Miracle-dz/UniFAR-FTUs huggingface dataset:
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni. cz/MotiveValidator.
The target spectrum of SdsR small RNA in Salmonella

Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these ‘core sRNAs’ of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σS and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.
Relationship Between Inter‐Arm Difference in Systolic Blood Pressure and Arterial Stiffness in Community‐Dwelling Older Adults

A significant inter‐arm difference in systolic blood pressure (IADSBP) has recently been associated with worse cardiovascular outcomes. The authors hypothesized that part of this association is mediated by arterial stiffness, and examined the relationship between significant IADSBP and carotid‐femoral pulse wave velocity (CF‐PWV) in a sample from the Baltimore Longitudinal Study of Aging. Of 1045 participants, 50 (4.8%) had an IADSBP ≥10 mm Hg at baseline, and 629 had completed data from ≥2 visits (for a total of 1704 visits during 8 years). CF‐PWV was significantly higher in patients with an IADSBP ≥10 mm Hg (7.3±1.9 vs 8.2±2, P=.002). Compared with others, patients with IADSBP ≥10 mm Hg also had higher body mass index, waist circumference, and triglycerides; higher prevalence of diabetes; and lower high‐density lipoprotein (HDL) cholesterol (P<.001 for all). A significant association with IADSBP ≥10 mm Hg was observed for CF‐PWV in both cross‐sectional (odds ratio [OR], 1.19; 95% confidence interval [CI], 1.06–1.87; P=.01) and longitudinal (OR, 1.15; 95% CI, 1.03–1.29; P=.01) multivariate analyses. Female sex, Caucasian race, high body mass index (plus diabetes and low HDL cholesterol only cross‐sectionally) were other independent correlates of IADSBP ≥10 mm Hg. Significant IADSBP is associated with increased arterial stiffness in community‐dwelling older adults.
An improved routing scheme for wireless sensor networks with Hybrid Energy Storage System

In This paper we proposed an improved routing metrics for wireless sensor networks (WSNs) based on Hybrid Energy Storage System (HESS) which merges Super capacitor (SC) and a Rechargeable Battery (RB). The proposed routing scheme assigns different metrics considering not only residual energy, harvesting rates and expected path length of next hop, but also the potential of the future hops. Simulations results show that the proposed scheme can obtain a better delivery of data packets while maintain low latency in some situation.
Usages des TIC pour la transmission des savoirs par des formateurs d'enseignants à l'ENS d'Abidjan

Cet article presente les resultats d'une etude qualitative portant sur les usages des TIC par des formateurs dans le cadre de la formation initiale des enseignants a l'Ecole normale superieure d'Abidjan. Neuf formateurs issus des departements des Sciences et Technologies, d'Histoire/Geographie et des Langues ont participe a la presente recherche. Les entretiens semidirectifs ont porte sur des usages des TIC que font ces formateurs dans le cadre de la formation initiale des enseignants a l'ENS d'Abidjan. Les divers usages mis en evidence peuvent etre regroupes dans la categorie des usages pedagogiques des TIC.
The morphological expression of temporality on the verb in French as a second language

Les recherches sur l’expression de la temporalité en langue seconde s’attachent depuis plusieurs décennies, à travers des perspectives diverses, à brosser un tab-leau des différentes étapes d’acquisition des moyens de référence à la temporalité, en fonction notamment des propriétés typologiques des langues source et cible de l’apprenant, et du contexte d’acquisition dans lequel se trouve ce dernier (milieu scolaire ou naturel, âge du début d’acquisition, etc.). Dans un premier temps, nous proposerons un bref bilan des principaux acquis du domaine, avant de présenter plus en détail le champ couvert dans ce numéro spécial qui porte tout particulièrement sur l’acquisition de la morphologie temporo-aspectuelle en français langue seconde (L2).
Adopted Adults Who Search for Background Information and Contact with Birth Relatives

As part of its work with adopters, adopted people and their birth relatives, the Children's Society Post-adoption and Care Counselling Research Project is engaged in a number of studies looking at adopted people's experiences of seeking background information and contact with birth relatives. Between 1988 and 1995, project workers provided advice and counselling beyond initial contact to 366 adopted people seeking information and possible reunion with a birth relative. In the following study, Julia Feast and David Howe analysed the agency's file records to determine the numbers and characteristics of adopted people who sought help from the project's counsellors. Findings are presented about the demographic characteristics of the adopted adults, their reasons for wanting the service, the type of contact established with a birth relative and the quality of relationship with their adoptive parents.
Gender and the State: Accommodating Difference and Equality

