Miracle-dz/UniFAR-FTUs huggingface dataset:
ICD10 Coding of Death Certificates with the NCBO and SIFR Annotator(s) at CLEF eHealth 2017 Task 1

The SIFR BioPortal is an open platform to host French biomedical ontologies and terminologies based on the technology developed by the US National Center for Biomedical Ontology (NCBO). The portal facilitates the use and fostering of terminologies and ontologies by offering a set of services including semantic annotation. The SIFR Anno-tator (http://bioportal.lirmm.fr/annotator) is a publicly accessible, easily usable ontology-based annotation tool to process French text data and facilitate semantic indexing. The web service relies on the ontology content (preferred labels and synonyms) as well as on the semantic of the ontologies (is-a hierarchies) and their mappings. The SIFR BioPortal also offers the possibility of querying the original NCBO Annotator for English text via a dedicated proxy that extends the original functionality. In this paper, we present a preliminary performance evaluation of the generic annotation web service (i.e., not specifically customized) for coding death certificates i.e., annotating with ICD-10 codes. This evaluation is done against the CepiDC/CDC CLEF eHealth 2017 task 1 manually annotated corpus. For this purpose, we have built custom SKOS vocabularies from the CePIDC/CDC dictionaries as well as training and development corpora, for all three tasks using a most frequent code heuristic to assign ambiguous labels. We then submitted the vocabularies to the NCBO and SIFR BioPortal and used the annotation services on task 1 datasets. We obtained, for our best runs on each corpus the following results: English raw corpus (69.08% P, 51.37% R, 58,92% F1); French raw corpus (54.11% P, 48.00% R, 50,87% F1); French aligned corpus (50.63% P, 52.97% R, 51.77% F1).
Ectopic expression of GATA6 bypasses requirement for Grb2 in primitive endoderm formation

Gene knockouts in mice have showed that Grb2 and GATA6 are essential for the formation of primitive endoderm in blastocysts. Here, we confirmed that implanted Grb2‐null blastocysts lack primitive or extraembryonic endoderm cells either at E4.5 or E5.5 stages. We analyzed the relationship between Grb2 and GATA6 in the differentiation of embryonic stem (ES) cells to primitive endoderm in embryoid body models. Upon transfection with GATA6 expression vector, Grb2‐null ES cells underwent endoderm differentiation as indicated by the expression of the extraembryonic endoderm markers Dab2 and GATA4. Transfection of GATA4 expression vector also had the same differentiation potency. When GATA6‐ or GATA4‐transfected Grb2‐null ES cells were allowed to aggregate, fragments of an endoderm layer formed on the surface of the spheroids. The results suggest that GATA6 is downstream of Grb2 in the inductive signaling pathway and the expression of GATA6 is sufficient to compensate for the defects caused by Grb2 deficiency in the development of the primitive and extraembryonic endoderm. Developmental Dynamics 240:566–576, 2011. © 2010 Wiley‐Liss, Inc.
Toxicological characterization of N‐methyl‐N‐nitrosourea‐induced cataract in rats by LC/MS‐based metabonomic analysis

Cataract is one of the most serious drug‐induced side effects that can terminate the development of drug candidates, and pharmaceutical companies consider it important to evaluate cataract‐inducing potential in the early phases. Metabonomics is expected to be a powerful approach for the safety evaluation of drug candidates. In this study, we conducted a toxicological characterization of N‐methyl‐N‐nitrosourea (MNU)‐induced cataract in rats by LC/MS‐based metabonomic analysis. MNU was intraperitoneally administered once to 15‐day old rats at 70 mg kg−1. After that, animals were kept for 3 weeks waiting for cataract formation. Lens samples for metabonomic analysis were collected on 7, 14 and 21 days after MNU administration. Comprehensive analyses of lens metabolites were conducted using an LC/MS system, and multivariate data for each sample were compared by principal component analysis (PCA) to find any changes in lens metabolites. Lens opacity was confirmed by ophthalmoscopy 14 days after dosing, and even by gross observation 21 days after dosing. PCA of the lens samples for the control and MNU‐treated groups revealed that the metabolite profiles of lens differed from each other, and several lens metabolites, such as lots of α‐amino acids and gluthathione, decreased after MNU treatment. In conclusion, metabonomic analysis enabled us to identify new marker candidates for cataract and provided a better understanding of the mechanism related to MNU‐induced cataract. It was considered that metabonomics is a useful approach for the characterization of drug‐induced toxicity. Copyright © 2011 John Wiley & Sons, Ltd.
Mechanism of Flake Drying and Its Correlation to Quality

