dataesr/scientific-paragraphs-categorization huggingface dataset:
). "Defense" (14. 71%) is also dominant, but only in the Level 2 dataset (Additional file 2). (iii) If domains are annotated to the clusters with codons under selection, F-box (22. 54% of all annotated domains in the dataset), Leucine rich repeats (LRR; 11. 27%), and NB-ARCs (8. 45%) are predominant. Again, this trend is mostly visible in the Level 2 dataset whereas potential domains are more diverse in the Level 1 dataset (Additional file 2).
Acknowledgements We are grateful to  Mathieu Rouard  for providing the GreenPhylDB data and the  SouthGreen bioinformatics platform  (http://www. southgreen. fr/)which was essential for our analysis. We also would like to thank two anonymous reviewers for their constructive comments on the manuscript. IF was granted by  ARCAD  ( Agropolis Resource Center for Crop Conservation, Adaptation and Diversity ), a flagship project of the  Agropolis Fondation , and  JD by scientific council of Montpellier SupAgro. This work was partially funded by the  French Agence Nationale de la Recherche :  ANR-11-BSV7-013-03 , TRANS and by the  French Agence Nationale de la Recherche Investissements d'avenir/ Bioinformatique :  ANR-10-BINF-01-02 ,  Ancestrome.
Objective: To report a series of cases of ulceration of the oral mucosa linked to direct contact with ferrous sulfate in elderly patients. Case summary: The first case report concerns the occurrence of widespread oral ulceration in an 87-year-old woman with Alzheimer's disease. The ulceration extended from the side of the tongue to the floor of the mouth. No clear explanation was found and various local treatments were ineffective. Once it was realized that the ferrous sulfate tablets (given as an iron supplement) were crushed prior to administration (due to the patient's deglutition disorder), withdrawal of this treatment led to rapid resolution of the ulceration. Nine other cases of oral ulcerations associated with ferrous sulfate were identified in the French National Pharmacovigilance Database.
Introduction In older patients, iron-deficiency anemia is associated with an elevated risk of mortality and various morbidities (such as cardiovascular disease and cognitive dysfunction). 1 Treatment of this type of anemia is based on oral iron supplementation (with ferrous sulfate tablets in most cases). Although iron supplementation is generally well-tolerated, mucosal injury to the upper gastrointestinal tract following iron overdose has often been described, particularly in children. 2, 3 ] [4] [5]  However, mucosal injury has very rarely been reported in patients receiving therapeutic dosages of ferrous sulfate, and the few case reports in the literature mainly concern gastric injury. 6 ceration of the oral mucosa following direct contact with ferrous sulfate in elderly patients: a case report and a review of the French National Pharmacovigilance Database Here, we report the case of an elderly patient in whom oral ulceration was induced by direct, prolonged contact with ferrous sulfate.
Review of the French National Pharmacovigilance Database We searched the French National Pharmacovigilance Database between July 1986 and July 2013 and found nine reports of mouth ulceration associated with the use of ferrous sulfate tablets (Table  1 ). The French National Pharmacovigilance system was established in 1973. A network of 31 regional centers receives spontaneous reports of "serious and/or unexpected" adverse drug reactions from health care professionals. Eight of the nine patients were women. The patients' mean age was 81. 5 years (range: 54-97 years). Dysphagia or prolonged presence of tablets in the mouth were reported in three cases and the use of crushed tablets was reported in two other cases. Ferrous sulfate was always the only medication suspected and all the cases of oral ulceration resolved or improved rapidly after withdrawal of this treatment.
No cases of oral ulceration  no concomitant drugs in addition to trospium was reported taken by the patient. Abbreviations: M, male; F, female. were associated with other iron salts (eg, iron fumarate and ascorbate, which are also widely prescribed) were found in the French National Pharmacovigilance Database. In accordance with the literature data mentioned, the database also featured cases of esophageal and gastric ulceration related to the administration of ferrous sulfate.
Phase 4: financial planning Due to budgetary limitations, funding for this venture was not available from either the hospital or the training facilities, which was unfortunate. However, this challenge was overcome using the following three approaches. First, many of the hardware items used in MDT meetings, such as personal computers, software, and audiovisual equipment, were members' personal property. Second, wherever possible, we made full use of free software. We utilized WhatsApp ® (WhatsApp Inc. , Mountain View, CA, USA) and Google Mail ® (Google Inc. , Mountain View, CA, USA) groups to coordinate MDT activities and disseminate information rapidly. Computed tomography images were viewed using OsiriX ® Digital Imaging and Communications in Medicine (DICOM) imaging software (v 5. 6; Pixmeo, Bernex, Switzerland), which is available freely on the internet.
