Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of microbial rhodopsins in retinal neurons with subcellular targeting motifs: for the study of the structure/function of aii amacrine cells and for vision restoration

EXPRESSION OF MICROBIAL RHODOPSINS IN RETINAL NEURONS WITH SUBCELLULAR TARGETING MOTIFS: FOR THE STUDY OF THE STRUCTURE/FUNCTION OF AII AMACRINE CELLS AND FOR VISION RESTORATION by CHAOWEN WU August 2011 Advisor: Dr. Zhuo-Hua Pan Major: Anatomy & Cell Biology Degree: Doctor of Philosophy Protein-targeting motifs serve as addresses for subcellular protein localization. This feature of targeting-motifs was used to study the retina. The first part of the dissertation reports in the axonless spiking AII amacrine cell of the mammalian retina a dendritic process sharing organizational and functional similarities with the axon initial segment, the typical site of action potential initiation. This process was revealed through viral-mediated expression of channelrhodopsin-2-GFP (ChR2-GFP) with the AIS-targeting motif of sodium channels (NavIIIII) and was shown to be the site of spike initiation. The second part of the dissertation aimed to improve microbial rhodopsin-mediated gene therapy for vision restoration by using targeting-motifs to recreate 87
Industrial Agglomeration and Spatial Persistence: Entry, Growth, and Exit of Software Publishers

We use geocoded administrative data from Texas on all business establishments to estimate the effects of localization economies on the spatial persistence of industrial employment for the software industry. We decompose this persistence into components arising from entry rates, firm growth, and exit rates. Unlike previous research that has used geographies based on county and MSA divisions, this analysis takes place at a very high level of spatial resolution in which the industrial composition is identified within areas as small as one mile in radius. The choice of the software industry allows us to isolate the effects arising from human capital spillovers and the effects arising from the labor pool channel from other sources of agglomeration economies. Moreover, the decomposition of the employment persistence in entry, growth and exit, and the high level of spatial resolution allow us to distinguish between these two effects and has a number of other advantages. The results suggest that a location, defined as a 1-mile radium circle, with an initial concentration of software industry employment, retains a disproportionate number of software industry employees 6 years later. Software industry employment in the surrounding area has a small and often insignificant effect, i.e., any agglomeration effects dissipate rapidly over space. The results are not driven by higher growth rates of software establishments in high concentration locations or by differences in the survival probabilities. Rather, they are fully accounted for by two factors: (i) the retention of jobs lost by an establishment in a location by other establishments in that same location and (ii) an increased propensity of software establishments to enter in or near locations with prior software establishment presence. The entry effect diminishes sharply beyond one mile. These findings are mostly consistent with labor channel effects, including the possibility of spin-offs locating near existing firms, but disembodied human capital spillovers might also be present to some extent.
Removing randomness from computational number theory

In recent years, many probabilistic algorithms (i.e., algorithms that can toss coins) that run in polynomial time have been discovered for problems with no known deterministic polynomial time algorithms. Perhaps the most famous example is the problem of testing large (say, 100 digit) numbers for primality. Even for problems which are known to have deterministic polynomial time algorithms, these algorithms are often not as fast as some probabilistic algorithms for the same problem. Even though probabilistic algorithms are useful in practice, we would like to know, for both theoretical and practical reasons, if randomization is really necessary to obtain the most e cient algorithms for certain problems. That is, we would like to know for which problems there is an inherent gap between the deterministic and probabilistic complexities of these problems. In this research, we consider two problems of a number theoretic nature: factoring polynomials over nite elds and constructing irreducible polynomials of speci ed degree over nite elds. We present new results that narrow the gap between the known deterministic and probabilistic complexities of these problems. One of our results is a deterministic polynomial time reduction from the latter problem to the former, giving rise to a deterministic algorithm for constructing irreducible polynomials that runs in polynomial time for elds of small characteristic. Another of our results is a new deterministic factoring algorithm whose worst-case running time is asymptotically faster than that of previously known deterministic algorithms for this problem. We also analyze the average-case running time of our algorithm (averaging over inputs), proving that it is just about as fast as the expected running time (averaging over coin tosses) of some of the fastest probabilistic algorithms. In particular, the average-case running time of our algorithm is polynomial. i Preface Some of the results in this thesis have previously appeared in [38] and [39]. I wish to thank my advisor, Eric Bach. Working with Eric has truly been a delight, and his encouragement and support were invaluable in conducting this research. Thanks also goes to Anne Condon, Jon Sorenson and John Strikwerda for providing me with corrections and insightful comments on an early draft of this thesis. I would like to also thank Hendrik Lenstra for sharing several of his ideas with me, and Hiroshi Gunji, in whose classes I learned quite a bit about algebra. This research was supported by NSF grants DCR-8504485 and DCR8552596. ii
Sample size calculations for micro‐randomized trials in mHealth

