dataesr/scientific-paragraphs-categorization huggingface dataset:
| MATERIAL S AND ME THODS Data from patients who underwent thyroidectomy at a single tertiary hospital and who had been studied preoperatively through thy- A thyroid ultrasound was performed preoperatively by 2 radiologists specialized in neck ultrasound to describe the presence or absence of the following parameters: echogenicity, microcalcifications, irregular borders, intranodular increase in central vascularization and presence of a halo. Echogenicity was determined as a function of the surrounding tissue and is classified as anechoic, hypoechoic, isoecotic, hyperechoic or heterogeneous echogenicity. The presence of micro-or macrocalcifications was determined. The shape of the nodule was classified as regular or irregular. Doppler echography was studied if there was an increase in vascularization at the intranodular level.
roid US and FNA was collected between March 2006 and January 2016. Demographic and clinical information was obtained through a retrospective review of medical records and a prospectively collected thyroid pathology database. Surgical interventions were performed by a team of 2 general surgeons from the Endocrine Surgery Unit at Santa Creu i Sant Pau Hospital in Barcelona, Spain. The surgical indication was made by individually assessing the patient's clinical, ultrasound and cytological data according to our centre's protocol. Patients with at least 1 of the following criteria were referred for surgery: high suspicion of malignancy, rapid nodule growth, compressive symptomatology, nodules larger than 4 cm, repeatedly nondiagnostic FNA, as well as those who expressed desire of being intervened either for aesthetic reasons or for uneasiness with the diagnosis.
Fluorescence and confocal microscopy imaging Images and Z-stacks of UMAMIT24-GFP and UMAMIT25-GFP for localization of UMAMIT24-GFP and UMAMIT25-GFP within the seed were taken using a Zeiss ® LSM 880 confocal laser-scanning microscope. Spatiotemporal expression of UMAMIT24-GFP and UMAMIT25-GFP was examined using an Olympus ® SZXZRFL3 stereomicroscope attached with the Olympus DP71 digital camera (Olympus ® America, NY, USA). Subcellular localization of UMAMIT24-GFP or UMAMIT25-GFP was imaged using an Olympus ® FV1000 confocal microscope equipped with an UPLSAPO ×60/1. 2 water immersion objective (for protoplats) or a ×20/0. 85 oil immersion objective (for thiodiethanol-cleared tissue), with the confocal pinhole size corresponding to 1 Airy unit. All images were taken using wavelengths as follows: GFP (excitation 488 nm, emission 500-530 nm), mCherry (excitation 543 nm, emission 565-615 nm), chlorophyll (excitation 488 nm, emission >650 nm), or Syto82 (excitation 543 nm, emission 565-615 nm), and merged using ZEN ® software (Zeiss), Olympus ® Fluoview (Olympus ® ), and ImageJ.
UMAMIT24 and 25 are expressed in distinct cell types in developing seeds Publicly available microarray data suggested that both UMAMIT24 and UMAMIT25 are expressed in seed and silique tissues 6 DAP, and show low expression in vegetative tissues  (Schmid et al. , 2005). To identify the cell types that express UMAMIT24 and 25 within the silique, UMAMIT24 or UMAMIT25 were tagged with GFP at the C-terminus and expressed under the control of their native promoter (UMAMIT24promoter:UMAMIT24-GFP and UMAMIT25promoter:UMAMIT25-GFP). Siliques were collected between 4 and 14 DAP, and GFP fluorescence was visualized in dissected siliques. UMAMIT24-GFP expression became visible at 6 DAP in the chalazal seed coat of developing seeds with little to no expression in the embryo, seed coat, or endosperm (Fig.
Acknowledgements We thank the  Salk Institute Genomic Analysis Laboratory  for providing the sequence-indexed Arabidopsis T-DNA insertion mutants, and the  ABRC  and  GABI-Kat III  for providing the T-DNA insertion line seeds. We thank  Cindy Denbow  and  Dr Eva Collakova  for their work on the yeast UPLC data,  Virginia Johnson  for her work on the plant HPLC data, and  Dr Ayumi Hyodo  for her work on the N and C enrichment experiments. The use of the  Microscopy and Imaging Center facility at Texas A&M University  is acknowledged. The Olympus FV1000 confocal microscope acquisition was supported by the  Office of the Vice President for Research at Texas A&M University. This work was supported by The  National Science Foundation   MCB 1052048  (GP and SO) and MCB1519094 (GP), the  Virginia Agricultural Experiment Station  and the  Hatch Program  of the  National Institute of Food and Agriculture, U.
