Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecotoxicological effects of activated carbon amendments on macroinvertebrates in nonpolluted and polluted sediments.

Amendment of contaminated sediment with activated carbon (AC) is a remediation technique that has demonstrated its ability to reduce aqueous concentrations of hydrophobic organic compounds. The application of AC, however, requires information on possible ecological effects, especially effects on benthic species. Here, we provide data on the effects of AC addition on locomotion, ventilation, sediment avoidance, mortality, and growth of two benthic species, Gammarus pulex and Asellus aquaticus , in clean versus polycyclic aromatic hydrocarbon (PAH) contaminated sediment. Exposure to PAH was quantified using 76 μm polyoxymethylene passive samplers. In clean sediment, AC amendment caused no behavioral effects on both species after 3-5 days exposure, no effect on the survival of A. aquaticus , moderate effect on the survival of G. pulex (LC(50) = 3.1% AC), and no effects on growth. In contrast, no survivors were detected in PAH contaminated sediment without AC. Addition of 1% AC, however, resulted in a substantial reduction of water exposure concentration and increased survival of G. pulex and A. aquaticus by 30 and 100% in 8 days and 5 and 50% after 28 days exposure, respectively. We conclude that AC addition leads to substantial improvement of habitat quality in contaminated sediments and outweighs ecological side effects.
Beyond TNF, Th1 and Th2 in inflammatory bowel disease

The last decade has seen rapid developments in the field of biological therapy for inflammatory bowel disease (IBD). Understanding the immunopathogenesis of IBD has led to identification of distinct immunological targets. Such targeted therapy with antitumour necrosis factor (TNF) monoclonal antibodies is now in widespread use for both Crohn’s disease (CD) and ulcerative colitis (UC). Beyond this, therapies with other anticytokines are in various stages of development, including antibodies against interleukin 6 (IL6), IL12/23 and interferon γ (IFNγ). The rationale for targeting these cytokines is largely derived from observations regarding the cytokine profile in intestinal tissues from patients with generally long-standing IBD, and from experiments utilising animal models of the disease. Analysis of the mucosal T cell phenotype had until recently largely supported the concept of CD as a Th1 disease, driven by IL12 and characterised by the production of the signature cytokine, IFNγ, and UC as an atypical Th2 disease characterised by production of cytokines such as IL13. More recently, the discovery of the Th17 lineage, driven by IL23 (as well as IL6 and transforming growth factor β) and characterised by IL17 production has led to a re-evaluation, and the realisation that a number of inflammatory conditions in which Th1 was previously considered central, may actually be Th17 dependent. Amongst these are several experimental models of colitis, and there is emerging evidence of CD as a Th17 disease. To add to the complexity, in contrast to mice, in humans a significant proportion of Th17 cells also secrete IFNγ, thus displaying a mixed Th17/Th1 cytokine phenotype, particularly in the gut.1 Furthermore, a number of observations regarding Th17 cells challenge our concepts of terminal T cell lineage commitment, with the demonstration that regulatory T cells can differentiate into inflammatory Th17 cells.2 A number of …
A back-to-back comparison of white light video endoscopy with autofluorescence endoscopy for adenoma detection in high-risk subjects

Objective To compare the sensitivity of autofluorescence endoscopy (AFE) and white light video endoscopy (WLE) for the detection of colorectal adenomas in high-risk patients belonging to Lynch syndrome (LS) or familial colorectal cancer (CRC) families. Methods This was a prospective single-centre study carried out in a tertiary referral centre. The subjects were 75 asymptomatic patients originating from LS or familial CRC families. Patients were examined with either WLE followed by AFE or AFE followed by WLE. Back-to-back colonoscopy was performed by two blinded endoscopists. All lesions were removed during the second endoscopic procedure. Lesions missed during the second procedure were identified and removed on third pass. The sensitivity calculations for colorectal adenomas were based on histology results. The main outcome measures were the difference in sensitivity between WLE and AFE for the detection of adenomas in patients with LS or familial CRC. Results At least one adenoma was detected in 41 (55%) patients. WLE identified adenomas in 28/41 patients and AFE in 37/41 patients, corresponding to a 32% increase. In total 95 adenomas were detected, 65 by WLE and 87 by AFE, resulting in a significantly higher sensitivity of AFE compared with WLE (92% vs 68%; p=0.001). The additionally detected adenomas with AFE were significantly smaller than the adenomas detected by WLE (mean 3.0 mm vs 4.9 mm, p<0.01). Conclusions AFE improves the detection of colorectal adenomas in patients with LS or familial CRC. The results of this study suggest that AFE may be preferable for surveillance of these high-risk patients.
A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA‐Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short‐read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole‐genome comparative evolutionary studies between crops and their wild‐related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen. fr/.
wisepair: a computer program for individual matching in genetic tracking studies