The use and development of mobile interventions are experiencing rapid growth. In “just‐in‐time” mobile interventions, treatments are provided via a mobile device, and they are intended to help an individual make healthy decisions ‘in the moment,’ and thus have a proximal, near future impact. Currently, the development of mobile interventions is proceeding at a much faster pace than that of associated data science methods. A first step toward developing data‐based methods is to provide an experimental design for testing the proximal effects of these just‐in‐time treatments. In this paper, we propose a ‘micro‐randomized’ trial design for this purpose. In a micro‐randomized trial, treatments are sequentially randomized throughout the conduct of the study, with the result that each participant may be randomized at the 100s or 1000s of occasions at which a treatment might be provided. Further, we develop a test statistic for assessing the proximal effect of a treatment as well as an associated sample size calculator. We conduct simulation evaluations of the sample size calculator in various settings. Rules of thumb that might be used in designing a micro‐randomized trial are discussed. This work is motivated by our collaboration on the HeartSteps mobile application designed to increase physical activity. Copyright © 2015 John Wiley & Sons, Ltd.
Phinding Phish: An Evaluation of Anti-Phishing Toolbars

There are currently dozens of freely available tools to help combat phishing and other web-based scams. Many of these tools come in the form of web browser extensions that warn users when they are browsing a suspected phishing site. We used verified phishing URLs and legitimate URLs to test the effectiveness of 10 popular antiphishing toolbars. Overall, we found that the anti-phishing toolbars that were examined in this study left a lot to be desired. SpoofGuard did a very good job at identifying fraudulent sites, but it also incorrectly identified a large fraction of legitimate sites as fraudulent. EarthLink, Google, Netcraft, Cloudmark, and Internet Explorer 7 identified most fraudulent sites correctly and had few, if any, false positives, but they still missed more than 15% of fraudulent sites. The TrustWatch, eBay, and Netscape 8 toolbars could correctly identify less than half the fraudulent sites, and McAfee SiteAdvisor did not correctly identify any fraudulent sites. Many of the toolbars we tested were vulnerable to some simple exploits as well. In this paper we describe the anti-phishing toolbar test bed we developed, summarize our findings, and offer observations about the usability and overall effectiveness of these toolbars. Finally, we suggest ways to improve anti-phishing toolbars.
Goal-Directed Modulation of Neural Memory Patterns: Implications for fMRI-Based Memory Detection

Remembering a past event elicits distributed neural patterns that can be distinguished from patterns elicited when encountering novel information. These differing patterns can be decoded with relatively high diagnostic accuracy for individual memories using multivoxel pattern analysis (MVPA) of fMRI data. Brain-based memory detection—if valid and reliable—would have clear utility beyond the domain of cognitive neuroscience, in the realm of law, marketing, and beyond. However, a significant boundary condition on memory decoding validity may be the deployment of “countermeasures”: strategies used to mask memory signals. Here we tested the vulnerability of fMRI-based memory detection to countermeasures, using a paradigm that bears resemblance to eyewitness identification. Participants were scanned while performing two tasks on previously studied and novel faces: (1) a standard recognition memory task; and (2) a task wherein they attempted to conceal their true memory state. Univariate analyses revealed that participants were able to strategically modulate neural responses, averaged across trials, in regions implicated in memory retrieval, including the hippocampus and angular gyrus. Moreover, regions associated with goal-directed shifts of attention and thought substitution supported memory concealment, and those associated with memory generation supported novelty concealment. Critically, whereas MVPA enabled reliable classification of memory states when participants reported memory truthfully, the ability to decode memory on individual trials was compromised, even reversing, during attempts to conceal memory. Together, these findings demonstrate that strategic goal states can be deployed to mask memory-related neural patterns and foil memory decoding technology, placing a significant boundary condition on their real-world utility.
Bloodborne Viral Hepatitis Infections among Drug Users: The Role of Vaccination

Drug use is a prevalent world-wide phenomenon and hepatitis virus infections are traditionally a major health problem among drug users (DUs). HBV and HCV, and to a lesser extent HAV, are easily transmitted through exposure to infected blood and body fluids. Viral hepatitis is not inevitable for DUs. Licensed vaccines are available for hepatitis A and hepatitis B. The purpose of this overview is to show some epidemiological data about HBV and the other blood-borne viral hepatitis among DUs and to summarize and discuss use of hepatitis vaccinations in this population. Successful vaccination campaigns among DUs are feasible and well described. We try to focus on the most significant results achieved in successful vaccination programs as reported in scientific literature. Vaccination campaigns among DUs represent a highly effective form of health education and they are cost-saving.
Fictional Narratives for Clinical App Development

