Miracle-dz/UniFAR-FTUs huggingface dataset:
Tools for Gene-Regulatory Analyses in the Marine Annelid Platynereis dumerilii

The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species.
L'impact de la solidarité familiale sur le niveau de vie et la pauvreté des personnes âgées au Mali

Si la solidarité « privée » est perçue comme très vivace en Afrique, la solidarité « publique », à travers un système de protection sociale des personnes vulnérables ou pauvres, est quasiment inexistante. La solidarité « privée » ou familiale se manifeste, au quotidien, par l'entraide, les visites, la mobilisation de tous les membres lors des événements heureux (mariage, naissance, etc.) ou malheureux (décès, maladies, etc.). Elle se traduit aussi par des transferts, en espèces ou en nature, entre les membres de la parentèle. Dans quelle mesure cette solidarité palie-t-elle efficacement à l'atonie de la solidarité publique, en particulier envers les personnes âgées ? Telle est la question principale de cette recherche. Nous mobilisons les données d'une enquête ménage réalisée au Mali en 2006. Les résultats montrent que les mécanismes de solidarité familiale ne semblent pas suffisants pour lutter efficacement contre la pauvreté des seniors. In Africa, a public social protection system that protects vulnerable or impoverished individuals is practically non-existent. On the other hand, everyday “private” protection is evident in interactions between family members at gatherings (such as marriages, funerals or births), visits, or in material exchanges. This leads to the following question: to what extent is this “private” solidarity successful in aiding the Malian population, particularly the elderly? Using data from a survey conducted in Mali in 2006, the author argues that familial ties do not appear to be sufficient or effective in alleviating the poverty experienced by the elderly in Mali.
Problems, communications, and common sense

Problem solving in the real world is a more general issue than what is currently understood under this notion in the majority of today's AI publications. Particularly, finding an appropriate formal representation of a given problem in the real world is very difficult even for humans. We think that this is reminiscent of the core difficulty of knowledge acquisition for knowledge acquisition for knowledge-based systems, i.e. modeling the real world. If a machine is to understand problem statements in natural language, much commonsense knowledge must be available. However, even if it were available, it would be very difficult to retrieve those chunks of knowledge necessary for the problem at hand. We propose a view of presenting a problem to a problem solver as an act of communication, which may provide hints for finding such knowledge.
The effects of school social mix: unpacking the differences

Whether school composition makes a difference for student outcomes has been the subject of much controversy. This article draws on Growing Up in Ireland data, a rich source of information on nine-year-old children along with the characteristics of their school and classroom teacher. In contrast to many studies which rely on a single measure of social background, the use of a range of measures (including social class, parental education and income) allows us to provide precise estimates of differences in performance between schools designated as disadvantaged and other schools. The analyses also provide new insights into the processes underlying such differences. Only the most disadvantaged schools, those in Urban Band 1, are found to have a contextual effect for both reading and mathematics. This achievement gap is found to reflect differences in teacher experience and turnover, the concentration of additional learning needs, absenteeism levels and children's engagement in school.
Body composition in male physical education university students in view of their physical activity level

Purpose. Body composition and fat distribution is specific for particular populations and social groups. However, one factor that significantly affects body composition is physical activity. The aim of the study was to assess the various components of body composition in male physical education students with regard to their physical activity level. Methods. A detailed questionnaire survey on physical activity was administered to 252 male students. Based on their responses, the participants were placed into two groups engaged in either moderate or vigorous physical activity. Anthropometric measurements included measures of body height and mass and also skinfold thickness. Body composition was assessed by bioelectrical impedance analysis. Statistical analysis was performed by comparing the groups’ mean values, standard deviations, and percentages of the components of body composition. Results. The groups did not differ significantly for mean body height and mass. No statistically significant differences were found in the absolute amounts of the various components of body composition (except for fat mass) between the groups. Both groups had 61.5 kg of fat-free mass (constituting 80.6% of body mass for the vigorously active and 78.7% of body mass for the moderately active students) and both had 44 kg of muscle mass (constituting 58.3% and 56.1% of body mass, respectively). Students who declared to be involved in vigorous physical activity had 2 kg less and 2% lower fat mass than those involved in moderate physical activity (based on BIA measurements). Measures of skinfold thickness found more subcutaneous fat tissue in the vigorously active group, but the use of a fat index based on body height found them to present less fat. Conclusions. The difference in fat content between physical education students who were more or less physically active was found to be 2 kg and 2%. The results found that physical activity level was not associated with body height, body mass, and the absolute amounts of the other studied components of body composition.
Single-value combinatorial auctions and algorithmic implementation in undominated strategies

