jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

BACKGROUND: DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies. RESULTS: Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation. CONCLUSIONS: jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/

Acute liver toxicity with ifosfamide in the treatment of sarcoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Ifosfamide is a chemotherapy agent infrequently associated with liver toxicity. To the best of our knowledge, this report is the first to describe serious liver toxicity associated with ifosfamide used in combination with doxorubicin that caused acute but fully reversible liver failure and encephalopathy. This report reviews the possible mechanisms by which ifosfamide causes this adverse effect.</p> <p>Case report</p> <p>A 61-year-old Caucasian woman who presented with an inoperable right neck mass due to synovial sarcoma was treated with standard-dose ifosfamide and doxorubicin. Within 24 hours of completing the first cycle of chemotherapy, she developed significant derangements in liver function, with a 250-fold increase in transaminase and associated synthetic function impairment and encephalopathy. No other causes of liver failure were identified. Both biochemical tests and encephalopathy were reversed after supportive management and treatment with <it>N</it>-acetylcysteine. No liver toxicity was observed with subsequent cycles of chemotherapy with doxorubicin alone.</p> <p>Conclusion</p> <p>This case highlights the possibility that chemotherapy agents can cause rare and idiosyncratic toxicities, so physicians must be vigilant for drug reactions, especially when patients do not respond to usual treatment.</p

Acute liver toxicity with ifosfamide in the treatment of sarcoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Ifosfamide is a chemotherapy agent infrequently associated with liver toxicity. To the best of our knowledge, this report is the first to describe serious liver toxicity associated with ifosfamide used in combination with doxorubicin that caused acute but fully reversible liver failure and encephalopathy. This report reviews the possible mechanisms by which ifosfamide causes this adverse effect.</p> <p>Case report</p> <p>A 61-year-old Caucasian woman who presented with an inoperable right neck mass due to synovial sarcoma was treated with standard-dose ifosfamide and doxorubicin. Within 24 hours of completing the first cycle of chemotherapy, she developed significant derangements in liver function, with a 250-fold increase in transaminase and associated synthetic function impairment and encephalopathy. No other causes of liver failure were identified. Both biochemical tests and encephalopathy were reversed after supportive management and treatment with <it>N</it>-acetylcysteine. No liver toxicity was observed with subsequent cycles of chemotherapy with doxorubicin alone.</p> <p>Conclusion</p> <p>This case highlights the possibility that chemotherapy agents can cause rare and idiosyncratic toxicities, so physicians must be vigilant for drug reactions, especially when patients do not respond to usual treatment.</p

Analysis of Software Patches Using Numerical Abstract Interpretation

International audienceWe present a static analysis for software patches. Given two syntactically close versions of a program, our analysis can infer a semantic difference, and prove that both programs compute the same outputs when run on the same inputs. Our method is based on abstract interpretation, and parametric in the choice of an abstract domain. We focus on numeric properties only. Our method is able to deal with unbounded executions of infinite-state programs, reading from infinite input streams. Yet, it is limited to comparing terminating executions, ignoring non terminating ones.We first present a novel concrete collecting semantics, expressing the behaviors of both programs at the same time. Then, we propose an abstraction of infinite input streams able to prove that programs that read from the same stream compute equal output values. We then show how to leverage classic numeric abstract domains, such as polyhedra or octagons, to build an effective static analysis. We also introduce a novel numeric domain to bound differences between the values of the variables in the two programs, which has linear cost, and the right amount of relationality to express useful properties of software patches.We implemented a prototype and experimented on a few small examples from the literature. Our prototype operates on a toy language, and assumes a joint syntactic representation of two versions of a program given, which distinguishes between common and distinctive parts

