dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods: Participants in the Finnish Public Sector study were linked to national registers. We included data for the years 1994-2011. We identified and followed 3468 adult patients with hypertension and 412 adult patients with type 2 diabetes for medication adherence for the 3 years before their retirement and the 4 years after their retirement (mean follow-up 6. 8 yr). Our primary outcome was proportion of patients with poor adherence to medication, which we defined as less than 40% of days covered by treatment. We determined these proportions before and after retirement using data from filled prescriptions.
Study population and design We used data from the Finnish Public Sector Study, which follwed a cohort of 151 901 employees of local government in 10 towns and 21 public hospitals. 17 These employees cover a wide range of occupational groups, from city mayors to semiskilled cleaners, the largest groups being nurses and teachers. The sex and age distribution of the members of the cohort correspond to those of all Finnish public sector employees (75% v. 77% women; mean age 44 v. 45 yr). A detailed description of the Finnish Public Sector Study and its context is provided in Appendix 1 (available at www. cmaj. ca /lookup /suppl /doi :10. 1503 /cmaj. 122012 /-/DC1). We linked the cohort members to national prescription and health registers from 1994 to 2011 through the unique personal identification codes assigned to all permanent residents of Finland.
Assessment of retirement Data on retirement were obtained from electronic records of the Finnish Centre for Pensions. All gainful employment is insured in a pension scheme and accrues a pension, and the centre coordinates all earnings-related pensions for permanent residents of Finland. These records provided virtually complete retirement data for all participants. We obtained the dates at which all participants started to receive old-age or disability pension and their ages at retirement from Jan. 1, 1996, to Dec. 31, 2010, irrespective of the participants' workplace before retirement.
Case definition for hypertension and type 2 diabetes Finnish National Health Insurance, coordinated by the Social Insurance Institution, covers all permanent residents of Finland and provides special reimbursement for additional costs associated with many chronic diseases, including hypertension and type 2 diabetes. Participants with hypertension or type 2 diabetes who required continuous medication were identified from the Social Insurance Institution Drug Reimbursement Register. This register contains data on all patients who have been granted reimbursement for medications in Finland, including antihypertensive and antidiabetic drugs, with the date on which the permission was granted (diagnostic details in Appendix 2, available at available at www. cmaj. ca /lookup /suppl /doi :10. 1503 /cmaj.
Assessment of adherence to treatment At the time of the study, all prescriptions were written by a physician. The Social Insurance Institution reimbursed 70%-100% of the costs of antihypertensive and antidiabetic drugs for patients granted special reimbursement, including the participants of the present study. We followed participants for adherence to treatment from 3 years before their retirement to up to 4 years after (the observation period). We used days covered by filled prescriptions to assess adherence to treatment, a valid measure of medical adherence in a closed pharmacy system, such as in Finland. 18 We defined poor medication adherence as less than 40% of days covered by treatment; we performed subsidiary analyses with alternative cut-offs of 20%, 30%, 50%, 60%, 70% and 80%. 10, 19, 20 e obtained data on all filled prescriptions of antihypertensive and antidiabetic drugs reimbursed to participants between Jan.
Other variables Preretirement covariates included sex, age at retirement, socioeconomic status, depression and cardiovascular comorbidity. We obtained data on sex and socioeconomic status (i. e. , manual v. nonmanual labour) from the employers' registers. An additional indicator for socioeconomic status was size of residence (< 80 v. ≥ 80 m 2 ), obtained from the Population Register Centre. We used the Finnish Hospital Discharge Register and the Social Insurance Institution registers to determine depression status (Appendix 2) and comorbid cardiovascular disease (at least 1 of coronary artery disease, coronary insufficiency, cardiac arrhythmia or cerebrovascular disease). Validation studies show the Finnish Hospital Discharge register to contain about 95% of all discharges, and records are correct in at least 95% of the dis-charges compared with the corresponding medical records.
