Miracle-dz/UniFAR-FTUs huggingface dataset:
From molecules to mastication: the development and evolution of teeth

Teeth are unique to vertebrates and have played a central role in their evolution. The molecular pathways and morphogenetic processes involved in tooth development have been the focus of intense investigation over the past few decades, and the tooth is an important model system for many areas of research. Developmental biologists have exploited the clear distinction between the epithelium and the underlying mesenchyme during tooth development to elucidate reciprocal epithelial/mesenchymal interactions during organogenesis. The preservation of teeth in the fossil record makes these organs invaluable for the work of paleontologists, anthropologists, and evolutionary biologists. In addition, with the recent identification and characterization of dental stem cells, teeth have become of interest to the field of regenerative medicine. Here, we review the major research areas and studies in the development and evolution of teeth, including morphogenesis, genetics and signaling, evolution of tooth development, and dental stem cells. WIREs Dev Biol 2013, 2:165–182. doi: 10.1002/wdev.63
Nonlinear Processes in Geophysics Scaling in the Space Climatology of the Auroral Indices: Is Soc the Only Possible Description?

The study of the robust features of the magneto-sphere is motivated both by new " whole system " approaches, and by the idea of " space climate " as opposed to " space weather ". We enumerate these features for the AE index, and discuss whether self-organised criticality (SOC) is the most natural explanation of the " stylised facts " so far known for AE. We identify and discuss some open questions, answers to which will clarify the extent to which AE's properties provide evidence for SOC. We then suggest an SOC-like reconnection-based scenario drawing on the result of Craig (2001) as an explanation of the very recent demonstration by Uritsky et al. (2001b) of power laws in several properties of spatiotemporal features seen in auroral images.
GPS-EM Sanctions for Serious Sex Offenders: The Application and Outcomes in the United States and Australia

ABSTRACT In the United States and, subsequently, in Australia the utilization of Global Positioning Systems—Electronic Monitoring (GPS-EM) proliferated in the mid-2000s as part of the populist “tough on crime” agenda. These surveillance-oriented sanctions are applied on serious sex offenders usually post their original sentences. This article critically examines the application and outcomes of GPS-EM sanctions in the United States and Australia. U.S. evaluations have indicated that to be successful, GPS-EM sanctions must contain offender treatment, be appropriately funded, and have an effectively run centralized monitoring center. Evaluative research on GPS-EM sanctions in Australia is yet to be conducted.
Determinants of Formin Homology 1 (FH1) Domain Function in Actin Filament Elongation by Formins*

Background: Formin FH1 domains deliver subunits to actin filament barbed ends. Results: The transfer rate of formin Bni1p depends on FH1 polyproline track sequences and positions. Conclusion: The two FH1 domains of formin dimers deliver actin independently of one another. Significance: Sequence features of other FH1 domains are similar to Bni1p, suggesting a common strategy to maximize actin polymerization rates. Formin-mediated elongation of actin filaments proceeds via association of Formin Homology 2 (FH2) domain dimers with the barbed end of the filament, allowing subunit addition while remaining processively attached to the end. The flexible Formin Homology 1 (FH1) domain, located directly N-terminal to the FH2 domain, contains one or more stretches of polyproline that bind the actin-binding protein profilin. Diffusion of FH1 domains brings associated profilin-actin complexes into contact with the FH2-bound barbed end of the filament, thereby enabling direct transfer of actin. We investigated how the organization of the FH1 domain of budding yeast formin Bni1p determines the rates of profilin-actin transfer onto the end of the filament. Each FH1 domain transfers actin to the barbed end independently of the other and structural evidence suggests a preference for actin delivery from each FH1 domain to the closest long-pitch helix of the filament. The transfer reaction is diffusion-limited and influenced by the affinities of the FH1 polyproline tracks for profilin. Position-specific sequence variations optimize the efficiency of FH1-stimulated polymerization by binding profilin weakly near the FH2 domain and binding profilin more strongly farther away. FH1 domains of many other formins follow this organizational trend. This particular sequence architecture may optimize the efficiency of FH1-stimulated elongation.
Nonparametric estimation of copula functions for dependence modelling

Copulas characterize the dependence among components of random vectors. Unlike marginal and joint distributions, which are directly observable, the copula of a random vector is a hidden dependence structure that links the joint distribution with its margins. Choosing a parametric copula model is thus a nontrivial task but it can be facilitated by relying on a nonparametric estimator. Here the authors propose a kernel estimator of the copula that is mean square consistent everywhere on the support. They determine the bias and variance of this estimator. They also study the effects of kernel smoothing on copula estimation. They then propose a smoothing bandwidth selection rule based on the derived bias and variance. After confirming their theoretical findings through simulations, they use their kernel estimator to formulate a goodness‐of‐fit test for parametric copula models.
Review on Feature Selection Techniques and the Impact of SVM for Cancer Classification using Gene Expression Profile

