Miracle-dz/UniFAR-FTUs huggingface dataset:
Stage-specific differentiation of iPSCs toward retinal ganglion cell lineage

Purpose As an alternative and desirable approach for regenerative medicine, human induced pluripotent stem cell (hiPSC) technology raises the possibility of developing patient-tailored cell therapies to treat intractable degenerative diseases in the future. This study was undertaken to guide human Tenon’s capsule fibroblasts-derived iPSCs (TiPSCs) to differentiate along the retinal ganglion cell (RGC) lineage, aiming at producing appropriate cellular material for RGC regeneration. Methods By mimicking RGC genesis, we deliberately administered the whole differentiation process and directed the stage-specific differentiation of human TiPSCs toward an RGC fate via manipulation of the retinal inducers (DKK1+Noggin+Lefty A) alongside master gene (Atoh7) sequentially. Throughout this stepwise differentiation process, changes in primitive neuroectodermal, eye field, and RGC marker expression were monitored with quantitative real-time PCR (qRT-PCR), immunocytochemistry, and/or flow cytometry. Results Upon retinal differentiation, a large fraction of the cells developed characteristics of retinal progenitor cells (RPCs) in response to simulated environment signaling (DKK1+Noggin+Lefty A), which was selectively recovered with manual isolation approaches and then maintained in the presence of mitogen for multiple passages. Thereafter, overexpression of ATOH7 further promoted RGC specification in TiPSC-derived RPCs. A subset of transfected cells displayed RGC-specific expression patterns, including Brn3b, iSlet1, calretinin, and Tuj, and approximately 23% of Brn3b-positive RGC-like cells were obtained finally. Conclusions Our DKK1+Noggin+Lefty A/Atoh7-based RGC-induction regime could efficiently direct TiPSCs to differentiate along RGC lineage in a stage-specific manner, which may provide a benefit to develop possible cell therapies to treat retinal degenerative diseases such as glaucoma.
Stars and gas in the very large interacting galaxy NGC 6872

The dynamical evolution of the. large (>100 kpc), barred spiral galaxy NGC 6872 and its small companion IC 4970 in the southern group Pavo is investigated. We present N-body simulations with stars and gas and 21 cm Hi observations carried out with the Australia Telescope Compact Array of the large-scale distribution and kinematics of atomic gas. Hi is detected toward the companion, corresponding to a gas mass of ∼1.3 x 10 9 Mo NGC 6872 contains ∼1.4 x 1010 M o of Hi gas, distributed in an extended rotating disk. Massive concentrations of gas (∼10 9 M O ) are found at the tip of both tidal tails and towards the break seen in the optical northern arm near the companion. We detect no Hi counterpart to the X-ray trail between NGC 6872 and NGC 6876, the dominant elliptical galaxy in the Pavo group located ∼8' to the southeast. At the sensitivity and the resolution of the observations, there is no sign in the overall Hi distribution that NGC 6876 has affected the evolution of NGC 6872. There is no evidence of ram pressure stripping either. The X-ray trail could be due to gravitational focusing of the hot gas in the Pavo group behind NGC 6872 as the galaxy moves supersonically through the hot medium. The simulations of a gravitational interaction with a small nearby companion on a low-inclination prograde passage are able to reproduce most of the observed features of NGC 6872, including the general morphology of the galaxy, the inner bar, the extent of the tidal tails and the thinness of the southern tail.
Recognition of A ffi ne Distorted Characters by Using A ffi ne-Invariant Local Descriptors

Camera-based character recognition has a possibility to realize a variety of applications and has been paid attention. However, character images are often taken from different angles and characters tend to be distorted. In such a case, recognition accuracy becomes worse. Therefore, we must find some methods to deal with this problem. In this paper, we experimentally evaluate some affine-invariant local descriptors by testing how well they can recognize affine distorted characters. As a result, affine-invariant local descriptors are robust to affine distorted characters to some extent.
SWAN-1, a Caenorhabditis elegans WD Repeat Protein of the AN11 Family, Is a Negative Regulator of Rac GTPase Function