This research focuses on experimental investigations of the drying and bending properties of wood flakes. Three species (southern yellow pine, sweetgum, and yellowpoplar) were tested. Experiments on flake drying and effect of flake properties (cutting direction and dimension) and an external factor (temperature) were used to evaluate the flake drying process. Drying experiments were conducted using a convection oven. Bending properties of dried flakes were also measured. Modulus of elasticity (MOE), modulus of rupture (MOR), and strength at proportional limit (SPL) of flakes were measured based on Methods of Testing Small Clear Specimens of Timber (ASTM D14394) using a miniature material tester. The drying curve was characterized by a second-order/quadratic equation. This equation was then differentiated to get the drying rate curve. Observation on drying and drying rate curves revealed that the rate of moisture loss consists of two falling rate periods; no constant rate drying period was observed. First falling rate drying period is controlled by convective heat transfer. Bound water diffusion controls the second falling rate drying period. Species, cutting direction, dimension, and temperature were found to have significant effect on drying rate of wood flakes. Southern yellow pine has the fastest drying rate followed by sweetgum then yellow-poplar. Differences in drying rate between species were attributed to differences in specific gravity and other factors. Radially-cut specimens have a slower drying rate than tangentially-cut specimens. There were also significant differences in drying rate between the four different flake dimensions. Thickness was found to be the more sensitive parameter in terms of dimensions. As expected, drying temperature also had highly significant effect on drying rate. An increasing trend in drying rate was observed as drying temperature increased.
Enteroviruses in Acute Myocardial Infarction

Background: Human enteroviruses (EVs) may have a role as a possible risk factor in the pathogenesis of MI. The aim of this study was to evaluate the presence of enterovirus genomic RNA in peripheral blood samples of patients with acute myocardial infarction (MI). Methods: We investigated the presence of enterovirus genomic RNA in the peripheral blood of 115 patients with acute MI hospitalized in the Coronary Care Unit of Imam Reza and Ghaem University Hospitals (Mashhad, Iran) by RT-PCR using the virus specific primers. Results: The subjects’ mean (±SD) age was 63.5 (±9.4) years (range: 38–82) and 38.3 % of the subjects were female. Of 115 patient specimens, 3 (2.6%) were positive in RT-PCR. Conclusion: The prevalence of enterovirus in MI patients is considerable. More investigations are needed to determine the causal role of enteroviruses in MI.
MRI characteristics and follow-up findings in patients with neurological complications of enterovirus 71-related hand, foot, and mouth disease.

OBJECTIVES This study aimed to investigate the magnetic resonance imaging (MRI) characteristics and clinical and MRI follow-up findings of patients with neurological complications of enterovirus 71-related hand, foot and mouth disease. METHODS Data were collected from 12 patients who developed neurological complications of enterovirus 71-related hand, foot, and mouth disease during an enterovirus-71 outbreak in Hainan Province, China, from May 2008 to October 2011. Patients were followed up for 2 years. RESULTS In the six patients with brainstem encephalitis, MRI showed posterior brainstem abnormalities with hyperintense areas on T2-weighted images and hypointense areas on T1-weighted images. In the four patients with acute flaccid paralysis but no brainstem encephalitis, sagittal MRI images showed linear hyperintense areas in the anterior spinal cord, transverse T2-weighted images showed hyperintense areas in the spinal cord, and contrast-enhanced axial T1-weighted images showed strong enhancement of the anterior horns or nerve roots. In the two patients with aseptic meningitis, MRI showed widening of the subarachnoid space and ventricles. The MRI and clinical signs of aseptic meningitis resolved within 4 weeks in both patients. Patients with isolated pontine abnormalities recovered faster than those with multiple brainstem abnormalities, patients with isolated brainstem encephalitis recovered faster than those with associated acute flaccid paralysis, patients with paralysis of one limb recovered faster than those with paralysis of multiple limbs, and patients with isolated thoracolumbar cord abnormalities recovered faster than those with cervical cord abnormalities. CONCLUSIONS MRI is useful for assessment of the neurological complications of enterovirus 71-related hand, foot, and mouth disease. Patients who develop neurological complications characteristically have MRI abnormalities of the posterior brainstem or bilateral anterior horns of parts of the spinal cord. The MRI findings can help to predict prognosis.
Integrating Object and Meta-Level Value Based Argumentation

