dataesr/scientific-paragraphs-categorization huggingface dataset:
DISCUSSION In this paper, we have introduced a method to record and process TLS and MSS data with the purpose of building a 3D reference model of a canal tunnel. A comparison between the SONAR and LASER device characteristics highlights differences that impact the quality of the data. In particular, it appears that MSS data have a much lower resolution than TLS data, and that the angular loss of resolution can be rather strong. Since the elongated shape of the tunnel generates unfavorable incidence angles, the quality of SONAR acquisitions becomes rather coarse at large distances from the scanner. Moreover, this technology tends to provide noisy data. To limit the effect of perturbations on the processing, we first perform a data denoising by meshing. More specifically, a coarseto-fine method, which gradually increases the resolution of the mesh, has been used.
, 2006)  seem appealing for this task. A second important issue is related to the co-registration of the point clouds provided by the scanners. While processing TLS data to obtain the above-water geo-reference 3D model is rather straightforward, this task is much more difficult for MSS data. Due to the low resolution of the data and to the angular loss of resolution, classical techniques such as ICP did not provide satisfactory results in our experiments. To alleviate this problem, its is possible to improve the experimental setup by reducing the distance between MMS stations: an interval of about 5 m would be recommended. Moreover, it is possible to immerse more tar-gets, such as the ladders that we used here, to provide additional references to help the registration. Our experiments show that the targets must be carefully chosen and placed on-site: for example, the ladders should be separated from the canal walls, unless their segmentation becomes problematic.
To obtain a geo-referenced global model of the canal-tunnel, registering MSS and TSS data is a crucial point. The main difficulty we are faced with in this application is that there is no overlap between the above and underwater models. We therefore proposed a 3-step procedure in which, first, geometrical entities are used to fix the attitude parameters. The second step uses the ladders to estimate the vertical correction: we proposed a robust method based on M-estimation to fit lines on the bars and rungs of the ladder using the noisy point cloud. We assessed the method by comparing the results of the fit with direct measurement of distances. In most cases, the error is less than 10 mm (with a maximum of 46 mm). Third, after having extracted the intersection lines between the water surface and the MSS and TLS models, we apply a 2D ICP algorithm limited to estimate the remaining 2D translations.
Background: Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. Methods: We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). Results: The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118).
The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Discussion and conclusions: Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.
A systematic review of those studies found no evidence of bias when restricting to English language literature in reviews of conventional medical interventions  [3]. A similar evaluation in the field of complementary and alternative medicine found that English-language studies tend to report smaller effects than those published in other languages  [4]. The Chinese biomedical literature has been continuously growing over the past decades. China's share in the world's total published scientific papers increased from less than 1% in 1980 to about 12% in 2011, currently ranking second behind the US  [5]. There is limited evidence that searching Chinese databases when performing systematic reviews leads to the identification of additional relevant studies and influences the outcome of meta-analysis.
Available studies are limited to the field of traditional Chinese medicine, and the results of such investigations have been conflicting  [6] [7] [8]. We here report on a case of two recently published independent systematic reviews on the same topic: one for which the authors did not search in Chinese databases and the other for which the authors did. We describe five major Chinese electronic biomedical literature databases, with regard to content, search features, and accessibility. We also evaluate to what extent Cochrane reviewers have included these Chinese databases in their search strategy.
In contrast with the review of Whiting et al. , the review from Gao et al. specifically aimed to evaluate the accuracy of anti-CCP antibodies in the Chinese population. The rationale for restricting the review to the Chinese population was a presumed variability in anti-CCP accuracy, related to the genetic or ethnic background. Gao   studies, of which 114 had been published in the Chinese language. Although Whiting and her colleagues thoroughly searched 10 databases (inception to 2009) without language restrictions and were able to include 151 studies (155 publications), only 5 of these were reported in the Chinese language. In total, the two reviews identified 269 unique studies. Surprisingly, only four primary studies can be found in both reviews (Figure  1 ). This discrepancy can be explained by the fact that Gao et al.
also searched CNKI, one of the largest Chinese biomedical databases, while Whiting et al. did not. The summary estimates of test accuracy generated by the two meta-analyses were comparable. Gao et al. reported a summary estimate of sensitivity of 65% (95% confidence interval (CI) 65% to 66%) at a specificity of 95% (95% to 96%). Most studies in this review had used multiple sets of patient inclusion criteria. Whiting et al. a subset of case-control studies in their review (n = 97) and reported summary estimates of 68% (65% to 71%) for sensitivity and 95% (94% to 96%) for specificity. A limitation when trying to compare the two anti-CCP reviews lies in the lack of details about the index tests under investigation in Gao's review. Whiting et al. provided a complete description of the different types of anti-CCP antibodies evaluated across primary studies (antifilaggrin antibodies; antikeratin antibodies; antiperinuclear factor; first, second, or third generation anti-CCP; mutated citrullinated vimentin) whereas Gao et al.