In this article, we are interested in general techniques for designing mechanisms that approximate the social welfare in the presence of selfish rational behavior. We demonstrate our results in the setting of Combinatorial Auctions (CA). Our first result is a general deterministic technique to decouple the algorithmic allocation problem from the strategic aspects, by a procedure that converts any algorithm to a dominant-strategy ascending mechanism. This technique works for any single value domain, in which each agent has the same value for each desired outcome, and this value is the only private information. In particular, for “single-value CAs”, where each player desires any one of several different bundles but has the same value for each of them, our technique converts any approximation algorithm to a dominant strategy mechanism that almost preserves the original approximation ratio. Our second result provides the first computationally efficient deterministic mechanism for the case of single-value multi-minded bidders (with private value and private desired bundles). The mechanism achieves an approximation to the social welfare which is close to the best possible in polynomial time (unless P=NP). This mechanism is an algorithmic implementation in undominated strategies, a notion that we define and justify, and is of independent interest.
IWantPrivacy : Widespread Violation of Privacy Settings in the Twitter Social Network

Twitter is a social network that focuses on creating and sharing short 140 character messages know as tweets. Twitter’s sole privacy policy is a binary option that either allows every message a user creates to be publicly available, or allows only a user’s followers to see posted messages. As the Twitter community grew, conventions organically formed that allowfor rich expressiveness with only 140 characters. Repeating wh at someone else says is called retweeting; this behavior facilitates the spread of information and commentary in real-time. We have performed a large-scale collection of data from the Twitter social network by means of the publicly available application programming interface (API) they provide. Our data set contains over 2.7 billion messages, 80 million user profi les, and a 2.6 billion edge social network. We analyze these data and uncover the growing trend where users defeat Twitter’s simple privacy mechanism of “protecting one’s tweets” by si mply retweeting a protected tweet. We have shown through quantitative and qualitative analysi s that these privacy-violating retweets are a growing problem. More than 4.42 million tweets exist in our corpus that expose protected information. As Twitter gains popularity over ti me, we see an increasing trend in the number of privacy-violating retweets. Although there are many users who are unaware that their private tweets are being broadcast to the public, ther e are some who are aware of this problem.
Behavioral analysis of CREB αΔ mutation on a B6/129 F1 hybrid background

The cyclic AMP (cAMP)‐response element binding protein (CREB) is an activity‐dependent transcription factor that plays a role in synaptic plasticity and memory storage in Aplysia, Drosophila, and rodents. Mice with targeted deletions of two CREB isoforms (α and Δ; CREB αΔ mice) have been characterized on a mixed genetic background of C57BL/6 (B6) and 129/SvEv (129), as well as on a defined F1 hybrid of B6 and FVB/N, and these results suggest that the phenotype of CREB αΔ mice depends critically on genetic background. In an examination of the hypothesis that the role of CREB in learning and memory can be influenced by strain differences, we analyzed mice with the CREB αΔ mutation on an F1 hybrid background of B6 and 129 strains. CREB αΔ mice on this background had impaired short‐term and long‐term cued and contextual fear conditioning and normal spatial learning in the Morris water maze. Our results suggest that at least some aspects of hippocampal function are normal in CREB αΔ mice, and that CREB αΔ mice on the B6/129 F1 background have alterations in amygdala function. These studies underscore the importance of controlling for genetic background in the behavioral analysis of knockout and transgenic mice. Hippocampus 2002;12:18–26. © 2002 Wiley‐Liss, Inc.
AP1B sorts basolateral proteins in recycling and biosynthetic routes of MDCK cells

The epithelial-specific adaptor AP1B sorts basolateral proteins, but the trafficking routes where it performs its sorting role remain controversial. Here, we used an RNAi approach to knock down the medium subunit of AP1B (μ1B) in the prototype epithelial cell line Madin–Darby canine kidney (MDCK). μ1B-knocked down MDCK cells displayed loss of polarity of several endogenous and exogenous basolateral markers transduced via adenovirus vectors, but exhibited normal polarity of apical markers. We chose two well characterized basolateral protein markers, the transferrin receptor (TfR) and the vesicular stomatitis virus G protein, to study the sorting role of AP1B. A surface-capture assay introduced here showed that μ1B-knocked down MDCK cells plated on filters at confluency and cultured for 4.5 d, sorted TfR correctly in the biosynthetic route but incorrectly in the recycling route. In contrast, these same cells missorted vesicular stomatitis virus G apically in the biosynthetic route. Strikingly, recently confluent MDCK cells (1–3 d) displayed AP1B-dependence in the biosynthetic route of TfR, which decreased with additional days in culture. Sucrose density gradient analysis detected AP1B predominantly in TfR-rich endosomal fractions in MDCK cells confluent for 1 and 4 d. Our results are consistent with the following model: AP1B sorts basolateral proteins in both biosynthetic and recycling routes of MDCK cells, as a result of its predominant functional localization in recycling endosomes, which constitute a post-Golgi station in the biosynthetic route of some plasma membrane proteins. TfR utilizes a direct route from Golgi to basolateral membrane that is established as the epithelial monolayer matures.
Application of Pharmaceutical QbD for Enhancement of the Solubility and Dissolution of a Class II BCS Drug using Polymeric Surfactants and Crystallization Inhibitors: Development of Controlled-Release Tablets

