Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequency-dependent selection drives HBeAg seroconversion in chronic hepatitis B virus infection

HBeAg seroconversion is an important stage in the evolution of a chronic hepatitis B virus (HBV) infection that usually leads to control of viral replication and a reduced risk for liver cirrhosis and cancer. Since current therapies for the HBV-associated liver inflammation that is known as chronic hepatitis B (CHB). Rarely induce permanent HBeAg seroconversion, there is a need to understand the mechanisms responsible for the purpose of identifying new therapeutic targets. Currently, the most widely accepted hypothesis is that the patient’s humoral and cellular immune responses to the HBV initiate HBeAg seroconversion. Although we accept that this hypothesis cannot be excluded, we propose an alternative that is consistent with published data on HBeAg seroconversion. We postulate, as others have, that the HBeAg suppresses the immune response to the HBV. However, production of the HBeAg incurs a metabolic cost to the hepatocyte which reduces the replicative capacity of the virus. Consequently, HBeAg-negative viruses replicate faster than HBeAg-positive viruses. HBeAg-negative variants arise de novo; and when their frequency in the population is low they have a replicative advantage. However, they also benefit from the immunosuppressive effects of the HBeAg-positive viruses in the population. As HBeAg-negative variants increase in frequency and HBeAg levels fall, the immune system recognizes the HBV, and HBeAg seroconversion occurs as a consequence of frequency-dependent selection acting on HBeAg-negative variants. This hypothesis explains the wide inter-individual variation in age of seroconversion, the increased rate of seroconversion during anti-viral treatment and the phenomena of both spontaneous and post-treatment HBeAg reversions (in which patients cycle between the HBeAg-positive and negative phases of their infection).
Consumer Preferences for Peach Attributes: Market Segmentation Analysis and Implications for New Marketing Strategies

Consumers in today's marketplace have seemingly endless choices with regards to produce. Peach growers and retailers in Ontario, Canada, have begun taking steps to increase demand for their products. This study investigates the impact of those strategies on the market. Using conjoint analysis and market simulations, we evaluate the peach market to identify key drivers of peach purchasing. The results indicate that the market is heterogeneous and that price, origin, and quality indicators are the most important drivers of purchases. Our simulations indicate that adoption of new plastic packaging by the industry is a viable strategy for increasing demand for local peaches.
Longitudinal development in the preterm thalamus and posterior white matter: MRI correlations between diffusion weighted imaging and T2 relaxometry

Infants born prematurely are at increased risk of adverse neurodevelopmental outcome. The measurement of white matter tissue composition and structure can help predict functional performance. Specifically, measurements of myelination and indicators of myelination status in the preterm brain could be predictive of later neurological outcome. Quantitative imaging of myelin could thus serve to develop biomarkers for prognosis or therapeutic intervention; however, accurate estimation of myelin content is difficult. This work combines diffusion MRI and multi‐component T2 relaxation measurements in a group of 37 infants born very preterm and scanned between 27 and 58 weeks equivalent gestational age. Seven infants have longitudinal data at two time points that we analyze in detail. Our aim is to show that measurement of the myelin water fraction is achievable using widely available pulse sequences and state‐of‐the‐art algorithmic modeling of the MR imaging procedure and that a multi‐component fitting routine to multi‐shell diffusion weighted data can show differences in neurite density and local spatial arrangement in grey and white matter. Inference on the myelin water fraction allows us to demonstrate that the change in diffusion properties of the preterm thalamus is not solely due to myelination (that increase in myelin content accounts for about a third of the observed changes) whilst the decrease in the posterior white matter T2 has no significant component that is due to myelin water content. This work applies multi‐modal advanced quantitative neuroimaging to investigate changing tissue properties in the longitudinal setting. Hum Brain Mapp 37:2479–2492, 2016. © The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
An Evaluation of Technological Pedagogical Content Knowledge (TPACK) of In-Service Teachers: A Study in Turkish Public Schools.