ANCA vasculitis induction management during the COVID-19 pandemic

As the severe acute respiratory syndrome coronavirus 2 pandemic evolved and became a global health threat, the safety of immunosuppression in antineutrophil cytoplasmic antibody-associated vasculitis (AAV) became of utmost important for clinicians and patients. Although timely initiation of immunosuppressive therapy is critical to quell the acute inflammation and prevent AAV-associated mortality and morbidity, concerns for increased susceptibility to Coronavirus Disease 2019 (COVID-19), delayed viral clearance, and decreased humoral response to infection led to speculation about modification in induction therapy practices may be deployed by physicians caring for patients with AAV. This international retrospective cohort study investigated the influence of the COVID-19 pandemic on AAV induction therapy and patient outcomes in different parts of the world by studying differences in treatment regimens in the United States, United Kingdom, and Europe

Does a referral from home to hospital affect satisfaction with childbirth? A cross-national comparison

<p>Abstract</p> <p>Background</p> <p>The Belgian and Dutch societies present many similarities but differ with regard to the organisation of maternity care. The Dutch way of giving birth is well known for its high percentage of home births and its low medical intervention rate. In contrast, home births in Belgium are uncommon and the medical model is taken for granted. Dutch and Belgian maternity care systems are compared with regard to the influence of being referred to specialist care during pregnancy or intrapartum while planning for a home birth. We expect that a referral will result in lower satisfaction with childbirth, especially in Belgium.</p> <p>Methods</p> <p>Two questionnaires were filled out by 605 women, one at 30 weeks of pregnancy and one within the first two weeks after childbirth, either at home or in a hospital. Of these, 563 questionnaires were usable for analysis. Women were invited to participate in the study by independent midwives and obstetricians during antenatal visits in 2004–2005. Satisfaction with childbirth was measured by the Mackey Satisfaction with Childbirth Rating Scale, which takes into account the multidimensional nature of the concept.</p> <p>Results</p> <p>Belgian women are more satisfied than Dutch women and home births are more satisfying than hospital births. Women who are referred to the hospital while planning for a home birth are less satisfied than women who planned to give birth in hospital and did. A referral has a greater negative impact on satisfaction for Dutch women.</p> <p>Conclusion</p> <p>There is no reason to believe Dutch women receive hospital care of lesser quality than Belgian women in case of a referral. Belgian and Dutch attach different meaning to being referred, resulting in a different evaluation of childbirth. In the Dutch maternity care system home births lead to higher satisfaction, but once a referral to the hospital is necessary satisfaction drops and ends up lower than satisfaction with hospital births that were planned in advance. We need to understand more about referral processes and how women experience them.</p

The Consumer Quality Index Hip Knee Questionnaire measuring patients' experiences with quality of care after a total hip or knee arthroplasty

<p>Abstract</p> <p>Background</p> <p>The Dutch Consumer Quality Index Hip Knee Questionnaire (CQI Hip Knee) was used to assess patients' experiences with and evaluations of quality of care after a total hip (THA) or total knee arthroplasty (TKA). The aim of this study is to evaluate the construct validity and internal consistency reliability of this new instrument and to assess its ability to measure differences in quality of care between hospitals.</p> <p>Methods</p> <p>Survey data of 1,675 subjects who underwent a THA or TKA were used to evaluate the psychometric properties. Exploratory factor analyses were performed and item-total correlations and inter-factor correlations were calculated to assess the construct validity of the instrument. Reliability analyses included tests of internal consistency (Cronbach's alpha coefficients). Finally, multilevel analyses were performed to assess the ability of the instrument to discriminate between hospitals in quality of care.</p> <p>Results</p> <p>Exploratory factor analyses indicated that the survey consisted of 21 items measuring five aspects of care (i.e. communication with nurses, communication with doctors, communication with general practitioner, communication about new medication, and pain control). Cronbach's alpha coefficients ranged from 0.76 to 0.90 indicating good internal consistency. The survey's ability to discriminate between hospitals was partly supported by multilevel analysis. Two scales (i.e. communication with nurses and communication with doctors) were able to measure differences between hospitals with respect to patients' experiences with quality of care. Logistic multilevel analyses indicated that hospitals explained part of the variation between patients in receiving information.</p> <p>Conclusion</p> <p>These findings suggest that the CQI Hip Knee is reliable and valid for use in Dutch health care. Health care providers or health plans can use this survey to measure patients' experiences with hospital care and to identify variations in care between hospitals.</p

