Miracle-dz/UniFAR-FTUs huggingface dataset:
Octopus arm movements under constrained conditions: adaptation, modification and plasticity of motor primitives

ABSTRACT The motor control of the eight highly flexible arms of the common octopus (Octopus vulgaris) has been the focus of several recent studies. Our study is the first to manage to introduce a physical constraint to an octopus arm and investigate the adaptability of stereotypical bend propagation in reaching movements and the pseudo-limb articulation during fetching. Subjects (N=6) were placed inside a transparent Perspex box with a hole at the center that allowed the insertion of a single arm. Animals had to reach out through the hole toward a target, to retrieve a food reward and fetch it. All subjects successfully adjusted their movements to the constraint without an adaptation phase. During reaching tasks, the animals showed two movement strategies: stereotypical bend propagation reachings, which were established at the hole of the Perspex box and variant waving-like movements that showed no bend propagations. During fetching movements, no complete pseudo-joint fetching was observed outside the box and subjects pulled their arms through the hole in a pull-in like movement. Our findings show that there is some flexibility in the octopus motor system to adapt to a novel situation. However, at present, it seems that these changes are more an effect of random choices between different alternative motor programs, without showing clear learning effects in the choice between the alternatives. Interestingly, animals were able to adapt the fetching movements to the physical constraint, or as an alternative explanation, they could switch the motor primitive fetching to a different motor primitive ‘arm pulling’. Summary: The ability of the motor system to adapt and modify motor primitives is shown by introducing a physical constraint to the octopus arm.
The Chemical Composition of Essential Oils from Cinnamomum camphora and Their Insecticidal Activity against the Stored Product Pests

To investigate the chemical composition and insecticidal activity of the essential oils of certain Chinese medicinal herbs and spices, the essential oils were extracted from the stem barks, leaves, and fruits of Cinnamomum camphora (L.) Presl, which were found to possess strong fumigant toxicity against Tribolium castaneum and Lasioderma serricorne adults. The essential oils of the plants were extracted by the method of steam distillation using a Clavenger apparatus. Their composition was determined by gas chromatography/mass spectrometric (GC-MS) analyses (HP-5MS column), and their insecticidal activity was measured by seal-spaced fumigation. D-camphor (51.3%), 1,8-cineole (4.3%), and α-terpineol (3.8%), while D-camphor (28.1%), linalool (22.9%), and 1,8-cineole (5.3%) were the main constituents of its fruits. The essential oils of the C. camphora all showed fumigant and contact toxicity. Other compounds exhibited various levels of bioactivities. The results indicate that the essential oils of C. camphora and its individual compounds can be considered a natural resource for the two stored-product insect management.
Developmental and hormonal regulation of NR2A mRNA in forebrain regions controlling avian vocal learning.

Developmental changes in the composition of NMDA receptors can alter receptor physiology as well as intracellular signal transduction cascades, potentially shifting thresholds for neural and behavioral plasticity. During song learning in zebra finches, NMDAR currents become faster, and transcripts for the modulatory NR2B subunit of this receptor decrease in lMAN, a region in which NMDAR activation is critical for vocal learning. Using in situ hybridization, we found that NR2A transcripts change reciprocally, increasing significantly in both lMAN (59%) and in another song region, Area X (38%), between posthatch day (PHD) 20 and 40, but not changing further at PHD60 or 80. In adjacent areas not associated with song learning, NR2A mRNA did not change between PHD20-80. Although early song deprivation (which extends the sensitive period for song learning) delays changes in NR2B gene expression and NMDAR physiology within the lMAN, it did not alter NR2A mRNA levels measured at PHD40, 45, or 60. Early testosterone (T) treatment, which disrupts vocal development and accelerates the maturation of both NR2B levels and NMDAR physiology in lMAN, also significantly increased NR2A transcripts measured at PHD35 in lMAN. In Area X, a similar effect of T approached significance. Together with our previous studies, these results show that in a pathway critical for vocal plasticity, the ratio of NR2A:NR2B mRNA rises abruptly early during the sensitive period for song learning. Furthermore, androgen regulation of NMDAR gene expression may alter thresholds for experience-dependent synaptic change.
WITH ENHANCED RESOURCE FINDING AND VISUAL EXPLORATION