Statistical analysis We analyzed a 7-year observation period including the 3 years before and the 4 years after the date of retirement. Periods during which participants stayed in hospital were excluded from follow-up. Participants were censored at death. We stratified data by sex and performed analyses separately for poor adherence in relation to hypertension and diabetes medications. The participants who received treatment for both hypertension and diabetes were included in both sets of analyses. We calculated annual prevalence estimates and prevalence ratios of poor medication adherence and their 95% confidence intervals (CIs) using a repeated-measures logbinomial regression with the generalized estimating equation (GEE) method and autoregressive correlation structure. GEE takes into account the intraindividual correlation between measurements and is not sensitive to missing measurements.
Results We identified 25 535 people who retired between 1996 and 2010, 21 052 of whom were alive at least 1 year after their retirement and were included in our analyses. Complete prescription data were available for all included participants. Of the 21 052 participants, 3889 had hypertension before their retirement, and 611 had type 2 diabetes before their retirement. We only included patients with hypertension (n = 3468) or type 2 diabetes (n = 412) whose diagnoses were made before the start of our observation period; thus, we excluded 421 patients with hypertension and 199 patients with diabetes whose diagnoses were made after the start of our observation period. Of the 3880 included participants, 2720 (70. 1%) were female, corresponding the sex distribution of the overall cohort (Table  1 ).
Most of the published data concern trade in hydrocarbons (petroleum and gas), which account for  12  This classification is preferred over the harmonized system as no data are available for Libya in the United Nations Commodity Trade Statistics Database (UN Comtrade). 13 This is a well-established approach that dates from the late 1960s following the work of Bhagwati (1967) and that is currently enjoying something of a revival as a result of new research into customs fraud. 14 For a wider discussion of the various explanations, see Raballand et al. (2013). 15 Data were provided for the period 2007 to 2010 only in COMTRADE. 91% of the value of Libyan exports to Tunisia according to the Libyan authorities and 84% of Tunisian imports from Libya according to Tunisian authorities. There are significant gaps in the trade flows reported by the Libyan and Tunisian authorities.
These gaps are particularly large for iron and steel bars (SITC code 676) and inorganic chemical elements (SITC code 522). For example, in 2008, exports of metal bars registered by the Libyan authorities as exported from Libya to Tunisia were 20 times higher than the number registered as imported by the Tunisian authorities. The high value of these trade flows is due primarily to the dominance of trade in hydrocarbons (gas and petroleum), which accounted on average for 70% of Algeria's exports to Tunisia according to the Algerian authorities and 76% of Tunisian imports according to the Tunisian authorities. This trade accounts for most of the gap in the total value of trade recorded by the two countries (or US$28. 4m higher according to the Tunisian authorities). 16 The Tunisian authorities recorded data for imports of 68 different categories of products on average, while their Algerian counterparts recorded export data for 82 categories.
Although there are gaps in the data (with 13 fewer categories on average per year), these are not as large as with Libya. However, there are significant gaps in terms of both value and volume. Table  2  (see Annex 2) lists the 20 largest recorded gaps for a single product. In the most extreme case (fresh fruit and vegetables), the export value was 30,000 times higher when recorded as exports by the Algerian authorities than when recorded as imports by the Tunisian authorities. In general, trade flows from Algeria to Tunisia are under-reported by the Tunisian authorities, with CIF figures lower than FOB in 55% of the cases. For the most part, gaps are found in the trade in products used mainly in the construction industry, such as categories 723 (civil engineering and contractors' plant and equipment), 747 (taps, cocks, valves, and similar appliances), 812 (plumbing and heating fixtures and fittings), and 273 (stone, sand, and gravel).
Estimates Based on Fieldwork As the data available are far from complete, it is not possible to estimate the scale of informal trade based on figures alone. For that reason, fieldwork was conducted at the Ras Ajdir crossing point on the Tunisia-Libya border and in the Kasserine governorate on the Tunisia-Algeria border. The aim of the interviews was to gather information on the current level of informal trade between Tunisia and its two neighbors. The estimates were made using two different methods, which yielded roughly similar results (at least TND 1. 8 bn including fuel from Algeria) (see Table  1 ). One estimate was based entirely on the information gathered during the fieldwork, while the second one was made using unit floor values based on data concerning modes of transport. The second method resulted in a higher estimate of the level of informal trade, most probably because of the under-reporting of value and/or volumes in the interviews.
