Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithmes pour la reconstruction de séquences de marqueurs conservés dans des données de métagénomique. (Algorithms for conserved markers sequences reconstruction in metagenomics data)

Les progres recents en termes de sequencage d’ADN permettent maintenant d’acceder au materiel genetique de communautes microbiennes extraites directement d’echantillons environnementaux naturels. Ce nouveau domaine de recherche, appele metagenomique, a de nombreuses applications en sante, en agro-alimentaire, en ecologie, par exemple. Analyser de tels echantillons demande toutefois de developper de nouvelles methodes bio-informatiques pour determiner la composition taxonomique de la communaute etudiee. L’identification precise des organismes presents est en effet une etape essentielle a la comprehension des ecosystemes meme les plus simples. Cependant, les technologies de sequencage actuelles produisent des fragments d’ADN courts et bruites, qui ne couvrent que partiellement les sequences completes des genes, ce qui pose un veritable defi pour l’analyse taxonomique a haute resolution. Nous avons developpe MATAM, une nouvelle methode bio-informatique dediee a la reconstruction rapide et sans erreurs de sequences completes de marqueurs phylogenetiques conserves, a partir de donnees brutes de sequencage. Cette methode est composee d’une succession d’etapes qui realisent la construction et l’analyse d’un graphe de chevauchement de lectures. Nous l’avons appliquee a l’assemblage de la petite sous-unite de l’ARN ribosomique sur des metagenomes simules, synthetiques et reels. Les resultats obtenus sont de tres bonne qualite et ameliorent l’etat de l’art.
Predicting soil organic matter stability 1 in agricultural fields through carbon 2 and nitrogen stable isotopes 3 4

30 In order to evaluate the sustainability and efficiency of soil carbon sequestration measures and 31 the impact of different management and environmental factors, inf ormation on soil organic 32 matter (SOM) stability and mean residence time (MRT) is required. However, this 33 information on SOM stability and MRT is expensive to determine vi a radiocarbon dating, 34 precluding a wide spread use of stability measurements in soil science. In this paper, we test 35 an alternative method, first developed by Conen et al. (2008) for undis t rbed Alpine grassland 36 systems, using C and N stable isotope ratios in more frequently dis urbed agricultural soils. 37 Since only information on carbon and nitrogen concentrations and their s table isotope ratios 38 is required, it is possible to estimate the SOM stability at greatly reduced costs compared to 39 radiocarbon dating. Using four different experimental sites locat ed in various climates and 40 soil types, this research proved the effectiveness of using the C/N ratio and δN signature to 41 determine the stability of mOM (mineral associated organic matter) relative to POM 42 (particulate organic matter) in an intensively managed agroecological setting. Combining this 43 approach with δC measurements allowed discriminating between different manage ment 44 (grassland vs cropland) and land use (till vs no till) systems. With increasing depth the 45 stability of mOM relative to POM increases, but less so unde r tillage compared to no-till 46 practises. Applying this approach to investigate SOM stability in different soi l aggregate 47 fractions, it corroborates the aggregate hierarchy theory as pr oposed by Six et al. (2004) and 48 Segoli et al. (2013). The organic matter in the occluded micr o-aggregate and silt & clay 49 fractions is less degraded than the SOM in the free micro-ag gregate and silt & clay fractions. 50 The stable isotope approach can be particularly useful for s oils with a history of burning and 51 thus containing old charcoal particles, preventing the use of C to determine the SOM 52 stability. 53
15 Years of Research on Redirected Walking in Immersive Virtual Environments

Virtual reality users wearing head-mounted displays can experience the illusion of walking in any direction for infinite distance while, in reality, they are walking a curvilinear path in physical space. This is accomplished by introducing unnoticeable rotations to the virtual environment-a technique called redirected walking. This paper gives an overview of the research that has been performed since redirected walking was first practically demonstrated 15 years ago.
Analytical formula for the pseudoinverse and its application for singular path tracking with a class of redundant robotic limbs