The aim of this study was to apply quality by design (QbD) for pharmaceutical development of felodipine solid mixture (FSM) containing hydrophilic carriers and/or polymeric surfactants, for easier development of controlled-release tablets of felodipine. The material attributes, the process parameters (CPP), and the critical quality attributes of the FSMs were identified. Box–Behnken experimental design was applied to develop space design and determine the control space of FSMs that have maximum solubility, maximum dissolution, and ability to inhibit felodipine crystallization from supersaturated solution. Material attributes and CPP studied were the amount of hydroxypropyl methylcellulose (HPMC; X1), amount of polymeric surfactants Inutec®SP1 (X2), amount of Pluronic®F-127 (X3) and preparation techniques, physical mixture (PM) or solvent evaporation (SE; X4). There is no proposed design space formed if the Pluronic® content was below 45.1 mg and if PM is used as the preparation technique. The operating ranges, for robust development of FSM of desired quality, of Pluronic®, Inutec®SP1, HPMC, and preparation technique, are 49–50, 16–23, 83–100 mg, and SE, respectively. The calculated value of f2 was 56.85, indicating that the release profile of the controlled-release (CR) tablet (CR-6) containing the optimized in situ-formed FSM was similar to that of the target release profile. Not only did the ternary mixture of Pluronic®, HPMC with Inutec®SP1 enhance the dissolution rate and inhibit crystallization of felodipine, but also they aided Carbopol®974 in controlling felodipine release from the tablet matrix. It could be concluded that a promising once-daily CR tablets of felodipine was successfully designed using QbD approach.
Vehicle following control design for automated highway systems

The purpose of this paper is to design and test a vehicle control system in order to achieve full vehicle automation in the longitudinal direction for several modes of operation, where the infrastructure manages the vehicle following. These modes include autonomous vehicles, cooperative vehicle following and platooning. The vehicle control system consists of a supervisory controller that processes the inputs from the driver, the infrastructure, other vehicles and the on-board sensors and sends the appropriate commands to the brake and throttle controllers. In addition, the controller makes decisions about normal, emergency and transition operations. Simulation results of some of the basic vehicle following manoeuvres are used to verify the claimed performance of the designed controllers.
The Evolving Impact of the Ogallala Aquifer: Agricultural Adaptation to Groundwater and Climate

Agriculture on the American Great Plains has been constrained by historical water scarcity. After World War II, technological improvements made groundwater from the Ogallala aquifer available for irrigation. Comparing counties over the Ogallala with nearby similar counties, groundwater access increased irrigation intensity and initially reduced the impact of droughts. Over time, land-use adjusted toward water-intensive crops and drought-sensitivity increased; conversely, farmers in water-scarce counties maintained drought-resistant practices that fully mitigated higher drought-sensitivity. Land values capitalized the Ogallala's value at $26 billion in 1974; as extraction remained high and water levels declined, the Ogallala's value fell to $9 billion in 2002.
Content Based Routing with Elvin4

Building on experience with a general-purpose notification service, we describe the design and implementation of a second-generation content-based messaging system. Elvin4 includes a novel security framework, internationalisation, a powerful subscription language, and a modular pluggable protocol stack. We discuss its evolution from previous versions, differences from related work, and describe the transition in underlying ideology from notification service to content-based routing and the effect this has had upon the
Acetaldehyde reinforcement and motor reactivity in newborns with or without a prenatal history of alcohol exposure