Estimates Based on Unit Values Estimates based on interviews alone are not sufficiently accurate due to a number of factors. In the case of interviews with transporters, for example, the quantities being transported are often underreported, and there is often a lack of knowledge of the real value of the goods concerned. In some cases, the sample is simply not large enough. As a result, we tried to determine the volume and scope of informal cross-border trade using other data sources and through cross-checking to arrive at a figure closer to the reality. We cross checked data on the number and type of means of transport used in this form of trade. This allows us to extrapolate the volume and value of goods concerned by informal trade. Nearly 1,000 Tunisian vehicles use the Ras Ajdir border crossing each day, specializing in informal trade between Libya and Tunisia.
Optical flow dissimilarity Instead of using tracklets, motion can also be estimated using an optical flow. The optical flow is computed by a pyramidal version of the Lucas-Kanade  [26]  algorithm, we use five levels for the image pyramids. Figure  3  shows an example of the estimated optical flow for a video of our dataset. Two optical flows are computed at each frame: one with the previous frame and the other with the next frame. The two obtained optical flows are then averaged to reduce the noise. The resulting velocity of a detection is estimated by the flow vector the most represented on the detection area. The motion dissimilarity from optical flow is defined as follows d m (z i , z j ) = 1 2 (|| x i + v i (t j -t i ) -x j || +|| x j + v j (t i -t j ) -x i ||) ( 13 ) where v i is the estimated optical flow vector of the detection i.
Performance of our dissimilarity measure Table  3  shows F-measures obtained with four versions of the presented algorithm. The first (basic) is the base algorithm without tracklets or optical flow, it just uses time,  The mean and standard deviation of F-measures are estimated over results obtained by varying the P e parameter, which is the probability to start (or stop) a cluster at a http://jivp. eurasipjournals. com/content/2013/1/10 given detection. This parameter is used to force the number of clusters. For these experiments we take 100 values of P e between 0. 04 and 25%. Results show that the quality does not appear to be very sensitive to the large P e variation. Although dataset videos have various false positive rates (from 1. 5 to 11%), we arbitrarily set the false positive parameter (β) to 1% for all the videos.
dataset because of the fast crossing and direction variation of pedestrians, and also the small size of detected faces (materials provided with this article contain these five videos). Video 6 a is part of a dataset built to evaluate the detection of abandoned baggage systems in Advanced Video and Signal Based Surveillance Conference. The frame rate of videos Additional file 1: Video 1, Additional file 2: Video 2, Additional file 3: Video 3 and Video 6 is 25 frames per second and 13 frames per second for videos Additional file 4: Video 4 and Additional file 5: Video 5. To extract faces, we use the classic Viola-Jones [31]  face detector implemented in OpenCV library. For all the videos, detections are rather small (from side 30 to 60 pixels) compared to the face recognition. It is close to the smallest face we can detect with the OpenCV implementation.
The CSF sample was bioassayed into three Swiss white mice. The CSF was centrifuged and resuspended in a saline solution containing penicillin G and streptomycin. This homogenate was inoculated i. p. (0. 5 mL/mouse) into three mice. Four weeks post-inoculation all three mice were still asymptomatic, however, the microscopic examination of their brain tissue revealed the presence of T. gondii cysts (Figure  2 ). The T. gondii strain was designated as ROU-H-001 and banked at the Toxoplasma Biological Resource Center under the Accession Number TgH113001. It was submitted to DNA extraction (Qiagen, Germany) for a genotyping analysis using 15 microsatellite markers distributed on 10 of 14 chromosomes of T. gondii, as described elsewhere  [3]. Briefly, for each primer pair, the forward one was 5 0 -end labeled with fluorescein to allow sizing of PCR products electrophoresed in an automatic sequencer.
