dataesr/scientific-paragraphs-categorization huggingface dataset:
Results and Discussion For our experiments, we utilized the Weibo check-in data set and used KDE to analyze the density of check-in data. The overall density of check-ins during January-March 2016 can be observed in Figure  4 , and it can be observed that the center of the city has a high density of check-ins, which is a normal behavior for a big city due to easy accessibility of transport (i. e. , subway) and living facilities (i. e. , food, entertainment). Moreover, the high density of check-ins can be observed near the district borders of Baoshan, Changning, Minhang, Putuo, and Pudong New Area as compared to the center of these district. To investigate the check-in frequency and behavior, we analyzed the data regarding gender (male and female) in 10 districts of Shanghai. Figure  5a ,b shows the overall weekly check-in trend; which depicts that female users prefer to use Weibo more as compared to male users during the whole week as well as during weekdays and weekends in all districts of Shanghai.
Furthermore, it is observed that during whole week check-in frequency increases a lot at night (  20   To investigate the check-in frequency and behavior, we analyzed the data regarding gender (male and female) in 10 districts of Shanghai. Figure  5a ,b shows the overall weekly check-in trend; which depicts that female users prefer to use Weibo more as compared to male users during the whole week as well as during weekdays and weekends in all districts of Shanghai. It is also observed that check-in frequency increases during Saturday and Sunday. Moreover, Figure  6a ,b shows the check-in density in Shanghai. It is observed that female users prefer to use Weibo as compared to male users and hence justifies the results of Figure  5. To investigate the check-in frequency and behavior, we analyzed the data regarding gender (male and female) in 10 districts of Shanghai.
Conclusions In the current study, we presented an in-depth empirical investigation of check-in behavior using intensity maps and trends using LBSN data. We investigated the check-in behavior from several different angles: the difference in gender, during weekdays and weekends, and daily and hourly patterns. In our results, we observe high rates of social media usage from female users and differences in check-in behavior during weekdays and weekends in all studied districts of Shanghai. Apart from the inherent limitations of LBSN data, we discuss here to what extent LBSN data can be exploited to observer check-in behavior. More specifically, compared to other data sources (such as survey, census, GPS traces and call detail records), LBSN check-in data have some advantages, such as low cost and high spatial precision.
However, check-in data also has some limitations, such as bias of gender, a low sampling frequency, and bias of location category. In summary, LBSN data is more likely to be a supplement to than a substitute of traditional data sources. Based on the results of the empirical study, LBSN data has the potential to provide a new outlook as a supplement to observe gender differences and intensity of check-ins (during weekdays and weekends) and can help policymakers to define policies regarding the supply of services in urban areas within a city. It can also help to observe variations in population density over the period and act as a tool to estimate the supply of services in the city. In the future, we plan to use LBSN data as a means to investigate the factors that influence the change in human check-in behavior within the city.
Of 71 declining lavenders tested, one L. angustifolia cv. Matherone plant of field MTF and one L. intermedia of cv. Grosso plant from field GS gave a positive 16S rRNA amplification, whereas 20 symptomless lavenders and 5 greenhouse-grown lavender seedlings tested negative. In both of the positive cases, the sequences were 100% identical to the 16S rRNA sequence of "Candidatus Phytoplasma trifolii" (GenBank accession number AY390261)  (19). Two "Candidatus Phytoplasma solani"-positive L. intermedia cv. Grosso plants from field RS (C T values of 28. 6 and 32. 5) gave 16S rRNA amplicons with sequence similarity of 99. 7% to "Ca. Phytoplasma solani" 16S rRNA (GenBank accession number AF248959) (2). To search for other bacteria associated with declining lavenders, the bacterial community present on healthy lavenders was compared to that of "Ca.
The primers were f-Cox (5=-CGTCGCATTCCAGATTATCCA-3=) and r-Cox (5=-CAACTACGGATATATAAGAGCCAAAACTG-3=). The COI TaqMan MGB probe (5=-TGCTTACGCTGGATGGAATGCCCT-3=) was 5= labeled with 6-carboxyfluorescein (FAM) as the reporter dye. Reactions were performed in a final volume of 20 l containing 10 l of QuantiTect multiplex PCR buffer (Qiagen, Hilden, Germany), 0. 2 M each primer and COI probe, 0. 4 M Stol probe, and 1 l of purified nucleic acid. Assays were performed on an MX 3005 apparatus (Stratagene, La Jolla, CA, USA). The cycling conditions were as follows: 15 min at 95°C for Hot Start Taq DNA polymerase activation, followed by 50 cycles of 94°C for 60 s and 59°C for 90 s. The estimation of the cycle threshold (C T ) was calculated with MXPro v4. 10 software (Stratagene, La Jolla, CA, USA).