Graphical Abstract Abstract This work introduces a novel formula for calculating the right pseudoinverse, proposed for a class of kinematically redundant robotic limbs with one degree of redundancy. The formula is derived from the Singularity-Consistent method and is expressed as a sum of scalable vector fields parameterized by the desired end link twist. Pseudoinverse properties are ensured by assigning proper vector field intensities. The formula is applied to the IK problem, whereby the end link tracks a degenerate singular path, i.e. a nontangential path that penetrates the workspace boundary, and thus resulting in an unavoidable kinematic singularity. Through this method, the instability of the conventional pseudoinverse solution and the stationary point problem obtained when the solution is stripped from the ill-conditioned denominator is avoided. In addition, the appearance of the ‘inner obstacle’ algorithmic singularity problem known from a previous work can be circumvented. The performance of the method is verified via numerical simulations with an S-R-S-type structure and the Barrett WAM.
The Effect of Lean‐Seafood and Non‐Seafood Diets on Fecal Metabolites and Gut Microbiome: Results from a Randomized Crossover Intervention Study

SCOPE The impact of dietary protein types on the gut microbiome is scarcely studied. The aim of the present study is therefore to examine the effects of lean-seafood and non-seafood proteins on the gut microbiome composition and activity and elucidate potential associations to cardiovascular disease (CVD) risk factors. METHODS A crossover intervention study in which 20 healthy subjects consumed two diets that varied in protein source was conducted. 1 H NMR spectroscopy and 16S rDNA sequencing analyses were applied to characterize fecal metabolites and gut microbiota composition, respectively. RESULTS A twofold increase in fecal trimethylamine excretion was observed after the lean-seafood diet period. Circulating TAG and the total to high-density lipoprotein (HDL) cholesterol ratio as well as circulating TMAO levels were each associated with specific gut bacteria. Following the non-seafood diet period, a decreased relative abundance of Clostridium cluster IV and a tendency toward an increased Firmicutes/Bacteroidetes ratio were found. CONCLUSIONS Lean-seafood and non-seafood diets differentially modulate the gut microbiome composition and activity. Furthermore, the gut microbiota composition seems to affect circulating TMAO levels and CVD risk factors.
Disclosure of Intellectual Capital Components in Integrated Reporting: An Empirical Analysis

The purpose of the study is to investigate how firms disclose information in their integrated report (IR) on intellectual capital (IC), regarding its components and their link with the value creation process. Therefore, by adopting a content analysis methodology, the study, which covers three years (2014–2016), is focused on IC. A sample of firms belonging to the financial services sector is investigated by analysing 135 integrated reports. The main findings show that firms, on the one hand, provide information on IC by adopting a classification close to those outlined by IC scholars; on the other hand, the vast majority of the investigated firms tends to adopt a superficial approach. More specifically, firms disclose a low amount of information about the link between IC and the value creation process, even though they are aware of its importance.
Association between community management of pneumonia and diarrhoea in high-burden countries and the decline in under-five mortality rates: an ecological analysis

Objective The objective of the paper is to explore if the adoption of national policies to use community-based health providers for the management of pneumonia and diarrhoea is associated with the decline in under-five mortality, including achievement of the Millennium Development Goal (MDG)4 target, in high-burden countries. Setting This country level analysis covers 75 high-burden low-income and middle-income countries which accounted for 98% of the 5.9 million global under-five deaths in 2015. One-fourth of these deaths were due to pneumonia and diarrhoea. Methods χ2 tests and multiple regression analysis were used to examine the association between reduction in under-five mortality rates and community case management of pneumonia and diarrhoea by adjusting for the influence of other possible determinants. Participants No patient or population interviewed/examined for this analysis. Countries were the unit of analysis. Interventions Community case management (CCM) of pneumonia and diarrhoea policies. Outcome measures Changes in under-five mortality rates over time. Results Countries that had adopted both CCM policies were three times more likely to achieve the MDG4 target than countries that did not have both policies in place. This association was further confirmed by the multivariate analysis (β-coefficient=10.4; 95% CI 2.4 to 18.5; p value=0.012). Discussion There is a statistically significant association between adoption of CCM policies for treatment of pneumonia and diarrhoea and the rate of decline in child mortality levels. It is important to promote CCM in countries lagging behind to achieve the new target of 25 or fewer deaths per 1000 live births by 2030.
Mineral Apposition Rates in Coronal Dentine of Mandibular First Molars in Soay Sheep: Results of a Fluorochrome Labeling Study