Individual‐based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A ‘permanent’ genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python‐based computer‐modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without‐reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.
Cardiovascular responses to insertion of the laryngeal mask

We have compared, in 40 healthy patients, the cardiovascular responses induced by laryngoscopy and intubation with those produced by insertion of a laryngeal mask. Anaesthesia was induced with thiopentone and maintained with enflurane and nitrous oxide in oxygen; vecuronium was used for muscle relaxation. Arterial pressure was measured with a Finapres monitor. The mean maximum increase in systolic arterial pressure after laryngoscopy and tracheal intubation was 51.3% compared with 22.9% for laryngeal mask insertion (p < 0.01). Increases in maximum heart rate were similar, (26.6% v 25.7%) although heart rate remained elevated for longer after tracheal intubation. We conclude that insertion of the laryngeal mask airway is accompanied by smaller cardiovascular responses than those after laryngoscopy and intubation and that its use may be indicated in those patients in whom a marked pressor response would be deleterious.
Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description

Next‐generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α‐ and β‐diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α‐ and β‐community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates.
No TGFBRII germline mutations in juvenile polyposis patients without SMAD4 or BMPR1A mutation

Juvenile polyposis (JPS) is an autosomal dominant disorder characterised by the presence of multiple gastro-intestinal juvenile polyps and an increased risk of colorectal cancer (CRC). 1 JPS is caused by germline mutation of SMAD4 or BMPR1 A, both involved in the transforming growth factor β/bone morphogenic protein (TGFβ/BMP) signalling pathway. A recent study by van Hattem et al , published in this journal ( Gut 2008; 57 :623–7), showed that a germline defect in one of these genes is found in approximately 50% of JPS patients, with 30–40% being a point mutation or small deletion and 10–15% a large genomic deletion. Since no germline defect is found in ∼50% of JPS patients, it is likely that other genes exist which cause JPS.2 Several candidate genes, mostly involved in TGFβ/BMP signalling, have been investigated for a role in JPS pathogenesis. No mutations have been found in these genes.3–6 (table 1) Recently, the TGFβ co-receptor endoglin was proposed as a JPS susceptibility gene, but other studies could …
Effect of levosimendan on estimated glomerular filtration rate in hospitalized patients with decompensated heart failure and renal dysfunction.

BACKGROUND Only limited data of the long-term effect of levosimendan on renal dysfunction in patients with decompensated heart failure (DHF) have been published previously. To date, there has been no similar study carried out in a Chinese population. DESIGN AND METHODS A prospective, randomized, placebo-controlled, and double-blind study was performed to investigate the effect of levosimendan on estimated glomerular filtration rate (eGFR) in DHF patients with renal dysfunction during a 30-day period. Sixty-six patients with left ventricular ejection fraction (LVEF) ≤40% and eGFR 15-89 mL/min/1.73 m(2) were randomized in a 1:1 ratio to receive a 24-h infusion with levosimendan or placebo. The B-type natriuretic peptide (BNP) and eGFR were determined at baseline and day 1, 3, 7, 14, 30 after the start of treatment. RESULTS The eGFR levels were obviously enhanced following levosimendan, peaked at 3 days, sustained for at least 14 days, and returned to baseline by day 30 after starting infusion. In contrast, placebo did not induce any significant changes in eGFR levels during the follow-up. In addition, levosimendan resulted in a distinct decrease in BNP levels in comparison with placebo, and the beneficial effect returned to baseline by day 14 and remained so at day 30 postinfusion. CONCLUSIONS A 24-h infusion with levosimendan transiently improved the renal dysfunction compared with placebo in patients with DHF, and its beneficial effects persisted for at least 14 days after the initiation of treatment.
Supplying injecting equipment to drug misusers: a survey of community pharmacists' attitudes, beliefs and practices