In the current study, the technological pedagogical content knowledge (TPACK) perceptions of Turkish in-service teachers working in public schools were investigated. The survey method was employed to investigate the in-servive teachers’ perceptions of TPACK in terms of some demographic variables. The participants of the study consisted of volunteering in-service teachers (n = 200) from different public elementary and high schools. The results of the study indicated that the in-service teachers’ TPACK perceptions were affected by their gender, occupational experience, educational level, teaching level, and taking educational computer and Internet use seminar variables. The results also revealed that the in-service teachers’ perceptions of TPACK were at a moderate level. The results suggested that further efforts are required to develop the in-service teachers’ TPACK perceptions in order to integrate ICTs into teaching and learning process effectively in the classroom.
A Two-Cycle Lock-In Time ADPLL Design Based on a Frequency Estimation Algorithm

This brief presents a frequency estimation algorithm (FEA) for an all-digital phase-locked loop (ADPLL) instead of the traditional binary frequency-searching algorithm. Based on the proposed FEA and a new fast-lock scheme, a fast-lock engine is designed to improve the lock-in time of an ADPLL design with two referenced clock cycles. An implementation of the proposed ADPLL design is realized by utilizing United Microelectronics Corporation (UMC) 0.18-μm 1P6M CMOS technology with a core area of 300 × 250 μm2, consisting of an acceptable input reference clock ranging from 220 kHz to 8 MHz. The ADPLL design has a frequency range of 28-446 MHz with an 8.8-ps digitally controlled oscillator resolution. Moreover, the peak-to-peak jitter of the ADPLL achieves 70 ps, respectively.
Endometrial maturation: the role of oestradiol and progesterone

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
A bifurcation study of the three-dimensional thermohaline ocean circulation: the double-hemispheric case

Within a low-resolution primitive-equation model of the three-dimensional ocean circulation, a bifurcation analysis is performed of double-hemispheric basin flows. Main focus is on the connection between results for steady two-dimensional flows in a nonrotating basin and those for threedimensional flows in a rotating basin. With the use of continuation methods, branches of steady states are followed in parameter space and their linear stability is monitored. There is a close qualitative similarity between the bifurcation structure of steady-state solutions of the two- and three dimensional flows. In both cases, symmetry-breaking pitchfork bifurcations are central in generating a multiple equilibria structure. The locations of these pitchfork bifurcations in parameter space can be characterized through a zero of the tendency of a particular energy functional. Although balances controlling the steady-state flows are quantitatively very different, the zonally averaged patterns of the perturbations associated with symmetry-breaking are remarkably similar for two-dimensional and three-dimensional flows, and the energetics of the symmetry-breaking mechanism is in essence the same.
Ribosomal DNA in the Grasshopper Podisma pedestris: Escape From Concerted Evolution

Eukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.
Mobility of research workers and knowledge diffusion as evidenced in patent data: the case of liquid crystal display technology

This paper analyses the nature of knowledge spillovers from research and development (R&D) in the field of liquid crystal display technology by estimating the impact of inventors' changing organizational and collaborative affiliations on the probability of citations in US patents filed between 1976? 1995, while controlling for geographic localization effects. It is argued that technology policy towards a particular industry must take the role of inventors' mobility in facilitating the flow of ideas across space and innovating organizations into account. Policy implications for the display industry are discussed against the background of previous experiences with government-sponsored R&D collaborations.
The Local Lyα Forest: Absorbers in Galaxy Voids

We have conducted pointed redshift surveys for galaxies in the direction of bright active galactic nuclei whose Hubble Space Telescope far-UV spectra contain nearby (cz ≲ 30,000 km s-1), low column density [12.5 ≤ log N(cm-2) ≤ 14.5] Lyα forest absorption systems. Here we present results for four lines of sight that contain nearby (cz ≲ 3000 km s-1) Lyα absorbers in galaxy voids. Although our data go quite deep [-13 ≤ MB(limit) ≤ -14] out to impact parameters of ρ ≲ 100-250 h kpc, these absorbers remain isolated and thus appear to be truly intergalactic, rather than part of galaxies or their halos. Since we and others have discovered no galaxies in voids, the only baryons detected in the voids are in the Lyα "clouds. " Using a photoionization model for these clouds, the total baryonic content of the voids is 4.5% ± 1.5% of the mean baryon density.
The Function of the Urban Informal Sector in Employment: Evidence from Colombia 1984-2000