Understanding the basic structure of a code base and a development team are essential to get new developers up to speed in a software development project. Developers do so through the process of early experimentation with code and the creation of mental models of technical and social structures in a project. However, getting up-to-speed in a new project can be challenging due to difficulties in: finding the right place to begin explorations, expanding the focus to determine relevant resources for tasks, and identifying dependencies across project elements to gain a high-level overview of project structures. In this thesis, I first identified six challenges that developers face during the process of developer onboarding from recent research studies and informal interviews with developers. To address these challenges, I implemented automated tool support with enhanced resource finding and visual exploration. Specifically, I proposed six functional requirements for supporting developers onboarding. I then extended the project tool Tesseract to support these functionalities to help novice developers find relevant resources (files, developers, bugs, etc.) and understand project structures when joining a new project. To understand how the onboarding func-tionalities work in supporting developers' onboarding process, I conducted a user study with typical onboarding tasks requiring early experimentation and internalizing project structures. The results indicated that enhanced search features, the ability to explore semantic relationships across repositories, and network-centric visualizations of project structures were very effective in supporting onboarding. iii ACKNOWLEDGMENTS First, I would like to thank my adviser, Dr. Anita Sarma, for all her support, encouragement , and guidance, without which I would never be able to achieve this. Dr. Sarma has everything you could ask for from an Adviser. She is patient, understanding , and knowledgeable. She is willing to help whenever possible. I feel lucky to be her first student and really appreciate this opportunity to work with her. I would also like to thank my committee members Dr. Gregg Rothermel and Dr. Witty Srisa-an, for offering great suggestions on my research and taking time reviewing my thesis. Dr. Srisa-an also advised me through the first year in my Master program, helping me adapt to the study and life here. Anthropology, who supported me during my first year of study. I would like to thank Larry Maccherone, who built much of the tool I used for my research. I would also like to thank my colleagues in the ESQuaReD Lab and the staff …
Information Structure and Statistical Information in Discrete Response Models

Discrete response models are of high interest in economics and econometrics as they encompass treatment effects, social interaction and peer effect models, and discrete games. We study the impact of the structure of information sets of economic agents on the Fisher information of (strategic) interaction parameters in such models. While in complete information models the information sets of participating economic agents coincide, in incomplete information models each agent has a type, which we model as a payoff shock, that is not observed by other agents. We allow for the presence of a payoff component that is common knowledge to economic agents but is not observed by the econometrician (representing unobserved heterogeneity) and have the agents' payoffs in the incomplete information model approach their payoff in the complete information model as the heterogeneity term approaches 0. We find that in the complete information models, there is zero Fisher information for interaction parameters, implying that estimation and inference become nonstandard. In contrast, positive Fisher information can be attained in the incomplete information models with any non-zero variance of player types, and for those we can also find the semiparametric efficiency bound with unknown distribution of unobserved heterogeneity. The contrast in Fisher information is illustrated in two important cases: treatment effect models, which we model as a triangular system of equations, and static game models. In static game models we show this result is not due to equilibrium refinement with an increase in incomplete information, as our model has a fixed equilibrium selection mechanism. We find that the key factor in these models is the relative tail behavior of the unobserved component in the economic agents' payoffs and that of the observable covariates.
Effect of Fuel Injection Strategy on the Carbonaceous Structure Formation and Nanoparticle Emission in a DISI Engine Fuelled with Butanol