This paper presents the use of fictional narratives in participatory design for health information technology (HIT). We used the case of an established occupational therapy assessment tool to investigate how fictional narratives can aid de-sign workshops and their outcomes in the health domain by means of participatory principles. The methodological findings show how a fictional narrative can be adopted in a di-verse manner across design workshops by practitioners and participants with a research background. Also, the importance of tailoring fictional narratives towards specific participants in the design process is emphasised.
Development of a New Cryptographic Construct Using Palmprint-Based Fuzzy Vault

The combination of cryptology and biometrics has emerged as promising component of information security. Despite the current popularity of palmprint biometric, there has not been any attempt to investigate its usage for the fuzzy vault. This paper therefore investigates the possible usage of palmprint in fuzzy vault to develop a user friendly and reliable crypto system. We suggest the use of both symmetric and asymmetric approach for the encryption. The ciphertext of any document is generated by symmetric cryptosystem; the symmetric key is then encrypted by asymmetric approach. Further, Reed and Solomon codes are used on the generated asymmetric key to provide some error tolerance while decryption. The experimental results from the proposed approach on the palmprint images suggest its possible usage in an automated palmprint-based key generation system.
In-vitro fermentation characteristics and methane reduction potential of mustard cake (Brassica juncea L.)

Aim: To assess the effect of mustard cake (Brassica juncea L.) levels in concentrate mixtures and in composite feed mixtures (CFMs) on in-vitro fermentation characteristics and methane production. Materials and Methods: Five concentrate mixtures were prepared with containing 30% oil cake, where linseed cake was replaced by mustard cake at the rate of 0%, 7.5%, 15.0%, 22.5%, and 30% in concentrate mixture. Mustard cake contained glucosinolate 72.58 µmol/g oil free dry matter (DM) and contents in diet were 0, 5.4, 10.9, 16.3, and 21.8 µmol/g of concentrate mixture, respectively. Concentrate mixture containing 15.0% mustard cake was found to produced minimum methane which was then used for the preparation of CFM containing 0%, 25%, 50%, and 75% levels with gram straw. Result: Increased levels of mustard cake in concentrate mixtures had a linear decrease (p<0.05) in the total gas production, and the 15% inclusion showed lowest methane concentration (quadratic, p<0.01). The degradability of DM and organic matter (OM) of concentrate mixtures did not change, however, pH and NH3-N concentrations of the fermentation medium showed linear (p<0.05) reductions with increased mustard cake levels. Increased levels of 15% mustard cake containing concentrate mixture in CFMs exhibited a trend (p=0.052) of increased gas production, whereas methane concentration in total gas, methane produced and degradability of DM and OM were also displayed a linear increase (p<0.05). However, the pH, NH3-N, and total volatile fatty acid levels decreased linearly (p<0.05) with increased levels of concentrate in CFMs. Conclusion: Reduction in methane production was evidenced with the inclusion of mustard cake in concentrate mixture at 15% level, and the CFMs with 25% concentrate, which contained 15% mustard cake, exhibited an improved fermentation and reduced methane production.
The Pro-Apoptotic BH3-Only Protein Bim Interacts with Components of the Translocase of the Outer Mitochondrial Membrane (TOM)

The pro-apoptotic Bcl-2-family protein Bim belongs to the BH3-only proteins known as initiators of apoptosis. Recent data show that Bim is constitutively inserted in the outer mitochondrial membrane via a C-terminal transmembrane anchor from where it can activate the effector of cytochrome c-release, Bax. To identify regulators of Bim-activity, we conducted a search for proteins interacting with Bim at mitochondria. We found an interaction of Bim with Tom70, Tom20 and more weakly with Tom40, all components of the Translocase of the Outer Membrane (TOM). In vitro import assays performed on tryptically digested yeast mitochondria showed reduced Bim insertion into the outer mitochondrial membrane (OMM) indicating that protein receptors may be involved in the import process. However, RNAi against components of TOM (Tom40, Tom70, Tom22 or Tom20) by siRNA, individually or in combination, did not consistently change the amount of Bim on HeLa mitochondria, either at steady state or upon de novo-induction. In support of this, the individual or combined knock-downs of TOM receptors also failed to alter the susceptibility of HeLa cells to Bim-induced apoptosis. In isolated yeast mitochondria, lack of Tom70 or the TOM-components Tom20 or Tom22 alone did not affect the import of Bim into the outer mitochondrial membrane. In yeast, expression of Bim can sensitize the cells to Bax-dependent killing. This sensitization was unaffected by the absence of Tom70 or by an experimental reduction in Tom40. Although thus the physiological role of the Bim-TOM-interaction remains unclear, TOM complex components do not seem to be essential for Bim insertion into the OMM. Nevertheless, this association should be noted and considered when the regulation of Bim in other cells and situations is investigated.
Efficient training of neural gas vector quantizers with analog circuit implementation

