Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health.

Functional Food Ingredients Against Colorectal Cancer is one of the first European Union funded Research Projects at the cross-road of functional genomics [comprising transcriptomics, the measurement of the expression of all messengers RNA (mRNAs) and proteomics, the measurement of expression/state of all proteins], nutrition and human health. The goal of Functional Food Ingredients Against Colorectal Cancer is to develop a colon epithelial cell line-based screening assay for nutrients with presumed anti-colorectal carcinogenic properties. Genes involved in colon carcinogenesis are identified at the RNA and protein level, using a variety of methods (subtractive hybridisation, DNA microarray, proteomics) in combination with models for colorectal cancer development (human biopsies, rat model for colorectal carcinogenesis, colorectal cancer epithelial cell lines). Secondly, colorectal cancer epithelial cell lines are selected, in terms of their capacity to undergo gene/protein expression changes representing different phases in the colorectal carcinogenesis. Thirdly, these cell lines are used to determine the effects of nutrients with presumed anti-carcinogenic properties (e.g. resveratrol, flavonoids) on functional genomics-derived endpoints. Once validated against the effects of these nutrients in in vivo animal models and classical biomarkers for colorectal carcinogenesis, these cell line models combined with functional genomics represent useful tools to study colorectal carcinogenesis and screen for nutrients with anti-carcinogenic properties.
Incidence and Prevalence of Childhood Obesity in Tehran, Iran in 2011

Background: The aim of this study was to determine the incidence and prevalence of obesity in Tehranian children. Methods: Data from children participated in Tehran Lipid and Glucose Study (TLGS) were evaluated. Cut off points for definition of obesity was the CDC’s standard thresholds of the 95th percentile and 85th percentile for overweight. Prevalence, annual incidence of obesity, cumulative incidence over 10 year and the incidence density (cases per person-years) totally were calculated. Results: The annual incidence of obesity was 1.9 and 3.4% per year in the first 3 yr and decreased to 0.9 and 2.5% in the last 3 yr of follow-up in girls and boys, respectively. Incidence density rates were in line with cumulative incidence, with a rate of 20.7 per 1000 person-years between the ages of 5.6 and 15.5 yr. The prevalence of obesity was higher among children who had obese parents (P=0.03). Among all ages, across the quartiles of parents’ BMI, the prevalence of obesity increased with rising in paternal (P=0.001) or maternal BMI (P=0.004). Physical activity of mothers affected the prevalence of obesity in children at mean ages of 5.3 and 9.1 yr. Across quartiles of mother’s physical activity, from heavy to light, the prevalence of obesity increased among children, from 4.4% to 5.9% in children, aged 5.3 (P=0.02) and from 11.6% to 13.0% in children, aged 9.1 yr (P=0.03). Conclusion: Prevalence of obesity among children increased with age. Cumulative incidence of obesity in children who were overweight at baseline was much higher than other children.
Control in time and space: Tramtrack69 cooperates with Notch and Ecdysone to repress ectopic fate and shape changes during Drosophila egg chamber maturation

Organ morphogenesis requires cooperation between cells, which determine their course of action based upon location within a tissue. Just as important, cells must synchronize their activities, which requires awareness of developmental time. To understand how cells coordinate behaviors in time and space, we analyzed Drosophila egg chamber development. We found that the transcription factor Tramtrack69 (TTK69) controls the fates and shapes of all columnar follicle cells by integrating temporal and spatial information, restricting characteristic changes in morphology and expression that occur at stage 10B to appropriate domains. TTK69 is required again later in oogenesis: it controls the volume of the dorsal-appendage (DA) tubes by promoting apical re-expansion and lateral shortening of DA-forming follicle cells. We show that TTK69 and Notch compete to repress each other's expression and that a local Ecdysone signal is required to shift the balance in favor of TTK69. We hypothesize that TTK69 then cooperates with spatially restricted co-factors to define appropriate responses to a globally available (but as yet unidentified) temporal signal that initiates the S10B transformations.
Slit2 and Robo3 modulate the migration of GnRH-secreting neurons