The aim of this paper is to analyze the function of the informal sector in employment, its relationship to urban employment, with illustrative evidence from Colombia. The analysis is done for the period 1984 - 2000, which includes phases of boom and economic crisis as well as the implementation of neoliberal reforms to national development. The paper summarizes four competing approaches to the conceptualization of the informal sector, and describes their measurement strategies. It argues that elements of state regulation are fundamental whereas firm size should not be considered as a defining element. Subsequently, it analyzes how the internal composition of the informal sector evolved, considering elements of state regulation, firm size, and dynamism of the economic activities. It examines the function of the informal sub-sectors in the urban labor market, using indicators such as relative earnings and size, and a crude indicator of labor mobility. At least three sub-sectors conforming the informal sector are identified: salaried workers of large and small firms, entrepreneurs and subsistence workers. It is argued that each sub-sector of the informal sector responds in different ways to prevailing economic conditions. The subsistence sub-sector supports the dualistic view, whereas the other two are integrated to the formal sector. No dominant sub-sector permits broadrange generalizations about the" informal sector. "
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.
Two-step biodiesel production using supercritical methanol and ethanol

Current industrial biodiesel production utilizes an alkali catalyst that can participate in saponification side reactions. The side reactions are reduced by using highly refined vegetable oil feedstocks. Also, the catalyst must be extracted from the final product in a washing step. A catalyst-free alternative for the production of biodiesel was developed. It involves two reaction steps: 1) triglyceride hydrolysis (fat splitting) at subcritical conditions to separate glycerol from fatty acids, and 2) fatty acid esterification in supercritical alcohol to form fatty acid alkyl esters. The catalyst-free process can potentially be used with a variety of low-cost vegetable and animal fats without undesired side reactions. The focus of this project was on the esterification reaction. Experiments were carried out with methanol and ethanol in a batch reaction system at supercritical conditions. High conversions could be attained at short reaction times. It was determined that the reaction followed second-order reversible kinetics. In addition, a novel Raman spectroscopic method was developed for the analysis of esterification reaction products. Abstract Approved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ DateApproved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date TWO-STEP BIODIESEL PRODUCTION USING SUPERCRITICAL METHANOL AND ETHANOL
Budgeting in Europe after Maastricht: patterns of reform and their effectiveness

Este trabajo analiza el desarrollo de las reglas e instituciones fiscales en los paises europeos durante la ultima decada. Hallamos que el grado de cambios de los procesos presupuestarios y de las reglas fiscales difiere mucho entre los distintos paises. Se evalua el patron de los cambios con respecto a los diferentes tipos ideales de gobernabilidad fiscal. Nuestro analisis muestra que los paises que adoptan reglas en consonancia con sus instituciones fiscales predichas consiguen mayores logros en el plano fiscal que otras naciones que no hacen eso. Tenemos, pues, una explicacion parcial de por que razon el efecto del marco fiscal europeo ha sido asimetrico en relacion con los paises miembros.
On the Random 1/2-Disk Routing Scheme in Wireless Ad Hoc Networks

Random 1/2-disk routing in wireless ad-hoc networks is a localized geometric routing scheme in which each node chooses the next relay randomly among the nodes within its transmission range and in the general direction of the destination. We introduce a notion of convergence for geometric routing schemes that not only considers the feasibility of packet delivery through possibly multi-hop relaying, but also requires the packet delivery to occur in a finite number of hops. We derive sufficient conditions that ensure the asymptotic \emph{convergence} of the random 1/2-disk routing scheme based on this convergence notion, and by modeling the packet distance evolution to the destination as a Markov process, we derive bounds on the expected number of hops that each packet traverses to reach its destination.
No . 1681 Is Disinflation Good for the Stock Market ?