A postal survey of 888 community pharmacists in one metropolitan administrative region of southern England investigated the pharmacists' involvement in the supply of injecting equipment to injecting drug misusers (IDMs). The survey response rate was 59 per cent. Of respondents, 58 per cent sold injecting equipment and almost 10 per cent supplied it via “exchange” schemes. The respondents' attitudes and beliefs towards provision of injecting equipment were measured on a five point scale. Providers of injecting equipment were significantly more likely than non‐providers to have a positive attitude towards supply, to perceive greater demand for injecting equipment, and to believe that “important others,” such as the pharmacy clientele and other health professionals, would like them to make equipment available. Certain demographic variables and specific beliefs were identified which differentiated between providers and non‐providers of injecting equipment. Pharmacists who did not supply injecting equipment were significantly more likely than providers to believe in negative outcomes of supply, such as theft from the pharmacy. The strong associations identified in this study, between service provision, attitudes and beliefs, have implications for shaping attitudes and encouraging pharmacists' future involvement in HIV‐prevention initiatives.
Medical students and foundation doctors need more exposure to basic urology

With few foundation doctors (FDs) expressing any interest in urology and the lack of a formal undergraduate curriculum in urology,1 it has been documented that undergraduate exposure to urology is inadequate2 and that FDs are unable to perform basic urological procedures,3 in which they should be competent as specified in the General Medical Council (GMC) publication Tomorrow’s Doctors.4
Pathological lesions in colonic biopsies during Parkinson’s disease

Parkinson’s disease (PD) is a neurodegenerative condition that affects 1% of the population over 65 years of age. The two pathological hallmarks of PD are a loss of dopaminergic neurons in the substantia nigra (SN) and the presence of cytoplasmic eosinophilic inclusions termed Lewy bodies (LBs), whose main component is phosphorylated α-synuclein.1 This degeneration of SN neurons leads to a dopamine deficiency responsible for the major motor symptoms. Nevertheless, it has become increasingly evident that PD is a multicentric neurodegenerative process that also affects neuronal structures outside the SN.2 In this context, various reports performed on surgical or autopsy specimens have shown that the enteric nervous system (ENS) is affected during PD.3 4 However, it is still a matter of debate whether these alterations occur early in the course of the disease. This is mainly due to a lack of accessibility to the ENS in the living patients. Therefore, demonstrating (1) the ability to study the ENS using routine colonic biopsies and (2) the presence of lesions characteristics …
Normal hematologic parameters and fetal hemoglobin silencing with heterozygous IKZF1 mutations.

To the editor: The multiple zinc finger-containing transcription factor, IKAROS/IKZF1, has multifaceted roles in hematopoiesis. [1][1] Numerous studies using both human primary hematopoietic cells and mouse models have suggested that IKZF1 plays a key role in erythropoiesis and the fetal-to-adult
Maternal and Newborn Vitamin D Status and Its Impact on Food Allergy Development in the German LINA Cohort Study

K Weisse, S Winkler, F Hirche. Maternal and newborn vitamin D status and its impact on food allergy development in the German LINA cohort study. Allergy. 2013;68(2):220–228 To investigate the relationship of maternal and cord blood vitamin D levels on atopic outcomes in early childhood. A total of 378 mother-infant pairs from Leipzig, Germany, a subgroup of the LINA (Lifestyle and environmental factors and their Influence on Newborns Allergy risk) cohort study, were included. Mothers with immune or infectious disease concerns during the pregnancy were excluded. Blood samples were collected from expectant mothers at the 34th week of gestation and from infant cord blood at delivery for …
Radioactive iodine-refractory differentiated thyroid cancer: unmet needs and future directions