PCR was carried out in a 25-lL reaction mixture consisting of 12. 5 lL of 2X QIAGEN Multiplex PCR Master Mix (Qiagen, France), 5 pmol of each primer, and 5 lL of DNA. Cycling conditions were 15 min at 95 °C; 30 s at 94 °C, 3 min at 61 °C, 30 s at 72 °C (35 cycles), and 30 min at 60 °C. PCR products were diluted 1:10 with deionized formamide. One microliter of each diluted PCR product was mixed with 0. 5 lL of a dye-labeled size standard (ROX 500, Applied Biosystems) and 23. 5 lL of deionized formamide (Applied Biosystems). This mixture was denatured at 95 °C for 5 min and then electrophoresed using an automatic sequencer (ABI PRISM 3130xl, Applied Biosystems). The sizes of the alleles in bp were estimated using GeneMapper analysis software (version 4. 0, Applied Biosystems). The analyzed T.
Relative light units (RLU) Figure  2  High-throughput screening data for gene delivery efficacy of PBAE polymers to IMR90 cells. Luciferase-encoding DNA is delivered and expression is measured as rlU. ratios 1. 05:1, 1. 1:1, 1. 2:1, 1:1, and 1:1. 05 refer to polymerization conditions and wt/wt is the weight ratio of polymer to DNa. graphs show the mean, n$4. Notes: acrylate monomers (Bx), amino-alcohol monomers (sy), and end-capping groups (ez). The number "x" following the acrylate monomers "B" refers to the number of carbons between acrylate groups in the monomer, the number "y" following the amino-alcohol monomers "s" refers to the number of carbons between the amine group and the alcohol group in the sidechain, and the number "z" following the end-capping groups "e" refers to an arbitrary number used to designate a particular end-capping group.
Using the particle size distribution data from nanoparticle tracking analysis measurements, the number of plasmids associated with a single PBAE-based nanoparticle was quantified. 21 It was observed that 30-100 plasmids were encapsulated in each nanoparticle depending on polymer structure. To identify polymers from the PBAE library with the ability to transfect human fibroblasts in an efficacious, rapid, and high-throughput manner, the PBAE library was screened on IMR-90 fetal lung fibroblasts using a 96-well plate assay. 26 PBAE/CMV-Luc nanoparticles were synthesized by varying the polymer to DNA weight ratio from 20 wt/wt to 100 wt/wt. Figure  2  shows the compiled transfection efficacy data reported as relative luminescence units per well. Several PBAE nanoparticle conditions had higher transfection efficacy than the commercial controls, ie, FuGENE HD, Lipofectamine 2000, and polyethylenimine.
The inclusion of persuasive features in eHealth has been shown to have positive trade-offs such as increased adherence  [20]. The roadmap consists of five phases (see Figure  1 ): 1. Contextual inquiry. Here, information on the context of use, the designated end users and the professionals that need to implement the eHealth intervention is collected. 2. Value specification. Data from the contextual inquiry is translated into stakeholder values and requirements for the technology. 3. Design. Prototypes of the eHealth technology are created on the basis of requirements and tested. 4. Operationalisation. The final version of the eHealth intervention is launched and additional resources (eg, user support) are mobilized. 5. Summative evaluation. Finally, the uptake and effect of the eHealth technology is evaluated.
Requirement(s) Attribute(s) Value User expression The system incorporates data from databases for patient and protocol/procedural information The system provides access to all (types of) information via one interface One-stop-portal for information Easy access Nurse 1: "But wouldn't it be nice if you have the medications in the electronic prescriptions system, and that you can click on the medication and just click on through. " Pharmacist: "that you can instantly…" Nurse2 : "directly…" Nurse3: "yes, that it is available directly" Pharmacist: "Yes, for prescribing [a medicine] I can imagine that he [the physician] needs the information from an indication-point of view. And for you I can imagine that you would want to have the information focused on the application; how to do it all. " Nurse 3: "What should I pay attention to.