Most would concur that the American state, from its very founding and still today, builds upon liberal principles asserting the fundamental equality of all individuals. What is more, social movements have been successful in demanding that the state treat all individuals the same “in spite of” their group differences, thereby promoting the inclusion of people initially discriminated against on the basis of their group difference. This is no small task, as history tells us. For example, we have recently celebrated the 50th anniversary of the March on Washington and the Civil Rights Movement, which exemplify the demand for equal treatment of individuals “in spite of” their race. John Lewis, an African-American civil rights activist, testifies, for example, as to how difficult this was, based on his experience fifty years ago. When he traveled during those times, he ran into racial segregation everywhere, including housing, hotels, restaurants, and public restrooms. His goal was desegregation—that is, to integrate public facilities so that all individuals would have access on equal bases with everyone else (Stolberg 2013).
Partial Automation of Sensitivity Analysis by Mutant Schemata Approach

According to Voas et al. testability is defined as the ease with in which faults may manifest themselves as failures when the software undergoes the testing process [39]. They also went further by introducing an approach for measuring sensitivity in terms of estimates from Propagation, Infection, and Execution (PIE) analyses of software and calculating the testability of a program through sensitivity estimate. Their testability calculations ‘by hand’ to determine the stability of the PIE analysis technique had drawbacks such as more time-consuming, high cost and less precision in the overall results [4]. Particularly the infection analysis part is one of the most expensive, sophisticated and time-consuming component of the PIE analysis technique. In order to solve this problem an investigation has been carried out by the author for establishing the feasibility of automating (or partially automating) the PIE analysis technique by means of a fast, and computationally less expensive Mutant Schemata Generation (MSG) approach [2]. An MSG-Infection tool has been developed to automate PIE analyses partially. This paper explains the use of MSG-Infection tool in automating the sensitivity analysis of C-programs and presents the results demonstrating the performance improvements achieved due to the MSG-Approach.
Identification of Genetic Variants in Endothelial Lipase in Persons With Elevated High-Density Lipoprotein Cholesterol

Background—Elevated high-density lipoprotein cholesterol (HDL-C) is associated with reduced risk of cardiovascular disease, and variation in HDL-C levels has been shown to be ≈50% heritable. Overexpression of endothelial lipase (EL), a member of the lipoprotein lipase gene family, markedly reduces HDL-C levels in mouse models. We hypothesized that genetic variation in EL might be associated with elevated HDL-C. Methods and Results—All exons and 1.2 kilobase of promoter of the EL gene were sequenced in 20 unrelated human subjects with high HDL-C levels. A total of 17 variants were identified. Six of these were potentially functional and were confirmed by restriction enzyme analysis. Four variants result in amino acid changes (Gly26Ser, Thr111Ile, Thr298Ser, and Asn396Ser,) and 2 variants were in the promoter (−303A/C and −410C/G). The genotype frequencies of each variant were determined in 176 black controls, 165 white controls, and 123 whites with high HDL-C. The Thr111Ile variant was the most common, with an allele frequency of 10.3% in blacks, 31.2% in white controls, and 32.6% in the high HDL-C group. The remaining variants all had allele frequencies <5.0% but differed in frequency among the 3 groups. Interestingly, Gly26Ser, Thr298Ser, and −303A/C were found in the black and high HDL-C white cohorts but were absent in the control white group. Conclusions—Six new potentially functional variants in EL were discovered through sequencing of the EL gene in subjects with high HDL-C levels. Differences in allele frequencies exist between blacks and whites and between control subjects and those with high HDL-C levels.
Advanced Analytics with the SAP HANA Database

MapReduce as a programming paradigm provides a simple-to-use yet very powerful abstraction encapsulated in two second-order functions: Map and Reduce. As such, they allow defining single sequentially processed tasks while at the same time hiding many of the framework details about how those tasks are parallelized and scaled out. In this paper we discuss four processing patterns in the context of the distributed SAP HANA database that go beyond the classic MapReduce paradigm. We illustrate them using some typical Machine Learning algorithms and present experimental results that demonstrate how the data flows scale out with the number of parallel tasks.
Regulation of Molecular Pathways in Ischemia-Reperfusion Injury After Liver Transplantation