Photodynamic therapy On PubMed, all studies proposed for "photodynamic therapy and peritoneal carcinomatosis" (n = 82) were analyzed. An initial evaluation of the title and abstracts were performed to exclude articles which didn't really evaluate these therapeutic for PM. Many articles were about photodynamic diagnosis and not therapy. We excluded articles about in vitro experimentations. Thirty-one articles were assessed for eligibility: 9 trials, 20 preclinicals studies, and 2 reviews. We analyzed only preclinicals studies and clinical trials. Full text was available for 8 trials and 19 preclinical studies. We included, finally, these 27 articles. On clinical trials, only 1 of the 2 trials proposed was really about the PDT (NCT02840331).
Acknowledgements: We want to thank  Dr Katrien Remaut  for her contribution in reading and correcting this paper. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. Research funding: None declared. Employment or leadership: M. Pocard is expert consultant for GAMIDA company. M. Pocard had commercial relation with ROCHE, SANOFI, ETHICON company, Capnomed. Honorarium: None declared.
TreM data For all study plots, each tree, including the stem and crown, was visually inspected for TreMs by two observers. Based on the typology of  Vuidot et al. (2011) , we created a list of 30 TreM types that we used to classify TreMs on our plots. All living trees with a DBH > 6 cm and snags located within the plots were searched for presence of TreMs (Appendix 2); we surveyed 13,640 living trees and snags in total. We arranged the TreM types into 12 groups for further analysis according to  Paillet et al. (2017) : crown deadwood, broken tops, conks of fungi, woodpecker cavities, non-woodpecker cavities, base cavities, bark characteristics, cracks, outgrowths, patches with exudates, epiphytes, and dendrothelms. All TreMs were surveyed in 2015 and 2016 during the period of June to September.
Data analyses Generalized linear mixed models (GLMMs) were used to assess the effect of local plot structure and spatial variability on diversity and density characteristics of TreMs. Fixed effects included tree species richness (i. e. , total number of tree species per plot), RMS DBH (root mean square diameter of trees at breast height in a given plot), proportion of snags (proportion of snags per plot versus total number of trees), and region (Dinarides and Carpathians). The random effects structure mirrored the spatial hierarchical nature of the sampling design, including plots nested within pairs of plots, which were nested within stands nested within regions. In the models of TreM density, the tree density per plot was treated as a nuisance variable to account for a trivial positive relationship between tree density and TreM density.
, 2017a) , may influence the presence of conks of fungi and even woodpeckers  (Jackson and Jackson, 2004 ). We also observed much higher densities of base cavities compared to  Paillet et al. (2017) ; because large cavities take more time to develop, higher rates of occurrence on very old trees would be expected, thus many primary forests would have higher numbers of older trees with longer periods of time since the last severe disturbance  (Siitonen et al. , 2012). In contrast, we found lower densities of outgrowths and bark characteristics in the Dinaric dataset compared to the French strict forest reserves  (Paillet et al. , 2017) ; outgrowths and bark characteristics tend to occur more frequently on oaks (Quercus spp. ), firs (Abies spp. ), and spruces (Picea spp. ) compared to beech  (Vuidot et al.
Acknowledgement: This project was supported by the institutional project  MSMT CZ. 02. 1. 01/0. 0/0. 0/16_019/0000803 ,  MSMT  project  LTC17055 , through the  Czech University of Life Sciences  (Grant IGA no. B09/17  and  CIGA  no. 20184304 ), by  institutional  project  MSMT EVA4. 0 CZ. 02. 1. 01/0. 0/0. 0/16_019/0000803  and by the  European Regional Development Fund-Project  " Mechanisms and dynamics of macromolecular complexes: from single molecules to cells " (No. CZ. 02. 1. 01/0. 0/0. 0/15_003/0000441 ).
People with intellectual disabilities (PWIDs) are now living longer; thus, the incidence of cancer within this population is increasing. Available data indicate an excess of digestive tract cancers in PWIDs, but colorectal cancer has rarely been specifically studied and has not been extensively reviewed. This is despite risk factors such as being overweight, obesity, and lack of exercise being more frequent in PWIDs. In this article, we examine the literature on the frequency, screening, and treatment of colorectal cancer in PWIDs by assessing 4 databases, Medline, EBSCO-CINHL, ASSIA, and PsychLIT, from 1970 to February 2017. Findings indicate that the frequency trends slightly higher than that found in the general population. Screening presents a unique opportunity to discover early colorectal cancer, but is underused in PWIDs compared to the general population.
