study. A multivariate analysis controlling for autologous marrow grafting showed that the dose of TBI was the only statistically significant predictor of grades III-IV RRT. Those patients who developed grade III RRT were unlikely to survive 100 days from transplant, though not all deaths could be attributed to RRT. Patients who developed grade II toxicity in three or more organs were more likely to die within 100 days than those developing grade II toxicity in two or less organs (P = .0027). This system was generally able to distinguish RRT from other toxicities observed in marrow recipients.
Comparative Analysis of Context-Dependent Mutagenesis in Humans and Fruit Flies

In general, mutation frequencies are context-dependent: specific adjacent nucleotides may influence the probability to observe a specific type of mutation in a genome. Recently, several hypermutable motifs were identified in the human genome. Namely, there is an increased frequency of T>C mutations in the second position of the words ATTG and ATAG and an increased frequency of A>C mutations in the first position of the word ACAA. Previous studies have also shown that there is a remarkable difference between the mutagenesis of humans and drosophila. While C>T mutations are overrepresented in the CG context in humans (and other vertebrates), this mutation regularity is not observed in Drosophila melanogaster. Such differences in the observed regularities of mutagenesis between representatives of different taxa might reflect differences in the mechanisms involved in mutagenesis. We performed a systematical comparison of mutation regularities within 2–4 bp contexts in Homo sapiens and Drosophila melanogaster and found that the aforementioned contexts are not hypermutable in fruit flies. It seems that most mutation contexts affect mutation rates in a similar manner in H. sapiens and D. melanogaster; however, several important exceptions are noted and discussed.
On Organizational Citizenship

Part 1 Preface Part 2 Acknowledgments Part 3 Introduction Chapter 4 1. Building the Construct Chapter 5 2. Social Paradigms Chapter 6 3. Government in Industrial Society Chapter 7 4. Applied Human Nature Chapter 8 5. Organizational Citizenship Behavior Chapter 9 6. Organizational Citizenship Chapter 10 7. Afterword Chapter 11 8. Why It is a Bad Idea To Run a College Like a Business Part 12 Reference Part 13 Index
System in-Package solution with Dielectric Resonator Antenna and Power Amplifier for a 60 GHz high data-rate transmitter

Performance of a System in-Package (SiP) module is evaluated in this paper. The solution consists of a Dielectric Resonator Antenna (DRA) excited by a Power Amplifier (PA). The impact of the bond wire and the closed proximity of the PA element have been considered in the simulation for the co-design of this highly integrated sub-system. Experimental results show a total EIRP of 21 dBm measured for the PA/DRA configuration.
The Personal Travel Assistant (PTA): Measuring the Dynamics of Human Travel Behavior

The fundamental research question that was addressed with the project is whether a simple, continuously collected GPS sequence can be used to accurately measure human behavior. We applied Hybrid Dynamic Mixed Network (HDMN) modeling techniques to learn behaviors given an extended GPS data stream. This research project was designed to be an important component of a much larger effort. Unfortunately, the promised funding from a commercial sponsor for the larger project did not materialize, and so we did not have the resources to deploy a prototype personal travel assistant system. Work focused on developing the HDMN model. The learning and inference steps using the HDMN model were much slower than would be acceptable in an operational Personal Travel Assistant (PTA) system. We conducted research into alternate formulations that would improve convergence, handle noisy data more robustly and reduce the need for human intervention. This report describes how this projectâ€™s results fit into the larger research context, details the work done for this UCTC grant, and outlines future directions of research based on the findings of this project.
A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral effects of neuronal ablations and genetic perturbations, as well as unexpected aspects of wild type behavior. The predictive success of the model indicates that random search in C. elegans can be understood in terms of a neuronal flip-flop circuit involving reciprocal inhibition between two populations of stochastic neurons. Our findings establish a unified theoretical framework for understanding C. elegans locomotion and a testable neuronal model of random search that can be applied to other organisms.
A low phase noise oscillator using SIW combline resonator

A low phase noise oscillator based on substrate integrated waveguide (SIW) combline resonator is presented. By taking high-Q advantage of the resonator's superior characteristics, the proposed oscillator possesses low phase noise performance with a compact size. For validating the idea, an oscillator operating at X-band is designed and fabricated. The measured results show that at the oscillation frequency of 10.07 GHz with − 0.7 dBm output power, the phase noise is −127.25 dBc/Hz at 1 MHz frequency offset.
Non-ignorable missing covariate data in parametric survival analysis