A recent extension to Dung's argumentation framework allows for arguments to express preferences between other arguments. Value based argumentation can be formalised in this extended framework, enabling meta-level argumentation about the values that arguments promote, and the orderings on these values. In this paper, we show how extended frameworks integrating meta-level reasoning about values can be rewritten as Dung frameworks, and show a soundness and completeness result with respect to the rewrites. We then describe how value orderings can emerge, or be 'formed', as a result of dialogue games based on the rewritten frameworks, and illustrate the advantages of this approach over existing dialogue games for value based argumentation frameworks.
The Importance of Cardiolipin Synthase for Mitochondrial Ultrastructure, Respiratory Function, Plant Development, and Stress Responses in Arabidopsis[W]

CARDIOLIPIN SYNTHASE (CLS) catalyzes the synthesis of cardiolipin, the signature phospholipid of the mitochondrial inner membrane. Through characterization of a cls mutant in Arabidopsis, this study shows that CLS is crucial for correct mitochondrial function and development in Arabidopsis under both optimal and stress conditions. Cardiolipin (CL) is the signature phospholipid of the mitochondrial inner membrane. In animals and yeast (Saccharomyces cerevisiae), CL depletion affects the stability of respiratory supercomplexes and is thus crucial to the energy metabolism of obligate aerobes. In eukaryotes, the last step of CL synthesis is catalyzed by CARDIOLIPIN SYNTHASE (CLS), encoded by a single-copy gene. Here, we characterize a cls mutant in Arabidopsis thaliana, which is devoid of CL. In contrast to yeast cls, where development is little affected, Arabidopsis cls seedlings are slow developing under short-day conditions in vitro and die if they are transferred to long-day (LD) conditions. However, when transferred to soil under LD conditions under low light, cls plants can reach the flowering stage, but they are not fertile. The cls mitochondria display abnormal ultrastructure and reduced content of respiratory complex I/complex III supercomplexes. The marked accumulation of tricarboxylic acid cycle derivatives and amino acids demonstrates mitochondrial dysfunction. Mitochondrial and chloroplastic antioxidant transcripts are overexpressed in cls leaves, and cls protoplasts are more sensitive to programmed cell death effectors, UV light, and heat shock. Our results show that CLS is crucial for correct mitochondrial function and development in Arabidopsis under both optimal and stress conditions.
Thermodynamic constraint on the depth of the global tropospheric circulation

Significance The study explores two fundamental problems in climate science: (i) The physical factors that govern the depth of the troposphere, and (ii) the response of clouds to climate change. Previous research has argued that tropical anvil temperatures are strongly constrained by the fundamental thermodynamic properties of water vapor. Here we argue that the same basic thermodynamic properties strongly constrain the depth of the troposphere, the temperature of high clouds, and the amplitude of large-scale dynamics throughout the globe. The results suggest that the positive climate feedbacks associated with tropical high clouds also operate in the extratropics, and that the top of the troposphere should remain at roughly the same temperature throughout the globe as the climate system warms. The troposphere is the region of the atmosphere characterized by low static stability, vigorous diabatic mixing, and widespread condensational heating in clouds. Previous research has argued that in the tropics, the upper bound on tropospheric mixing and clouds is constrained by the rapid decrease with height of the saturation water vapor pressure and hence radiative cooling by water vapor in clear-sky regions. Here the authors contend that the same basic physics play a key role in constraining the vertical structure of tropospheric mixing, tropopause temperature, and cloud-top temperature throughout the globe. It is argued that radiative cooling by water vapor plays an important role in governing the depth and amplitude of large-scale dynamics at extratropical latitudes.
Evaluation of the diagnostic accuracy of UBC® Rapid in bladder cancer: a Swedish multicentre study