only characterized assays by manufacturer (Eurimmun vs. non-Eurimmun tests). Yet the fact that the summary accuracy estimates are almost identical in both reviews suggests that the same kind of index tests were reviewed. In this case, a very large body of evidence (114 studies) was missed through not searching in a Chinese database, but this additional evidence seemed to be of no influence on summary accuracy estimates. Here, the results were similar and it may therefore be unnecessary to search Chinese databases, but no claim is made that this would apply to all cases. It is largely unknown whether Chinese databases contain relevant clinical data for systematic reviews and whether including this data would affect the outcomes and conclusions. Further research is needed to resolve this question, especially in fields other than complementary and alternative medicine.
Wu et al. previously reported on a case of two independent reviews evaluating the effectiveness of acupuncture for chronic asthma  [8]. While the first review only searched English language databases, the other also searched Chinese databases. This strategy almost doubled the number of included trials  (12 vs. 22)  and led to an almost ninefold increase in the number of included patients (350 vs. 3,058). The review that searched in Chinese databases found a significant effect of acupuncture on spirometry parameters whereas the other review found no evidence favoring acupuncture. It is highly likely that the amount of data in Chinese databases and their effect on the summary estimates differ by topic of interest and across study types (for example, interventions, diagnostic test accuracy, and prognostic and omics marker evaluations).
Chinese biomedical databases Xia et al. have extensively described five major biomedical databases originating from China: CNKI, Chinese Biomedical Literature (CBM), Chinese Medical Current Content (CMCC), VIP, and WANFANG (China Online Journals)  [15]. They reported that less than 6% of the 2,500 journals indexed in these databases were also indexed in MED-LINE. All databases had advanced search features that allowed combining keywords with Boolean and proximity operators. Four databases had even more advanced search features that allowed command-line-style queries with keywords, fields, Boolean, and proximity operators. All databases accepted English-written queries but all were also language sensitive. In terms of accessibility, all databases but CBM gave free access to study abstracts and offered the possibility to purchase full-text articles without full subscription to the database.
CBM search features were accessible to subscribers only. In another recent evaluation of the relevance of searching Chinese biomedical databases (CBM, CNKI, VIP, and WANFANG) when conducting systematic reviews, Ai et al. found that CBM and CNKI were the two databases that covered the most journals (1,784 and 1,126, respectively)  [16]. The authors recommended CBM for reviewers who aim to search for studies in Chinese and CNKI for non-Chinese-speaking researchers.
Searching Chinese databases: current practice among Cochrane reviewers The Cochrane Collaboration recommends searching without language restrictions to avoid language bias. It also suggests searching regional databases when relevant, citing CBM as an example of a Chinese database  [2]. We aimed to evaluate whether authors of published Cochrane reviews had searched Chinese databases. Study selection was performed by searching the full text of Cochrane reviews for any reference to at least one of the five major Chinese databases. On October 8, 2014, we searched the Cochrane Library from inception using full text screening for the words 'China National Knowledge Infrastructure' , 'China Academic Journals' (former name of CNKI), 'cnki' , 'Chinese Biomedical Literature Database' , 'cbm' , 'Chinese Medical Current Content' , 'cmcc' , 'VIP' , 'Wanfang' , or 'Wan fang'.
Protocols were excluded. Data extraction was performed by one author (JFC or DAK) using a standardized form. We extracted the name of the first author and publication year, whether the reviewers had applied any language restrictions, which of the five Chinese databases were searched, and whether any review author had a Chinese affiliation. We also extracted whether the review addressed a complementary or alternative medicine topic (as defined by Kemper et al. )  [17]. Among 8,680 published reviews indexed in the Cochrane Library, only 243 (3%) had searched at least one of the five major Chinese databases. These were retained for further analysis. All included Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation and 118 (49%) addressed a topic in complementary or alternative medicine.
About half of reviewers had searched multiple Chinese databases (135, 56%). CNKI and CBM were most frequently searched (in 185 [76%] and 162 [67%] cases, respectively) while CMCC was searched in only 21 cases (9%). The great majority of the reviews, 213 (88%), explicitly declared not to have applied any language restrictions, compared to one review that did, while 29 reviews did not make any statement on language restrictions. A limitation to this study is that we only investigated Cochrane systematic reviews, which may stand apart from other reviews because of high standards for the conduct and reporting of literature search. A comparable evaluation of search strategies used in 235 systematic reviews of diagnostic test accuracy published in China before 2011 found that Chinese reviewers had searched Chinese databases (with or without English language databases) in 205 (87%) cases  [18].