When countries attempt to stabilize annual inflation rates that are greater than 40 percent, the domestic stock market appreciates by 24 percent on average. The present value of the long-run benefits to shareholders of reducing high inflation outweighs the present value of the short-run costs. In contrast, the average market response is economically weak and statistically insignificant, if the pre-stabilization inflation rate is less than 40 percent. Stock market responses also help predict the change in inflation and output in the year following stabilization efforts. This additional result indicates that the stock market evidence for the 81 episodes studied is not spurious. Assistant Professor of Economics, Stanford Business School and Hoover National Fellow 2000-2001: Stanford, CA 94305-5015; (650) 723-0905; pbhenry@stanford.edu. I would like to thank Paul Romer for detailed comments on earlier drafts. I also thank Richard Clarida, Pat Conway, Bob Flanagan, Bob Hall, Helene Rey, Tom Sargent, Ken Singleton, Ewart Thomas, Jim Van Horne, and seminar participants at the Hoover Institution, London Business School, the NBER, and the Stanford Macro Lunch for helpful comments. Serkan Arslanap, Joanna Campbell, Begna Gebreyes, Chad Milner, Nora Richardson, and Laura Veldkamp provided stellar research assistance. All remaining errors are my own.
In Vivo Biotinylation of the Toxoplasma Parasitophorous Vacuole Reveals Novel Dense Granule Proteins Important for Parasite Growth and Pathogenesis

ABSTRACT Toxoplasma gondii is an obligate intracellular parasite that invades host cells and replicates within a unique parasitophorous vacuole. To maintain this intracellular niche, the parasite secretes an array of dense granule proteins (GRAs) into the nascent parasitophorous vacuole. These GRAs are believed to play key roles in vacuolar remodeling, nutrient uptake, and immune evasion while the parasite is replicating within the host cell. Despite the central role of GRAs in the Toxoplasma life cycle, only a subset of these proteins have been identified, and many of their roles have not been fully elucidated. In this report, we utilize the promiscuous biotin ligase BirA* to biotinylate GRA proteins secreted into the vacuole and then identify those proteins by affinity purification and mass spectrometry. Using GRA-BirA* fusion proteins as bait, we have identified a large number of known and candidate GRAs and verified localization of 13 novel GRA proteins by endogenous gene tagging. We proceeded to functionally characterize three related GRAs from this group (GRA38, GRA39, and GRA40) by gene knockout. While Δgra38 and Δgra40 parasites showed no altered phenotype, disruption of GRA39 results in slow-growing parasites that contain striking lipid deposits in the parasitophorous vacuole, suggesting a role in lipid regulation that is important for parasite growth. In addition, parasites lacking GRA39 showed dramatically reduced virulence and a lower tissue cyst burden in vivo. Together, the findings from this work reveal a partial vacuolar proteome of T. gondii and identify a novel GRA that plays a key role in parasite replication and pathogenesis. IMPORTANCE Most intracellular pathogens reside inside a membrane-bound vacuole within their host cell that is extensively modified by the pathogen to optimize intracellular growth and avoid host defenses. In Toxoplasma, this vacuole is modified by a host of secretory GRA proteins, many of which remain unidentified. Here we demonstrate that in vivo biotinylation of proximal and interacting proteins using the promiscuous biotin ligase BirA* is a powerful approach to rapidly identify vacuolar GRA proteins. We further demonstrate that one factor identified by this approach, GRA39, plays an important role in the ability of the parasite to replicate within its host cell and cause disease. Most intracellular pathogens reside inside a membrane-bound vacuole within their host cell that is extensively modified by the pathogen to optimize intracellular growth and avoid host defenses. In Toxoplasma, this vacuole is modified by a host of secretory GRA proteins, many of which remain unidentified. Here we demonstrate that in vivo biotinylation of proximal and interacting proteins using the promiscuous biotin ligase BirA* is a powerful approach to rapidly identify vacuolar GRA proteins. We further demonstrate that one factor identified by this approach, GRA39, plays an important role in the ability of the parasite to replicate within its host cell and cause disease.