Within the context of ever wider expansion of direct injection in spark ignition engines, this investigation was aimed at improved understanding of the correlation between fuel injection strategy and emission of nanoparticles. Measurements performed on a wall guided engine allowed identifying the mechanisms involved in the formation of carbonaceous structures during combustion and their evolution in the exhaust line. In-cylinder pressure was recorded in combination with cycle-resolved flame imaging, gaseous emissions and particle size distribution. This complete characterization was performed at three injection phasing settings, with butanol and commercial gasoline. Optical accessibility from below the combustion chamber allowed visualization of diffusive flames induced by fuel deposits; these localized phenomena were correlated to observed changes in engine performance and pollutant species. With gasoline fueling, minor modifications were observed with respect to combustion parameters, when varying the start of injection. The alcohol, on the other hand, featured marked sensitivity to the fuel delivery strategy. Even though the start of injection was varied in a relatively narrow crank angle range during the intake stroke, significant differences were recorded, especially in the values of particle emissions. This was correlated to the fuel jet-wall interactions; the analysis of diffusive flames, their location and size confirmed the importance of liquid film formation in direct injection engines, especially at medium and high load.
Metallothioneins as dynamic markers for brain disease in lysosomal disorders

To facilitate development of novel disease‐modifying therapies for lysosomal storage disorder (LSDs) characterized by nervous system involvement such as metachromatic leukodystrophy (MLD), molecular markers for monitoring disease progression and therapeutic response are needed. To this end, we sought to identify blood transcripts associated with the progression of MLD.
Positive and negative transcriptional control by heme of genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae

Responses of the yeast genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase, HMG1 and HMG2, to in vivo changes in heme concentrations were investigated. Expression of the genes was determined by direct measurement of the mRNA transcribed from each gene, by direct assay of the enzyme activity encoded by each gene, and by measurement of the expression of lacZ fusions to the control regions of each gene. These studies indicated that expression of HMG1 was stimulated by heme, whereas expression of HMG2 was repressed by heme. The effect of heme on HMG1 expression was mediated by the HAP1 transcriptional regulator and was independent of HAP2. Thus, the genes encoding the 3-hydroxy-3-methylglutaryl coenzyme A reductase isozymes join a growing list of gene pairs that are regulated by heme in opposite ways.
Dissociation Dynamics of XPC-RAD23B from Damaged DNA Is a Determining Factor of NER Efficiency

XPC-RAD23B (XPC) plays a critical role in human nucleotide excision repair (hNER) as this complex recognizes DNA adducts to initiate NER. To determine the mutagenic potential of structurally different bulky DNA damages, various studies have been conducted to define the correlation of XPC-DNA damage equilibrium binding affinity with NER efficiency. However, little is known about the effects of XPC-DNA damage recognition kinetics on hNER. Although association of XPC is important, our current work shows that the XPC-DNA dissociation rate also plays a pivotal role in achieving NER efficiency. We characterized for the first time the binding of XPC to mono- versus di-AAF-modified sequences by using the real time monitoring surface plasmon resonance technique. Strikingly, the half-life (t1/2 or the retention time of XPC in association with damaged DNA) shares an inverse relationship with NER efficiency. This is particularly true when XPC remained bound to clustered adducts for a much longer period of time as compared to mono-adducts. Our results suggest that XPC dissociation from the damage site could become a rate-limiting step in NER of certain types of DNA adducts, leading to repression of NER.
Meaning development versus predefined meanings in language evolution models

This paper investigates the effect of predefining semantics in modelling the evolution of compositional languages versus allowing agents to develop these semantics in parallel with the development of language. The study is done using a multi-agent model of language evolution that is based on the Talking Heads experiment. The experiments show that when allowing a co-evolution of semantics with language, compositional languages develop faster than when the semantics are predefined, but compositionality appears more stable in the latter case. The paper concludes that conclusions drawn from simulations with predefined meanings, which most studies use, may need revision.
Informative art: information visualization in everyday environments

