Miracle-dz/UniFAR-FTUs huggingface dataset:
Endoscopic ultrasonography: impact in diagnosis, staging and management of pancreatic tumors. An overview.

The incidence of pancreatic adenocarcinoma(PA) is increasing and represents the fourthleading cause of cancer death in Westerncountries. The aggressive nature of thedisease and late diagnosis make incidencerates almost identical to mortality rates.This malignancy is currently difficult to treat,because only a few patients (5-20%) haveresectable disease at the moment of diagnosis,with a 5-year survival rate of less than 25%. In the last few years, much effort has beenmade to achieve an optimal standardalgorithm for pancreatic cancer staging.Careful preoperative staging is essential inorder to plan the best treatment, selectingpatients who can benefit from surgery andthose who will need palliative treatment.The regional anatomy of the pancreas iscomplex to study and cytology samples aredifficult to obtain because of itsretroperitoneal location.Endoscopic ultrasonography (EUS), atechnique in which an ultrasonographic probeis placed at the tip of an oblique viewingendoscope, was introduced in the early ‘80s toovercome the limitations of trans-abdominalultrasonographic imaging of the pancreascaused by intervening air, fat and bone.The ability to position the echographictransducer in direct proximity to the pancreasby means of the stomach and duodenum,combined with the use of high-frequencyprobes, produces detailed high-resolutionimages of the pancreas which far surpassthose of other imaging techniques such ascomputed tomography (CT) and magneticresonance (MR). Even if new radiological devices such as dual-phase helical-CT (h-CT) have beenintroduced, EUS still remains the bestinstrument for studying pancreatic cancer,with a T-stage accuracy of 78-94% and an N-accuracy of 64-82% [1, 2]. In a review comparing EUS versus h-CT instaging pancreatic cancer, Hunt and Faigel [3]found EUS to be more accurate in detecting(97% vs. 73%) and predicting tumorresectability (91% vs. 83%) and moresensitive in detecting vascular invasion (91%vs. 64%). A recent retrospective study comparing multi-detector spiral CT to EUS and EUS-FNA hasshown an overall accuracy of CT of 74%while EUS had an accuracy of 94% [4]. Maybe, with the introduction of a multi-detector CT scanner with a narrow collimatorand faster scanning, the ability of CT to showthe pancreas will improve, but more studiesare needed to establish the real applications ofmulti-detector CT.We have to remember that EUS is operator-dependent and several factors can influenceits staging accuracy, such as the experience ofthe endosonographer, imaging artifacts, and
Bivalve Biomarker W orkshop : overview and discussion group summaries

A. H. RINGWOOD1, M. J. HAMEEDI2, R. F. LEE3, M. BROUWER4, E. C. PETERS5, G. I. SCOTT6, S. N. LUOMA7 and R. T. DIGIULIO8 1 Marine Resources Research Institute, 217 Fort Johnson Road, Charleston, SC 29412, USA 2 NOAA, National Ocean Service, 1305 East-West Highway, Silver Springs, MD 20910, USA 3 University of Georgia, Skidaway Institute of Oceanography, 10 Ocean Science Drive, Savannah, GA 31411, USA 4 University of Southern Mississippi, Institute of Marine Sciences, Department of Coastal Sciences, 703 East Beach Drive, Ocean Springs, MS 39564, USA 5 Tetra Tech, Inc., 10306 Eaton Place, Suite 340, Fairfax, VA 22030, USA 6 NOAA/NOS, 219 Fort Johnson Road, Charleston, SC 29412, USA 7 MS465, US Geological Survey, 345 Middleeld Road, Menlo Park, CA 94025, USA 8 Duke University, School of Environment, PO Box 90328, LSRC, Durham, NC 27708, USA
Analyse de requêtes en langue naturelle et extraction d'informations bibliographiques pour une recherche de livres orientée contenu efficace