Gonadotropin-releasing hormone (GnRH) neurons are born in the nasal placode and migrate along olfactory and vomeronasal axons to reach the forebrain and settle in the hypothalamus, where they control reproduction. The molecular cues that guide their migration have not been fully identified, but are thought to control either cell movement directly or the patterning of their axonal substrates. Using genetically altered mouse models we show that the migration of GnRH neurons is directly modulated by Slit2 and Robo3, members of the axon guidance Slit ligand and Robo receptor families. Mice lacking Slit2 or Robo3 have a reduced number of GnRH neurons in the forebrain, but a normal complement of their supporting axons, pointing to a direct role for these molecules in GnRH neuron migration.
Mitochondrial genome nucleotide substitution pattern between domesticated silkmoth, Bombyx mori, and its wild ancestors, Chinese Bombyx mandarina and Japanese Bombyx mandarina

Bombyx mori and Bombyx mandarina are morphologically and physiologically similar. In this study, we compared the nucleotide variations in the complete mitochondrial (mt) genomes between the domesticated silkmoth, B. mori, and its wild ancestors, Chinese B. mandarina (ChBm) and Japanese B. mandarina (JaBm). The sequence divergence and transition mutation ratio between B. mori and ChBm are significantly smaller than those observed between B. mori and JaBm. The preference of transition by DNA strands between B. mori and ChBm is consistent with that between B. mori and JaBm, however, the regional variation in nucleotide substitution rate shows a different feature. These results suggest that the ChBm mt genome is not undergoing the same evolutionary process as JaBm, providing evidence for selection on mtDNA. Moreover, investigation of the nucleotide sequence divergence in the A+T-rich region of Bombyx mt genomes also provides evidence for the assumption that the A+T-rich region might not be the fastest evolving region of the mtDNA of insects.
Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design

Biologically relevant macromolecules, such as proteins, do not operate as static, isolated entities. On the contrary, they are involved in numerous interactions with other species, such as proteins, nucleic acid, membranes, small molecule ligands, and also, critically, solvent molecules. These interactions often display a remarkable degree of specificity and high affinity. Fundamentally, the biological processes rely on molecular organisation and recognition events. Binding between two interacting partners has both enthalpic (H) and entropic (-TS) components, which means the recognition event is associated with changes of both the structure and dynamics of each counterpart. Like any other spontaneous process, binding occurs only when it is associated with a negative Gibbs' free energy of binding ( G  ), which may have differing thermodynamic signatures, varying from enthalpyto entropy-driven. Thus, the understanding of the forces driving the recognition and interaction require a detailed description of the binding thermodynamics, and a correlation of the thermodynamic parameters with the structures of interacting partners. Such an understanding of the nature of the recognition phenomena is of a great importance for medicinal chemistry and material research, since it enables truly rational structure-based molecular design. This chapter is organised in the following way. The first part of it introduces general principles which govern macromolecular associations under equilibrium conditions: the free energy of binding and its enthalpic and entropic components, the contributions from both interacting partners, interaction energy of the association, and specific types of interactions – such as hydrogen bonding or van der Waals interactions, ligand and protein flexibility, and ultimately solvent effects (e.g. solute-solvent interactions, solvent reorganisation). The second part is dedicated to methods applied to assess particular contributions, experimental as well as computational. Specifically, there will be a focus on isothermal titrational calorimetry (ITC), solution nuclear magnetic resonance (NMR), and a discussion of computational approaches to the estimation of enthalpic and entropic contributions to the binding free energy. I will discuss the applicability of these methods, the approximations behind them, and their limitations. In the third part of this chapter, I will provide the reader several examples of ligand-protein interactions and focus on the forces driving the associations, which can be very different from case to case. Finally, I will address several practical aspects of assessing the thermodynamic parameters in molecular design, the
Learning Semantic Representations for the Phrase Translation Model