The DNA microarray technology has modernized the approach of biology research in such a way that scientists can now measure the expression levels of thousands of genes simultaneously in a single experiment. Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. But compared to the number of genes involved, available training data sets generally have a fairly small sample size for classification. These training data limitations constitute a challenge to certain classification methodologies. Feature selection techniques can be used to extract the marker genes which influence the classification accuracy effectively by eliminating the un wanted noisy and redundant genes This paper presents a review of feature selection techniques that have been employed in micro array data based cancer classification and also the predominant role of SVM for cancer classification.
Low-complexity frame-level joint source-channel distortion optimal, adaptive intra refresh

Error resilient, low latency video coding for interactive video applications requires progressive intra coding of macroblocks (MBs) to contain the error propagation. Both refresh MB selection (RMS) and refresh rate selection (RRS) impact the subjective video quality in the presence of packet losses. Joint source-channel rate distortion optimization methods attempt to find the best trade-off between compression efficiency and end-to-end distortion at an MB-level and are typically computationally expensive in addition to not being optimal at a picture level. While probabilistic error propagation tracking is used for refresh MB selection in previous work, these picture-level optimal RRS methods model source-channel distortion by mimicking the effect of periodic intra frame coding which does not match well with content adaptive refresh MB selection. In this paper, we propose a frame-level approach to RRS that aligns the joint source-channel rate-distortion trade-off modeling with an enhanced RMS process to achieve an optimal end-to-end distortion that is content, bit-rate and channel adaptive. For typical videoconferencing content, the proposed approach is quite low in complexity, works on par with off-line multi-pass identification of the optimal fixed refresh rate and is quite competitive when compared to the H.264 joint modelpsilas lossy rate-distortion optimization technique.
Framework for Analyzing Effects of Spring Load Restrictions

Spring load restrictions (SLR) impose restrictions on heavy trucks during the spring thaw period. Although the policies have been implemented for many years, their economic effects on truckers remain uncertain. This study provides an overview of practices around the world and sets up a framework to estimate the benefit-cost of the SLR policy. A freight demand model in Minnesota was built to estimate the impacts of SLR on the freight transportation pattern. The model allows various policy scenarios to be tested before being put into practice. A preliminary result of the freight demand model indicates the SLR policy increased truck vehicle kilometers of travel in Lyon County, Minnesota, by about 13%.
Gender diversity within the workforce in the microfinance industry in Africa: Economic performance and sustainability

This study examines the relationship of gender diversity within the workforce and the sustainability of economic performance within the microfinance industry in Africa as compared to the rest of the world. Measuring economic performance helps to demonstrate whether resources are effectively utilized to achieve social performance objectives. We use ROA—the most common measure of profit for financial institutions—to capture financial performance, and OpEx—the most widely used indicator of efficiency—to capture operating efficiency. We measure gender diversity within the microfinance workforce at two hierarchical levels. Our analysis of a data set of 1,389 observations in 1,053 firms suggests that gender diversity enhances economic performance, especially in Africa. We propose that policymakers and practitioners consider these results to determine how to best deploy women within the microfinance workforce to deliver sustainable economic performance. Copyright © 2016 ASAC. Published by John Wiley & Sons, Ltd. Resume Cette etude examine la relation entre la diversite des sexes au sein du personnel et la durabilite de la performance economique dans l'industrie de la microfinance en Afrique, par comparaison au reste du monde. La mesure de la performance economique permet de demontrer que les ressources sont efficacement utilisees pour atteindre les objectifs de la performance sociale. La ROA— la mesure la plus courante permettant d'evaluer le profit des institutions financieres — est utilisee pour cerner la performance financiere et l'OpEx— l'indicateur d'efficacite la plus repandue — est utilisee pour determiner l'efficacite operationnelle. L'etude montre que la mesure de la diversite des genres au sein du personnel de la microfinance s'opere a deux niveaux hierarchiques. L'analyse de 1389 observations provenant de 1053 firmes indique que la diversite des genres ameliore la performance economique, notamment en Afrique. L'article propose aux decideurs et aux gestionnaires de s'inspirer de nos resultats pour mieux deployer la gent feminin dans le personnel des microfinances afin d'atteindre des performances economiques durables. Copyright © 2016 ASAC. Published by John Wiley & Sons, Ltd.
Bidirectional LSTM-CRF Models for Sequence Tagging