PHILIPPINES Emmalocera sp. (Lepidoptera: Pyralidae) This stemborer was collected at 1 location in Laguna Province and 1 location in Quezon Province during a survey in Jul 2013. Its closest match in GenBank was E. latilimbella (Ragonot), but with only a 93% sequence similarity and an "E" value of 0. 0. Emmalocera latilimbella is only known from Australia and Papua New guinea (BOLDSYSTEMS 2016; global Information System on Pyraloidea 2016), and a literature search revealed no records of larval host plants. With a 93% similarity, it seems unlikely that the borer is E. latilimbella, but based on similarity among other Lepidoptera  (Kim et al. 1999; Cognato 2006) , it is probably in the genus Emmalocera.
Chilo sp. (Lepidoptera: Crambidae) During a survey in the Philippines in Mar 2015, crambid larvae were found boring in the stems of cogongrass near Binan, Laguna Province, causing damage similar to that described above for Acrapex species. Based on the CO1 gene, the closest species in GenBank was Chilo partellus (Swinhoe), a notorious pest of corn and sorghum in southern Asia and East and southern Africa  (Kfir et al. 2002; Sharma et al. 2007 ) that is not known to occur in the Philippines. However, the sequence similarity was only 92% (E value = 0. 0), suggesting that the insect was not C. partellus. This was confirmed by morphological identification as a Chilo sp. , but taxonomically distinct from C. partellus. A collection of 30 larvae was sent to the Fort Pierce quarantine facility, where they were placed on cut stems of cogongrass.
Acknowledgments We would like to thank several people for assistance with taxonomic identifications;  Yutaka Yoshiyasu  for Acrapex azumai,  Junichi Yukawa  for Contarinia sp. ,  James Hayden  for Chilo sp. ,  Kevin Williams  for Aprostocetus sp. and Prospicroscytus mirficus, and  Peter Buhl  for Platygaster orseoliae. Funding was provided by grants from the  Florida Agricultural Experiment Station ,  Florida Fish and Wildlife Conservation Commission , the  Florida Department of Agriculture and Consumer Services , and  USDA-NIFA  grant # 2012-67013-19340.
Objectives: We investigated the neural basis of hallucinations Alzheimer's disease (AD) by applying voxel-based morphometry (VBM) to anatomical and functional data from the AD Neuroimaging Initiative. Methods: AD patients with hallucinations, based on the Neuropsychiatric Inventory (NPI-Q) (AD-hallu group; n539), were compared to AD patients without hallucinations matched for age, sex, educational level, handedness and MMSE (AD-c group; n539). Focal brain volume on MRI was analyzed and compared between the two groups according to the VBM method. We also performed voxellevel correlations between brain volume and hallucinations intensity. A similar paradigm was used for the PET analysis. ''Core regions'' (i. e. regions identified in both MRI and PET analyses, simply done by retaining the clusters obtained from the two analyses that are overlapping) were then determined.
Ethic These data were analyzed anonymously. All subjects gave written, informed consent prior to participation through the local institutional review boards at participating institutions. For the purpose of this study we used the Alzheimer's Disease Neuroimaging Initiative (ADNI) data that were previously collected across 50 sites. Study subjects gave written informed consent at the time of enrolment for data collection and completed questionnaires approved by each participating site's Institutional Review Board (IRB). The complete list of ADNI sites' IRBs can be found in the link: http://adni. loni. ucla. edu/about/data-statistics/. Specifically, they are: Albany Medical College, Banner Alzheimer's Institute,.
Subjects from the Alzheimer's Disease Neuroimaging Initiative Database Data used in the preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (adni. loni. ucla. edu). The ADNI was launched in 2003 by the National Institute on Aging (NIA), the National Institute of Biomedical Imaging and Bioengineering (NIBIB), the Food and Drug Administration (FDA), private pharmaceutical companies and non-profit organizations, as a $60 million, 5-year public-private partnership. The primary goal of ADNI has been to test whether serial magnetic resonance imaging (MRI), positron emission tomography (PET), other biological markers, and clinical and neuropsychological assessment can be combined to measure the progression of mild cognitive impairment (MCI) and early Alzheimer's disease (AD).