Screening was also added to the search terms since bowel screening was in place in some countries. Four databases (Medline, ASSIA, EBSCO-CINHL, and PsychLIT) were used for this review as these incorporated medical databases related to PWIDs  [21, 22]. The terms were used in combination and were adjusted to suit the terminology of the database searched. To capture the "grey literature," and ensure total coverage of the data, searches of professional organizations (e. g. , Foundation for People with Learning Disabilities), government bodies (e. g. , Learning Disabilities Observatory, England), and special interest groups were performed   [23]. Hand searches were also undertaken by reviewing the reference lists of the articles retrieved by the database searches. It should be noted that due to the limited literature available all types of studies and interventions were considered  [22].
In addition, rather than review the empirical literature, the authors wanted to update current knowledge on colon cancer and bowel screening; hence, articles were included that had an educational slant as well as information booklets aimed at supporting the PWID and the caregiver. The number of articles retrieved by each database and search term is shown in Figure  1. The inclusion criteria consisted of all studies being written in English and relating specifically to colon/bowel screening/cancer screening in PWID. It should be noted that 2 articles, 1 French and 1 Japanese, were included due to their relevance and availability of translations. Exclusion criteria extended to other cancers/cancer screening. Titles and abstracts were screened to ensure adherence to the inclusion criteria and eligibility to the final literature review.
3 were expected (SIR 95% CI 0. 4-1. 7), and 6 patients with rectal cancers were observed while 7 were expected (SIR 95% CI 0. 3-1. 9) [5]. The second study, conducted in Western Australia on 9,409 PWIDs between 1982 and 2001, was another data linkage study, linking an intellectual disability database to a cancer registry. There were 14 male patients with colon or rectal cancers when 9. 38 were expected, indicating an increased SIR of 1. 39 (95% CI 0. 14-2. 37). Nine cases were observed for women when 2. 9 were expected, indicating an increased SIR of 3. 10 (95% CI 1. 42-5. 88) [6]. Both authors noted the small sample size as a limitation. A mortality study conducted in the UK reviewed records from the Leicestershire Intellectual Disability Database between 1993 and 2006. It included patients with moderate to profound intellectual disabilities living mainly in institutions but also with their family or independently in the community  [26].
Institutional Population More data are available for PWIDs living in institutions than for the general population of PWIDs. Data from 3 consecutive British studies by the Stoke Park group of hospitals used cause of death of their residents as documented in hospital records over a 65-year period. However, it should be noted that these studies did not use the international classification of diseases, did not report incidence by age, and standardised mortality measures were not employed. Results suggested an increased frequency of colon and rectal cancer in PWIDs compared to the general population. Among 61 PWIDs who died from cancer during the 40-year period from 1936 to 1975, 10 (12%) succumbed to colon (n = 5; 1 male, 4 female) and rectal (n = 5; 4 male, 1 female) malignancies. The authors emphasized that, compared to the general population, relatively more PWIDs die from these cancers (17 vs.
An Israeli study reviewed 450 records of death in 53 residential centres between 1991 and 2005. The findings revealed 74 cancer deaths from people with mild, moderate, or severe IDs living in institutions. Colorectal cancers accounted for 9. 4% of these cancer deaths  [31]. A limitation was that those who died at home or in a foster family were not included in this study. A recent study in France used data from a large survey of 1,519 institutions, finding 3 cases of colorectal cancer among a total of 32 cancers, while 1 colorectal cancer was expected, suggesting a non-significant increase with an associated SIR of 3 (95% CI 0. 6-8. 76) [32]. A Japanese study found PWIDs not to be at more risk of adenomatous polyposis syndrome (APS) or colon cancer  [33]. Colonoscopy screening was undertaken in an institution of 134 patients (age range 32-69 years).
6% in PWIDs, lower than the 50. 4% uptake in the general population  [52]. This is in contrast with other work in the UK published a year earlier and again obtained from the JHSCSAF, which suggested lower rates for bowel screening in PWIDs (28. 1%) compared to the general population (40. 5%)  [53]. Canadian work comparing 15,791 PWIDs and 791,792 without IDs from administrative health and social services datasets for Ontario residents aged between 50 and 64 years has suggested lower colorectal cancer screening rates for PWIDs (32%) than in the general population. Of those PWIDs, 18. 5% had undergone a FOBT compared to 26. 4% of the nondisabled population between 2008 and 2009  [54]. It must again be remembered that the population in these studies only reflects those in contact with services or appearing on social service records.