This paper presents a novel semantic-based phrase translation model. A pair of source and target phrases are projected into continuous-valued vector representations in a low-dimensional latent semantic space, where their translation score is computed by the distance between the pair in this new space. The projection is performed by a multi-layer neural network whose weights are learned on parallel training data. The learning is aimed to directly optimize the quality of end-to-end machine translation results. Experimental evaluation has been performed on two Europarl translation tasks, English-French and German-English. The results show that the new semantic-based phrase translation model significantly improves the performance of a state-of-the-art phrase-based statistical machine translation sys-tem, leading to a gain of 0.7-1.0 BLEU points.
Immunoproteomics and immunoinformatics analysis of Cryptococcus gattii: novel candidate antigens for diagnosis.

AIM To identify immunoreactive proteins of Cryptococcus gattii genotype VGII and their B-cell epitopes. MATERIALS & METHODS We combined 2D gel electrophoresis, immunoblotting and mass spectrometry to identify immunoreactive proteins from four strains of C. gattii genotype VGII (CG01, CG02, CG03 and R265). Next, we screened the identified proteins to map B-cell epitopes. RESULTS Sixty-eight immunoreactive proteins were identified. The strains and the number of proteins we found were: CG01 (12), CG02 (12), CG03 (18) and R265 (26). In addition, we mapped 374 peptides potentially targeted by B cells. CONCLUSION Both immunoreactive proteins and B-cell epitopes of C. gattii genotype VGII that were potentially targeted by a host humoral response were identified. Considering the evolutionary relevance of the identified proteins, we may speculate that they could be used as the initial targets for recombinant protein and peptide synthesis aimed at the development of immunodiagnostic tools for cryptococcosis.
Recursive Hashing and One-Pass, One-Hash n-Gram Count Estimation

Many applications use sequences of n consecutive symbols (n-grams). We review n-gram hashing and prove that recursive hash families are pairwise independent at best. We prove that hashing by irreducible polynomials is pairwise independent whereas hashing by cyclic polynomials is quasi-pairwise independent: we make it pairwise independent by discarding n− 1 bits. One application of hashing is to estimate the number of distinct n-grams, a view-size estimation problem. While view sizes can be estimated by sampling under statistical assumptions, we desire a statistically unassuming algorithm with universally valid accuracy bounds. Most related work has focused on repeatedly hashing the data, which is prohibitive for large data sources. We prove that a one-pass onehash algorithm is sufficient for accurate estimates if the hashing is sufficiently independent. For example, we can improve by a factor of 2 the theoretical bounds on estimation accuracy by replacing pairwise independent hashing by 4-wise independent hashing. We show that recursive random hashing is sufficiently independent in practice. Maybe surprisingly, our experiments showed that hashing by cyclic polynomials, which is only quasi-pairwise independent, sometimes outperformed 10-wise independent hashing while being twice as fast. For comparison, we measured the time to obtain exact n-gram counts using suffix arrays and show that, while we used hardly any storage, we were an order of magnitude faster. The experiments used a large collection of English text from Project Gutenberg as well as synthetic data.
The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma

Five years after the last prostatic carcinoma grading consensus conference of the International Society of Urological Pathology (ISUP), accrual of new data and modification of clinical practice require an update of current pathologic grading guidelines. This manuscript summarizes the proceedings of the ISUP consensus meeting for grading of prostatic carcinoma held in September 2019, in Nice, France. Topics brought to consensus included the following: (1) approaches to reporting of Gleason patterns 4 and 5 quantities, and minor/tertiary patterns, (2) an agreement to report the presence of invasive cribriform carcinoma, (3) an agreement to incorporate intraductal carcinoma into grading, and (4) individual versus aggregate grading of systematic and multiparametric magnetic resonance imaging-targeted biopsies. Finally, developments in the field of artificial intelligence in the grading of prostatic carcinoma and future research perspectives were discussed.
Cloning and characterization of the Salmonella typhimurium ada gene, which encodes O6-methylguanine-DNA methyltransferase