Rac GTPases are key regulators of cell shape and cytoskeletal organization. While some regulators of Rac activity are known, such as GTPase-activating proteins (GAPs) that repress Rac activity, other Rac regulators remain to be identified. The novel Caenorhabditis elegans WD-repeat protein SWAN-1 was identified in a yeast two-hybrid screen with the LIM domains of the Rac effector UNC-115/abLIM. SWAN-1 was found to also associate physically with Rac GTPases. The swan-1(ok267) loss-of-function mutation suppressed defects caused by the hypomorphic ced-10(n1993) allele and enhanced ectopic lamellipodia and filopodia formation induced by constitutively active Rac in C. elegans neurons. Furthermore, SWAN-1(+) transgenic expression suppressed the effects of overactive Rac, including ectopic lamellipodia and filopodia formation in C. elegans neurons, ectopic lamellipodia formation in cultured mammalian fibroblasts, and cell polarity and actin cytoskeleton defects in yeast. These studies indicate that SWAN-1 is an inhibitor of Rac GTPase function in cellular morphogenesis and cytoskeletal organization. While broadly conserved across species, SWAN-1 family members show no sequence similarity to previously known Rac inhibitors.
Are Efficient Taxes Responsible for Big Government? Evidence from Tax Withholding

The paper examines the claim that more efficient taxes lead to bigger government by studying the effects of income tax withholding, a particular technological shock to tax efficiency. We exploit the variation in the timing of the adoption of withholding by state governments in the United States during the 1940’s through 1970’s. Due to improved compliance and other factors, withholding immediately and permanently increased income tax collections by 24 percent at given tax rates. We find that this efficiency shock caused a large increase in income tax revenues, although much of the increase occurred through a shift in the composition of revenues towards a heavier reliance on the income tax. We also find that the revenue from other taxes increased when withholding was adopted, which we intepret as evidence that the adoption of withholding was motivated by higher demand for government spending. We use the theory to disentangle the causal effect from withholding to higher taxes and the reverse causality from higher demand to withholding. The causal effect accounts for at most one half of the 8 percent increase in total revenue. Contrary to claims that withholding was the thing that enabled the post-war explosion of income taxation, we conclude that it accounts for approximately 9 percent of the growth of state income taxes during the period in question.
Finding Plagiarism by Evaluating Document Similarities

In this paper we discuss the approach we have used for finding plagiarized passages of text during the PAN'09 plagiarism detection competition. We describe the existing anti-plagiarism system we use in the Czech National Archive of Graduate Theses. We then discuss the modifications to this system which have been necessary in order to fit the results to the competition rules. We also present a performance data of the described system, and the possible improvement for our production systems, which result from the code written for the PAN'09 competition.
Cluster-Based Relevance Feedback: Legal Track 2011

This is our second participation in the TREC Legal Track. The TREC Legal Track 2011 featured only the Learning Task. We participated in Topics 401 and 403. We used Lemur 4.11 1 for Boolean retrieval and followed it with a clustering technique, where we chose members from each cluster (which we called seeds ) for relevance judgement by the TA and assumed all other members of the cluster whose seeds are assessed as relevant to be relevant. Based on the relevance information from seeds and their clusters, we applied Rocchio relevance feedback technique implemented in Terrier 3.0 2 . Then, we used the feedback terms for the expansion of both the text queries and the Boolean queries. Finally, we used Z-fusion[4], a data fusion technique, on two of our runs.
The CARMEN e-Science pilot project: Neuroinformatics work packages

The CARMEN (Code Analysis, Repository and Modelling for e-Neuroscience) project aims to apply e-Science technology to Neurophysiology to enable the sharing of data resources and the services for processing this data. This paper describes the application oriented services: the companion paper [1] describes the technology underpinning this application. Overall, the CARMEN project is developing a Neuroinformatics resource which will change the way data is processed in experimental Neuroscience by providing archiving and a set of powerful services, supporting collaborative neurophysiology research.
The molecular chaperone DnaK accelerates protein evolution