Participation in FOBT was 7. 5% for PWIDs aged 18-76 years, but data for people aged 51-74 years was not reported. The findings, however, have several weaknesses; for example, the non-responders may be a different population, surveys were only sent to those in contact with services, and there is always the possibility of recall bias or interpretation issues of the questions posed. Work in terms of facilitating bowel screening is limited and comes mainly from the UK. One study reviewed records from a local Direct Enhanced Service register and identified 238 clients aged 60-74 years who were eligible for FOB screening, of whom 19 (8%) had participated in the screening  [58]. Information was collected from 31 of 47 GP practices, with no indication of why all practices were not consulted. Another study reported within the paper used health promotional materials aimed at increasing the uptake of FOB screening.
ACKNOWLEDGEMENTS This research was funded by a sub-contract from  Florida International University  to MSABI (Subcontract No. 800000246-05 ). J. T. conceived and designed the laboratory experiments and small community test trial. J. T. and F. M. conducted the laboratory experiments, test trial and analysed the data. K. H. conceived, designed the MSABI test kit and conducted the community education intervention. J. T. and F. M. supported the intervention trial with laboratory support for test production. K. H. and J. M. analysed the intervention data. J. M, F. M. and K. H. wrote the paper. The authors declare no conflict of interest. The founding sponsors had no role in the design of the study, data collection, analysis or writing the manuscript.
Naming, reporting, and pathogenicity of mutations The consistent use of nomenclature in managing DNA sequence mutations is essential for concise communication of diagnostic testing and genetic risk assessment. 60 In clinical practice, aberrations are often referred to as mutations, and are referred to such in clinical reports. However, one must note that the more accurate technical term is 'variant'. It is recommended that mutations are named according to the Human Genome Variation Society guidelines, or according to American College of Medical Genetics guidelines on mutations and mutation pathology in the case of germline mutations. 86, 87 escription of mutations at the DNA level using the stable Locus Reference Genomic reference sequence is recommended to enable comparison across studies and databases.
TP53 locus-specific databases are available and are important tools for analyzing and assessing the pathogenicity of TP53 mutations. These are the IARC TP53 database (http://p53. iarc. fr/), the TP53 website (http://p53. fr/), and the Seshat online software (http://p53. fr/tp53-database/seshat). The Seshat online software, for example, provides a quality check of the mutation nomenclature, generates a description of the mutation, and assesses the pathogenicity of each mutation with the use of specific algorithms. Structural and functional information for each mutation is also produced. 35, 89.
5 months (prespecified Pneumonia (13%) with R/R CLL/SLL Median age (range): 107/116 (92%) (prespecified primary (prespecified primary primary analysis) Hypertension (13%) and del(17)p 64 (57-72) analysis, median analysis) Anemia (10%) Ibrutinib 420 mg OD ECOG score: 11. 5 months follow-up) Thrombocytopenia (8%) NCT01744691 0: 49 (34%) ≥1: 95 (66%) Atrial fibrillation (6%) (24-month extended analysis) Pharmacyclics LLC. Median prior regimens Janssen Research (IQR): 2 (1-3) & Development, LLC RESONATE: a phase 3, Adult patients with del(17p) ORR in del(17p) Median PFS in del(17p) Median OS in Grade 3-5 AE occurred (18, 99) open-label, multicenter R/R CLL/SLL 127/391 (32%) patients treated and/or TP53 patients del(17p) or TP53 in 56% of patients study of ibrutinib versus (n=391) with ibrutinib: 89% not reached at patients not treated with idelalisib ofatumumab in Ibrutinib arm.
19 months follow-up reached + rituximab and 48% treated patients with Median age (range): ORR in del(17p) in patients treated at 19 months with placebo + rituximab previously treated 67 (30-86) patients treated with with ibrutinib follow-up in Grade 3-5 AE occurred CLL/SLL ECOG score: ofatumumab: 20% patients treated in >5% of patients: Ibrutinib 420 mg 0: 79 (41%) (median follow-up Median PFS in del(17p) with ibrutinib Idelalisib + rituximab OD versus ofatumumab 1: 116 (59%) 19 months) and/or TP53 patients Neutropenia (34%) Median prior 5. 8 months in patients Median OS not Thrombocytopenia (10%) NCT01578707 regimens: 3 (1-12) treated with ofatumumab reported in Placebo + rituximab Ofatumumab arm. del(17p) or TP53 Neutropenia (22%) Pharmacyclics LLC. Median age (range): Patients with both del17p patients treated Thrombocytopenia (16%) Janssen Research & 67 (37-88) and TP53 mutation with ofatumumab Anemia (14%) (overall Development, LLC ECOG score: (n=38) had worse study population) 0: 80 (41%) PFS compared with 1:116 (59%) patients with neither of Median prior regimens: these abnormalities 2 (1-13) (n=68) (P=0.