Determination of sensitive and specific markers of very early AD progression is intended to aid researchers and clinicians to develop new treatments and monitor their effectiveness, as well as lessen the time and cost of clinical trials. The Principal Investigator of this initiative is Michael W. Weiner, MD, VA Medical Center and University of California -San Francisco. For up-to-date information, see www. adni-info. org. ADNI is a large multicenter, longitudinal, observational trial taking place across the United States and Canada, launched in 2003, in which subjects with normal cognition, amnestic mild cognitive impairment (MCI), and mild AD are followed up with periodic neuropsychological testing, multiple imaging techniques, and fluid biomarkers. Subjects with complete baseline clinical datasets (n5765; including 387 amnestic MCI, 200 controls and 178 mild AD) were included in the current study.
MRI Acquisition Standard 1. 5T T1-weighted images obtained using volumetric 3D MPRAGE protocol with resolutions ranging from 0. 9 mm60. 9 mm61. 20 mm to 1. 3 mm61. 3 mm61. 20 mm were included from the ADNI database. For detailed information on the MRI protocols and preprocessing steps, see Jack et al  [25]. It is of importance to notice that a major effort was devoted in establishing the MRI protocol specifications to standardize 3D T1-weighted sequences across sites and platforms in order to enable the scientific community to carry out relevant multicentric morphometric study (see  [25]  for details). In our work, we choose to restrict our analysis to 1. 5 MRI scans only (3T MRI examination were discarded) in order to have even more consistent data.
MRI image analysis For MRI analysis, 39 patients with hallucinations (AD-hallu group) were compared to 39 control patients (AD-c group). Each of these two groups was preliminary compared to the group of 39 healthy elderly controls (HC). Focal brain atrophy of gray mater (GM) and white matter (WM) was compared between groups using the VBM (voxel-based morphometry) method provided in SPM12b (Statistical Parametric Mapping, Wellcome Department of Cognitive Neurology, London, U. K. ) and ran under Matlab R2010a software (The MathWorks, Natick, MA). We also performed voxel-level correlations between GM/WM atrophy and hallucinations intensity. Voxel-based morphometry analyses included image pre-processing and statistical analyses. Anatomical MRI images were spatially pre-processed using standard procedures  [27].
PET image analysis For FDG-PET analysis, 19 patients with hallucinations (AD-hallu subgroup) were compared to 20 control patients (AD-c subgroup). Each group was also compared to 20 healthy elderly controls (HC subgroup) Focal brain metabolism was compared between groups and voxel-level correlations between brain metabolism and hallucinations intensity were performed within AD-hallu group. To this end, all PET images were spatially normalized to the Montreal Neurological Institute (MNI) space. This was done by first registering each PET image on the corresponding MRI image for each subject using an affine transformation. Then, the transformations estimated from MRI analysis using Dartel algorithm were then applied on the affinely registered PET images. By this way, we benefit from the structural information of MRI data to accurately match all PET images.
MRI and PET image analysis: ''core regions'' We define as "core regions" the regions that were identified in both MRI and PET analyses. This is simply done by retaining the clusters obtained from the two analyses that are overlapping. We looked for these "core regions" either for the comparison between AD-hallu and AD-cor for the correlation analyses with the intensity of hallucinations. MNI Space Utility (MSU, http://www. ihb. spb. ru/,pet_lab/MSU/MSUMain. html), xjView software (http://www. alivelearn. net/xjview8/) and Talairach software (http://www. talairach. org/index. html ) were used to create reports about cluster localization in terms of Talairach Daemon anatomical region labels for both MRI and PET analysis.
Statistical analysis The Statistical Package for Social Sciences software (SPSS ver. 21. 0. 0. 0, http:// www-01. ibm. com/software/analytics/spss/) was used for further statistical evaluation as required. Where appropriate, differences in demographic and clinical data were assessed using parametric (ANOVA, t-tests) and non-parametric tests (Kruskall-Wallis H, Mann-Whitney U). Post-hoc analysis were applied: Tukey post-hoc test for ANOVA and Kruskall-Wallis post-hoc test for H. For categorical measures, x 2 tests were applied. For each test statistic, a probability value of P,0. 05 was regarded as significant.