Abstract Objective: The aim of this study was to determine the diagnostic accuracy of UBC® Rapid – a urine-based marker for bladder cancer – in patients with bladder cancer and controls, and to compare the test results across risk groups. Materials and methods: This prospective phase II study was conducted at four Swedish hospitals. UBC Rapid was evaluated in four groups: A, newly diagnosed bladder cancer (n = 94); B, follow-up of non-muscle-invasive bladder cancer (n = 75); C, benign urinary tract diseases (n = 51); and D, healthy controls (n = 50). Tumours were divided into high risk (carcinoma in situ, TaG3, T1, T2 and T3) and low risk (low malignant potential, TaG1 and TaG2). Urine samples were quantitatively analysed by UBC Rapid. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated based on optimal cut-off (receiver operator characteristics curve analysis). A linear regression compared the UBC Rapid results in the different risk groups. Results: The optimal cut-off was 8.1 μg/l. The median UBC Rapid values were 9.3 μg/l [interquartile range (IQR) 30.9] and 4.3 μg/l (IQR 7.8) in patients with positive and negative cystoscopy, respectively (p < .001). The value for group A was 15.6 μg/l (IQR 37.9), group B 5.6 μg/l (IQR 8.6), group C 5.1 μg/l (IQR 9.0) and group D 3.3 μg/l (IQR 7.1). Sensitivity was 70.8%, specificity 61.4%, PPV 71.3% and NPV 60.8%. The high-risk group had significantly higher UBC Rapid values than the low-risk group: 20.5 μg/l (IQR 42.2), sensitivity 79.2% and specificity 61.4% versus 7.0 μg/l (IQR 9.9), sensitivity 60.0% and specificity 61.4% (p = .039). Conclusions: The UBC Rapid urine-based marker for bladder cancer gave higher values in patients with positive than in those with negative cystoscopy. The diagnostic accuracy was better in patients with high-risk than in those with low-risk tumours, and was better during primary detection than during surveillance.
Inverted Meckel’s diverticulum mimicking an ulcerated pedunculated polyp: detection by single-balloon enteroscopy

hospital because of recurrent obscure gastrointestinal bleeding. Abdominal computed tomography revealed one heterogeneous lesion with soft tissue and accumulation of fluid over the distal ileum (●" Fig. 1). Physical examinations showed mild tenderness in the right lower quadrant region of abdomen, and laboratory data revealed microcytic anemia. Single-balloon enteroscopy with an anal approach showed one ulcerated pedunculated polyp (about 2 cm in size) with a long stalk located at around the distal ileum (●" Fig. 2a,b; ●" Video 1). Polypectomy was performed during enteroscopy (●" Fig. 2c). One diverticularlike orifice occurred after polypectomy, and one small hole on the tip of this diverticulum was visualized. The woman received emergent laparotomy because of iatrogenic gut perforation. The operation disclosed one diverticulum with iatrogenic perforation about 60 cm from the ileocecal valve (●" Fig. 3a). Segmental resection of the ileum was performed. The pathologic examination of specimens from laparotomy and polypectomy confirmed the diagnosis of Meckel’s diverticulum with ectopic pancreatic tissue (●" Fig. 3b) and gastric tissue (●" Fig. 3c) with ulceration. Meckel’s diverticulum is the most common congenital anomaly of the gastrointestinal tract (1%–3% of the population); it is generally asymptomatic. Bleeding is themost commoncomplication, especially in children. However, accurate diagnosis remains difficult. In addition to conventional Technetium-99m pertechnetate scintigraphy, capsule or balloon-assisted enteroscopy is another diagnostic tool to directly observe the diverticulum [1–3]. Inverted Meckel’s diverticulum is extremely rare, especially that containing both pancreatic and gastric tissues [4,5]. In the present case, the inverted Meckel’s diverticulum with ectopic tissues was clearly viewed by single-balloon enteroscopy, but this lesion mimicked an ulcerated pedunculated polyp. Polypectomy caused subsequent gut perforation. Therefore, inverted Meckel’s diverticulum should be considered and treated carefully in a patient with an elongated pedunculated polyp in the distal ileum.
Cell Damage and Death by Autoschizis in Human Bladder (RT4) Carcinoma Cells Resulting from Treatment with Ascorbate and Menadione