Thanks to advances in display technologies, it will soon be possible to have electronic information displays virtually everywhere. We have developed the concept of Informative Art as a way to integrate information visualization in the everyday human environment. Informative Art combines a dynamically updated information display with the decorative role of visual art, such as posters and paintings. We present four examples of Informative Art, where we borrowed the styles of various modern artists to show different kinds of information. For instance, a composition similar to the style of an abstract painter, Piet Mondriaan, showed the current weather in six different cities, while a piece of "landscape art" in the style of Richard Long gave a view of the last 30 days of global earthquake activity. We discuss how designing information visualizations for everyday environment introduces requirement that are different from those of graphical user interfaces for desktop computers.
Generalized Optical Flow Model for Scattering Media

This paper proposes a novel methodology to estimate the optical flow in scattering media, which consists on new formulation based on the classical Horn-Schunk approach and the optical image formation model. Our formulation is able to deal with the hard problem of tracking points in a medium where there is absorption and scattering effects. This approach generalizes assumptions of the Horn-Schunk model in order to tackle both non-scattering and scattering media. Our approach uses the Dark Channel Prior to estimate the scene transmission, which attains a significant improvement in the optical flow estimation in scattering media. We show that our approach outperformed state-of-the-art models and we provide a detailed analysis of our technique that shows its applicability to image sequences acquired both in simulated and real scenes.
PENNER SEQUENCES AND ASYMPTOTICS OF MINIMUM DILATATIONS FOR SUBFAMILIES OF THE MAPPING CLASS GROUP

Let Fm ⊂ Mod(Sm) be a collection of subsets of the mapping class group of a compact oriented surface Sm of genus gm, where gm is unbounded. We say F = ⋃ m Fm admits asymptotically small dilatations if there exists a sequence φm ∈ Fm of pseudo-Anosov elements so that λ(φm)m is bounded. In this paper, we describe Penner’s construction for producing sequences of pseudo-Anosov mapping classes whose normalized dilatations converge and apply the construction to the setting of handlebody mapping class groups and mapping classes with trivial homological dilatation.
Assessment of Advanced Age as a Risk Factor in Microvascular Breast Reconstruction

Background:The population of elderly people is the fastest growing population in the United States. Because breast cancer typically affects the elderly population, surgeons will be performing more mastectomies in older patients. In this study, we evaluate the risks of microvascular breast reconstruction as a function of increasing age. Methods:Between July 2002 and September 2009, a retrospective analysis of 818 free-flap breast reconstructions was used to assess the risk of age on surgical outcomes. Patient comorbidities, the American Society of Anesthesiologists (ASA) classification, and length of hospital stay were used to assess the rates of complications among our age cohorts. Results:Advanced age was not associated with increased complications (P > 0.69). ASA class was a significant predictor of overall complications (P < 0.03) as well as the rate of fat necrosis (P < 0.01) and hematoma (P < 0.001). Flap loss occurred in 1.5% of operations, but there was no difference among the various age groups. Previous surgery was associated with an increased risk of flap loss (P < 0.001), and hypertension also increased the risk of thrombosis (P < 0.04). There was no difference in mean length of hospital stay (4.27 days). Conclusions:Advanced age should not be considered a risk factor for microvascular breast reconstruction. Because ASA status did predict overall surgical complications, surgeons should consider the patients' overall health status in deciding whether to operate.
Determination of Ionizing Radiation Exposure Levels within Four Local Mining Sites Selected from Sardauna Local Government Area of Taraba State - Nigeria