Au cours des dernieres annees, le Web a connu une enorme croissance en matiere de contenus et d'utilisateurs. Ce phenomene a entraine des problemes lies a la surcharge d'information face a laquelle les utilisateurs ont des difficultes a trouver les bonnes informations. Des systemes de recommandation ont ete developpes pour resoudre ce probleme afin de guider les utilisateurs dans ce flux d'informations. Les approches de recommandation se sont multipliees et ont ete mises en œuvre avec succes, notamment au travers d’approches telles que le filtrage collaboratif. Cependant, il existe encore des defis et des limites qui offrent des opportunites pour de nouvelles recherches. Parmi ces defis, la conception de systemes de recommandation de lectures est devenue un axe de recherche en pleine expansion suite a l’apparition des bibliotheques numeriques.Traditionnellement, les bibliotheques jouent un role passif dans l’interaction avec les lecteurs et ce, faute d’outils efficaces de recherche et de recommandation. Dans ce manuscrit, nous nous sommes penchee sur la creation d’un systeme de recommandation de lectures. Nos objectifs portent sur :- ameliorer la comprehension des besoins utilisateurs exprimes au sein des requetes en langage naturel de recherches de livres, articles et billets ; - pallier l'absence de liens explicites entre ouvrages et articles de revues par la detection et l'analyse automatique des references bibliographiques afin de proposer des liens ; - parvenir a un systeme de recommandation de lectures s'appuyant sur des donnees textuelles permettant de fournir une liste de recommandations personnalisees aux utilisateurs actifs.
Identifying compliance incentives for screening and treatment of tuberculosis.

A significant proportion of the residents of the Downtown East Side in the city of Vancouver is at a comparatively high risk of contracting tuberculosis (TB) due to various psychosocial factors. Based on data from three case-finding studies of a small segment of this population, it was suspected that this area contained many undetected cases. One study revealed a prevalence rate as high as 300 per 100,000, as compared with a prevalence rate of 34 per 1,000,000 in the metropolitan Vancouver area. To effectively control TB and to reduce the high rate of TB in this area, an ongoing screening program was instituted to identify individuals with TB and to initiate and supervise treatment. This area is characterized by a relatively high incidence of social and economic problems including alcohol and drug addiction and unemployment. The age of the population is predominantly in the 30- to 60-year range; the population is highly transient. Consequently, drawing high-risk individuals into the screening program presents difficulties, and many individuals have difficulty adhering to the prescribed treatment regimen. This article describes various strategies employed to encourage these individuals to be screened and also examines selected components of community health nursing practice utilized to determine what factors contribute to adherence to treatment. A significant proportion of the residents of the Downtown East Side (DES), an urban area in the city of Vancouver, is at a comparatively high risk of contracting tuberculosis (TB) due to various physical and psychosocial factors. This area encompasses about 382 square blocks and includes the popularly known areas of Gastown, Skid Row, Granville Mall, and Chinatown. Based on data from three case-finding studies of a small segment of this population, it was suspected that this area contained a large number of undetected cases. This area is characterized by a relatively high incidence of social and economic problems including alcohol and drug addiction and unemployment. The age of the
Meta-analysis To Define a Core Microbiota in the Swine Gut

The results of this meta-analysis demonstrate that “study” and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits. ABSTRACT The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design. Therefore, we performed a meta-analysis using 20 publically available data sets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Next to the “study” itself, the gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota (P = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, and Ruminococcus and the RC9 gut group were found in 99% of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum were shared by >90% of all GI samples, suggesting a so-called “core” microbiota for commercial swine worldwide. IMPORTANCE The results of this meta-analysis demonstrate that “study” and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits.
Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward

We recently reported a dramatic increase in the prevalence of carbapenem-resistant Acinetobacter baumannii infections in the intensive care unit (ICU) of a Vietnamese hospital. This upsurge was associated with a specific oxa23-positive clone that was identified by multilocus VNTR analysis. Here, we used whole-genome sequence analysis to dissect the emergence of carbapenem-resistant A. baumannii causing ventilator-associated pneumonia (VAP) in the ICU during 2009–2012. To provide historical context and distinguish microevolution from strain introduction, we compared these genomes with those of A. baumannii asymptomatic carriage and VAP isolates from this same ICU collected during 2003–2007. We identified diverse lineages co-circulating over many years. Carbapenem resistance was associated with the presence of oxa23, oxa40, oxa58 and ndm1 genes in multiple lineages. The majority of resistant isolates were oxa23-positive global clone GC2; fine-scale phylogenomic analysis revealed five distinct GC2 sublineages within the ICU that had evolved locally via independent chromosomal insertions of oxa23 transposons. The increase in infections caused by carbapenem-resistant A. baumannii was associated with transposon-mediated transmission of a carbapenemase gene, rather than clonal expansion or spread of a carbapenemase-harbouring plasmid. Additionally, we found evidence of homologous recombination creating diversity within the local GC2 population, including several events resulting in replacement of the capsule locus. We identified likely donors of the imported capsule locus sequences amongst the A. baumannii isolated on the same ward, suggesting that diversification was largely facilitated via reassortment and sharing of genetic material within the localized A. baumannii population.
Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp.