Molecular chaperones, also known as heat-shock proteins, refold misfolded proteins and help other proteins reach their native conformation. Thanks to these abilities, some chaperones, such as the Hsp90 protein or the chaperonin GroEL, can buffer the deleterious phenotypic effects of mutations that alter protein structure and function. Hsp70 chaperones use a chaperoning mechanism different from Hsp90 and GroEL, and it is not known whether they can also buffer mutations. Here, we show that they can. To this end, we performed a mutation accumulation experiment in Escherichia coli, followed by whole-genome resequencing. Our sequence data shows that overexpression of the Hsp70 chaperone DnaK increases the tolerance of its clients for nonsynonymous nucleotide substitutions and nucleotide insertions and deletions. We also show that this elevated mutational buffering on short evolutionary time scales translates into differences in evolutionary rates on intermediate and long evolutionary time scales. To this end, we compared the evolutionary rates of DnaK clients and nonclients using the genomes of E. coli, Salmonella typhimurium, and 83 other gamma-proteobacterial species. We find that clients that interact strongly with DnaK evolve faster than weakly interacting clients. Our results imply that all three major chaperone classes can buffer mutations and affect protein evolution. They illustrate how an individual protein like a chaperone can have a disproportionate effect on proteome evolution.
Bridging the Gap between User Requirements and Configuration Requirements

The Service Availability Forum supports the realization of Highly Available systems by means of standards like the Availability Management Framework (AMF), a middleware service that manages the high availability of services provided by applications through the coordination of their redundant components. AMF configurations for applications, capable of providing and protecting services, can be generated from the software and from a set of configuration requirements (CR). The specification of CR requires a good knowledge of the AMF specification. Users/Customers may not have this AMF knowledge and are usually acquainted to specifying high level characteristics of services of interest. This paper introduces an approach aiming at bridging the gap between user requirements and configuration requirements for the design of AMF configurations.
Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels

Genotype imputation is a vital tool in genome-wide association studies (GWAS) and meta-analyses of multiple GWAS results. Imputation enables researchers to increase genomic coverage and to pool data generated using different genotyping platforms. HapMap samples are often employed as the reference panel. More recently, the 1000 Genomes Project resource is becoming the primary source for reference panels. Multiple GWAS and meta-analyses are targeting Latinos, the most populous, and fastest growing minority group in the US. However, genotype imputation resources for Latinos are rather limited compared to individuals of European ancestry at present, largely because of the lack of good reference data. One choice of reference panel for Latinos is one derived from the population of Mexican individuals in Los Angeles contained in the HapMap Phase 3 project and the 1000 Genomes Project. However, a detailed evaluation of the quality of the imputed genotypes derived from the public reference panels has not yet been reported. Using simulation studies, the Illumina OmniExpress GWAS data from the Los Angles Latino Eye Study and the MACH software package, we evaluated the accuracy of genotype imputation in Latinos. Our results show that the 1000 Genomes Project AMR + CEU + YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1000 Genomes Project panel for Latinos. Our results serve as a guide to future imputation based analysis in Latinos.
Practical principled FRP: forget the past, change the future, FRPNow!

We present a new interface for practical Functional Reactive Programming (FRP) that (1) is close in spirit to the original FRP ideas, (2) does not have the original space-leak problems, without using arrows or advanced types, and (3) provides a simple and expressive way for performing IO actions from FRP code. We also provide a denotational semantics for this new interface, and a technique (using Kripke logical relations) for reasoning about which FRP functions may "forget their past", i.e. which functions do not have an inherent space-leak. Finally, we show how we have implemented this interface as a Haskell library called FRPNow.
The influence of decentralized taxes and intergovernmental grants on local spending volatility