Miners and the people living close to mining sites are exposed to elevated levels of ionizing radiation with or without their consent. This study determined the background ionizing radiation of four mining sites from Sardauna local government area of Taraba state using an inspector alert nuclear radiation meter manufactured by S.E. International, Inc USA with serial number 35440. The meter has a halogen- quenched Geiger Muller tube with a ± 45 mm effective diameter and mica window density of 1.5- 2.0 mg/cm3. The Geiger tube in the meter generates a pulse of electrical current each time radiation is incident on the tube and causes ionization. The measured values ranged from 0.19 - 0.40 mSv/yr across all the mining sites and 500 m away from the sites. These results were found to be far less than the standard of 1.0 mSv/yr set by International Commission on Radiological Protection (ICRP) for the general public and 20.0 mSv/yr set by the Nigeria Basic Ionization Radiation Regulation (NiBIRR) for the whole body of adult radiation protection workers which means that the miners and inhabitants of this areas are safe. Nevertheless, there could be long term variations in the consequences arising from the effects of ionizing radiation among the miners and even the inhabitants. Strong correlations were found between the equivalent doses at the excavating and the processing points of the sites which mean that the miners and people living close to these mining sites are subjected to uniform distribution of consequences arising from ionizing radiation. We do recommend that policy makers and regulatory bodies should apply mitigation measures to the effects by means of creating awareness to the miners at various mining sites and the use of modern mining strategies to protect other natural resources especially water.
A hierarchical approach with feature selection for emotion recognition from speech

We examine speaker independent emotion classification from speech, reporting experiments on the Berlin database across six basic emotions. Our approach is novel in a number of ways: First, it is hierarchical, motivated by our belief that the most suitable feature set for classification is different for each pair of emotions. Further, it uses a large number of feature sets of different types, such as prosodic, spectral, glottal flow based, and AM-FM ones. Finally, it employs a two-stage feature selection strategy to achieve discriminative dimensionality reduction. The approach results to a classification rate of 85%, comparable to the state-of-the-art on this dataset.
Genetic Determinants Associated With Early Age of Diagnosis of IBD

BACKGROUND: Inflammatory bowel disease (IBD) is typically diagnosed at 20 to 40 years of age. However, very young versus elderly patients with IBD may have different mechanisms of disease that may affect prognosis and care. OBJECTIVES: The purpose of this work was to identify single nucleotide polymorphisms associated with age of onset of Crohn’s disease and ulcerative colitis. DESIGN: Patients were genotyped using a custom microarray chip containing 332 IBD-associated single nucleotide polymorphisms. Age at diagnosis as a continuous variable was assessed using linear regression. Patients were then subgrouped by age at diagnosis and compared by the Fisher exact test. Bonferroni correction was used in all of the analyses. SETTINGS: This study was conducted at a tertiary academic hospital. PATIENTS: Sixty patients with Crohn’s disease and 26 with ulcerative colitis were ⩽16 years old, 259 patients with Crohn’s disease and 248 with ulcerative colitis were 17–60 years old, and 10 patients with Crohn’s disease and 20 with ulcerative colitis were >60 years old at diagnosis and included in this study. MAIN OUTCOME MEASURES: Age at diagnosis and single nucleotide polymorphism correlations were measured in this study. RESULTS: The NOD2 single nucleotide polymorphism rs2076756 was associated with younger age at Crohn’s disease diagnosis (p = 0.0002). Patients with the AA/wild-type genotype were diagnosed at 31.9 ± 1.23 years, AG heterozygotes at 25.6 ± 0.99 years, and GG/at-risk allele homozygotes at 22.6 ± 1.32 years. Depending on age categories compared, single nucleotide polymorphisms in POU5F1, TNFSF15, and HLA DRB1*501 were associated with age of Crohn’s disease diagnosis. No genetic associations were seen between ulcerative colitis and linear age at diagnosis; however, the G allele of the LAMB1 single nucleotide polymorphism rs886774 was found to be associated with ulcerative colitis diagnosed at ⩽16 versus >17 years old (p = 0.008). LIMITATIONS: This study was limited to known IBD single nucleotide polymorphisms. CONCLUSIONS: This analysis reaffirms the association between NOD2, a molecule of innate immunity, and early Crohn’s disease onset. This is the first report of a possible association between early Crohn’s disease and the POU5F1, TNFSF15, and HLA DRB1*501 genes. The LAMB1 gene, associated with mucosal basement membrane integrity, was associated with early onset ulcerative colitis and, thus, suggests a fundamentally different mechanism of early disease pathogenesis in ulcerative colitis versus Crohn’s disease.