In each PCR plaque, three healthy lavenders and three "Ca. Phytoplasma solani"-positive lavenders were used as controls. Samples with C T of Ͻ40 were considered positive. For a time course quantitative survey of "Ca. Phytoplasma solani" infection, a quantitative reference was added to the assay. It consisted of a plasmid containing the gene target as the insert. Amplification of a 976-bp fragment of the "Ca. Phytoplasma solani" strain PO map gene was achieved using primers adkF2 (5=-GTTGGTCGCAGAATTTGTCC-3=) and if1R2 (5=-CCAGAAACATAAGCGGTAATCGT-3=) for 35 cycles (94°C for 40 s, 55°C for 40 s, 72°C for 40 s). The map PCR product was cloned in pGEM-T easy plasmid (Promega, Charbonnières-les-Bains, France) according to the manufacturer's instructions. Results were analyzed using MxPro QPCR software (Agilent, Les Ulis, France).
Amplified products were directly sequenced on both strands on the MegaBACE capillary sequencer by Beckman Coulter Genomics (Takeley, UK). Raw chromatograms were assembled and edited using the Phred-Phrap-Consed package  (42) (43) (44). "Ca. Phytoplasma solani" secY sequence accession numbers are indicated on Fig. S1  in the supplemental material [see also "Accession number(s)" below]. The "Ca. Phytoplasma solani" strain Champlong transmitted to C. roseus periwinkle and the LD strain Dep transmitted to C. roseus in 1970 were further characterized by nested-PCR amplification and sequencing of the housekeeping gene tuf and the two genes vmp1 and STAMP gene, encoding variable surface proteins, according to previously published procedures  (24, 41, 45, 46). Deep sequencing of V4V5-amplified 16S rRNA.
Pools of lavender total nucleic extracts from autumn 2009 consisted of mixtures of equal volumes of 22 extracts of "Ca. Phytoplasma solani"-free nonsymptomatic lavenders (pool NS) and of 30 extracts of "Ca. Phytoplasma solani"-free declining lavenders from the same fields (pool S). Pool NS contained 7 L. angustifolia plants (fields MT, MTF, RJ, CC) and 16 L. intermedia plants (fields GS, GD, SP, RS, SB, AA, AS), whereas pool S contained 12 L. angustifolia and 21 L. intermedia plants from the same fields. Total nucleic acid concentration was adjusted to 50 ng/l in each pool and submitted to amplification of the V4V5 region of bacterial 16S rRNA  (47)  and Solexa sequencing performed on an Illumina MiSeq apparatus. After trimming for phred quality 30 and minimum length of 100 bases, reads were clustered into operational taxonomic units (OTUs) using CROP (clustering 16S rRNA for OTU prediction) at a 97% similarity threshold  (48) , and taxonomic assignments were performed by BLAST comparison against the GenBank database.
The representation of OTUs was the number of reads of each pool constituting a given OTU. Phylogenetic analysis of Hymenobacter sp. OTUs was conducted as described below. Diversity analysis of Hymenobacter sp. gyrB sequences and quantification of hymenobacters. Conserved regions within gyrB gene sequences were identified by aligning Hymenobacter species gyrB sequences. gyrB GenBank accession numbers are indicated on Fig. S2B  in the supplemental material. Two sets of primers were designed in these conserved regions to conduct nested-PCR amplification carried out with New England BioLabs Taq DNA polymerase. Total nucleic acids of pool S and pool NS were submitted to a first amplification with distal degenerated primers HYBGyrB-F0B (5=-GTRGARGTRGCSYT SCARTACAA-3=) and HYBGyrB-R0B (5=-CGGTTRCGGCCYTGYTTGGC-3=) with PCR conditions of 3 min at 95°C and 35 cycles of 30 s at 95°C, 30 s at 60°C, and 30 s at 72°C.
