dataesr/scientific-paragraphs-categorization huggingface dataset:
Since the end of the 1990's, the monitoring of HCV RNA after treatment initiation has played a critical role in defining guidelines to tailor treatment duration  11. Recently, a proof-of-concept trial was conducted in HCV patients to evaluate the possibility of using on-treatment HCV RNA levels to define the duration of triple DAA-based treatment and the results were promising  12. In that study involving Chinese patients all infected with HCV genotype 1b without cirrhosis, all 18 patients who achieved a viral load <500 IU/mL by day 2 with triple DAA regimens were cured after only 3 weeks of treatment  12. This suggests (but does not demonstrate) that viral kinetic models could be relevant to optimize therapy or to identify patients eligible for therapy as short 2-4 weeks. Here we analyzed the viral kinetics observed during treatments with SOF + LDV + GS-9669/GS-9451 for 6 weeks, SOF + LDV for 12 weeks (Synergy trial) and SOF + ribavirin (RBV) for 24 weeks (SPARE trial: ClinicalTrials.
gov, number NCT01441180) using mathematical modeling. By comparing the kinetics observed with these different treatment strategies we aim to decipher the biological origin of the rapid treatment response in short duration treatment and to evaluate if the in vitro finding that NS5A and protease inhibitors can reduce infectious virus is consistent with in vivo observations. We also evaluate whether the success of triple therapies could be predicted and whether it is possible to identify patients eligible for shorter treatment using a viral kinetic modeling approach.
Prediction intervals were obtained by generating 1000 datasets of N = 50 patients. We assumed by construction that SVR rates of 95% were obtained after after 8 weeks of SOF+LDV or 6 weeks of SOF+LDV+GS-9669/GS-9451 (see Methods). profiles but it could reflect the influence of the assay used for HCV RNA measurements on viral kinetic estimates. Here, we relied only on the Abbott real time HCV assay, which is generally considered as more sensitive and has smaller lower limit of detection than the Roche Taqman assay  16, 17. Consequently, viral load may remain detectable for longer period of time which leads to lower estimates for the rate of viral decline during the terminal phase of the viral kinetics, i. e. , the loss rate of infected cells. Another very surprising observation was that 35% of patients treated for 12 weeks and as many as 55% treated for 6 weeks had detectable HCV RNA levels at EOT.
Materials and Methods Patients and study design. We used data from the SYNERGY and SPARE trials (ClinicalTrials. gov, numbers NCT01805882 and NCT01441180, respectively)  6, 37. Written or oral informed consent from all participants was obtained. The clinical studies were approved by the institutional review board of the National Institute of Allergy and Infectious Diseases (NIAID) and were done in compliance with the Good Clinical Practice guidelines, the Declaration of Helsinki, and regulatory requirements. More details can be found in the primary papers  6, 37. The SPARE trial was conducted in two parts. In the first part, patients with a moderate stage of liver fibrosis were treated for 24 weeks with SOF (400 mg/day) once a day and a weight-based RBV regimen. In the second part, patients with all stages of liver fibrosis were randomized to receive the same dose of SOF in combination with either weight-based or low-dose RBV (600 mg/day) for 24 weeks  37.
Acknowledgements We thank  Graham Cooke ,  Jean -Michel Pawlotsky  and  Sarah Walker  for reviewing the manuscript. Portions of this work were performed under the auspices of the  U. S. Department of Energy  under contract  DE-AC52-06NA25396. This work was funded by  National Institutes of Health  grants  R01-AI078881 ,  R01-AI116868 ,  R01-AI028433  and  R01-OD011095.
The intervention consists in offering financial incentives conditional on attending scheduled pregnancy follow-up consultations. Clusters are 2-month periods with random turnover across centres. A composite outcome of maternal and neonatal morbidity and mortality is the primary endpoint. Secondary endpoints include maternal or neonatal outcomes assessed separately, qualitative assessment of the perception of the intervention and cost-effectiveness analysis for which children will be followed to the end of their first year through the French health insurance database. The study started in June 2016, and based on an expected decrease in the primary endpoint from 18% to 14% in the intervention group, we plan to include 2000 women in each group. Ethics and dissemination Ethics approval was first gained on 28 September 2014.