We studied the spatio‐temporal variation of mineral apposition rate (MAR) in postnatally formed coronal dentine of mandibular first molars from Soay sheep repeatedly injected with different fluorochromes. MAR declined along the cuspal to cervical crown axis, and from early to late formed dentine, that is, from the dentine at the enamel‐dentine‐junction (EDJ) to the dentine adjacent to the dentine‐pulp‐interface (DPI). Highest mean MARs (about 21 µm/day) were recorded in cuspal dentine formed in the period of 28‐42 days after birth. Lowest values (<2 µm/day) were recorded in late‐formed (secondary) dentine close to the DPI. The high MARs recorded in the dentine of the cuspal crown portions enable the formation of a large tooth crown within a relatively short period of less than one year. The established MARs in the dentine of the different crown portions of sheep molars will allow a precise determination of the timing of stress events affecting dentine formation. They are also helpful for devising sampling protocols in studies of trace element or stable isotope distributions in sheep dentine aimed at assessing temporal variation of incorporation into forming dentine. Such data are useful in a variety of contexts, including, for example, the exposure to pollutants and the reconstruction of husbandry practices or feeding regimes. Anat Rec, 301:902–912, 2018. © 2017 Wiley Periodicals, Inc.
Prototype of a Zero-Field-Cooled YBCO Bearing With Continuous Ring Permanent Magnets

Based on the levitating design of the Zero-Field-Cooled (ZFC) Maglev previously developed, a novel horizontal ZFC superconductor magnetic bearing (SMB) is currently being developed. However, simulations have shown that its stator and rotor made of YBCO bulks and NdFeB permanent magnets (PM), respectively, present significant magnetic discontinuities. These produce asymmetries on the bearing rotation and several stable and unstable position angles that prevent the SMB from rotating smoothly, leading to a step motor like sort of rotation. Those drawbacks are now avoided by using ring shape PMs, leading not only to a smooth rotation of the SMB but also increasing its stability. New three-dimensional finite element method simulations and a set of experimental tests with the new SMB show in this paper the viability and increased performance when ring shape PMs are used. Finally, experimental results using the prototype also show that the model fits very well with the laboratory test results.
A High-Bandwidth Back-Drivable Hydrostatic Power Distribution System for Exoskeletons Based on Magnetorheological Clutches

Exoskeletons are increasingly interesting for human assistance applications ranging from rehabilitation to force enhancement. However, today's exoskeletons are relatively slow and lack the mechanical transparency required to complete several daily tasks, mainly due to their bulky and non-back-drivable actuation mechanisms. To improve upon conventional exoskeleton designs, this letter presents a novel power-distribution system that combines magnetorheological (MR) clutches and low-friction hydrostatic transmissions using rolling diaphragms. In such a system, MR clutches are used to rapidly modulate the torque provided from a centralized power source and distribute it to each joint through a high-bandwidth, back-drivable, and low-inertia transmission. The main objective of this letter is to investigate the transparency performance of the MR-hydrostatic power distribution in terms of its force-bandwidth and back-drivability with the aim of being used in future exoskeletons. Experiments with a custom one degree-of-freedom haptic joint are supported by an analytical model that demonstrates the high bandwidth (>40 Hz) and good backdrivability (2–11% of peak force) of an MR-hydrostatic system.
Short article: Presence, extent and location of pancreatic necrosis are independent of aetiology in acute pancreatitis