However, even if there are no clinical data in the ADNI on the type of hallucinations in patients, it is known that in AD visual hallucinations are more frequent than auditory verbal hallucinations  [16]. Moreover, since hallucinations are less frequent in AD than in other neurodegenerative diseases, such as DLB, the only way that one can study so many patients with AD and hallucinations is to have recourse to a cohort as large as the ADNI. The second limitation is that, among the patients with brain MRI (n539), only a half had brain FDG-PET. Thus, the "core region" reflect a much smaller subset of patients, and this could introduce substantial bias. This limitation is inherent in the ADNI cohort, in which only about half of the patients have FDG-PET. In our study, the presence of hallucinations in AD (or AD and DLB) was correlated with a vast anterior-posterior network, with a predominant right brain involvement.
We suppose that patients have a top-down control failure, and also a dysfunction of the bottom-up visual processes. Top-down mechanisms are underlain by the right anterior insula and the right frontal lobe known to be involved in false attribution of a source to a stimulus and deficient intuitive judgment. Bottom-up mechanisms are involved in visuo-perceptual processing with posterior regions. Taken together, all these data are consistent with previously published data on hallucinations in neurodegenerative diseases. Further studies are now needed to elucidate more precisely the anatomic and functional connections underlying hallucinations in AD patients. the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report.
Growth and Analysis of Plant Material Arabidopsis thaliana seeds were obtained from the Nottingham Arabidopsis Stock Centre (NASC), except for promABI3::GUS and promABI4::GUS (Penfield et al. , 2006) (from Dr. Steve Penfield, Exeter University, UK), map1A  (Ross et al. , 2005)  (from Dr. Carmela Giglione; CNRS, France), and rap2. 3  (Ogawa et al. , 2007)  (from Dr. Atsuko Miyagi; University of Tokyo, Japan). prt6-1, prt6-5, ate1-2ate2-1, hre1 (SALK_039484), hre2 (SALK_052858), rap2. 2-1, rap2. 3-1, noa1-2, nia1nia2, and noa1-2nia1nia2 mutants and UBI-X-GUS and MX-HRE2 transgenic lines were described previously  (Hess et al. , 2011; Hinz et al. , 2010; Holman et al. , 2009; Licausi et al. , 2010; Lozano-Juste and Leon, 2010; Ogawa et al. , 2007). New transfer DNA (T-DNA) line accession numbers are rap2.
Stomatal Aperture Analyses and NO Measurements Stomatal aperture measurements were carried out as described previously  (Chater et al. , 2011; McAinsh et al. , 1991). Where required, opening buffer was supplemented with fumagillin (5 mM), SNAP (100 mM), or solvent (0. 001% ethanol). All solutions were perfused with CO 2 -free air. After 2 hr, the length and width of stomatal pores were measured using light microscopy and ImageJ software. Aperture was calculated as an ellipse. Significant differences between SNAP treatment and same-genotype controls were determined using an unpaired t test. NO accumulation was assessed using the specific NO dye DAF2-DA (Calbiochem) as described previously  (Desikan et al. , 2002). Data were analyzed by using ImageJ software. For all assays, measurements from 120 stomata were analyzed in three replicate experiments.
Hypocotyl Length Measurements Seeds were sown on MES-buffered MS, 1% sucrose, 0. 8% agar plates. After 4 days of stratification at 4 C, germination was synchronized by 6 hr light treatment at 21 C. Plates were transferred to a tightly sealed chamber with 300 ppm of pure NO gas (99. 5% pure nitric oxide; Linde), and a replica plate was kept untreated. Plates were maintained under darkness at 21 C for 4 days. Seedlings were harvested and scanned, and hypocotyl length was measured using ImageJ software. Values of hypocotyl length are means ± SD of 16-20 seedlings. Significant differences between NO treatment and same-genotype controls were determined using an unpaired t test. Chromatin Immunoprecipitation and Quantitative PCR Amplification Wild-type Col-0 and 35S::MA-RAP2. 3-HA seedlings (4 days old) grown at 22 C in darkness were used for ChIP analyses.
ChIP was performed as described previously  (Saleh et al. , 2008) , using Dynabeads Protein A (Invitrogen) and an anti-HA (hemagglutinin) polyclonal antibody (ab9110; Abcam). Relative enrichment was calculated by normalizing the amount of target DNA, first to the internal control gene CNX5 (At5g55130) and then to the corresponding amount in the input. Data are mean and SD of three technical replicates from a representative experiment from two biological replicates. Primers used are in Table  S2.