An independent data security and monitoring committee has been established. Results of the main trial and each of the secondary analyses will be submitted for publication in a peer-reviewed journal. trial registration number NCT02402855; pre-results. strengths and limitations of this study ► Inadequate prenatal care has been associated with poor pregnancy outcomes, and in high-income countries, socioeconomically disadvantaged women have increased rates of both unattended pregnancy follow-up visits and pregnancy-related adverse outcomes. Among interventions that aim to promote adequate prenatal care, financial incentives have the potential to overcome some of the barriers, but data on the reality and the magnitude of such an effect on pregnancy outcomes are sparse. ► A cluster-randomised clinical trial, using a Zelen design, will run in about 40 public maternity units all over France, with the aim to include a total of 4000 women.
The intervention group will receive a €30 incentive for each scheduled prenatal visit they have attended. The control group will be followed according to the national recommendations and local practices. ► The main outcome is a composite of maternal and neonatal adverse outcomes. Secondary outcomes will include qualitative assessments and the costeffectiveness of intervention. ► The definition of the low socioeconomic group relies on the type of healthcare insurance alone; no individual assessment will be conducted. ► Follow-up of children until their first birthday will only rely on electronic data from the French Health Insurance database.
Control group Women in the control group receive prenatal care according to the standard practice, as set out in national guidelines. Women's personal medical history and pregnancy medical data are collected up to 1 month Figure  1  Scheduled prenatal care visits and time window for financial incentives. If a woman shows up for a scheduled visit more than 2 weeks after her standard preplanned visit, she will receive the incentive for the next visit. This means that she will not attend a scheduled visit without receiving an incentive (with the limit of no more than one incentivised visit per month), but she may receive fewer incentive payments than the maximum she could have obtained. 26WG, 26 weeks of gestation; FU, follow-up. Open Access postdischarge after delivery, whereas data for their child will be collected up to their first birthday.
Number of prenatal consultations following the French standard care recommendations. All outpatient visits, including those prospectively scheduled by the study protocol, will be retrieved using the French Health Insurance database (Système National d'Informations Inter Régimes de l'Assurance Maladie (SNIIR-AM)). 4. Qualitative assessment of barriers to adequate prenatal follow-up and the perception of the intervention by some of the participating women and health professionals. 5. Differential cost-effectiveness ratio associated with financial incentive versus no compensation and expressed in terms of cost per complication avoided. 6. Overall budget impact. participant timelines Women will be followed according to the official antenatal care programme and to requests from their obstetrician.
No additional visits or tests of any type will be requested because of their participation in the trial. Data will be recorded from inclusion to discharge from the maternity ward. Newborns will be followed up to discharge from hospital. For the cost-effectiveness study, data on health resources utilisation, that is, outpatient clinics, blood or imaging tests performed and medication purchased, will be collected through the national health insurance database, up to the first year of age for the children. Figure  2  shows the overall management of women included in the study according to the randomisation group.
Open Access We hypothesised an intracluster correlation coefficient (ICC) of 0. 01, meaning that 1526 women are necessary. 28 llowing for 20% attrition, 1900 women per group are needed, and we set the sample size at 2000 per group. An ICC of 0. 01 was selected because the trial assesses an intervention aimed directly at the patient and an outcome measurement for which the variance between practices is low compared with the variability between patients within a practice. recruitment All eligible women registering for maternity care at the trial sites during the study period will be invited to participate in the study. The list of the participating centres can be found on ClinicalTrials. gov (NCT02402855). Information sheet and consent form for the intervention group (online supplementary annex 1) and the control group (online supplementary annex 2) are available in 18 languages.
Outcomes Efficacy is a composite criterion that includes complications of the child during his/her first year of life (such Open Access as perinatal death, prematurity or neurological impairment) and maternal adverse events (including postpartum haemorrhage, endometritis). Direct costs will be considered from a societal perspective. The effectiveness of the intervention will be expressed in terms of cost per complication avoided. The time horizon of the study will be at most 1 year and 9 months, corresponding to the period of pregnancy and a 1-year postdelivery follow-up period. Given the relatively short duration of follow-up, costs and effectiveness will not be updated. In addition to data collected in the CRF (CAse Report Form), all direct medical costs up to 1 year postdelivery will be retrieved from the National Health Insurance database.
MEthods: dAtA CollECtIon MAnAgEMEnt And AnAlysIs data collection methods Data will be collected through the eCRF. Inclusion and non-inclusion criteria, as well as attendance at each scheduled visit in the intervention group, will be prospectively entered into the eCRF. All other data, for maternal and neonatal outcomes, will be extracted from individual pregnancy records, in each of the participating centres, and collected into the eCRF by clinical research assistants. For the cost-effectiveness study, data for the first year of life will be extracted from the French Hospitalisation (Le Programme de Médicalisation des Systèmes d'Information) and Health Insurance (SNIIR-AM) databases and analysed at Dijon University Health Centre.
