Miracle-dz/UniFAR-FTUs huggingface dataset:
An experimental investigation into the mechanisms of bacterial evolution

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneousmutation, in the bacterium Escherichia coli through novel experimental assays andmathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneousmutation through qPCR assay of competition betweenwildtype and mutator phenotype E. coli. Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability.
Spectrum Harvesting and Sharing in Multi-Hop CRNs Under Uncertain Spectrum Supply

The essential impediment to apply cognitive radio (CR) technology for efficient spectrum utilization lies in the uncertainty of licensed spectrum supply. In this paper, we propose a novel architecture for spectrum harvesting and sharing, and investigate the joint routing and frequency scheduling problem in multi-hop cognitive radio networks (CRNs) under uncertain spectrum supply. We introduce a new service provider, Secondary Service Provider (SSP), to facilitate the accessing for secondary users (SUs). We model the vacancy of available bands with a series of random variables, and mathematically describe the corresponding frequency scheduling and flow routing constraints. From the SSP's point of view, we characterize the CRN performance with a pair of parameters (α, β), and present an optimization problem to minimize the required network-wide spectrum resource at the (α,β) level. Given that (α, β) level is specified, we obtain a lower bound for the optimization problem and develop a threshold based coarse-grained fixing algorithm for a feasible solution. Simulation results show that (i) for any (α,β) level, the proposed algorithm provides a near-optimal solution to the formulated NP-hard problem, and (ii) the (α,β) based solution is better than the expected bandwidth based one in terms of blocking ratio and spectrum utilization in multi-hop CRNs.
Learning Civics in the Community

ABSTRACTTo test the effects of an out-of-classroom experiential learning program on adolescents' knowledge and attitudes about local government, high school students serving as interns to local government officials were compared to students selected to participate in the same program at a later time. Regression analyses controlling for pretest scores yielded statistically significant differences in favor of the interns for knowledge and political efficacy but not attitudes toward local government. Comparisons among four intern programs and with conventional civics classes confirmed the attribution of gains to participation in the programs and indicated the importance of seminars and of a close relationship between interns and their sponsors. Although these results cannot be generalized to nonvoluntary programs or to other subjects, they are strong enough to recommend further testing of experiential approaches, contrary to current emphasis on conventional classroom instruction.
Behavioural and family systems interventions in developmental disability: towards a contemporary and integrative approach

While behavioural intervention is effective in the treatment of challenging behaviour, in developmental disability it can have significant limitations in the family setting. Families can sometimes find it difficult to make lifecycle transitions or respond to other stressful life events and become stuck in patterns of interaction that include the presenting behaviour. The aim of this paper is to present a theoretical and working model of intervention that integrates more contemporary behavioural and systemic orientations. Four stages for intervention are provided, each consisting of practical guidelines for the clinician. Three detailed case studies are also included.
The third planet

This paper examines the conceptions of planetary phenomena related to temperature change as held by primary school teacher trainees at the Department of Teacher Education of Jyvaskyla University. The data were collected by means of an essay test, supplemented by interviews. The results show that very few students have internalized these phenomena in accordance with present‐day scientific concepts. The significance of the Earth's sphericity seems particularly obscure. The influence of the angle of inclination of the Earth's axis is misunderstood. Similarly, temperature differences are erroneously attributed to the distance from the sun of the Earth or of a particular place. The students do not reach their conclusions by inference, but rather attempt to remember what they have been taught. There are defects in their logical thought, several answers contained no explanation whatsoever, and cause‐and‐effect relationships are reversed.
Thermal rejuvenation in metallic glasses

Abstract Structural rejuvenation in metallic glasses by a thermal process (i.e. through recovery annealing) was investigated experimentally and theoretically for various alloy compositions. An increase in the potential energy, a decrease in the density, and a change in the local structure as well as mechanical softening were observed after thermal rejuvenation. Two parameters, one related to the annealing temperature, Ta/Tg, and the other related to the cooling rate during the recovery annealing process, Vc/Vi, were proposed to evaluate the rejuvenation phenomena. A rejuvenation map was constructed using these two parameters. Since the thermal history of metallic glasses is reset above 1.2Tg, accompanied by a change in the local structure, it is essential that the condition of Ta/Tg ≥ 1.2 is satisfied during annealing. The glassy structure transforms into a more disordered state with the decomposition of icosahedral short-range order within this temperature range. Therefore, a new glassy structure (rejuvenation) depending on the subsequent quenching rate is generated. Partial rejuvenation also occurs in a Zr55Al10Ni5Cu30 bulk metallic glass when annealing is performed at a low temperature (Ta/Tg ~ 1.07) followed by rapid cooling. This behavior probably originates from disordering in the weakly bonded (loosely packed) region. This study provides a novel approach to improving the mechanical properties of metallic glasses by controlling their glassy structure.
Automatic creation of stock market lexicons for sentiment analysis using StockTwits data