Discussion Our case report highlights that large numbers of publications may be missed when not searching Chinese databases. In a systematic literature survey, we found that Cochrane reviewers searching Chinese databases are an exception, mainly limited to review teams with an author with a Chinese affiliation, and focusing on interventions in complementary or alternative medicine. A major hurdle to searching Chinese databases is the amount of resources and personnel needed. Systematic review projects often suffer from time and budget constraints, which may conflict with authors' willingness to maximize the amount of evidence relevant to their clinical question. Searching Chinese databases and extracting data from large amounts of Chinese publications implies having at least one Chinese language reviewer on board or resources to work with biomedical-oriented professional translators.
Balk et al. found that Google Translate may be helpful in extracting data from non-English literature (Chinese, French, German, Japanese, and Spanish)  [19]. Unfortunately, Chinese translations provided the least accurate data in this comparison, with about one out of five items incorrectly extracted more than half of the times when using Google Translate, as compared to extraction performed by a fluent speaker. The credibility and integrity of the studies that can be additionally included when searching Chinese databases should also be taken into account. We are not aware of any direct way to evaluate the reliability of the data contained in biomedical journals and databases. One can only evaluate indirect evidence, such as evidence of scientific misconduct. A number of cases of scientific fraud and misconduct in China have been reported in the past few years, including plagiarism, falsification, and fabrication of data  [20].
et al. only searched for studies reported in English or Chinese, whereas the review from Whiting et al. had no geographical or language restrictions. The most striking finding when comparing the two reviews is the large number of studies published in the Chinese language identified by Gao et al. but not by Whiting et al. Gao and colleagues searched two biomedical databases (MEDLINE and China National Knowledge Infrastructure (CNKI), 2000 to 2010) and included 118 Comparison of Whiting et al. 's and Gao et al. 's systematic reviews.
2010[12]Gao et al. 2012[11]Primary aim To compare the accuracy of anti-CCP antibodies and rheumatoid factor in diagnosing rheumatoid arthritis in patients with early symptoms of the disease To determine the accuracy of anti-CCP antibody in diagnosis of patients with rheumatoid arthritis in a Chinese population Databases searched MEDLINE, Embase, Science Citation Index, BIOSIS, ISI Web of Science, System for Information on Grey Literature in Europe, Zetoc, National Technical and Information System, Dissertation Express MEDLINE, CNKI a 151 studies corresponding to 155 publications were included; b Estimates from case-control studies (n = 97). Anti-CCP, anti-cyclic citrullinated peptide; CI, confidence interval; CNKI, China National Knowledge Infrastructure.
INTRODUCTION Multiplexing considerably reduces the costs of highthroughput sequencing (HTS) for amplicon-based studies, but its results are often subject to a pervasive and overlooked bias. The samples labelled during the polymerase chain reaction (PCR) amplification by the incorporation of tag sequences appended to PCR primers are prone to cross-contamination. This is due to a phenomenon that consists in switching of the tags among amplicons and re-ferred to as mistagging  (1). A comprehensive solution is urgently needed since various multiplexing strategies are extensively being applied for microbial ecology  (2) , environmental biomonitoring  (3, 4)  and biomedical diagnosis  (5). This can become critical when interpreting HTS data sets in terms of species presence-absence and even more when used as a decisive basis for health care or ecosystem management.
Computational analysis Quality filtering and paired-end reads assembly. In order to keep a maximum of reads for deeper insights into the understanding of mistagging biases, we kept sequences with a mean Phred quality score above 20, but no ambiguous base call. We compared the tagged primers using Needleman-Wunsch alignments, allowing up to one and two errors in the tag and primer sequences, respectively. If we could not find a matching tagged primer, the corresponding pair was discarded. Then, we reconstructed the sequence from each paired reads according to the Needleman-Wunsch alignment resulting in the best overlap, with at least 12 bp and up to five differences. We removed sequences of less than 20 nucleotides. Clone sequence assignment. We computed a reference, hashing tree structure containing all the sequences of the clones, our extensive foraminiferal database and the PR2 database  (30).