ABSTRACT The influence of decentralized taxes and intergovernmental grants on local spending volatility. Regional Studies. This paper studies what affects the volatility of sub-central public spending in 20 Organisation for Economic Co-operation and Development (OECD) countries. The evidence based on data from 1972 to 2007 shows that the volatility of intergovernmental grants from upper levels is positively associated with the volatility of local expenditure. On the other hand, the volatility of local tax revenues – mainly that of property taxes – exerts the opposite effect. These findings suggest that making local governments rely more on grants than own tax revenues adversely affects their spending stability. Allowing them to levy autonomously taxes relying on responsive tax bases provides incentives to smooth their expenditure.
Direct observation of steady-state microtubule dynamics

Different types of unusual dynamic behavior have been reported for steady-state microtubules. While almost all earlier reports relied on kinetic measurements of bulk polymerization, we have directly visualized the steady-state addition of subunits to individual microtubules through the use of tubulin derivitized with biotin. Biotinylated tubulin was used both as an internal "seed" for polymerization and as a marker for assembly onto the ends of microtubules composed of purified tubulin. Biotinylated segments were distinguished from unmodified tubulin by double-label immunofluorescence. Microtubule lengths, number concentrations, and segment lengths have been monitored with time at steady state under two buffer conditions. The results indicate that the microtubule steady state under these conditions is a balance between a majority of slowly growing microtubules and a minority of rapidly depolymerizing ones as described by the "dynamic instability" model (Mitchison T., and M. Kirschner, 1984, Nature (Lond.). , 312:232-242). Microtubules show no evidence of treadmilling; instead most show progressive growth off both ends at steady state. Although solvent conditions markedly influence the growth rates, qualitatively the behavior is unchanged.
The Informative Versus Persuasive Role of Marketing Communication in New Product Categories: An Application to the Prescription Antihistamines Market

Marketing communication plays a major role in influencing consumer purchases in new product categories. An important question about this communication is whether it plays an informative or a persuasive role over the life cycle of the new product category. We expect that consumers are not well informed about product quality in the early stages of the product life cycle but they become better informed over time. The informative role of marketing communication is likely to have a much larger effect with uninformed consumers than with consumers who are better informed. Therefore, we conjecture that marketing communication plays a predominantly informative role initially and a predominantly persuasive role later. We develop a structural model of demand that allows for the differential impact of informative and persuasive roles of marketing communication over time. In addition, we control for the possibility that product experience also contributes to learning in such categories. We estimate our model on market-level data for the prescription antihistamines category. In our model, physician learning about new antihistamines occurs through marketing communication (detailing and meetings/seminars), and experience (past prescriptions). Specifically, our model is a random coefficients discrete choice model that allows for category expansion. The model also incorporates a Bayesian learning process through which physicians learn about the efficacy of this new class of drugs. We estimate our model using a GMM-based methodology. We find that, on average, physicians are most sensitive to detailing relative to other promotional activities. However, more interestingly, we find evidence for both informative and persuasive effects of detailing on physicians' prescription behavior. In addition, we find that detailing plays a primarily informative role in the introductory phase (typically 6-14 months post introduction) but the persuasive role dominates later on. The finding that persuasive effects are significant may explain why firms continue to detail long after a drug is introduced. In terms of resource allocation for detailing over time, our results suggest that firms should follow a pattern of heavier detailing at the introduction phase followed by lower levels.
A Model of Continuous Intention Grounding for HRI

We present a formal model of intention grounding for robots in HRI which models the user and robot’s own current intentions simultaneously. Central to the model are interactive state machines, and strength-of-evidence functions, which are evaluations of the degree to which an agent’s current intention is being communicated publicly. The model has so far been used in a simple pick-and-place robot with a speech interface, but we argue this can be generalized to other robots such as semi-autonomous vehicles, providing potential for automatic evaluation and active learning.
Systematic Evaluation of O-glycosylation Mediated Enhancement and Modulation of the Cel7A Carbohydrate Binding Module Function