Sentiment analysis has been increasingly applied to the stock market domain. In particular, investor sentiment indicators can be used to model and predict stock market variables. In this context, the quality of the sentiment analysis is highly dependent of the opinion lexicon adopted. However, there is a lack of lexicons adjusted to microblogging stock market data. In this work, we propose an automatic procedure for the creation of such lexicon by exploring a large set of labeled messages from StockTwits, a popular financial microblogging service, and using four statistical measures: adaptations of the known TF-IDF, Information Gain, Class Percentage, and a newly proposed Weighted Class Probability. The obtained lexicons are competitive when compared with a set of six reference lexicons. Moreover, we verified that it is beneficial to use continuous sentiment scores instead of sentiment labels.
Interrelations between thyrotropin levels and iodine status in thyroid-healthy children.

BACKGROUND Worldwide, iodine prophylaxis measures have improved iodine status in populations. Several studies have reported an increase in thyrotropin (TSH) levels coinciding with this prophylaxis. Whether this implies an increased risk for hypothyroidism or simply reflects a physiologic TSH adaptation mechanism is not clear. METHODS Data on iodine and thyroid status of 6-17 year old children and adolescents (n=9175), collected between 2003 and 2006 in the German-wide Health Interview and Examination Survey for Children and Adolescents (KiGGS) Study, provided the basis for the analyses of mutual relationships of urinary iodine status (assessed by iodine/creatinine ratio in spot urines), serum TSH levels, and thyroid volume (determined by ultrasound). For data analyses (multivariable linear regression analysis), only those children were included for whom none of the available parameters (including free triiodothyronine [fT3], free thyroxine [fT4], and thyroperoxidase antibody [TPO-Ab] measurements) indicated a potential pathophysiologic thyroid status (n=6101). RESULTS In this population-based sample of thyroid-healthy children, higher urinary iodine excretion was associated with higher TSH levels (p<0.05), adjusted for sex, age, body surface area, body mass index, fT3/fT4 ratio, and time of blood sampling. Higher TSH levels were not associated with a higher prevalence of TPO-Ab but with lower thyroid volume (p<0.001, fully adjusted). For the present study sample, one-time spot measurements of urinary iodine excretion were not related to thyroid volume, the long-term marker of iodine status. CONCLUSION Our findings show for the first time in thyroid-healthy children that smaller thyroid volume is associated with higher normal TSH levels. A decreased thyroid cell mass and cell amount, as induced by an improved iodine status, does presumably require a higher TSH signal to maintain a constant thyroid hormone production, suggesting an underlying physiologic adaptation. Correspondingly, an increased TSH level should not be used as the single criterion to evaluate the prevalence of hypothyroidism, and the repeatedly observed parallel increases of iodine supply and TSH levels should not readily be interpreted as evidence for an increased hypothyroidism risk. These insights, contradicting conventional interpretations, may contribute to dispel uncertainties about the safety of iodine prophylaxis measures.
A New Perspective on the Small-World Phenomenon: Greedy Routing in Tree-Decomposed Graphs

Milgram’s experiment (1967) demonstrated that there are short chains of acquaintances between individuals, and that these chains can be discovered in a greedy manner. Kleinberg (2000) gave formal support to this so-called “small world phenomenon” by using meshes augmented with long-range links chosen randomly according to harmonic distributions. In this paper, we propose a new perspective on the small world phenomenon by considering arbitrary graphs augmented according to distributions guided by tree-decompositions of the graphs. We show that, for any n-node graph G of treewidth ≤ k, there exists a tree-decomposition-based distribution D such that greedy routing in the augmented graph (G,D) performs in O(k log n) expected number of steps. We argue that augmenting a graph with long-range links chosen according to a tree-decomposition-based distribution is plausible in the context of social networks. However, social networks can have unbounded treewidth. Nevertheless, we note that these networks have few long chordless cycles because of their high clustering coefficient. We prove that if G has chordality ≤ k, then the tree-decomposition-based distribution D insures that greedy routing in (G,D) performs in O((k + log n) logn) expected number of steps. In particular, for any n-node graph G of chordality O(log n) (e.g., chordal graphs), greedy routing in the augmented graph (G,D) performs in O(log n) expected number of steps. This latter result stresses the fact that our model may well explain why greedy routing is so efficient in social networks, such as observed in Milgram’s experiment.
Using Self-Assessments in Early Intervention Training