Approximately 90% of thyroid cancers are differentiated (DTCs) and have papillary, follicular or Hürthle cell morphology. Although treatment with surgery and radioactive iodine (I-131; RAI), as appropriate, is associated with significant cure rates and survival benefits, clonal disease progression with development of refractoriness to RAI poses a major therapeutic challenge in about 15% of patients. Traditional chemotherapeutic agents are relatively ineffective and are associated with significant toxicities. Molecular studies have demonstrated that the development and progression of DTC are associated with a series of consistent abnormalities in pathways such as MAPK/ERK and PI3/Akt, which govern cellular growth, proliferation, apoptosis and angiogenesis. Small molecular inhibitors that target these pathogenic pathways, without many of the impairments associated with cytotoxic chemotherapy, have demonstrated efficacy in a variety of malignancies, including renal cell carcinoma, hepatocellular carcinoma, non-small-cell lung cancer and chronic myelogenous leukemia. Several targeted therapeutic agents are in development for the treatment of RAI-refractory DTC. Sorafenib and lenvatinib are being studied in placebo-controlled Phase III trials based on encouraging efficacy results observed in single-arm Phase II studies.
Central aortic blood pressure and augmentation index: comparison between Vasotens ® and SphygmoCor ® technology

Correspondence: Anatoliy N Rogoza Cardiology Research Complex, 3rd Cherpkovskaya str, 15a 121552, Moscow, Russian Federation Tel +7 4991490806 Fax +7 8312961415 Email rogoza@24h-monitoring.com Introduction: The aim of this study is the comparison of Vasotens technology as used in a device with an oscillometric method of blood pressure measurement (BPLab, Petr Telegin Ltd, Nizhny Novgorod, Russian Federation) against the validated tonometric system (SphygmoCor, AtCor Medical Pty Ltd, West Ryde, Australia). Methods: The examinations were carried out in two medical centers. Exclusion criteria included atrial fibrillation, severe cardiac anomalies, heart failure, arrhythmia, decompensated diabetes, the presence of an artificial pacemaker, pregnancy, and BMI . 30. Overall, 160 patients and healthy volunteers were examined. Central aortic systolic blood pressure (aSBP) and augmentation index (aAIx) were obtained by means of applanation tonometry and the oscillometric method was compared. Results: aSBP and aAIx measured using the BPLab device equates significantly with the same parameters measured by SphygmoCor. Conclusion: This finding allows the recommendation of Vasotens technology, which can be used with the 24-hour BPLab monitoring system for wide clinical use.
Differential expression of microRNAs in plasma of patients with colorectal cancer: a potential marker for colorectal cancer screening

Objective: MicroRNAs (miRNAs) have been shown to offer great potential in the diagnosis of cancer. We investigated whether plasma miRNAs could discriminate between patients with and without colorectal cancer (CRC). Methods: This study was divided into three phases: (1) marker discovery using real-time PCR-based miRNA profiling on plasma, corresponding cancerous and adjacent non-cancerous colonic tissues of five patients with CRC, along with plasma from five healthy individuals as controls; (2) marker selection and validation by real-time quantitative RT-PCR on a small set of plasma; and (3) independent validation on a large set of plasma from 90 patients with CRC, 20 patients with gastric cancer, 20 patients with inflammatory bowel disease (IBD) and 50 healthy controls. Results: Of the panel of 95 miRNAs analysed, five were upregulated both in plasma and tissue samples. All the five miRNAs were validated on the plasma of 25 patients with CRC and 20 healthy controls. Both miR-17-3p and miR-92 were significantly elevated in the patients with CRC (p<0.0005). The plasma levels of these markers were significantly reduced after surgery in 10 patients with CRC (p<0.05). Further validation with an independent set of plasma samples (n = 180) indicated that miR-92 differentiates CRC from gastric cancer, IBD and normal subjects. This marker yielded a receiver operating characteristic curve area of 88.5%. At a cut-off of 240 (relative expression in comparison to RNU6B snRNA), the sensitivity was 89% and the specificity was 70% in discriminating CRC from control subjects. Conclusion: MiR-92 is significantly elevated in plasma of patients with CRC and can be a potential non-invasive molecular marker for CRC screening.