Animal models have shown that early ontogeny seems to be a period of enhanced affinity to ethanol. Interestingly, the catalase system that transforms ethanol (EtOH) into acetaldehyde (ACD) in the brain, is more active in the perinatal rat compared to adults. ACD has been found to share EtOH's behavioral effects. The general purpose of the present study was to assess ACD motivational and motor effects in newborn rats as a function of prenatal exposure to EtOH. Experiment 1 evaluated if ACD (0.35 μmol) or EtOH (0.02 μmol) supported appetitive conditioning in newborn pups prenatally exposed to EtOH. Experiment 2 tested if prenatal alcohol exposure modulated neonatal susceptibility to ACD's motor effects (ACD dose: 0, 0.35 and 0.52 μmol). Experiment 1 showed that EtOH and ACD supported appetitive conditioning independently of prenatal treatments. In Experiment 2, latency to display motor activity was altered only in neonates prenatally treated with water and challenged with the highest ACD dose. Prenatal EtOH experience results in tolerance to ACD's motor activity effects. These results show early susceptibility to ACD's appetitive effects and attenuation of motor effects as a function of prenatal history with EtOH, within a stage in development where brain ACD production seems higher than later in life.
Trimester specific reference intervals for thyroid function tests in normal Indian pregnant women

Context: Accurate assessment of thyroid function during pregnancy is critical, for initiation of thyroid hormone therapy, as well as for adjustment of thyroid hormone dose in hypothyroid cases. Aims: We evaluated pregnant women who had no past history of thyroid disorders and studied their thyroid function in each trimester. Settings and Design: 86 normal pregnant women in the first trimester of pregnancy were selected for setting reference intervals. All were healthy, euthyroid and negative for thyroid peroxidase antibody (TPOAb). These women were serially followed throughout pregnancy. 124 normal nonpregnant subjects were selected for comparison. Material and methods: Thyrotropin (TSH), free thyroxine (FT4), free triiodothyronine (FT3) and anti-TPO were measured using Roche Elecsys 1010 analyzer. Urinary iodine content was determined by simple microplate method. The 2.5th and 97.5th percentiles were calculated as the reference intervals for thyroid hormone levels during each trimester. Statistical Analysis: SPSS (version 14.0, SPSS Inc., Chicago, IL, USA) was used for data processing and analysis. Results: The reference intervals for the first, second and third trimesters for the following parameters: TSH 0.09-6.65, 0.51-6.66, 0.91-4.86 µIU/mL, FT4 9.81-18.53, 8.52-19.43, 7.39-18.28 pM/L and FT3 3.1-6.35, 2.39-5.12, 2.57-5.68 pM/L respectively. Thyroid hormone concentrations significantly differed during pregnancy at different stages of gestation. The pregnant women in the study had median urinary iodine concentration of 150-200 µg/l during each trimester. Conclusions: The trimester-specific reference intervals for thyroid tests during pregnancy have been established for pregnant Indian women serially followed during pregnancy using 2.5th and 97.5th percentiles.
Phenomics of cardiac chloride channels: the systematic study of chloride channel function in the heart

Recent studies have identified several chloride (Cl−) channel genes in the heart, including CFTR, ClC‐2, ClC‐3, CLCA, Bestrophin, and TMEM16A. Gene targeting and transgenic techniques have been used to delineate the functional role of cardiac Cl− channels in the context of health and disease. It has been shown that Cl− channels may contribute to cardiac arrhythmogenesis, myocardial hypertrophy and heart failure, and cardioprotection against ischaemia–reperfusion. The study of physiological or pathophysiological phenotypes of cardiac Cl− channels, however, may be complicated by the compensatory changes in the animals in response to the targeted genetic manipulation. Alternatively, tissue‐specific conditional or inducible knockout or knockin animal models may be more valuable in the phenotypic studies of specific Cl− channels by limiting the effect of compensation on the phenotype. The integrated function of Cl− channels may involve multi‐protein complexes of the Cl− channel subproteome and similar phenotypes can be attained from alternative protein pathways within cellular networks, which are influenced by genetic and environmental factors. Therefore, the phenomics approach, which characterizes phenotypes as a whole phenome and systematically studies the molecular changes that give rise to particular phenotypes achieved by modifying the genotype (such as gene knockouts or knockins) under the scope of genome/proteome/phenome, may provide a more complete understanding of the integrated function of each cardiac Cl− channel in the context of health and disease.
Chapter 1 BAYESIAN METHODS FOR TRACKING AND LOCALIZATION

This chapter presents a tutorial-type introduction to dynamic Bayesian networks (DBNs), which provide a computational framework for the analysis of stochastic dynamic systems. The first part of the chapter provides a short overview of the work on probabilistic state estimation and system identification. The second part presents two example applications where the DBNs lead to elegant algorithms: robot localization and tracking of multiple persons with multiple cameras.