This paper presents an algorithm for training vector quantizers with an improved version of the neural gas model, and its implementation in analog circuitry. Theoretical properties of the algorithm are proven that clarify the performance of the method in terms of quantization quality, and motivate design aspects of the hardware implementation. The architecture for vector quantization training includes two chips, one for Euclidean distance computation, the other for programmable sorting of codevectors. Experimental results obtained in a real application (image coding) support both the algorithm's effectiveness and the hardware performance, which can speed up the training process by up to two orders of magnitude.
A sample of radio-loud active galactic nuclei in the Sloan Digital Sky Survey

A sample of 2712 radio-luminous galaxies is defined from the second data release of the Sloan Digital Sky Survey (SDSS) by cross-comparing the main spectroscopic galaxy sample with two radio surveys: the National Radio Astronomy Observatories (NRAO) Very Large Array (VLA) Sky Survey (NVSS) and the Faint Images of the Radio Sky at Twenty centimeters (FIRST) survey. The comparison is carried out in a multistage process and makes optimal use of both radio surveys by exploiting the sensitivity of the NVSS to extended and multicomponent radio sources in addition to the high angular resolution of the FIRST images. A radio source sample with 95 per cent completeness and 98.9 per cent reliability is achieved, far better than would be possible for this sample if only one of the surveys was used. The radio source sample is then divided into two classes: radio-loud active galactic nuclei (AGN) and galaxies in which the radio emission is dominated by star formation. The division is based on the location of a galaxy in the plane of 4000-A break strength versus radio luminosity per unit stellar mass and provides a sample of 2215 radio-loud AGN and 497 star-forming galaxies brighter than 5 mJy at 1.4 GHz. A full catalogue of positions and radio properties is provided for these sources. The local radio luminosity function is then derived both for radio-loud AGN and for star-forming galaxies and is found to be in agreement with previous studies. By using the radio to far-infrared (FIR) correlation, the radio luminosity function of star-forming galaxies is also compared to the luminosity function derived in the FIR. It is found to agree well at high luminosities but less so at lower luminosities, confirming that the linearity of the radio to FIR correlation breaks down below about 10 22 W Hz -1 at 1.4GHz.
Cost estimation for global software development

Global software development has gathered pace in recent years. Many software projects now involve asynchronous collaboration among geographically distributed teams several time zones apart. Software costestimation for such projects becomes challenging due to factors such as effort expended in team building and knowledge transfer, creating an architecture of the software product that can be easily distributed and that minimizes cross-site communication, facilitating communication among remote teams collaborating on parts of the architecture that are interrelated and their day-to-day governance.In this paper we structure the additional cost drivers of distributed development and examine the significance of each of these factors as a contributor to the overall cost of a software development project. We suggest ways in which COCOMO II, the most widely used software development cost estimation model, can be tailored to account for these additional complexities.
APTITUDE TREATMENT INTERACTION TERHADAP KEMAMPUAN PEMAHAMAN MATEMATIS SISWA

Kemampuan pemahaman yang menjadi salah satu bagian penting justru faktanya masih rendah. Telah banyak berbagai studi, baik dari skala nasional maupun pada skala internasional yang menunjukkan bahwa prestasi Indonesia terutama dalam pemahaman masih sangat memprihatinkan. Dalam tes yang dilaksanakan Trends In International Mathematics an Science Study (TIMSS), peserta Indonesia masih lemah dalam menyelesaikan soal-soal yangberkaitan dengan mengaplikasikan objek, menjelaskan keterkaitan konsep, menggunakan, memanfaatkan, dan memilih prosedur atau operasi tertentu. Hal tersebut berkaitan dengan pemahaman konsep matematis siswa, maka hasil dari TIMSS dapat menunjukan masih rendahnya pemahaman konsep matematis siswa yang dimiliki oleh siswa SMP di Indonesia. Pada penelitian ini menggunakan metode eksperimen, sebagai populasinya yaitu siswa siswa kelas VIII SMP Negeri 1 Tarogong Kidul tahun ajaran 2015/2016. Pada penelitian ini terpilih kelas eksperimen 1 yaitu kelas VIIIE yang pembelajarannya menggunakan Aptitude Treatment Interaction sedangkan kelas kontrolyaitu kelas VIIB yang pembelajarannya menggunakan Pembelajaran konvensional. Desain penelitian ini yaitu pretest-posttest dengan instrumen penelitian tipe uraian. Berdasarkan hasil analisis data dan pengujian hipotesis, “Terdapat perbedaan kemampuan pemahaman konsep matematis siswa yang mendapat model pembelajaran Aptitude Treatment Interaction dengan siswa yang mendapat model pembelajaran konvensional, sehingga dapat disimpulkan bahwa model pembelajaran Aptitude Treatment Interactionpada penelitian ini telah berpengaruh positif terhadap pembelajaran”.