Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Performance of Wells Score Combined With Point‐of‐care Lung and Venous Ultrasound in Suspected Pulmonary Embolism

OBJECTIVE Lung and venous ultrasound are bedside diagnostic tools increasingly used in the early diagnostic approach of suspected pulmonary embolism (PE). However, the possibility of improving the conventional prediction rule for PE by integrating ultrasound has never been investigated. METHODS We performed lung and venous ultrasound in consecutive patients suspected of PE in four emergency departments. Conventional Wells score (Ws) was adjudicated by the attending physician, and ultrasound was performed by one of 20 investigators. Signs of deep venous thrombosis (DVT) at venous ultrasound and signs of pulmonary infarcts or alternative diagnoses at lung ultrasound were considered to recalculate two items of the Ws: signs and symptoms of DVT and alternative diagnosis less likely than PE. The diagnostic performances of the ultrasound-enhanced Ws (USWs) and Ws were then compared after confirmation of the final diagnosis. RESULTS A total of 446 patients were studied. PE was confirmed in 125 patients (28%). USWs performed significantly better than Ws, with a sensitivity of 69.6% versus 57.6% and a specificity of 88.2% versus 68.2%. In combination with D-dimer, USWs showed an optimal failure rate (0.8%) and a significantly superior efficiency than Ws (32.3% vs. 27.2%). A strategy based on lung and venous ultrasound combined with D-dimer would allow to avoid CT pulmonary angiography in 50.5% of patients with suspected PE, compared to 27.2% when the rule without ultrasound is applied. CONCLUSIONS A pretest risk stratification enhanced by ultrasound of lung and venous performs better than Ws in the early diagnostic process of PE.
Risk factors for colonization and infection by Pseudomonas aeruginosa in patients hospitalized in intensive care units in France

Pseudomonas aeruginosa (P.aeruginosa) remains a prominent nosocomial pathogen responsible for high morbi-mortality in intensive care units (ICUs). P.aeruginosa transmission is known to be partly endogenous and exogenous. Main factors have been highlighted but the precise role of environment in regard to antibiotics use remained unclear. Objective To assess the role of environment, medical care and individual risks factors for P. aeruginosa colonization and infection. Study design and setting A French multicentric prospective study involved ten ICUs for a five months period. Every adult patient newly hospitalized in ICUs with no P. aeruginosa carriage up to 48 hours after admission was included and weekly screened before discharge or death. Screening swabs were either rectal, sputum or oropharyngeal samples. Hydric environment was also sampled each week. Data on patient clinical features, environmental and device exposures, and antibiotics supports were regularly collected. Multivariate analysis was performed with a multistate model. Results The overall prevalence of P. aeruginosa carriage was 15.3% (201/1314). Risk factors associated with patient colonization were: use of inactive antibiotics against P. aeruginosa (HR = 1.60 [1.15–2.21] p<0.01), tap water contamination at the entry in the room (HR = 1.66 [1.01–2.27] p<0.05) and mechanical invasive ventilation (HR = 4.70 [2.66–8.31] p<0.0001). Active antibiotics prevented from colonization (HR = 0.67 [0.48–0.93] p = 0.02) and from infection (HR = 0.64 [0.41–1.01] p = 0.05). Interaction between hydric environment antibiotics support was not statistically associated with patient colonization. Conclusion Hydric contamination and antibiotics pressure seem to remain key independent risk factors in P. aeruginosa colonization. These results advocate the need to carry on preventive and targeted interventions toward healthcare associated infections.
The Analysis of Polyploid Genetic Data

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.
Prognostic effect of transarterial chemoembolization–induced complete pathological response in patients undergoing liver resection and transplantation for hepatocellular carcinoma