Data acquisition and analysis were handled by the LightCycler 480 software release 1. 5. 0. (Roche, La Rochelle, France), which automatically calculates the number of gyrB gene copies in each sample by comparison with the standard range. gyrB is known to occur as a single copy in bacterial genomes. Comparison of the data and statistical significance were determined using one-way analysis of variance (ANOVA) with the software R (Development Core Team, 2014) and the package R Commander  (49). Phylogenetic analyses. Multiple alignments of homologous sequences retrieved from GenBank were performed for "Ca. Phytoplasma solani" secY and STAMP gene sequences, Hymenobacter sp. 16S rRNA, and gyrB sequences using ClustalW  (50). Phylogenetic analyses were conducted with MEGA6 using the maximum parsimony method and bootstrapping 250 times to estimate branching stability  (51, 52).
Accession number(s). Genes for the antigenic membrane protein STAMP of "Candidatus Phytoplasma solani" have been deposited in the NCBI database under BioProject PRJEB25879. Genes for the preprotein translocase SecY have been deposited in the NCBI database under accession numbers FN813271 to FN813290 and HF969329 to HF969334.
ACKNOWLEDGMENTS This work was funded by the  French Ministry of Agriculture Food and Fisheries (MAAF)  under the  Rural and Agricultural Development (DAR) initiative ,  FranceAgriMer , and the  Regional Council of Provence Alpes Côte d'Azur (PACA). We thank  Christophe Hubert  for  V4V5 16S  rRNA amplification and Illumina sequencing at the  Genome Transcriptome Facility of the University of Bordeaux  and  Elisabeth Boudon-Padieu  and  Marie-Thérèse Cousin  for helpful scientific discussions.
This research must be patient-related so that rapid feedback to the bedside is achieved and should aim to identify clinical-, biological-and tumor-related factors that are associated with treatment resistance. Finally, this research should also seek to explain epidemiological and social facets of disease behavior. Methods: The prospective FREGAT database, established by the French National Cancer Institute, is focused on adult patients with carcinomas of the esophagus and stomach and on whatever might be the tumor stage or therapeutic strategy. The database includes epidemiological, clinical, and tumor characteristics data as well as follow-up, human and social sciences quality of life data, along with a tumor and serum bank. Discussion: This innovative method of research will allow for the banking of millions of data for the development of excellent basic, translational and clinical research programs for esophageal and gastric cancer.
Consequently, a study of the mechanisms of resistance in esophageal and gastric cancers requires the use of a prospective database dedicated to patients with esophageal or gastric cancers that contains medical and surgical clinical data as well as epidemiological, psychological, emotional, social and biological data (collection of blood and tumor samples): the FREGAT clinico-biological database (FREGAT CBD). This sustained activity and the visibility of the FRE-GAT network meant that, in 2012, funding was obtained from the Institut National du Cancer (National Cancer Institute) for FREGAT CBD, the only worldwide project of this scale; this allowed research on esophageal and gastric cancers to be approached from an innovative angle. Unlike randomized trials, which attempt to answer a question asked a priori following what is often a long inclusion period of patient selection, the CBD-type approach allows for wide-ranging and prospective collection of information about non-selected consecutive patients.
The FREGAT clinico-biological database The FREGAT CBD is registered as Bio-Medical Research excluding health products with the Agence Nationale de Sécurité du Médicament et des produits de santé (French Medical Products Agency) and has a dedicated internet site (https://www. fregat-database. org/). The FREGAT CBD aims to enroll a mean of 500 patients per year. Inclusions began in early 2015, and each patient is followed-up for 3 years. This research comprises the following: - The questionnaires on Human and Social Sciences and Quality of Life are given to every patient by the investigator at each center and are identified by a unique patient number. They are then collected by the sponsor who is responsible for entering the data in the electronic case report form (e-CRF).