Background Ischemia-reperfusion (I/R) injury is a multifactorial phenomenon that occurs during the transplant event and frequently compromises early graft function after liver transplantation (LT). Current comprehension of molecular mechanisms and regulation processes of I/R injury lacks clarity. MicroRNA (miRNA) regulation results critical in several biological processes. Methods This study evaluated gene expression and miRNA expression profiles using microarrays in 34 graft biopsies collected at preimplantation (L1) and at 90 min postreperfusion (L2) from consecutives deceased-donor LT recipients. miRNA profiles were first analyzed. Data integration analysis (gene expression/miRNA expression) aimed to identify potential target genes for each identified miRNA from the L1/L2 differential gene expression profile. Results Pairwise comparison analyses identified 40 miRNAs and 3168 significantly differentially expressed genes at postreperfusion time compared with preimplantation time. Pathway analysis of miRNAs associated these profiles with antiapoptosis, inhibition of cellular proliferation, and proinflammatory processes. Target analysis identified an miRNA-associated molecular profile of 2172 genes involved in cellular growth and proliferation modulation by cell cycle regulation, cell death and survival, and proinflammatory and anti-inflammatory processes. miRNA-independent genes involved proinflammatory molecules. Conclusion We identified a miRNA profile involved in posttranscriptional regulatory mechanisms in I/R injury post-LT. A better understanding of these molecular processes involved in I/R may contribute to develop new strategies to minimize graft injury.
Sensorless rotor temperature estimation of permanent magnet synchronous motor

The work proposes a method for estimation of the magnet temperature in permanent-magnet synchronous machines by exploiting the d-axis saturation effects in the steel stator core produced by the d-current and rotor flux excitation. The method implies an intermittent injection of a voltage pulse in the d-axis of the motor. The resulting d-current response is a function of both the initial value of the d-current itself and the magnetization level of the magnets. Thus, a temperature dependent variation in the magnetization level of the permanent magnets is reflected in a variation of the d-current slope upon the voltage pulse. Experimental validation of the method is demonstrated with surface permanent-magnet motor.
Genesis of Neuronal and Glial Progenitors in the Cerebellar Cortex of Peripuberal and Adult Rabbits

Adult neurogenesis in mammals is restricted to some brain regions, in contrast with other vertebrates in which the genesis of new neurons is more widespread in different areas of the nervous system. In the mammalian cerebellum, neurogenesis is thought to be limited to the early postnatal period, coinciding with end of the granule cell genesis and disappearance of the external granule cell layer (EGL). We recently showed that in the rabbit cerebellum the EGL is replaced by a proliferative layer called ‘subpial layer’ (SPL) which persists beyond puberty on the cerebellar surface. Here we investigated what happens in the cerebellar cortex of peripuberal rabbits by using endogenous and exogenously-administered cell proliferation antigens in association with a cohort of typical markers for neurogenesis. We show that cortical cell progenitors extensively continue to be generated herein. Surprisingly, this neurogenic process continues to a lesser extent in the adult, even in the absence of a proliferative SPL. We describe two populations of newly generated cells, involving neuronal cells and multipolar, glia-like cells. The genesis of neuronal precursors is restricted to the molecular layer, giving rise to cells immunoreactive for GABA, and for the transcription factor Pax2, a marker for GABAergic cerebellar interneuronal precursors of neuroepithelial origin that ascend through the white matter during early postnatal development. The multipolar cells are Map5+, contain Olig2 and Sox2 transcription factors, and are detectable in all cerebellar layers. Some dividing Sox2+ cells are Bergmann glia cells. All the cortical newly generated cells are independent from the SPL and from granule cell genesis, the latter ending before puberty. This study reveals that adult cerebellar neurogenesis can exist in some mammals. Since rabbits have a longer lifespan than rodents, the protracted neurogenesis within its cerebellar parenchyma could be a suitable model for studying adult nervous tissue permissiveness in mammals.
Paper Title Optimal Farm Size under an Uncertain Land Market: the Case of Kyrgyz Republic Authors

of the paper The paper illustrates a theoretical model of real option value applied to the problem of land development. Making use of the 199882001 Kyrgyz Household Budget Survey, we show that when the hypothesis of decreasing return to scale holds, the relation between the threshold value of revenue per hectare and the amount of land cultivated is positive. In addition to that, the relation between the threshold and the amount of land owned is positive in the case of continuous supply of land and negative when there is discontinuous supply of land. The direct consequence is that, in the first case, smaller farms will be more willing to rent land and exercise the option where, in the second case, larger farms will exercise first. The results corroborate the findings of the theoretical model and suggest three main conclusions: (i) the combination of uncertainty and irreversibility is a significant factor in the land development decisions, (ii) farmers' behaviour is consistent with the continuous profit maximization model, (iii) farming unit revenue tends to be positively related to farm size, once uncertainty is properly accounted for.
Physical-layer authentication for wireless security enhancement: current challenges and future developments