Within any epidemiological study missing data is almost inevitable. This missing data is often ignored; however, unless we can assume quite restrictive mechanisms, this will lead to biased estimates. Our motivation are data collected to study the long-term effect of severity of disability upon survival in children with cerebral palsy (henceforth CP). The analysis of such an old data set brings to light statistical difficulties. The main issue in this data is the amount of missing covariate data. We raise concerns about the mechanism causing data to be missing. We present a flexible class of joint models for the survival times and the missing data mechanism which allows us to vary the mechanism causing the missing data. Simulation studies prove this model to be both precise and reliable in estimating survival with missing data. We show that long term survival in the moderately disabled is high and, therefore, a large proportion will be surviving to times when they require care specifically for elderly CP sufferers. In particular, our models suggest that survival from diagnosis is considerably higher than has been previously estimated from this data. This thesis contributes to the discussion of possible methods for dealing with NMAR data.
Early Aqueous Humor Analysis in Patients with Human Ocular Toxoplasmosis

ABSTRACT To evaluate the diagnostic sensitivity of a panel of laboratory tests for ocular toxoplasmosis performed at the time of presentation, paired samples of aqueous humor and serum were collected from 49 consecutive episodes of ocular toxoplasmosis with a clinical course of less than 3 weeks. Total immunoglobulin G (IgG) andToxoplasma gondii-specific IgG, IgM, and IgA were quantified by enzyme-linked immunosorbent assay. The avidity ofT. gondii-specific IgG was determined, and DNA extracted from aqueous humor was amplified for detection of a glycoprotein B gene sequence of T. gondii. The diagnosis was confirmed for 73% (36 of 49) of the patients; this rate rose to 79.5% if data from a later analysis of aqueous humor derived from five of the negative patients were included. The analysis of serum (detection of T. gondii-specific IgM and analysis of consecutive serum samples) alone did not contribute to the diagnosis. Calculation of local antibody production lacked diagnostic sensitivity when it was determined less than 3 weeks after the manifestation of clinical symptoms (28 of 49 patients [57%]), but this rose to 70% after an analysis of a second aqueous humor sample. The antibody avidity index attained diagnostic significance in only 8 of 43 instances (19%), andT. gondii DNA was amplified from no more than 6 of 39 (16%) aqueous humor samples. However, T. gondii-specific IgA was found within the aqueous humors of 11 of 43 patients (26%); measurement of the T. gondii-specific IgA level thus contributed substantially to the diagnostic sensitivity of the laboratory tests.
Forbearance Across Culture

FORBEARANCE ACROSS CULTURE By Yin Lin, M.S., M.A. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2015. Major Director: Everett L. Worthington, Jr., Ph.D. Professor Department of Psychology Forbearance is defined for the purpose of the present dissertation as, “the attempt to suppress the visible signs of negative emotion (i.e., emotional expression) and visible behaviors (i.e., the expression of negative vengeful or avoidant motives) in response to a hurt or offense, often (but not always) for the sake of group harmony. ” I reviewed the literature on forbearance and cross-cultural studies in suppression of emotion or emotional expression under the framework of New Big Five personality processes and cultural models of self and relating. Then I offered three propositions about forbearance. Furthermore, I collected three samples and described four studies to develop and test the construct validity of Forbearance Scale as well as the Group-Harmony Forbearance Index. Last but not least, I discussed implications for future research and practice related to forbearance.
Investigating Progression in Substance Use Initiation Using a Discrete-Time Multiple Event Process Survival Mixture (MEPSUM) Approach

The order and timing of substance initiation have significant implications for later problematic patterns of use. Despite the need to study initiation from a multivariate framework, survival analytic methods typically cannot accommodate more than two substances in one model. The discrete-time multiple event process survival mixture (MEPSUM) model represents an advance by incorporating more than two outcomes and enabling establishment of latent classes within a multivariate hazard distribution. Employing a MEPSUM approach, we evaluated patterns of tobacco, alcohol, and cannabis initiation in the National Longitudinal Study of Adolescent to Adult Health (N = 18,923). We found four classes that differed in their ages and ordering of peak initiation risk. Demographics, externalizing psychopathology, and personality significantly predicted class membership. Sex differences in the association between delinquency and initiation patterns also emerged. Findings support the utility of the MEPSUM approach in elucidating developmental pathways underlying clinically relevant phenomena.
Flexibility and torsional behaviour of rotary nickel-titanium PathFile, RaCe ISO 10, Scout RaCe and stainless steel K-File hand instruments.