The ada gene of Escherichia coli encodes O6-methylguanine-DNA methyltransferase, which serves as a positive regulator of the adaptive response to alkylating agents and as a DNA repair enzyme. The gene which can make an ada-deficient strain of E. coli resistant to the cell-killing and mutagenic effects of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) has been cloned from Salmonella typhimurium TA1538. DNA sequence analysis indicated that the gene potentially encoded a protein with a calculated molecular weight of 39,217. Since the nucleotide sequence of the cloned gene shows 70% similarity to the ada gene of E. coli and there is an ada box-like sequence (5'-GAATTAAAACGCA-3') in the promoter region, we tentatively refer to this cloned DNA as the adaST gene. The gene encodes Cys-68 and Cys-320, which are potential acceptor sites for the methyl group from the damaged DNA. The multicopy plasmid carrying the adaST gene significantly reduced the frequency of mutation induced by MNNG both in E. coli and in S. typhimurium. The AdaST protein encoded by the plasmid increased expression of the ada'-lacZ chromosome fusion about 5-fold when an E. coli strain carrying both the fusion operon and the plasmid was exposed to a low concentration of MNNG, whereas the E. coli Ada protein encoded by a low-copy-number plasmid increased it about 40-fold under the same conditions. The low ability of AdaST to function as a positive regulator could account for the apparent lack of an adaptive response to alkylation damage in S. typhimurium.
DISTURBANCE OBSERVER BASED CLOSED LOOP FORCE CONTROL FOR HAPTIC FEEDBACK

Most commonly used impedance-type haptic interfaces employ open-loop force control under the assumption of pseudostatic interactions. Advanced force control in such interfaces can increase simulation fidelity through improvement of the transparency of the device, and can further improve robustness. However, closed loop force-feedback is limited both due to the bandwidth limitations of force sensing and the associated cost of force sensors required for its implementation. In this paper, we propose the use of a nonlinear disturbance observer for estimation of contact forces during haptic interactions. This approach circumvents the traditional drawbacks of force sensing while exhibiting the advantages of closed-loop force control in haptic devices. The feedback of contact force information further enables implementation of advanced robot force control techniques such as robust hybrid impedance and admittance control. Simulation and experimental results, utilizing a PHANToM Premium 1.0A haptic interface, are presented to demonstrate the efficacy of the proposed approach.
Evaluating Efficiency‐Equality Tradeoffs for Mobile Source Control Strategies in an Urban Area

In environmental risk management, there are often interests in maximizing public health benefits (efficiency) and addressing inequality in the distribution of health outcomes. However, both dimensions are not generally considered within a single analytical framework. In this study, we estimate both total population health benefits and changes in quantitative indicators of health inequality for a number of alternative spatial distributions of diesel particulate filter retrofits across half of an urban bus fleet in Boston, Massachusetts. We focus on the impact of emissions controls on primary fine particulate matter (PM2.5) emissions, modeling the effect on PM2.5 concentrations and premature mortality. Given spatial heterogeneity in baseline mortality rates, we apply the Atkinson index and other inequality indicators to quantify changes in the distribution of mortality risk. Across the different spatial distributions of control strategies, the public health benefits varied by more than a factor of two, related to factors such as mileage driven per day, population density near roadways, and baseline mortality rates in exposed populations. Changes in health inequality indicators varied across control strategies, with the subset of optimal strategies considering both efficiency and equality generally robust across different parametric assumptions and inequality indicators. Our analysis demonstrates the viability of formal analytical approaches to jointly address both efficiency and equality in risk assessment, providing a tool for decisionmakers who wish to consider both issues.
Performance analysis of a hierarchical quorum consensus algorithm for replicated objects