3 Introduction 4 i. Crystalline Cellulose Affinity Enhancement by O-­‐glycosylation of Cel7A CBM 6 ii. O-­‐glycan Modulation of Cel7A CBM Cellulose Specificity 9 iii. Lignin Non-­‐productive Adsorption by Cel7A CBM and Modulation by O-­‐glycosylation.12 Materials and Methods 14 Results and Discussion 20 i. Synthesis and Characterization of CBM Glycoforms 20 ii. Cel7A CBM O-­‐Mannosylation Confers Adsorption Enhancement Towards Crystalline Cellulose 20 iii. O-­‐Mannose Modulation of Cel7A CBM Specificity for Model Cellulose Systems.26 iv. CBM Glycoform Non-­‐productive Adsorption on Kraft Lignin 30 Concluding Remarks and Future Directions 33 Acknowledgements 35 References 36 Appendix I 48 Appendix II 49
A comprehensive simulation study of slotted CSMA/CA for IEEE 802.15.4 wireless sensor networks

In this paper, we analyze the performance limits of the slotted CSMA/CA mechanism of IEEE 802.15. 4 in the beacon-enabled mode for broadcast transmissions in WSNs. The motivation for evaluating the beacon-enabled mode is due to its flexibility for WSN applications as compared to the non-beacon enabled mode. Our analysis is based on an accurate simulation model of the slotted CSMA/CA mechanism on top of a realistic physical layer, with respect to the IEEE 802.15. 4 standard specification. The performance of the slotted CSMA/CA is evaluated and analyzed for different network settings to understand the impact of the protocol attributes (superframe order, beacon order and backoff exponent) on the network performance, namely in terms of throughput (S), average delay (D) and probability of success (Ps). We introduce the concept of utility (U) as a combination of two or more metrics, to determine the best offered load range for an optimal behavior of the network. We show that the optimal network performance using slotted CSMA/CA occurs in the range of 35% to 60% with respect to an utility function proportional to the network throughput (S) divided by the average delay (D).
Stock prices and exchange rates in Sri Lanka: some empirical evidence

This paper examines the relationship between stock prices and exchange rates in Sri Lanka. The author uses monthly data on four foreign exchange rates and the All Share Price Index (ASPI) of the Colombo Stock Exchange in the empirical analysis. The Johansen’s cointegration test finds no long-run relationships between stock prices (ASPI) and any of the four exchange rates during the sample period. Therefore, the paper proceeded to test for short-run in-sample causal relationships between stock prices and exchange rates and found one unidirectional relationship from stock prices to the US dollar exchange rate. In addition, the author performed a variance decomposition analysis to get insights into the out-of-sample causal relationships between exchange rates and stock prices. The results indicate that most of the variance of the ASPI, particularly, at longer horizons is explained by the Indian rupee with the other currencies explaining a very little variation of the ASPI. The study also examined whether the ASPI has any role in explaining the variations in any of the four exchange rates. It is found that the ASPI has the most explanatory power in relation to the US dollar exchange rate.
Nonlinear Modeling for Distortion Analysis in Silicon Bulk-Mode Ring Resonators

A distributed modeling approach has been developed to describe the dynamic behavior of ring resonators. The model includes the effect of large amplitudes around primary resonance frequencies, material and electrostatic nonlinearities. Through a combination of geometric and material nonlinearities, closed-form expression for third-order nonlinearity in mechanical stiffness of bulk-mode ring resonators is obtained. Moreover, to avoid dynamic pull-in instability, the choices of the quality factor, ac-drive and DC-bias voltages of the ring resonators, with a given geometry are limited by a resonant pull-in condition. Using the perturbation technique and the method of harmonic balance, the expressions for describing the effect of nonlinearities on the resonance frequency and displacement are derived. The results are discussed in detail, showing the effect of varying operating conditions and the quality factor on the harmonic distortions and third-order intermodulation distortion. The detailed nonlinear modeling and distortion analysis are applied as appropriate tools to design bulk-mode ring resonators with low motional resistance and high linearity.