Criteria for inclusion -Patients with carcinoma of the esophagus, esophagogastric junction or stomach, those who were newly diagnosed by biopsy, no matter the cancer subtype, tumor stage or envisaged treatment. -Man or woman ≥ 18 years of age. -Treatment-naive in relation to these particular cancers. -Covered by the social welfare scheme. -Patients who voluntarily signed an informed consent form for retrieval of blood samples, completion of questionnaires and collection of patient information. Failing this, a patient who has received neoadjuvant treatment may be included in the FREGAT CBD, but this is subject to the recovery of pre-treatment data and whether all possible efforts have been made to access the tumor samples (tumor blocks) generated prior to any treatment. Patients who have participated in a clinical trial may be included in the FREGAT CBD.
Statistical plan The sample size should be large enough to allow detection of factors related to 3-year relapse, whatever could be the disease stage, the tumoral location or the therapeutic strategy. Because of the nature of the study, being a prospective database, our aim is to include a large number of gastric and esophageal cancer patients to observe enough events allowing us to identify a large panel of variables associated with tumoral relapse at 3 years. The estimated inclusion rate of 500 new cases per year of esophageal and gastric cancer at a national level is estimated to be feasible based on the national incidence of esophageal and gastric seen in France per year in participating centers. With a 10-year inclusion period, a sample size of 5000 patients will be available, based on the following assumptions: X% of gastric and Y% of esophageal cancer patients will be included in the database over the study period, with P% of patients expected to be lost of follow-up and/or with not analyzable data.
Variables collected Clinical, biological and epidemiological data and the treatment characteristics of the patients are collected in the e-CRF (https://fregat. ctd-cno. org/CSOnline/). The variables collected are described below: - -The information gathered in the database extends from the point when the clinical follow-up of the patients begins, with the usual visits and follow-up methods, at each investigator center. The information must be updated on an annual basis. In addition, the information must be updated when an event such as relapse or death occurs. Finally, this list of variables, which have been established a priori, can be amended to reflect the research projects initiated by the scientific committee once these projects have been validated.
How the research is conducted in practice After the criteria are verified for inclusion and noninclusion, the investigator provides the patient with information and gathers two copies of his or her signed consent (https://fregat. ctd-cno. org/CSOnline/). To proceed to inclusion, after the consent is signed, the investigator completes the inclusion form on the e-CRF to obtain the unique FREGAT CBD inclusion number, which is automatically generated by the Data Processing Centre and is transcribed on all the FREGAT CBD documents and questionnaires. This will be the only way to identify a patient. The frequency of examinations and the point when the self-assessment questionnaires are submitted depends on the patient's treatment regimen, as described in Fig. 1. -T1: On inclusion These examinations must be performed once a patient is included, when the questionnaires are submitted, or at the very latest, on the date the first treatment is administered (surgery, chemo(radio)therapy).
Collection of biological samples The FREGAT research project links the clinical data of patients with information that pertains to the clinical, biological and tumor data. All the data contained in the FREGAT research project is gathered when the patients undergo normal treatment procedures. The biological collection is maintained by the centers who accept the samples and by the Clinical Investigation Centre/Biological Resources Center at the corresponding center. Their roles are to: -Gather, prepare and conserve biological samples under optimum conditions to make them available to clinicians/researchers and when subsequent scientific projects are conducted. -Identify the sample in a unique manner: the sample belongs to a particular study and patient, and thus, the sample is identified using a specific label.
The current list of declared investigators is available on the FREGAT website (https://www. fregat-database. org/). At present, the partners involved in the FREGAT CBD research are as follows: -37 participating centers, (i. e. , 50 teams) -The network of tumor banks -The Biological Resource Centers -The Data Processing Centers from the North-West Cancéropôle (Cancer Research Cluster) It is also supported on designated platforms: -Lille University -Human and Social Sciences platform -Caen Epidemiology platform -Lille University -Methodology and Biostatistics platform -Besançon Quality of Life platform How should a scientific research project be filed? The form used to file a Scientific Research Project is available on the internet site (https://www. fregat-databa se. org/). The completed project will be sent to proofreaders from the scientific committee, and feedback will be sent to the investigator during the month after the project was filed.
Availability to non-French centers The first stage was to organize and establish the FRE-GAT CBD in France and to launch this scientific dynamic using national fund. Any interested foreign center may join the FREGAT dynamic provided it obtains the favorable opinion of the steering group and reaches a financial agreement. Any non-French team that wishes to access the data may file a Scientific Research Project; the appropriate form is available on the website https:// www. fregat-database. org/ and is available in both French and English.