Transarterial chemoembolization (TACE)–induced complete pathological response (CPR) is known to improve postresection outcomes of hepatocellular carcinoma (HCC). We aimed to assess the prognostic effects of CPR after preoperative TACE for HCC in patients who underwent hepatic resection (HR) or liver transplantation (LT). The clinical outcomes of patients showing CPR after HR (n = 110) or LT (n = 233) were analyzed. The control groups comprised patients with minimal recurrence risk as naïve single HCC ≤ 2 cm for HR (n = 476), and 1 or 2 HCCs ≤ 2 cm for LT (n = 184). Among HR study patients, 1‐, 3‐, and 5‐year tumor recurrence rates were 18.5%, 50.6%, and 58.7% respectively, which were higher than those of controls (P < 0.001). The 1‐, 3‐, and 5‐year patient survival rates were 97.8%, 82.0%, and 69.1%, respectively, which were lower than those of controls (P < 0.001). Among LT study patients, 1‐, 3‐, and 5‐year tumor recurrence rates were 4.1%, 7.9%, and 7.9%, respectively, which were higher than those of controls (P = 0.019). The 1‐, 3‐, and 5‐year patient survival rates were 92.7%, 89.2%, and 86.9%, respectively, which were not different than those of controls (P = 0.11). LT recipients had lower recurrence and higher survival rates compared with HR patients (P < 0.001). The tumor recurrence site was mainly intrahepatic in HR patients. There was no difference between the incidences of extrahepatic recurrence in the HR study group and all‐site recurrence in the LT study group (P = 0.61). We concluded that the prognostic effect of TACE‐induced CPR for HCC patients appears to be limited to downstaging. LT recipients benefited more from CPR than HR patients. Liver Transplantation 23 781–790 2017 AASLD.
JRE4 is a master transcriptional regulator of defense‐related steroidal glycoalkaloids in tomato

Steroidal glycoalkaloids (SGAs) are specialized anti-nutritional metabolites that accumulate in Solanum lycopersicum (tomato) and Solanum tuberosum (potato). A series of SGA biosynthetic genes is known to be upregulated in Solanaceae species by jasmonate-responsive Ethylene Response Factor transcription factors, including JRE4 (otherwise known as GAME9), but the exact regulatory significance in planta of each factor has remained unaddressed. Here, via TILLING-based screening of an EMS-mutagenized tomato population, we isolated a JRE4 loss-of-function line that carries an amino acid residue missense change in a region of the protein important for DNA binding. In this jre4 mutant, we observed downregulated expression of SGA biosynthetic genes and decreased SGA accumulation. Moreover, JRE4 overexpression stimulated SGA production. Further characterization of jre4 plants revealed their increased susceptibility to the generalist herbivore Spodoptera litura larvae. This susceptibility illustrates that herbivory resistance is dependent on JRE4-mediated defense responses, which include SGA accumulation. Ethylene treatment attenuated the jasmonate-mediated JRE4 expression induction and downstream SGA biosynthesis in tomato leaves and hairy roots. Overall, this study indicated that JRE4 functions as a primary master regulator of SGA biosynthesis, and thereby contributes toward plant defense against chewing insects.
The Vertebrate RCAN Gene Family: Novel Insights into Evolution, Structure and Regulation

Recently there has been much interest in the Regulators of Calcineurin (RCAN) proteins which are important endogenous modulators of the calcineurin-NFATc signalling pathway. They have been shown to have a crucial role in cellular programmes such as the immune response, muscle fibre remodelling and memory, but also in pathological processes such as cardiac hypertrophy and neurodegenerative diseases. In vertebrates, the RCAN family form a functional subfamily of three members RCAN1, RCAN2 and RCAN3 whereas only one RCAN is present in the rest of Eukarya. In addition, RCAN genes have been shown to collocate with RUNX and CLIC genes in ACD clusters (ACD21, ACD6 and ACD1). How the RCAN genes and their clustering in ACDs evolved is still unknown. After analysing RCAN gene family evolution using bioinformatic tools, we propose that the three RCAN vertebrate genes within the ACD clusters, which evolved from single copy genes present in invertebrates and lower eukaryotes, are the result of two rounds of whole genome duplication, followed by a segmental duplication. This evolutionary scenario involves the loss or gain of some RCAN genes during evolution. In addition, we have analysed RCAN gene structure and identified the existence of several characteristic features that can be involved in RCAN evolution and gene expression regulation. These included: several transposable elements, CpG islands in the 5′ region of the genes, the existence of antisense transcripts (NAT) associated with the three human genes, and considerable evidence for bidirectional promoters that regulate RCAN gene expression. Furthermore, we show that the CpG island associated with the RCAN3 gene promoter is unmethylated and transcriptionally active. All these results provide timely new insights into the molecular mechanisms underlying RCAN function and a more in depth knowledge of this gene family whose members are obvious candidates for the development of future therapies.
Serum cystatin C is an independent biomarker associated with the renal resistive index in patients with chronic kidney disease