Microarray Analyses Three biological replicates and their corresponding negative controls were hybridized to ATH1 microarrays (Affymetrix). The raw. cel files were background corrected and normalized using the Robust Multiarray Averaging (RMA) procedure  (Irizarry et al. , 2003) , with a custom chip definition file (. cdf) from the Custom CDF project (Ath1121501_At_TAIRG. cdf v14. 0. 0, released March 22, 2011)  (Dai et al. , 2005) , using the Bioconductor ''affy'' package in the programming language R. This CDF remaps the individual probes on the Affymetrix chip to their corresponding genes, using recent sequencing information from the Arabidopsis Information Resource (TAIR). For each sample pair (treatment/mutant and appropriate control), a two-way t test was performed for each gene, with mean expression at least 6 (log 2 , noise/signal transition informed by a histogram of the data) in one of the samples.
ACKNOWLEDGMENTS M. J. H. , S. P. P. , D. J. G. , G. M. M. , J. V. C. , and C. S. C. were supported by  UK Biotechnology and Biological Sciences Research Council (BBSRC)  grants  BB/G02488X/1 ,  BB/G010595/1 ,  BB/F006934/1 , and  BB/K000144/1  (including financial support from  SAB Miller plc ); J. E. G. was supported by  BB/K000063/ 1 ; N. M. I. by a  MARA PhD fellowship  from the  Malaysian government ; S. B. by a  University of Nottingham  PhD fellowship; and M. M. by a  University of Sheffield Faculty of Science Studentship. D. J. G. was supported by a  Nottingham Advanced Research Fellowship  for part of this work. J. L. -J. , A. C. , and J. L. were supported by grants  CSD2007-00057  and  BIO2011-27526  from the  Spanish government. G. W. B. was supported by a  Marie Curie IIF Fellowship.
The work of A. B. was supported by the  Austrian Science foundation FWF  (grants  P21215  and  P25488 ). Rothamsted Research receives grant-aided support from the  BBSRC. D. F. A. T. and J. B. were funded by  BBSRC  grant  BB/ G015066/1. N. M. -d. l. R. and D. A. were supported by grants from the  Spanish Ministry of Science and Innovation  ( BIO2010-15071 ). We thank  Susan Liddell  ( Sutton Bonington Proteomics Facility ) and  Pauline Roubira  for technical assistance.
An overview of the potential discovery space offered by LOFT as a general observatory cannot be given here. Below we just illustrate by example in figures the quality of science data expected from both the LAD and the WFM. LOFT core science will take less than 50% of the mission observing time. Consequently, observatory science will be able to exploit the superb mission capabilities for more than 25 Ms in 3 years. In addition to that, the data of the WFM will be made immediately publicly available: this will provide data for >130 gamma ray burst per year, >5000 type I Xray bursts and long-term timing and spectroscopic information on hundreds of X-ray sources of all classes.
Background The background of the LAD experiment is a critical requirement for some of the science objectives, namely those related to the observation of dim sources (Active Galactic Nuclei), aimed at studying the variations of the 6 keV Iron line, via spectral-timing. The intrinsic scientific requirement is actually related to the amount of residual background in the source data after proper subtraction, usually referred to as background systematics. In LOFT this is controlled by two requirements: the absolute level of the background and the residual fraction, 10 mCrab and 0. 25%, respectively. The LAD background level and spectral distribution were estimated by means of a Monte Carlo simulation using the GEANT code with a detailed mass model of the satellite and instrument. The methods and the results are described in detail in Campana et al.
The Science Ground Segment The Science Ground Segment (SGS) for the LOFT mission follows the traditional structure of ESA astrophysics mission. The Mission Operation Center and the Science Operation Center (SOC) are under the responsibility of ESA, while the Instrument Operation Centers (IOCs) and the Science Data Center (SDC) will be provided by the LOFT Consortium. The satellite will be commanded by ESA through the ground station in Kourou, which will receive part of the data downlink, the rest being received at the Malindi ground station. The telemetry data will be downloaded every orbit (100 minutes) to the two ground stations and analyzed at SOC and SDC to identify special events, deserving a rapid reaction of LOFT or a quick dissemination to the science community. The maximum required reaction time for Target of Opportunities is 12 working hours, although based on similarly operated past missions a faster reaction is anticipated.