Each sequence found in the hashing tree was de-replicated and statistics associated with the reference sequence name, number of reads and tagged primers were updated. If no hit was found, the new sequence was appended in the tree and assigned by Needleman-Wunsch alignments against our databases. First, we searched the clone sequences database relying on a hard threshold of 95% similarity for unambiguous assignment, according to the pairwise distances of the selected clones (Supplementary Figure  S3 ). Then, we checked the complete distance set with a soft threshold of 90% similarity. If no match was found in the clone sequences database, we repeated this procedure on the foraminiferal and PR2 databases. If still no hit was found, we searched for Basic Local Alignment Search Tool (BLAST) hits of least 90% identity and 90% coverage against (i) the sequences of the hashing tree, (ii) the National Center for Biotechnology Information (NCBI) nucleotide database and (iii) the PhiX genome.
We analysed the remaining unassigned sequences to screen for the presence of chimeras and repeated motifs of at least seven bases. First, based on the BLAST results, we considered a sequence as chimeric if different parents form heat shock proteins sep-arated by less than two nucleotides and had an identity threshold above 90%. Subsequently, we ran UChime  (31)  in database mode and considered a sequence as chimeric above a score of 0. 3. Finally, we searched for repeated subsequences of at least seven nucleotides, starting with the detection of primer sequence motifs. If we found no match throughout these steps, we considered the sequence as unknown. Mistagging-based filter. Our filtering procedure is designed to discriminate critical mistags from true sequences based on the information conveyed by the occurrences of non-critical mistags.
This means that if the same ISU is found in several samples, a different threshold for this ISU will be computed for each of the samples in which it was found. Therefore, the relative proportions of reads in each sample are accounted implicitly. To compute these thresholds, we gather for each sequence labelled with an expected combination the distribu-tion of abundance of this sequence labelled with all unexpected combinations that share at least one primer with the current expected combination. This leads to a set of abundances from which we compute a non-parametric rejection region to decide whether the corresponding sequence is genuine or a critical mistag (see Computational Methods). All the analysed raw read data sets are submitted to the NCBI BioProject ID 245467. All software used to produce the data or generate LSD experimental planning is available at https://github.
A trade-off between the number of samples and the amount of replication must be considered to ensure that rare species sequences remain unfiltered from replicates. Finally, it should be noted that the same amount of caution towards mistagging and applying alleviating measures should also be taken into account for non-environmental studies pooling together the tagged specimens  (48). In conclusion, we propose a few recommendations to increase the accuracy of HTS data sets based on multiplexed amplicon libraries: (i) Proscribe single-tagging and saturated double-tagging designs. (ii) Choose tagged primer combinations according to LSD to maximize the mistagging information. (iii) Minimize the sample saturation to reduce the proportion of critical mistags. (iv) Incorporate at least two PCR replicates to remove error ISUs.
5). Based on the holotype, an isolated skull, the total length is estimated to reach 1. 5 meter if proportion of Tselfatia is used. Teleosts indeterminate. Based on its mouth morphology, without marginal teeth and a small gape, Erfoudichthys rosae was probably very low in the trophic level. We use the trophic level of Chanos, 2, for this species. Based on the proportion of Chanos, the total size of E. rosae was ca. 45 cm. Fig  13  and Table  1  show the trophic position (or level) and body size of the Kem Kem taxa. assemblages on the basis of data from Fishbase (S1 Table ), with comparable value for the Kem Kem assemblage as estimated above.
Acknowledgments The authors thank  Mr. Rjimati , from the  Ministery of Energy, Mines, Water and Environment  for providing authorizations to reach the studied area. We acknowledge the driver team of Transport  Touristique Bakabou  and the team of volunteers from  SESNE Society of Elbeuf  for assistance with excavations during the 2008 fieldtrip. Patrice Raboeuf  is thanked for providing the articulated specimen of Obaiichthys. Some uncatalogued specimens previously housed in the musée des dinosaures of Espéraza, France, were donated to the  University Moulay Ismaïl  and are catalogued under UNI numbers. We thank both reviewers,  Bouziane Khalloufi  (Paris) and  Paulo Brito  ( Rio de Janeiro ) for their suggestions and corrections.
Remote sensing is one of the most common ways to extract relevant information about the Earth and our environment. Remote sensing acquisitions can be done by both active (synthetic aperture radar, LiDAR) and passive (optical and thermal range, multispectral and hyperspectral) devices. According to the sensor, a variety of information about the Earth's surface can be obtained. The data acquired by these sensors can provide information about the structure (optical, synthetic aperture radar), elevation (LiDAR) and material content (multi and hyperspectral) of the objects in the image. Once considered together their complementarity can be helpful for characterizing land use (urban analysis, precision agriculture), damage detection (e. g. , in natural disasters such as floods, hurricanes, earthquakes, oil-spills in seas), and give insights to potential exploitation of resources (oil fields, minerals).