A human bladder carcinoma cell line RT4 was sham-treated with buffer or treated with ascorbate (VC) alone, menadione alone (VK3), or a combination of ascorbate:menadione (VC+VK3) for 1, 2, and 4 h. Cytotoxic damage was found to be treatment-dependent in this sequence: VC+VK3>VC>VK3>sham. The combined treatment induced the greatest oxidative stress, with early tumor cell injury affecting the cytoskeletal architecture and contributing to the self-excisions of pieces of cytoplasm freed from organelles. Additional damage, including a reduction in cell size, organelle alterations, nuclear damage, and nucleic acid degradation as well as compromised lysosome integrity, is caused by reactivation of DNases and the redox cycling of VC or VC+VK3. In addition, cell death caused by VC+VK3 treatment as well as by prolonged VC treatment is consistent with cell demise by autoschizis, not apoptosis. This report confirms and complements previous observations about this new mode of tumor cell death. It supports the contention that a combination of VC+VK3, also named Apatone, could be co-administered as a nontoxic adjuvant with radiation and/or chemotherapies to kill bladder tumor cells and other cancer cells without any supplementary risk or side effects for patients.
Spatial Patterns of Avian Malaria Prevalence in Zonotrichia capensis on the Western Slope of the Peruvian Andes

Abstract Environmental heterogeneity largely dictates the spatial distributions of parasites and therefore the susceptibility to infection of host populations. We surveyed avian malaria infections in Rufous-collared sparrows (Zonotrichia capensis) across replicated altitudinal and latitudinal transects along the western slope of the Peruvian Andes to assess geographic patterns of prevalence. We found malaria infection prevalence peaked at midelevations along all 3 altitudinal transects (x̄ ≈ 2,733 m), with highest overall prevalence observed in the northern transect. We observed low levels of malarial parasite diversity, with 94% of infected birds carrying a single Haemoproteus (subgenus Parahaemoproteus) strain. The remaining infected birds harbored either a single alternate Haemoproteus or 1 of 2 Plasmodium strains. Our data suggest that temperature and precipitation are the primary drivers of the spatial patterns in avian malaria prevalence along the western slope of the Andes.
Neural correlates of visual extinction or awareness in a series of patients with right temporoparietal damage

Patients with visual extinction following right-hemisphere damage can typically detect left visual field stimulation when it is presented in isolation, but tend to miss this when it is paired with competing concurrent right visual stimulation. Some single-case studies have provided preliminary evidence that right visual cortex may show residual activation for contralesional, extinguished visual stimuli. Here we go beyond prior work by using individual retinotopic mapping and online eye-tracking during fMRI to study activity in stimulus-responsive retinotopic visual cortex for a case series of four extinction patients. We found consistent activation of retinotopic right visual cortex for bilateral visual stimulation that resulted in left extinction. This residual unconscious activation included areas V1 to V3 and was not due to inadvertent eye movements. We also provide further evidence for the emerging view that awareness may require activity of frontal and parietal regions well beyond visual cortex.
[Long-term treatment with intravitreal ranibizumab for exudative age-related macular degeneration].

INTRODUCTION The results of intravitreal ranibizumab treatment for exsudative age-related macular degeneration have been favourable until this time. AIM To evaluate the two-year functional and anatomic results of intravitreal ranibizumab treatment. METHOD 46 patients (age: 75 ± 9.1 years) were included in a prospective single center study. Treatment regimen was the following: monthly 0.5 mg ranibizumab was administered in the first 3 months, and later as required (pro re nata). The change of best corrected visual acuity and central retinal thickness was followed. RESULTS The visus change at the end of the follow-up time was not statistically significant compared to baseline (p = 0.760) and the at the end of the first year (p = 0.154). Central retinal thickness decreased significantly compared to baseline (p = 0.000001), but the change was not statistically significant compared to the end of the first year (p = 0.875). CONCLUSIONS Patients with neovascular macular degeneration treated with intravitreal ranibizumab using pro re nata regimen have stable visus for long term, and the exsudation could be reduced efficiently.
Cloning , Characterization , and Sequence Analysis of the clcE Gene Encoding the Maleylacetate Reductase of Pseudomonas sp . Strain B 13

A 3,167-bp PstI fragment of genomic DNA from Pseudomonas sp. strain B13 was cloned and sequenced. The gene clcE consists of 1,059 nucleotides encoding a protein of 352 amino acids with a calculated mass of 37,769 Da which showed maleylacetate reductase activity. The protein had significant sequence similarities with the polypeptides encoded by tcbF of pP51 (59.4% identical positions), tfdF of pJP4 (55.1%), and tftE of Burkholderia cepacia AC1100 (53.1%). The function of TcbF as maleylacetate reductase was established by an enzyme assay.