The Individuals with Disabilities Education Act (1997) addresses the importance of training personnel in special education through the development and implementation of a Comprehensive System of Personnel Development (CSPD) for each state. States often use self-assessment by the learner as a means of assessing training priorities and evaluating the effectiveness of inservice initiatives for the CSPD. This article describes the implementation of a self-assessment process based on competencies and validated behavioral indicators used statewide in Georgia for personnel in early intervention. Investigators analyzed 3500 self-assessment forms completed during a 2-year period that covered five Part C content areas. Changes in self-assessments are described and the utility of self-assessments is discussed.
A Survey of Wireless Security

Constant increase in use of wireless infrastructure networks for business purposes created a need for strong safety mechanisms. This paper describes WEP (Wired Equivalent Privacy) protocol for the protection of wireless networks, its security deficiencies, as well as the various kinds of attacks that can jeopardize security goals of WEP protocol: authentication, confidentiality and integrity. The paper, also, gives a summary of security improvements of WEP protocol that can lead to the higher level of wireless network infrastructure protection. Comparative analysis shows the advantages of the new 802.11i standard in comparison to the previous security solutions.
Plasma homocysteine, apolipoprotein E status and vascular disease in elderly patients with mental illness

Abstract Background: Total plasma homocysteine (tHcy) concentration is increased in elderly patients with mental illness. Also, patients with vascular disease have significantly higher plasma tHcy concentration compared with patients without vascular disease. Apolipoprotein E (apoE) status is associated with cardiovascular disease and a major genetic risk factor is inheritance of the e4 allele. In the present study, we investigated the association between plasma tHcy and apoE status. Methods: The relation between apoE status, plasma tHcy and vascular disease was investigated in a cohort of consecutively enrolled elderly patients with mental illness (n=328). Results: Plasma tHcy concentrations were increased (p<0.01) in carriers of APOE4 (13.6 μmol/L; 9.2–21.7 μmol/L) compared to non-carriers (12.4 μmol/L; 8.3–19.9 μmol/L). The proportion of patients with vascular disease was significantly (p<0.001) increased among carriers (61%) compared to non-carriers (42%). An increased percentage (p<0.001) of APOE4 carriers was observed in patients with Alzheimer's disease (AD) with (71%) or without vascular disease (42%), and in patients with vascular dementia (VaD) (54%) compared to a reference group (34%). Conclusions: Since carriers of APOE4 showed an increased likelihood of vascular disease, these patients need more intensive control of other modifiable vascular risk factors. Furthermore, the association between plasma tHcy and the presence of APOE4 might be attributed to an increased proportion of vascular disease in APOE4 carriers. Clin Chem Lab Med 2010;48:129–35.
The impact of an end-point committee in a large multicentre, randomized, placebo-controlled clinical trial: results with and without the end-point committee's final decision on end-points.

BACKGROUND A multicentre study permits rapid recruitment of a large number of patients. However, there is a risk of heterogeneities in end-point evaluations, as complex definitions of criteria are interpreted by several local investigators from different hospitals. Reports discussing end-point evaluation are sparse. The TRIM trial was a multicentre trial of a thrombin inhibitor in patients with unstable angina or non-Q myocardial infarction. In this study, an independent end-point committee evaluated all the reported events of death, acute myocardial infarction and refractory angina pectoris in order to obtain uniform judgements of major end-points. STUDY AIMS To describe the work of the end-point committee, to analyse its possible effect on the final study results and to discuss the impact on the design of future trials. METHOD The end-point committee consisted of four members, one from each participating country. After the data were processed by the study monitors, completed case record forms and patient files for patients with reported end-points were mailed to the national member of the end-point committee for judgement. The end-point committee met regularly and made final decisions about the end-points. The work of the end-point committee was documented on a separate case record form. RESULTS The end-point committee assessed 246 events of death, acute myocardial infarction and refractory angina pectoris in 187 of the 1209 patients (15.5%) in the TRIM trial. Misinterpretation of the index event, an inclusion myocardial infarction, as an early cardiac event was found in 12 patients. After end-point committee judgements, the number of patients with acute myocardial infarction or refractory angina pectoris during 30 days of follow-up was reduced from 177 to 153 (13. 6% reduction). The classification of events was changed in 53 of 187 patients (28.3%) with death, acute myocardial infarction or refractory angina pectoris. The data assessed by the safety committee was significantly different from the final database after end-point committee judgements. CONCLUSION The end-point committee corrected misinterpretations in such a high proportion of cases that the final results differed significantly from the preliminary results delivered to the safety committee. End-point judgements by an end-point committee should be performed in multicentre clinical trials to improve the quality and reliability of study results.
Character-driven story generation in interactive storytelling