A class of algorithms for synchronizing a large number of identical copies of an object is described, and its performance is evaluated. The method is based on organizing a group of objects into a multilevel hierarchy and extending the quorum consensus algorithm to such an environment. The performance of the algorithm is compared, in terms of availability and message cost, with that of two other methods, majority voting and dynamic voting using a simulation model. Although the author's method uniformly outperforms the other two methods in terms of average message cost, no single method is found to dominate in terms of availability. The conditions under which each method performs well are identified. <<ETX>>
Neural Basis of Empathy and Its Dysfunction in Autism Spectrum Disorders (ASD)

Abstract : The most human of emotions are defined by how we feel about others. Such other-regarding preferences (ORP), in the parlance of economics, both permit and necessitate the institutions that form the core of modern society. Abnormal functionalities associated with ORP in the brain are also thought to be a critical component underlying neuropsychiatric disorders marked by social deficits. The primary objectives of the research project are to develop an animal model of ORP (Objective 1), and investigate the functional contributions of the brain circuits (Objectives 2-3) and neuropeptide oxytocin (OT) (Objective 4). We have successfully developed a rhesus macaque model of ORP and demonstrated that rhesus monkeys care about rewards delivered to another monkey (Chang et al., 2011). We then for the first time demonstrated that inhaled OT using a pediatric nebulizer effectively reaches the central nervous system of rhesus macaques, providing a proof of concept for a clinical OT treatment method well-tolerated by children. Subsequently, we showed the inhaled OT promotes prosocial preferences and social gaze rates (Chang et al., 2012). Furthermore, we have recorded single neuron activity from OFC as well as the anterior cingulate sulcus (ACCs) and gyrus (ACCg) during the ORP task (Chang and Platt, 2013). Finally, we have inactivated OFC and ACCg and found differential causal contribution to social behaviors between these brain regions. Our results begin to elucidate neural mechanisms underlying ORP and open up future research aimed at understanding how therapeutic OT treatments in individuals with autism spectrum disorders work in their brains.
Combined static and dynamic variance adaptation for efficient interconnection of speech enhancement pre-processor with speech recognizer

It is well known that automatic speech recognition performs poorly in presence of noise or reverberation. Much research has been undertaken on model adaptation and speech enhancement to increase the robustness of speech recognizers. Model adaptation is effective to remove static mismatch between speech features and acoustic model parameters, but may not cope well with dynamic mismatch. Speech enhancement approaches can reduce dynamic perturbations, but often do not interconnect well with speech recognizer. There seems to be a lack of optimal way to combine these two approaches. In this paper we propose introducing the dynamic capabilities of speech enhancement into a static adaptation scheme. We focus on variance adaptation, and propose a novel parametric variance model that includes static and dynamic components. The dynamic component is derived from a speech enhancement pre-process, and the parameters of the model are optimized using an adaptive training scheme. An evaluation of the method with a speech dereverberation for preprocessing revealed that a 80 % relative error rate reduction was possible compared with the recognition of dereverberated speech, and the final error rate was 5.4 % which is close to that of clean speech (1.2%).
Smart sensing technology: opportunities and challenges

‘Smart’ sensors with embedded microprocessors and wireless communication links have the potential to change fundamentally the way civil infrastructure systems are monitored, controlled, and maintained. Indeed, a 2002 National Research Council report noted that the use of networked systems of embedded computers and sensors throughout society could well dwarf all previous milestones in the information revolution. However, a framework does not yet exist that can allow the distributed computing paradigm offered by smart sensors to be employed for structural health monitoring and control systems; current algorithms assume that all data is centrally collected and processed. Such an approach does not scale to systems with densely instrumented arrays of sensors that will be required for the next generation of structural health monitoring and control systems. This paper provides a brief introduction to smart sensing technology and identifies some of the opportunities and associated challenges. Copyright © 2004 John Wiley & Sons, Ltd.