Fit Criteria Requirements are a translation of end users' and stakeholders' needs and wishes into design, and should therefore be checked. Fit criteria are measures of success for this translation and are the basis of evaluations. Often, functional requirements cannot be evaluated with users as they are simply implemented or not (like a requirement specifying that type of data x is collected from database y). In this case, formulating a fit criterion is useless. In the other cases, whether or not a fit criterion is formulated or not depends on its priority (when there is no possibility to evaluate all requirements, only those with a high priority, or controversial requirements should be evaluated), and whether or not the prototypical version of the system that will be used supports evaluating the fit criterion (eg, testing for usability with a simple prototype will yield very limited results).
thaliana genome database revealed that the diversity pattern in this Leavenworthia genomic region resembles the SRK/SCR S-locus region of other characterized Brassicaceae species  [41]. The LaLal2 and LaSCRL genes themselves have high sequence diversity, but are flanked (at least on the right of LaLal2) by highly conserved regions (Figure  4A ). If we define the core S locus as being the region of low sequence similarity between the three haplotypes and comprising LaLal2 and LaSCRL, the size of the S locus is 14 kb in the a4 haplotype, the only one for which sequence information on both sides of the S locus is available. Because the upstream sequences of the core S locus of the a1-1 and a2 haplotypes are currently undetermined, their sizes remain unknown, but are at least 15. 3 kb in the a1-1 haplotype and 11.
Then, the original SRK/SCR S locus could have later been lost in Leavenworthia (perhaps following polyploidization). These two scenarios both fit the pattern of earlier divergence of Lal2 seen in the gene phylogeny (Figure  2 ), and are compatible with the evidence of relatively low diversity of Lalal2 alleles, and detection of strong selection in hypervariable regions of LaLal2  [28]. The data from this study are insufficient to know whether SI was lost in the lineage leading to Leavenworthia (Scenario I), or whether it was retained without interruption of the SI response (Scenario II), but there are several reasons to consider that SI may have been lost in the Leavenworthia lineage before being regained. First, the loss of SI is indeed common in the flowering plants and in the Brassicaceae-it has been estimated that half the species in  the family are self-compatible  [56, 57] , and thus, the possible loss of SI within Leavenworthia cannot be considered as an atypical event.
DNA Sequencing and Sequence Analysis Sanger, Illumina, and 454 sequencing were performed at the McGill University and Genome Quebec Innovation Centre. The genomes of Leavenworthia alabamica (a4 race), Sisymbrium irio, and the Leavenworthia short read data were gathered as part of an ongoing comparative genomics investigation involving these and other Brassicaceae species (Blanchette et al. , unpublished data). The sequences of the a1-1, a2, and a4 fosmid clones were also assembled from 454 data. In the case of the genomes, reads were generated in accordance with the Illumina protocols, with special attention paid to gentle shearing of mate-pair circular DNA to ensure. 500 nt fragments, thereby reducing the probability of a read fragment-join chimera. Paired end (26105, nominal 64 nt gap) Illumina reads were generated to a depth of 806 for each genome, trimmed for quality (39 trimming where Q,32) and assembled with the Ray assembler  [74]  using automatic coverage depth profiling and a Kmer of 31.
Scaffolding of Ray contigs was then undertaken with the SOAPdeNovo (BGI) assembler using a combination of 5 and 10 KBase mate pair reads (Blanchette et al. , unpublished data). Assembly of the fosmid sequences was undertaken in batches of pooled barcoded libraries covered by 1/8 of a flowcell of 454 sequencing (2006 coverage). After stripping vector contaminants Newbler (Roche) was used to assemble the reads into ,40 Kbase contigs using essentially default assembly parameters. Comparison of targeted fosmid assemblies (454) and short read whole genome assemblies (Illumina-Ray) from L. alabamica of the a4 race demonstrated high levels of concordance. Standard sequence analyses were done using the Geneious v. 5. 4. 6 software (Auckland, New Zealand)  [75]. Amino acid and nucleotide sequences were aligned with MUSCLE  [76].
Fosmid sequences were aligned using VISTA  [77]. Annotation of fosmid sequences was done by sequence blast against the Arabidopsis thaliana genome. Because of the high sequence diversity of LaSCRL, this gene could not be detected by blast search but was found by eye examination of short ORFs obtained from different translation frames for the presence of eight cysteines. The Mauve Genome Alignment software v. 2. 2. 0  [78]  was used to compare the S locus of A. thaliana with syntenic genome region of Leavenworthia and the S locus of Leavenworthia with syntenic genome region of A. lyrata. Protein domains were determined by submitting gene amino acid sequences to the SMART/Pfam prediction tools  [31].