We describe a fully implemented prototype for interactive storytelling using the Unreal/sup TM/ engine. We describe the important mechanisms involved in the variability of plot instantiations, within a scenario of sitcom genre. We also provide an evaluation of the concepts of how the dynamic interactions between agents and/or the user influence the generation of story, with first results of examples.
Latent and lytic infection of isolated guinea pig enteric ganglia by varicella zoster virus

Varicella zoster virus (VZV) has been demonstrated to infect guinea pig enteric neurons in vitro. Latent infection of isolated enteric neurons is established when the cultures predominantly consist of neurons and they are exposed to cell‐free VZV. Neurons harboring latent infection survive for weeks in vitro and express mRNA encoding ORFs 4, 21, 29, 40, 62, and 63, but not 14(gC) or 68 (gE) (although DNA encoding the glycoproteins is present). The expressed proteins are the same as those that are also expressed in human sensory neurons harboring latent VZV. In addition to mRNA, the immunoreactivities of ORFs 4, 21, 29, 62, and 63 can be detected. ORF 62 and 29 proteins are cytoplasmic and not intranuclear. VZV does not preferentially infect and/or become latent in intrinsic enteric primary afferent neurons indicating that the virus is latent in these neurons. Lytic infection occurs when mixed cultures of neurons and non‐neuronal cells of the bowel wall are exposed to cell‐free VZV or when isolated enteric neurons are exposed to cell‐associated VZV. When lytic infection occurs, enteric neurons die within 48 hr. Prior to their death, neurons express VZV glycoproteins, including gE and gB, and ORF 62 and 29 proteins are intranuclear. This new animal model should facilitate studies of VZV latency and the efficacy of therapies designed to prevent VZV infecion, latency, and reactivation. J. Med. Virol. 70:S71–S78, 2003. © 2003 Wiley‐Liss, Inc.
Synthesis and Preliminary Biologic Evaluation of 5‐Substituted‐2‐(4‐substituted phenyl)‐1,3‐Benzoxazoles as A Novel Class of Influenza Virus A Inhibitors

The diversity‐oriented chemistry synthesis together with the random screening approach has permitted the discovery and optimization of novel antiviral lead compounds. In this paper, a series of novel 5‐substituted‐2‐(4‐substituted phenyl)‐1,3‐benzoxazoles was synthesized and evaluated for their in vitro anti‐influenza A virus and anti‐influenza B virus activity. The activity was monitored by the MTS assay in the Madin–Darby canine kidney cells. Compound 7h showed excellent inhibitory activity and selective index against A/H3N2 (EC50 = 37.03 μm, SI > 5), which were all higher than that of the reference drug oseltamivir (EC50 > 59.00 μm, SI > 1). However, no compound displays inhibitory activity against influenza B virus.
Improving Image-Space Caustics Via Variable-Sized Splatting

Interactivity requires tradeoffs to achieve the right balance between rendering quality and speed. In practice, today’s applications restrict lighting to mainly direct illumination, sometimes augmented by precomputed transfer techniques for diffuse global effects. Dynamic high-frequency specular effects, such as caustics, are largely lacking due to the high costs for recomputation each frame. Recent work has introduced a variety of related caustics approximations that interactively render light-space photons into a photon buffer, gather them into a caustic map, and project this map onto the scene similar to shadow mapping. While the process is simple and straightforward, the discretization of light into a finite number of uniformly-distributed photons leads to undersampling and aliasing artifacts. This paper examines two techniques for reducing these artifacts using varying sized photon splats. Conceptually, these are similar to the variable-radius k-nearest neighbor search used in photon mapping, allowing noise reduction in areas of low photon density while maintaining crisp caustics at focal points. Our techniques improve image quality at a modest cost that is significantly cheaper than supersampling the photon buffer.
Getting to Know Poor Fathers Who Do Not Pay Child Support

About 2.5 million nonresident fathers are poor and do not pay child support. Most of them face multiple employment barriers, just like poor custodial mothers, but are significantly less likely than those mothers to participate in work‐support programs such as training, education, job search activities, or income security programs. Without access to work‐support programs, these fathers will remain unable to provide the financial support that their children need. Given that Congress expects poor nonresident fathers to support their children, it may want to consider directing work‐support programs to them so that they can fulfill their financial obligations to their children.