Analysis of qualitative survey Raw data are analysed according to a thematic analysis method. From this progressive work of conceptualisation and continuous comparison of the different situations, a theoretical system responding to our problems will be defined. A triangulation of data will be done as two sociologists will code the interview transcriptions. Nvivo software, which allows the creation of a code and has been well validated for qualitative analyses, will be used. 30 Qualitative data will be analysed during the data collection. The collection of data will continue until concept saturation is reached. Theoretical saturation will be assessed. 31 ractically, saturation is reached when no new data could add more information to meet the research objectives. Data will be analysed by two researchers, and the collection of data will end when two consecutive interviews have not generated any new information.
Research ethics approval Ethics approval was given by the Dijon Ethics Committee (CPP Est-1) on 18 September 2014, and the protocol was amended thereafter. The study obtained funding from the French Ministry for Health in December 2014 (PREPS-14-0173) and the study is promoted by Dijon Bourgogne University Hospital (France). Authorisation for holding the computerised databases was granted on 21 March 2016 by CNIL. This long delay was due to conflict between the reasoning of CNIL, for which the preservation of private life is its top priority, and the French source of public funding, which needs to know precisely to whom public money, in this case the financial incentive, is being given. It was registered in ClinicalTrials. gov with the identifier NCT02402855, on 17 March 2015, at the French Medicines Agency with identifier 2014-A01319-38 and at CNIL with request for authorisation number 915385.
In each case, for each lot, oysters were cultivated comparing two different systems (basket and cemented). Mortality was recorded during all the study time especially before and after the virus events, as well as at the end of the production process. Mortality of other stocks (different origin, size, and cultivation method) cultivated in the same raft were also recorded for comparison (Table  4 ). Furthermore, other IRTA spat lots grown by other four producers were also surveyed during the study period (Table  3 ). Finally, spat origin, cultivation method, and mortality of non-IRTA spat grown by different producers were also recorded (Table  4 ). Mortality data for larger IRTA spat sizes (>20 mm) immersed was also surveyed, however those large sizes reached sizes higher than 35-40 mm at the time of virus episodes and were not critical regarding herpesvirus associated mortality and thus are not presented in the present manuscript.
ACKNOWLEDGMENTS This research was funded primarily by the project  BIVALDAR  ( DAAM, Generalitat de Catalunya ), as well as with IRTA internal funds. Furthermore,  BIVALIFE  ( EU FP7 ) funds also contributed to the epidemiological survey. Funds from the  Monitoring Program in Shellfish growing areas of Catalonia , executed by IRTA for the  General Direction of Fisheries and Marine Affairs of Catalonia (Government of Catalonia ) also contributed to the presented data. Special thanks are given to the producers  Lorena Casanova  and  Antonio Vergés  from the production company  Vergés & Casanova  (http://vergesicasanova. es) from the  Ebro Delta (Spain) , for taking care of the oysters, transferring detailed information and following accurately all the advice provided to them for this study. Thanks also to the other producers who have also contributed to the data of this study ( Carlos Bori ,  Santiago Tomás ,  Francisco Curto ,  Carles Férnandez ,  Tomás Pinyol , and  Jesús Carles ).
The databases included medical claims (ie, facility and professional services) and outpatient pharmacy claims from private US health plans. Data from Shea et al. 13  with the incidence dramatically higher in persons with severe COPD (forced expiratory volume in 1 second [FEV 1 ] 50% of expected). 15, 16 In Sweden, the risk of severe/invasive pneumococcal disease (IPD) was fivefold higher in persons with COPD or pulmonary fibrosis and twice as high in persons with asthma than in the general population. 17 OPD patients may be more susceptible to respiratory infections, because their mucociliary clearance mechanisms are impaired, and production of the specific cell adhesion molecules that mediate attachment of bacteria and viruses is increased in their airways. Expression of platelet adhesion factor receptor (a cell adhesion molecule for Streptococcus pneumoniae and untypable Haemophilus influenza) and more recently ICAM1 (a cell adhesion molecule for rhinovirus) have been found to be significantly elevated in COPD patients and smokers compared to normal controls.