Discussion Despite efforts to optimize therapeutic strategies for better locoregional and systemic disease control, esophageal and gastric cancers still have a poor prognosis, as tumors are frequently diagnosed at an advanced stage, and there is often a delay between the appearance of initial symptoms and diagnosis. Even after multimodality treatments that combine endoscopy, surgery, chemotherapy, radiotherapy and immunotherapy are used to varying degrees, most patients experience disease persistence or recurrence related to treatment resistance of the tumor. The causes of such resistance are numerous and require urgent evaluation. In addition, the development of effective targeted treatments has been slow. The FREGAT prospective database, which is dedicated to esophageal and gastric cancers and which include tumor and serum banking, was created out of a need to identify specific epidemiological characteristics of esophageal and gastric cancer and to evaluate their impact on a given therapeutic strategy.
Creation of this database was also necessary for the identification of biological, clinical and tumor paradigms that explain resistance to treatment, and the identification of social and behavioral factors that result in a delay between first symptoms and diagnosis. The availability of biospecimens is critical to epidemiologic research for the identification, development, and validation of biomarkers for cancer susceptibility, precursor states, carcinogenic exposures, and cancer progression and recurrence. Biomarkers are key in studies of the molecular pathways that lead to cancer development and progression, and they may serve as surrogate markers for drug efficacy and toxicity, and as targets for cancer prevention, diagnosis, and treatment. Personalized medicine in esophageal and gastric cancer is just beginning and needs to be further developed.
Since esophageal and gastric cancers are complex cancers with multiple pathological and therapeutic drivers, resistance is common and multiple targeted therapies, which combine local and system approaches, will be required. This will rely on new clinico-epidemiological and biological studies. A comprehensive bench-to-bedside treatment-guided algorithm could provide for the optimum preoperative and/or postoperative combination of cytotoxic and targeted agents. Large specialized tumor banks and biobanks are mandatory for such projects. The prospective FREGAT CBD, established by the French National Cancer Institute, relies on different well-known and currently active networks. This database is dedicated to adult patients with carcinomas of the esophagus and stomach, no matter the tumor stage or therapeutic strategy.
It includes prospective data on epidemiology, clinical information, tumor characteristics, follow-up, human and social sciences and quality of life along with tumor and serum banking. The major aims of the FREGAT database are to (i) identify new prognostic and predictive factors based on clinical, biological and histological data, (ii) analyze the molecular mechanisms of drugs to discover and develop novel therapies, (iii) validate the promising markers already identified, (iv) evaluate the impact of each therapeutic strategy and the combination of strategies at a national level in different clinical and histological subgroups of esophageal and gastric cancer patients; this would thus strengthen the personalized therapeutic approach, (v) identify epidemiological, human and social sciences determinants that may have an impact on suboptimal access to care and delays in initiation of treatment, and (vi) evaluate the impact of the therapeutic strategies on the healthrelated quality of life of patients.
Acknowledgements This manuscript is dedicated to our colleague and friend  Prof. Christophe MARIETTE. We thank the actors of the FREGAT database:  Olivier Glehen 15  ,  Nicolas Carrere 16  ,  Jacques Jougon  17 , Denis Collet 18 , François Paye 19 ,  Denis Pezet 20  ,  Bernard Meunier 21  ,  Frédéric Di Fiore 22 , Xavier Benoît D'journo 23  ,  Olivier Bouché 24  ,  Marie-Pierre Galais   25  ,  Gil Lebreton 26  , Nicolas.
Estimating daily energy expenditure Tri-axial accelerometers (little Leonardo D3GT, AXY3 and Gulf Coast Data Concepts X8) were used to estimate DEE in a subset of the birds used for the hormone assay. Accelerometers were set to record at 25 or 50 Hz and attached on the midline of the mid back of individuals (as close to the centre of gravity as possible) using Tesa tape. All birds were successfully recaptured and accelerometers were retrieved after 3 days of deployment. Energy expenditure was estimated for diving, flying and resting [the main activities of European shags  (Sakamoto et al. , 2009) ] using behaviour-specific calibrations derived from respirometry calibrations with heart rate and accelerometry (see  Hicks et al. , 2017  for behaviour-specific calibrations and detailed methods).