Objective The most common aetiologies of acute pancreatitis (AP) are gallstones, alcohol and idiopathic. The impact of the aetiology of AP on the extent and morphology of pancreatic and extrapancreatic necrosis (EXPN) has not been clearly established. The aim of the present study was to assess the influence of aetiology on the presence and location of pancreatic necrosis in patients with AP. Patients and methods We carried out a post-hoc analysis of a previously established multicentre cohort of patients with AP in whom a computed tomography was available for review. Clinical data were obtained from the medical records. All computed tomographies were revised by the same expert radiologist. The impact of aetiology on pancreatic and EXPN was calculated. Results In total, 159 patients with necrotizing pancreatitis were identified from a cohort of 285 patients. The most frequent aetiologies were biliary (105 patients, 37%), followed by alcohol (102 patients, 36%) and other aetiologies including idiopathic (78 patients, 27%). No relationship was found between the aetiology and the presence of pancreatic necrosis, EXPN, location of pancreatic necrosis or presence of collections. Conclusion We found no association between the aetiology of AP and the presence, extent and anatomical location of pancreatic necrosis.
Virtual Double Staining Based Learning for Segmentation of Tumors in Primary Immunohistochemical Biomarkers

We propose a deep learning-based segmentation method of tumor for WSI biomarker quantification of Ki67. The model is evaluated by comparing with the clinical score and other statistical measures of an existing method based on Virtual Double Staining (VDS). The results show a 98.85% agreement between the two methods with no significant difference.
Strategic procurement and international collaboration to improve access to medicines

Efficient procurement of medicines is more than just obtaining the lowest price. It is about creating a healthy market where products of good quality are available at affordable prices on a sustainable basis and at the right time.1 In this context, a strategic approach to procurement is vital. Such an approach should encompas all activities that might improve the efficiency of procurement – e.g. activities to minimize low-value repetitive purchases, increase the benefit of economies of scale and reduce transaction and transport costs.2 Here, we will provide examples of the experiences of countries in the World Health Organization’s European Region in improving the efficiency of procurement of medicines. We will also explain how international collaboration could help improve individual country’s efforts.
Evolution of antimicrobial resistance of Salmonella enteritidis (1972-2005).

With the extensive use of antibiotics in livestock production, surveillance revealed an increase in Salmonella resistance to the commonly used antimicrobials in veterinary and public health. This serious threat to health care is further exacerbated by the limited epidemiological information about the common zoonotic agent, Salmonella enteritidis, required to determine antibiotic therapy. The aim was to characterise the antimicrobial resistance patterns of S. enteritidis isolates across different timelines (1972-2005) with accompanying genetic changes being investigated. Thirty-seven stored S. enteritidis isolates were collected from the Central Veterinary Laboratory, Harare, with antimicrobial susceptibility determined against eight antibiotics. Plasmids were isolated to analyse any genetic variation. An overall significant increase in resistance (p < 0.05) to nalidixic acid (0% - 10%), ampicillin (14.3% - 50%), tetracycline (14.3% - 30%) and erythromycin (71.4% - 100%) was observed across the timeline. However, the highest rates of susceptibility were maintained for gentamicin, sulphamethoxazole-trimethoprim, kanamycin and chloramphenicol. We report an increase in multidrug resistance (MDR) of 14.2% - 50% with an increase in resistotypes and plasmid profiles across the timeline. Eleven plasmid profiles were obtained in the 37 isolates studied with a minority of isolates (21.6%, 8/37) harbouring a 54 kb plasmid, commonly serovar-specific. A concerning increase in antimicrobial resistance to commonly administered drugs was observed across the timeline. The surge in MDR is of great concern and implies the need for consistent antimicrobial stewardship. No correlation was observed between the plasmid and antibiotic profiles.
Entwicklung eines Common Criteria Schutzprofils für elektronische Wahlgeräte mit Paper Audit Trail