While the open nature of radio propagation enables convenient “anywhere” wireless access, it becomes the root of security vulnerabilities in wireless communications. In light of this, physical-layer authentication, which is based on exploitation of the dynamics of physical layer attributes, is emerging as an effective approach to enhancing wireless security. In this article, we first review the existing physical-layer authentication techniques and identify their current limitations, ranging from low authentication reliability to the difficulties of integrating these techniques with the existing wireless infrastructure and applying them in complex future networks. We then present three promising research areas in addressing these challenges. Specifically, we propose the use of the multi-attribute multi-observation technique for enhancing the authentication reliability. In order to apply pointto- point physical-layer authentication techniques into existing wireless networks, we propose a cross-layer authentication approach relying on a composite security key that can seamlessly integrate physical-layer and upper-layer authentication schemes. We also discuss possible ways of invoking physical-layer authentication to reduce both the complexity and latency of the security processes in complex heterogeneous networks with the aid of the proposed physical security context sharing.
Absence of an Immediate G1/S Checkpoint in Primary MEFs Following γ-irradiation Identifies a Novel Checkpoint Switch

DNA double-strand breaks caused by ionizing radiation have been shown to induce G1/S,intra-S-phase, and G2/M cell-cycle checkpoints. However, analysis of the immediate inductionof G1/S checkpoint at a cellular level has been hampered by the inability to distinguish cells thatwere already replicating DNA at the time of damage from cells that entered S phase followingthe DNA damage. We have developed a novel strategy for assessing the initiation of the G1/Scheckpoint following γ-irradiation within asynchronous, low passage, primary mouse embryonicfibroblast cultures (MEFs) using a staggered CldU/IdU double-labelling protocol. Contrary tothe current model of the G1/S checkpoint, we found that 65% of late-G1 primary MEFs stillproceed into S phase after a γ-irradiation dose of 5 Gy. The delayed p53-dependent G1/Scheckpoint is intact in these cells, and a G2/M checkpoint that over 90% effective was inducedwithin 1 h and maintained through 6 h post-irradiation. Furthermore, these cells also exhibitedan intra-S-phase replication slow-down, as there is a decrease in the S/G2 transition frequency ofprimary MEFs following ? -irradiation. The absence of an immediate G1/S checkpoint inprimary MEFs suggests that in late G1 these cells may predominantly respond to DNA damageat the level of individual replication origins, rather than by inducing a complete shut-down of Sphaseentry.
Globalisation, knowledge economy and comparative education

This paper seeks to introduce this special issue by setting out what seem to be some of the major theoretical and methodological issues raised for comparative education by the increasing prominence of the discourses of the knowledge economy, which, it is argued, represent a particularly strong version of globalisation and its possible relationships to education systems, and hence an especially acute challenge to comparative education. It focuses on the possible implications of these changes for each of the three elements of ‘national education system’. In terms of the ‘national’ it discusses the nature and consequences of methodological nationalism, and emphasises the emerging pluri‐scalar nature of the governance of education. In terms of ‘education’, it argues that education is now being asked to do different things in different ways, rather than the same things in different ways. In terms of ‘system’, it is suggested that the constitution of education sectors may be in the process of changing, with a development of parallel sectors at different scales with different responsibilities. Overall, the article suggests that we may be witnessing the development of a new functional, scalar and sectoral (non zero sum) division of the labour of educational governance. Finally, it addresses the question ‘what is now to be compared’ and considers the consequences for both ‘explaining’ and ‘learning’ through comparative education.
Toward understanding the genetic basis of neural tube defects

Neural tube defects (NTDs) represent a common group of severe congenital malformations that result from failure of neural tube closure during early development. Their etiology is quite complex involving environmental and genetic factors and their underlying molecular and cellular pathogenic mechanisms remain poorly understood. Animal studies have recently demonstrated an essential role for the planar cell polarity pathway (PCP) in mediating a morphogenetic process called convergent extension during neural tube formation. Alterations in members of this pathway lead to NTDs in vertebrate models, representing novel and exciting candidates for human NTDs. Genetic studies in NTDs have focused mainly on folate‐related genes based on the finding that perinatal folic acid supplementation reduces the risk of NTDs by 60–70%. A few variants in these genes have been found to be significantly associated with an increased risk for NTDs. The candidate gene approach investigating genes involved in neurulation has failed to identify major causative genes in the etiology of NTDs. Despite this history of generally negative findings, we are achieving a rapid and impressive progress in understanding the genetic basis of NTDs, based mainly on the powerful tool of animal models.