AIM To assess and compare the flexibility and torsional resistance of PathFile, RaCe ISO 10 and Scout RaCe instruments in relation to stainless steel K-File hand instruments. METHODOLOGY Rotary PathFile (sizes 13, 16 and 19; .02 taper), Race ISO 10 (size 10; 0.02, 0.04 and 0.06 tapers), Scout RaCe (sizes 10, 15 and 20; 0.02 taper) and hand K-File (sizes 10, 15 and 20; 0.02 taper) instruments were evaluated. Alloy chemical composition, phases present and transformation temperatures were determined for the NiTi instruments. For all instruments, diameters at each millimetre from the tip as well as cross-sectional areas at 3 mm from the tip were measured based on ANSI/ADA Specification No. 101 using image analysis software. Resistance to bending and torsional resistance were determined according to specification ISO 3630-1. Vickers microhardness measurements were also taken in all instruments to assess their strength. Data were analysed using analysis of variance (α = 0.05). RESULTS The alloys used in the manufacture of the three types of NiTi instruments had approximately the same chemical composition, but the PathFile instruments had a higher Af transformation temperature and contained a small amount of B19' martensite. All instruments had diameter values within the standard tolerance. The bending and torsional resistance values were significantly increased relative to the instrument diameter and cross-sectional area. CONCLUSIONS PathFile instruments were the most flexible and the least torque resistant, whilst the stainless steel instruments were the least flexible although they were more torque resistant than the NiTi instruments.
Transversals as generating sets in finitely generated groups

We explore transversals of finite index subgroups of finitely generated groups. We show that when $H$ is a subgroup of a rank $n$ group $G$ and $H$ has index at least $n$ in $G$ then we can construct a left transversal for $H$ which contains a generating set of size $n$ for $G$, and that the construction is algorithmic when $G$ is finitely presented. We also show that, in the case where $G$ has rank $n \leq3$, there is a simultaneous left-right transversal for $H$ which contains a generating set of size $n$ for $G$. We finish by showing that if $H$ is a subgroup of a rank $n$ group $G$ with index less than $3 \cdot 2^{n-1}$, and $H$ contains no primitive elements of $G$, then $H$ is normal in $G$ and $G/H \cong C_{2}^{n}$.
Reconsidering Michael Polanyi’s Philosophy

The chemist and philosopher Michael Polanyi (1891-1976) was one of the first twentieth-century scientists to propose a program to resolve the internal conflict of the modern Enlightenment: scientific detachment and moral nihilism with humanist values. Stefania Jha's intellectual biography places Polanyi in the context of his time and culture, analyzes his key philosophical ideas, and explicates the application - and at times misappropriation - of his work. Polanyi's method was not laid out in his published works, and his vocabulary tends to make his writings difficult to understand. By exposing the structure of his theory of tacit knowing, and by tracing the growth of his thinking, Jha shows how the various elements of his thought are integrated. Through examination of his philosophical roots in Kant and the complexity of his evolving thought, she counteracts the popular notion that Polanyi's philosophy stands apart from the western philosophic tradition. Jha's deep analysis makes Polanyi's shift of focus from science to philosophy more intelligible, his philosophy more approachable, and the causes he championed - such as the freedom of science and cultural freedom - more understandable. Applying his notion of tacit knowing in practical directions, Jha seeks to bring the study of Polanyi's philosophy out of the specialists' enclave and into such fields as ethics and clinical medicine.
Acoustic Communications for Regional Undersea Observatories

Undersea observatories connected to shore with fiber-optic cable will provide scientists with long-term measurements from deep-ocean sensors. Proposed regional observatories include NEPTUNE which will traverse a three thousand kilometer path on the Juan de Fuca plate in the North Pacific. The NEPTUNE backbone includes nodes spaced approximately 100 km apart where additional branches may be added, and a variety of sensors supporting different scientific disciplines will located at each node and along the branches. The fiber optic and power cable creates a backbone that easily supports many smaller regions (cells) covered by wireless communication. An acoustic system extends the reach of the observatory in the area around each cell, allowing additional instruments to be added without installing dedicated cables. The utility of the wireless extension is highly dependent upon the range of the link, its energy efficiency and the total capacity of a cell. The objective of this paper is to explore these issues and discuss design, implementation, and performance of the wireless network.