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum (Fo). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. “Super Marmande,” while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. “Rio Grande. ” Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on “SM” tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively.
Combined Effects of Cigarette Smoking and Alcohol Consumption on Perinatal Outcome

Background: An increase in various congenital abnormalities associated with cigarette smoking and the use of alcohol during pregnancy has been reported in many studies. These exposures also increase the risk of pregnancy complications such as abruptio placentae, unexplained stillbirth, preterm labor and intrauterine growth restriction. However, very few studies have addressed the combined effect of smoking and drinking on pregnancy outcomes. Methods: In this review, the adverse effects of smoking or drinking on pregnancy were obtained from publications in which both substances were addressed in the same study population. A special effort was made to find studies in which the combined effect of these substances was investigated. Results: Preterm labor occurred more frequently in women who drank and smoked during pregnancy. This increased odds ratio was more than the sum of the effects of either smoking or drinking, indicating that the use of both substances by the same woman has a synergistic effect that increases the risk of preterm labor. This synergistic effect was also found for low birth weight and growth restriction. Conclusions: As most of the women who drink during pregnancy also smoke cigarettes, attention should be given to the prevention or reduced use of both substances during pregnancy.
Relation between the thermal conductivity and grain size in a polycrystalline silicene sheet

Silicene, a two-dimensional allotrope of silicon, has outstanding mechanical and electrical properties which have triggered extensive research on its application in the field of developing faster computer chips, more efficient solar cells, improved medical technologies, vehicle, and aircraft parts, etc. In this work, we have demonstrated a way to use large-scale molecular dynamics to explore the effective thermal conductivity of nano-grained polycrystalline 2-D Silicene sheets and compare it with a pristine one. By performing non-equilibrium molecular dynamics (NEMD) simulations, the effect of grain size on the thermal conductivity of polycrystalline Silicene sheets has been investigated. For both pristine and polycrystalline Silicene sheet, structures of 30 nm × 30 nm are considered and Stillinger-Weber potential is used to investigate the atoms’ interaction with theneighborhood. The temperature profiles are used to find the thermal conductivity by Fourier’s Law of conduction. Comparing with the pristine Silicene sheet we have found a very intriguing result. Our results reveal that the ultra-fine nano-grained Silicene structures have an increasing trend for thermal conductivity commensurate with grain size. Larger the grain size becomes, higher the thermal conductivity is. However, for very small grain size the thermal conductivity is considerably less than the pristine structure. It is also noticed that the thermal conductivity of smaller grain size structures shows more grain size dependency while the thermal conductivity for larger grain size exhibits trivial gradient and almost converges to some certain range of values.The grain size based rising trend is then evaluatedby specific heat calculation.The density of states (DOS) is ultimately calculated for different grain sizes to verify the trend of changing thermal conductivities on the basis of noise sensitivity.Silicene, a two-dimensional allotrope of silicon, has outstanding mechanical and electrical properties which have triggered extensive research on its application in the field of developing faster computer chips, more efficient solar cells, improved medical technologies, vehicle, and aircraft parts, etc. In this work, we have demonstrated a way to use large-scale molecular dynamics to explore the effective thermal conductivity of nano-grained polycrystalline 2-D Silicene sheets and compare it with a pristine one. By performing non-equilibrium molecular dynamics (NEMD) simulations, the effect of grain size on the thermal conductivity of polycrystalline Silicene sheets has been investigated. For both pristine and polycrystalline Silicene sheet, structures of 30 nm × 30 nm are considered and Stillinger-Weber potential is used to investigate the atoms’ interaction with theneighborhood. The temperature profiles are used to find the thermal conductivity by Fourier’s Law of conduction. Comparing with the pristine.
Reaction of surface-applied superphosphate with soil. I. The fertilizer solution and its initial reaction with soil