1%) (overall study population) NCT01203930 Median prior regimens: 0 Both del(17p) and Gilead Sciences TP53 mutation: 4/64 (6. 3%) Study 116: a randomized, Adult patients with R/R del(17p) and/or ORR in del(17p) Median PFS in del(17p) Not reported in Grade 3-5 AE occurred (19, 23) double-blind, placebo-CLL not eligible TP53 mutations and/or TP53 patients and/or TP53 patients del(17p) and/or in 56% of patients controlled study of for cytotoxic treated with treated with idelalisib TP53 patients treated with idelalisib idelalisib in agents (n=220); Idelalisib + rituximab Idelalisib plus plus rituximab: + R and 48% treated combination with PD within 24 months 46/110 (42%) rituximab: 77% not reached with placebo + rituximab rituximab for previously of last treatment Grade 3-5 AE occurred treated CLL Idelalisib + rituximab Rituximab: ORR in del(17p) Median PFS in del(17p) in >5% of patients: Idelalisib 150 mg Median age (range): 50/110 (45%) and/or TP53 patients and/or TP53 patients Idelalisib + rituximab arm: BD plus rituximab versus 71 (48-90) treated with treated with rituximab: Neutropenia (34%) placebo plus rituximab ECOG score/Karnofsky rituximab: 15% 4.
0 months (second Thrombocytopenia (10%) status: not reported (second interim interim analysis) Placebo + rituximab arm: NCT01539512 Median prior regimens: analysis, median Neutropenia (22%) 3 (1-12) exposure 5 months Thrombocytopenia (16%) Gilead Sciences Placebo + rituximab arm. with idelalisib, Anemia (14%) Median age (range):.
, 2012) ; http://www. endtb. org/clinical-trial; ClinicalTrials. gov), and thus has the potential to become a pivotal TB drug. We have recently shown that MXF kills non-replicating Mtb persisters in ex vivo caseum  (Sarathy et al. , 2018)  at concentrations that are achieved clinically in caseous foci  (Prideaux et al. , 2015a; Heinrichs et al. , 2018). Understanding the complex partitioning of MXF and other FQs in the cellular compartments of these lesions where intracellular pathogens reside constitutes one of the major remaining knowledge gaps to fully elucidate the lesion-centric pharmacokinetics and pharmacodynamics of this drug class. Here we combine high resolution MALDI MSI with histology staining, and quantitative image analysis, to study the spatial distribution of small molecule drugs in distinct cellular clusters of TB lesions and understand spatial drug partitioning in relation to where the pathogen resides.
Lastly, in the MALDI MSI ion map, we measured the relative abundance (drug/internal standard ion counts) of MXF in each ROI, expressed as the mean pixel intensity per ROI (each ROI containing 48 to 429 pixels, Figure  3C ). We found that average MXF contents were significantly different across the majority of ROIs (Figure  3 -figure  supplement 4A ) with a between-ROI variability of 43. 4%. These data were compiled to search for correlations between MXF abundance, measured as mean pixel intensity, and each of the recorded parameters (i. e. fraction of histiocytes, lymphocytes, neutrophils, epithelial cells and necrotic area, and distance from lesion outer edge, Figure  3 -source data 1), with the objective of identifying the major drivers of MXF distribution in TB lesions. Using Spearman rank correlation, we found a positive association between MXF abundance and the fraction of macrophages, and an inverse correlation with the relative distance from lesion border and the necrosis fraction (Figure  3 -source data 2 and Figure  3 -figure supplement 4B).
There was no significant association between MXF intensity signal and the percentage of other immune cell types in ROIs (Figure  3 -figure supplement 4C). These observations prompted us to use a nonlinear modeling approach to broadly interrogate the dataset and build a model of MXF partitioning in lesions. Using nonlinear mixed effect modeling (nonMEM) with the full dataset, we found that accounting for histiocyte fraction reduced the between-ROI MXF variability from 44. 0% to 28. 3%, which further decreased to 20. 0% when relative distance of ROI to lesion edge was integrated in the model. This was consistent with vascular function and small molecule penetration decreasing as the distance from the granuloma outer edge increases  (Datta et al. , 2015). Factoring the fraction of the ROI occupied by necrotic tissue further reduced the variability from 20.