Cystatin C is a cysteine protease inhibitor that is produced by nearly all human cells. The serum level of cystatin C is a stronger predictor of the renal outcome and the risk of cardiovascular events than the creatinine level. The resistive index (RI) on renal Doppler ultrasonography is a good indicator of vascular resistance as well as the renal outcomes in patients with chronic kidney disease (CKD). However, it is unclear whether serum cystatin C is associated with signs of vascular dysfunction, such as the renal RI. We measured the serum cystatin C levels in 101 CKD patients and investigated the relationships between cystatin C and markers of vascular dysfunction, including the renal RI, ankle-brachial pulse wave velocity (baPWV), intima-media thickness (IMT), and cardiac function. The renal RI was significantly correlated with the serum cystatin C level (p < 0.0001, r = 0.6920). The serum cystatin C level was found to be a significant determinant of the renal RI (p < 0.0001), but not the baPWV, in a multivariate regression analysis. The multivariate odds ratio of the serum cystatin C level for a renal RI of more than 0.66 was statistically significant (2.92, p = 0.0106). The area under the receiver-operating characteristic curve comparing the sensitivity and specificity of cystatin C for predicting an RI of more than 0.66 was 0.882 (cutoff value: 2.04 mg/L). In conclusion, the serum cystatin C level is an independent biomarker associated with the renal RI in patients with CKD.
Neuro-symbolic representation learning on biological knowledge graphs

Motivation : Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph‐structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein‐protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. Availability and implementation : https://github.com/bio‐ontology‐research‐group/walking‐rdf‐and‐owl Contact : robert.hoehndorf@kaust.edu. sa Supplementary information: Supplementary data are available at Bioinformatics online.
Visual Working Memory Capacity and Proactive Interference

Background Visual working memory capacity is extremely limited and appears to be relatively immune to practice effects or the use of explicit strategies. The recent discovery that visual working memory tasks, like verbal working memory tasks, are subject to proactive interference, coupled with the fact that typical visual working memory tasks are particularly conducive to proactive interference, suggests that visual working memory capacity may be systematically under-estimated. Methodology/Principal Findings Working memory capacity was probed behaviorally in adult humans both in laboratory settings and via the Internet. Several experiments show that although the effect of proactive interference on visual working memory is significant and can last over several trials, it only changes the capacity estimate by about 15%. Conclusions/Significance This study further confirms the sharp limitations on visual working memory capacity, both in absolute terms and relative to verbal working memory. It is suggested that future research take these limitations into account in understanding differences across a variety of tasks between human adults, prelinguistic infants and nonlinguistic animals.
Gait Analysis of Symptomatic Flatfoot in Children: An Observational Study

Background Flatfoot deformity is a lever arm disease that incurs kinetic inefficiency during gait. The purpose of this study was to measure the degree of kinetic inefficiency by comparing the gait analysis data of a flatfoot group with a normal control group. Methods The patient group consisted of 26 children (21 males and 5 females) with symptomatic flatfoot. They were examined with gait analysis between May 2005 and February 2014. Exclusion criteria were patients with secondary flatfoot caused by neuromuscular disorders, tarsal coalition, vertical talus, or others. Patients' mean age was 9.5 years (range, 7 to 13 years). The gait analysis data of the study group and the normal control group were compared. Results The mean vertical ground reaction force (GRF) in the push-off phase was 0.99 for the patient group and 1.15 for the control group (p < 0.05). The mean ankle moment in the sagittal plane during the push-off phase was 0.89 for the patient group and 1.27 for the control group (p < 0.05). The mean ankle power in the sagittal plane during the push-off phase was 1.38 for the patient group and 2.52 for the control group (p < 0.05). The aforementioned results show that patients with pes planovalgus had a reduction of moment, power, and GRF in the push-off phase during gait. Conclusions Symptomatic flatfeet had a moment inefficiency of 30% and power inefficiency of 45% during gait compared to feet with preserved medial longitudinal arches.
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree

Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in the Tree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Parada's (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species. These problems predictably result in distorted estimates of gene trees, species trees, bootstrap support, and branch lengths. Correction of these errors resulted in robust support for conventional relationships in Pinnipedia and Yangochiroptera. Phylogenomic data sets are not immune to the problems of homology errors in sequence alignments. Rather, sequence alignments underlie all inferences in molecular phylogenetics and evolution and should be spot-checked for obvious errors via manual inspection of alignments and gene trees.
Rice OsMYB5P improves plant phosphate acquisition by regulation of phosphate transporter

Myeloblastosis (MYB) transcription factors play central roles in plant developmental processes and in responses to nutrient deficiency. In this study, OsMYB5P, an R2R3-MYB transcription factor, was isolated and identified from rice (Oryza sativa L. ‘Dongjin’) under inorganic phosphate (Pi)-deficient conditions. OsMYB5P protein is localized to the nucleus and functions as a transcription activator in plant development. Overexpression of OsMYB5P in rice and Arabidopsis (Arabidopsis thaliana Col-0) increases tolerance to phosphate starvation, whereas OsMYB5P knock-out through RNA interference increases sensitivity to Pi depletion in rice. Furthermore, shoots and roots of transgenic rice plants overexpressing OsMYB5P were longer than those of wild plants under both normal and Pi-deficient conditions. These results indicate that OsMYB5P is associated with the regulation of shoot development and root- system architecture. Overexpression of OsMYB5P led to increased Pi accumulation in shoots and roots. Interestingly, OsMYB5P directly bound to MBS (MYB binding site) motifs on the OsPT5 promoter and induced transcription of OsPT5 in rice. In addition, overexpression of OsMYB5P in Arabidopsis triggered increased expression of AtPht1;3, an Arabidopsis Pi transporter, in shoots and roots under normal and Pi-deficient conditions. Together, these results demonstrate that overexpression of OsMYB5P increases tolerance to Pi deficiency in plants by modulating Pi transporters at the transcriptional level in monocots and dicots.
High temperature crack growth behavior in a Cr-Mo steel weldment

Creep deformation and creep crack growth experiments have been conducted on Cr-Mo steel weldment in order to provide information on residual life prediction of structural component weldment containing cracks. The stress exponent of creep deformation equation for the base metal and weldment at 823K were found to be 10.2 and 7.3, respectively. The creep rate of the weldment was much lower than that of the base metal. The creep crack growth rate of the weldment was almost twice as high as that of base metal under a fixed value of C. This may indicate that the weldment is stronger than the base metal in view of creep deformation and is more brittle during creep crack growth due to the intrinsic bainite microstructure.
Psychometric testing of the Italian and French versions of the Care Dependency Scale

Aim. The aim of this study was to test psychometrically the Italian and French versions of the Care Dependency Scale. Background. The Care Dependency Scale assesses changes in patients’ level of care dependency including important functional and mental dimensions. Evaluation of the psychometric properties of the Italian version is still ongoing. The French version has to date not been validated. Design. Nationwide cross-sectional point prevalence study. Method. Data were extracted from the national, annual prevalence survey of hospital-acquired pressure ulcers and inpatient falls in Swiss acute care hospitals in 2011. A total of 799 Italian and 1068 French-speaking patients were included in the analysis. For the evaluation, the psychometric properties were tested for each language both separately and conjointly. Results. The scales revealed high internal consistency. Factor analysis presented a one-factor solution for both versions separately as well as combined. Comparison of internal structure revealed an excellent degree of equivalence between the versions. Highly significant Spearman correlations between the Care Dependency Scale and the Braden Scale sum scores indicated satisfactory criterion validity. Conclusion. Both the Italian and the French versions of the Care Dependency Scale showed satisfactory psychometric properties and a high level of equivalence. Further psychometric testing, using modern test theory approaches, is required. However, the scale is recommended as a valid instrument for further use in Italian and French.