The phosphorus and calcium contents of the fertilizer solution from surfaceapplied superphosphate in contact with moist soil were shown to be similar to those of the metastable triple-point solution (MTPS) produced when an excess of monocalcium phosphate is shaken with water. The average phosphorus, calcium, and sulphur concentrations of saturated aqueous extracts of superphosphate at 20°C were 4.0M, 1.5M , and 0.023M respectively. The pH of these extracts ranged from 1.60 to 1.92 (0.15-0.47 units higher than that of MTPS). The sulphur content of the fertilizer solution was generally one-fiftieth to one-hundredth of the phosphorus content. In the absence of leaching both diffusion and capillarity were involved in the movement of phosphate from superphosphate particles into moist soil. The fertilizer solutes entered the soil mainly by diffusion but on soils of low moisture content the increase in pore size of the fertilizer particles, which resulted from the dissolution of monocalcium phosphate, led to a reversal of the suction gradient between soil and particle which caused movement of some of the fertilizer solution into the soil by capillarity. Leaching of superphosphate applied to dry soils by rainwater is likely to yield fertilizer solutions which have higher pH, lower phosphorus and calcium contents, and higher sulphur contents than the saturated solutions arising from superphosphate particles in contact with moist soil. When synthetic fertilizer solution reacted with acid soils the rate of removal of phosphate and calcium from solution depended upon the phosphate sorption capacity of the soil. In calcareous soil the calcium carbonate played a major part in phosphate precipitation. Appreciable amounts of iron and particularly aluminium were dissolved from each of the soils studied by the synthetic fertilizer solution to give solutions which, on standing, readily formed precipitates of phosphate. Both sulphate and organic sulphur compounds were displaced from the acid soils by the fertilizer solution but, in the calcareous soil, sulphate was coprecipitated with the phosphate.
Novel evolutionary pathways of sex‐determining mechanisms

Evolutionary transitions between sex‐determining mechanisms (SDMs) are an enigma. Among vertebrates, individual sex (male or female) is primarily determined by either genes (genotypic sex determination, GSD) or embryonic incubation temperature (temperature‐dependent sex determination, TSD), and these mechanisms have undergone repeated evolutionary transitions. Despite this evolutionary lability, transitions from GSD (i.e. from male heterogamety, XX/XY, or female heterogamety, ZZ/ZW) to TSD are an evolutionary conundrum, as they appear to require crossing a fitness valley arising from the production of genotypes with reduced viability owing to being homogametic for degenerated sex chromosomes (YY or WW individuals). Moreover, it is unclear whether alternative (e.g. mixed) forms of sex determination can persist across evolutionary time. It has previously been suggested that transitions would be easy if temperature‐dependent sex reversal (e.g. XX male or XY female) was asymmetrical, occurring only in the homogametic sex. However, only recently has a mechanistic model of sex determination emerged that may allow such asymmetrical sex reversal. We demonstrate that selection for TSD in a realistic sex‐determining system can readily drive evolutionary transitions from GSD to TSD that do not require the production of YY or WW individuals. In XX/XY systems, sex reversal (female to male) occurs in a portion of the XX individuals only, leading to the loss of the Y allele (or chromosome) from the population as XX individuals mate with each other. The outcome is a population of XX individuals whose sex is determined by incubation temperature (TSD). Moreover, our model reveals a novel evolutionarily stable state representing a mixed‐mechanism system that has not been revealed by previous approaches. This study solves two long‐standing puzzles of the evolution of sex‐determining mechanisms by illuminating the evolutionary pathways and endpoints.
An experimental comparison of linear non-Gaussian causal discovery methods and their variants

Many multivariate Gaussianity-based techniques for identifying causal networks of observed variables have been proposed. These methods have several problems such that they cannot uniquely identify the causal networks without any prior knowledge. To alleviate this problem, a non-Gaussianity-based identification method LiNGAM was proposed. Though the LiNGAM potentially identifies a unique causal network without using any prior knowledge, it needs to properly examine independence assumptions of the causal network and search the correct causal network by using finite observed data points only. On another front, a kernel based independence measure that evaluates the independence more strictly was recently proposed. In addition, some advanced generic search algorithms including beam search have been extensively studied in the past. In this paper, we propose some variants of the LiNGAM method which introduce the kernel based method and the beam search enabling more accurate causal network identification. Furthermore, we experimentally characterize the LiNGAM and its variants in terms of accuracy and robustness of their identification.