In this paper, we propose a variety of Long Short-Term Memory (LSTM) based models for sequence tagging. These models include LSTM networks, bidirectional LSTM (BI-LSTM) networks, LSTM with a Conditional Random Field (CRF) layer (LSTM-CRF) and bidirectional LSTM with a CRF layer (BI-LSTM-CRF). Our work is the first to apply a bidirectional LSTM CRF (denoted as BI-LSTM-CRF) model to NLP benchmark sequence tagging data sets. We show that the BI-LSTM-CRF model can efficiently use both past and future input features thanks to a bidirectional LSTM component. It can also use sentence level tag information thanks to a CRF layer. The BI-LSTM-CRF model can produce state of the art (or close to) accuracy on POS, chunking and NER data sets. In addition, it is robust and has less dependence on word embedding as compared to previous observations.
A pilot study of the Personality Assessment Inventory (PAI) in corrections: assessment of malingering, suicide risk, and aggression in male inmates.

Provision of mental health services to correctional populations places considerable demands on clinical staff to provide efficient and effective means to screen patients for severe mental disorders and other emergent conditions that necessitate immediate interventions. Among the highly problematic behaviors found in correctional settings are forms of acting out (e.g., suicide and aggression towards others) and response style (e.g., motivations to malinger). The current study examined the usefulness of the Personality Assessment Inventory (PAI) in assessing problematic behaviors in a corrections-based psychiatric hospital. As evidence of criterion related validity, selected PAI scales were compared to (a) evidence of malingering on the Structured Interview of Reported Symptoms (SIRS), (b) suicidal threats and gestures, and (c) ratings of aggression on the Overt Aggression Scale (OAS). In general, results supported the use of the PAI for the assessment of these problematic behaviors.
Repression of Dpp targets in the Drosophila wing by Brinker

Patterning along developing body axes is regulated by gradients of transcription factors, which activate or repress different genes above distinct thresholds. Understanding differential threshold responses requires knowledge of how these factors regulate transcription. In the Drosophila wing, expression of genes such as omb and sal along the anteroposterior axis is restricted by lateral-to-medial gradients of the transcriptional repressor Brinker (Brk). omb is less sensitive to repression by Brk than sal and is consequently expressed more laterally. Contrary to previous suggestions, we show that Brk cannot repress simply by competing with activators, but requires specific repression domains along with its DNA-binding domain. Brk possesses at least three repression domains, but these are not equivalent; one, 3R, is sufficient to repress omb but not sal. Thus, although sal and omb show quantitative differences in their response to Brk, there are qualitative differences in the mechanisms that Brk uses to repress them.
Stability of Helicopters in Compliant Contact Under PD-PID Control

Aerial vehicles are difficult to stabilize, especially when acted upon by external forces. A hovering vehicle interacting with objects and surfaces must be robust to contact forces and torques transmitted to the airframe. These produce coupled dynamics that are distinctly different from those of free flight. While external contact is generally avoided, extending aerial robot functionality to include contact with the environment during flight opens up new and useful areas such as perching, object grasping, and manipulation. These mechanics may be modeled as elastic couplings between the aircraft and the ground, represented by springs in R3×SO(3). We show that proportional derivative and proportional integral derivative (PID) attitude and position controllers that stabilize a rotorcraft in free flight will also stabilize the aircraft during contact for a range of contact displacements and stiffnesses. Simulation of the coupled aircraft dynamics demonstrates stable and unstable modes of the system. We find analytical measures that predict the stability of these systems and consider, in particular, the planar system in which the contact point is directly beneath the rotor. We show through explicit solution of the linearized system that the planar dynamics of the object-helicopter system in vertical, horizontal, and pitch motion around equilibrium remain stable, within a range of contact stiffnesses, under unmodified PID attitude control. Flight experiments with a small-scale PID-stabilized helicopter fitted with a compliant gripper for capturing objects affirm our model's stability predictions.
Movement‐related frequency modulation of beta oscillatory activity in the human subthalamic nucleus

Event‐related changes of brain electrical rhythms are typically analysed as amplitude modulations of local field potential (LFP) oscillations, like radio amplitude modulation broadcasting. In telecommunications, frequency modulation (FM) is less susceptible to interference than amplitude modulation (AM) and is therefore preferred for high‐fidelity transmissions. Here we hypothesized that LFP rhythms detected from deep brain stimulation (DBS) electrodes implanted in the subthalamic nucleus (STN) in patients with Parkinson's disease could represent movement‐related activity not only in AM but also in FM. By combining adaptive autoregressive identification with spectral power decomposition, we were able to show that FM of low‐beta (13–20 Hz) and high‐beta (20–35 Hz) rhythms significantly contributes to the involvement of the human STN in movement preparation, execution and recovery, and that the FM patterns are regulated by the dopamine levels in the system. Movement‐related FM of beta oscillatory activity in the human subthalamic nucleus therefore provides a novel informational domain for rhythm‐based pathophysiological models of cortico‐basal ganglia processing.
A comparative study of word order in Old Romance