Chronic OVA allergen challenged Siglec-F deficient mice have increased mucus, remodeling, and epithelial Siglec-F ligands which are up-regulated by IL-4 and IL-13

Abstract Background In this study we examined the role of Siglec-F, a receptor highly expressed on eosinophils, in contributing to mucus expression, airway remodeling, and Siglec-F ligand expression utilizing Siglec-F deficient mice exposed to chronic allergen challenge. Methods Wild type (WT) and Siglec-F deficient mice were sensitized and challenged chronically with OVA for one month. Levels of airway inflammation (eosinophils), Siglec-F ligand expresion and remodeling (mucus, fibrosis, smooth muscle thickness, extracellular matrix protein deposition) were assessed in lung sections by image analysis and immunohistology. Airway hyperreactivity to methacholine was assessed in intubated and ventilated mice. Results Siglec-F deficient mice challenged with OVA for one month had significantly increased numbers of BAL and peribronchial eosinophils compared to WT mice which was associated with a significant increase in mucus expression as assessed by the number of periodic acid Schiff positive airway epithelial cells. In addition, OVA challenged Siglec-F deficient mice had significantly increased levels of peribronchial fibrosis (total lung collagen, area of peribronchial trichrome staining), as well as increased numbers of peribronchial TGF-β1+ cells, and increased levels of expression of the extracellular matrix protein fibronectin compared to OVA challenged WT mice. Lung sections immunostained with a Siglec-Fc to detect Siglec-F ligand expression demonstrated higher levels of expression of the Siglec-F ligand in the peribronchial region in OVA challenged Siglec-F deficient mice compared to WT mice. WT and Siglec-F deficient mice challenged intranasally with IL-4 or IL-13 had significantly increased levels of airway epithelial Siglec-F ligand expression, whereas this was not observed in WT or Siglec-F deficient mice challenged with TNF-α. There was a significant increase in the thickness of the peribronchial smooth muscle layer in OVA challenged Siglec-F deficient mice, but this was not associated with significant increased airway hyperreactivity compared to WT mice. Conclusions Overall, this study demonstrates an important role for Siglec-F in modulating levels of chronic eosinophilic airway inflammation, peribronchial fibrosis, thickness of the smooth muscle layer, mucus expression, fibronectin, and levels of peribronchial Siglec-F ligands suggesting that Siglec-F may normally function to limit levels of chronic eosinophilic inflammation and remodeling. In addition, IL-4 and IL-13 are important regulators of Siglec-F ligand expression by airway epithelium

Drug safety of rosiglitazone and pioglitazone in France: a study using the French PharmacoVigilance database

International audienceBackgroundThiazolidinediones (TZDs), rosiglitazone (RGZ) and pioglitazone (PGZ) are widely used as hypoglycemic drugs in patients with type 2 diabetes mellitus. The aim of our study was to investigate the profile of adverse drug reactions (ADRs) related to TZDs and to investigate potential risk factors of these ADRs.MethodsType 2 diabetic patients were identified from the French Database of PharmacoVigilance (FPVD) between 2002 and 2006. We investigated ADR related to TZD, focusing on 4 ADR: edema, heart failure, myocardial infarction and hepatitis corresponding to specific WHO-ART terms.ResultsAmong a total of 99,284 adult patients in the FPVD, 2295 reports concerned type 2 diabetic patients (2.3% of the whole database), with 161 (7%) exposed to TZDs. The frequency of edema and cardiac failure was significantly higher with TZDs than in other patients (18% and 7.4% versus 0.8% and 0.1% respectively, p ConclusionsThiazolidinediones exposure is associated with an increased risk of edema and heart failure in patients with type 2 diabetes even when recommendations for use are respected. In contrast, the risk of hepatic reactions and myocardial infarction with this class of drugs seems to be similar to other hypoglycemic agents