Mit dem Urteil vom 3. Marz 2009 hat das Bundesverfassungsgericht die bislang in der Bundesrepublik Deutschland eingesetzten Wahlgerate fur verfassungswidrig erklart. Grund fur dieses Urteil war die fehlende Umsetzung des Prinzips der Offentlichkeit der Wahl. Mit dem Urteil erklarte das Gericht jedoch nicht grundsatzlich den Einsatz elektronischer Wahlgerate fur verfassungswidrig. Im Rahmen des von der DFG geforderten Projekts ’VerKonWa’ wurde das EasyVote System entwickelt, welches den Offentlichkeitsgrundsatz durch sogenannte Paper Audit Trails umsetzt. Im Rahmen dieser Arbeit berichten wir uber die Erfahrung bei der Entwicklung eines Common Criteria Schutzprofils fur elektronische Wahlgerate mit Paper Audit Trails.
Unequal Political Participation Worldwide

Introduction 1. Unequal participation around the world 2. Heterogeneous consequences of contexts on participation 3. The difficulty of the voting procedure 4. Government fragmentation and media systems 5. Trade unions in the highly educated membership era 6. Income inequality and the participation of lower-status groups 7. Consequences of unequal participation for representation Conclusions.
Lung Volume Reduction Coil Treatment in Chronic Obstructive Pulmonary Disease Patients with Homogeneous Emphysema: A Prospective Feasibility Trial

Background: In patients with heterogeneous emphysema, surgical and bronchoscopic lung volume reduction (LVR) treatments are available. However, for patients with homogeneous emphysema these treatments are hardly investigated and seem less effective. Bronchoscopic LVR coil treatment has been shown to be effective in patients with heterogeneous emphysema, but this treatment has not been exclusively investigated in homogeneous emphysema. Objectives: The aim of this study was to investigate the safety and efficacy of LVR coil treatment in patients with homogeneous emphysema. Methods: In this single-arm, open-label study, patients received a maximum of 12 LVR coils (PneumRx Inc., Mountain View, Calif., USA) in each upper lobe in two sequential procedures. Tests were performed at baseline and at 6 months. The primary endpoint was the improvement from baseline in 6-min walking distance (6MWD) after treatment. Results: Ten patients with severe airway obstruction and hyperinflation were treated. A median of 11 (range 10-12) coils were placed in each lung. Two chronic obstructive pulmonary disease exacerbations and one small pneumothorax were recorded as serious adverse events. At 6 months, 6MWD had improved from 289 to 350 m (p = 0.005); forced vital capacity from 2.17 to 2.55 liters (p = 0.047); residual volume from 5.04 to 4.44 liters (p = 0.007) and St. George's Respiratory Questionnaire from 63 to 48 points (p = 0.028). Conclusion: LVR coil treatment in homogeneous patients improves hyperinflation, airway resistance, exercise capacity and quality of life with an acceptable safety profile. The benefit of LVR coil treatment is not limited to patients with heterogeneous emphysema, and patients with homogenous emphysema can benefit as well.
Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases

Genes and proteins are known to have differences in their sensitivity to alterations. Despite numerous sequencing studies, proportions of harmful and harmless substitutions are not known for proteins and groups of proteins. To address this question, we predicted the outcome for all possible single amino acid substitutions (AASs) in nine representative protein groups by using the PON‐P2 method. The effects on 996 proteins were studied and vast differences were noticed. Proteins in the cancer group harbor the largest proportion of harmful variants (42.1%), whereas the non‐disease group of proteins not known to have a disease association and not involved in the housekeeping functions had the lowest number of harmful variants (4.2%). Differences in the proportions of the harmful and benign variants are wide within each group, but they still show clear differences between the groups. Frequently appearing protein domains show a wide spectrum of variant frequencies, whereas no major protein structural class‐specific differences were noticed. AAS types in the original and variant residues showed distinctive patterns, which are shared by all the protein groups. The observations are relevant for understanding genetic bases of diseases, variation interpretation, and for the development of methods for that purpose.