The main objective of this article is to discuss word-order phenomena in Old French, Old Spanish, Old Portuguese, and Old Occitan from a comparative perspective. In particular, the following are examined: (i) the empirical evidence in order to assess the theoretical arguments for and against a verbsecond analysis of the Old Romance languages; (ii) verb movement in Old Romance; and (iii) whether the changes in the word-order patterns in the history of the Romance languages can be captured as yet another instance of grammaticalisation. By means of a uniform methodology and statistical analysis of novel data, it is claimed that: (a) Old Romance does not possess a Germanic V2; (b) there is variation in terms of word order among Old Romance languages, which is shown to be linked to the individual history of the languages; (c) V2 order is mostly an epiphenomenon of the discourse mechanisms and the nature of the left functional field in these languages.
Changes of Functional Brain Networks in Major Depressive Disorder: A Graph Theoretical Analysis of Resting-State fMRI

Recent developments in graph theory have heightened the need for investigating the disruptions in the topological structure of functional brain network in major depressive disorder (MDD). In this study, we employed resting-state functional magnetic resonance imaging (fMRI) and graph theory to examine the whole-brain functional networks among 42 MDD patients and 42 healthy controls. Our results showed that compared with healthy controls, MDD patients showed higher local efficiency and modularity. Furthermore, MDD patients showed altered nodal centralities of many brain regions, including hippocampus, temporal cortex, anterior cingulate gyrus and dorsolateral prefrontal gyrus, mainly located in default mode network and cognitive control network. Together, our results suggested that MDD was associated with disruptions in the topological structure of functional brain networks, and provided new insights concerning the pathophysiological mechanisms of MDD.
Modeling shared care plans using CONTsys and openEHR to support shared homecare of the elderly

This case report describes how two complementary standards, CONTsys (European Standard EN 13940-1 for continuity of care) and the reference model of openEHR, were applied in modeling a shared care plan for shared homecare based on requirements from the OLD@HOME project. Our study shows that these requirements are matched by CONTsys on a general level. However, certain attributes are not explicit in CONTsys, for example agents responsible for performing planned interventions, and support for monitoring outcome of interventions. We further studied how the care plan conceptual model can be implemented using the openEHR reference model. The study demonstrates the feasibility of developing shared care plans combining a standard concept model, for example CONTsys with an electronic health records (EHR) interoperability specification, that is the openEHR, while highlighting areas that need further exploration. It also explores the reusability of existing clinical archetypes as building blocks of care plans and the modeling of new shared care plan archetypes.
Uniform first-order definitions in finitely generated fields

We prove that there is a first-order sentence in the language of rings that is true for all finitely generated fields of characteristic 0 and false for all fields of characteristic >0. We also prove that for each n in N, there is a first-order formula psi_n(x_1,.,x_n) that when interpreted in a finitely generated field K is true for elements x_1,. ,x_n in K if and only if the elements are algebraically dependent over the prime field in K.
3D Proximal Tubule Tissues Recapitulate Key Aspects of Renal Physiology to Enable Nephrotoxicity Testing

Due to its exposure to high concentrations of xenobiotics, the kidney proximal tubule is a primary site of nephrotoxicity and resulting attrition in the drug development pipeline. Current pre-clinical methods using 2D cell cultures and animal models are unable to fully recapitulate clinical drug responses due to limited in vitro functional lifespan, or species-specific differences. Using Organovo's proprietary 3D bioprinting platform, we have developed a fully cellular human in vitro model of the proximal tubule interstitial interface comprising renal fibroblasts, endothelial cells, and primary human renal proximal tubule epithelial cells to enable more accurate prediction of tissue-level clinical outcomes. Histological characterization demonstrated formation of extensive microvascular networks supported by endogenous extracellular matrix deposition. The epithelial cells of the 3D proximal tubule tissues demonstrated tight junction formation and expression of renal uptake and efflux transporters; the polarized localization and function of P-gp and SGLT2 were confirmed. Treatment of 3D proximal tubule tissues with the nephrotoxin cisplatin induced loss of tissue viability and epithelial cells in a dose-dependent fashion, and cimetidine rescued these effects, confirming the role of the OCT2 transporter in cisplatin-induced nephrotoxicity. The tissues also demonstrated a fibrotic response to TGFβ as assessed by an increase in gene expression associated with human fibrosis and histological verification of excess extracellular matrix deposition. Together, these results suggest that the bioprinted 3D proximal tubule model can serve as a test bed for the mechanistic assessment of human nephrotoxicity and the development of pathogenic states involving epithelial-interstitial interactions, making them an important adjunct to animal studies.