Vaccination with The Danish National Patient Registry was used to identify all first-time inpatient hospitalizations for pneumonic AECOPD (pAECOPD; 18,968 patients) and nonpneumonic AeCOPD (npAeCOPD; 33,552 patients). All COPD hospitalizations were categorized according to whether they included a primary or secondary diagnosis of pneumonia. Data from Søgaard et al. 26  (B) Median ICU length of stay (LOS) in COPD patients due to pAeCOPD or npAeCOPD. Data were obtained from a retrospective analysis of all hospitalizations in 2005 in the departments of internal and respiratory medicine in one Swedish and two Norwegian hospitals. A total of 1,144 hospital admissions (731 patients) were identified from the patient administrative systems: 237 were for pAECOPD (mean age 75. 3 years) and 472 for npAECOPD (mean age 71.
7 years). *P0. 001. Data from Andreassen et al. 25  (C) 30-Day mortality among the 52,520 patients described in A, with adjustments for age, sex, comorbidity, and respiratory medications. Data from Søgaard et al. 26  (D) In-hospital and 90-day mortality in COPD patients following hospitalization for npAeCOPD or pAeCOPD in the UK in 2008. UK National COPD audit data were used to determine in-hospital and 90-day mortality rates of patients admitted with npAeCOPD (542 of 7,833 patients and 951 of 7,504 patients, respectively) or pAeCOPD (160 of 1,505 patients and 247 of 1,441 patients, respectively). A total of 9,338 admissions were assessed, with a mean age of 73 years. *P0. 001. Data from Myint et al. 27  PPV produces an immunoresponse that is limited to B-cell stimulation and antibody production.
A total of 1,144 hospital admissions (731 patients) were identified from the patient administrative systems: 237 were for pAECOPD (mean age 75. 3 years) and 472 for npAECOPD (mean age 71. 7 years). *P0. 001. Data from Andreassen et al. 25  (C) 30-Day mortality among the 52,520 patients described in A, with adjustments for age, sex, comorbidity, and respiratory medications. Data from Søgaard et al. 26  (D) In-hospital and 90-day mortality in COPD patients following hospitalization for npAeCOPD or pAeCOPD in the UK in 2008. UK National COPD audit data were used to determine in-hospital and 90-day mortality rates of patients admitted with npAeCOPD (542 of 7,833 patients and 951 of 7,504 patients, respectively) or pAeCOPD (160 of 1,505 patients and 247 of 1,441 patients, respectively). A total of 9,338 admissions were assessed, with a mean age of 73 years.
Acknowledgments The content of this article is based on a symposium (sponsored by  Pfizer Inc. , Paris, France) held at the ERS International Congress in London in September 2016. The authors take full responsibility for the content of this article and thank  Dr Kurt Liittschwager  ( 4Clinics, Paris, France ) for scientific writing services and assistance in preparing the manuscript in close collaboration with the authors. The authors also thank  Dr Tin Tin Htar  ( Pfizer ) for valuable comments and suggestions. Financial support for the preparation of this manuscript was provided by  Pfizer.
marginatum salivary gland proteins but not against R. microplus tick cell proteins (Figure  3B ). These results agreed with the ELISA results showing that both patients have antibodies against tick proteins (Figures  2B  and 2C ), but suggested a patient-specific antibody response to tick species responsible for the reported anaphylactic reaction to tick bite (i. e. Rhipicephalus spp. in patient 1 and H. marginatum in patient 2). The R. microplus BME/CTVM23 tick cells and H. marginatum salivary gland proteins were then used for higher resolution 2-D gel Western blots and mass spectrometry (MS) to identify proteins differentially recognized by IgE in patients but not control sera and reacting with anti-α-Gal antibodies (Figures  4  and 5 ). A total of 139 R. microplus BME/CTVM23 tick cell proteins were identified from the 20 spots recognized by patient 1 or control sera and by anti-α-Gal antibodies in the 2-D gels (Figure  4  and Supporting information Data Set 1).
marginatum salivary gland proteins, in which 51% of the proteins could not be assigned to a biological process (Figure  7B ). For example, although protein folding was present in both datasets (Figures  6B  and 7B ), translation and glycolytic processes were better represented in H. marginatum than in R. microplus proteins. Nevertheless, protein processing in general was highly represented in both R. microplus and H. marginatum identified unique proteins (Figures  6B  and 7B ). Six proteins were identified in spots positive for α-Gal (Figure  5  and Supporting information Data Set 1), and as in R. microplus proteins (Figures  6A  and 6C ), showed a similar representation for molecular function (Figure  7C ) than for all identified unique proteins (Figure  7A ). For the biological process ontology of proteins identified in spots positive for α-Gal (Figure  7D ), the most represented processes such as cytoskeleton organization, ATP synthesis/hydrolysis, proton transport, glycolytic process, cell migration, muscle contraction, and embryonic development accounting for 90% of all proteins were also represented in all H.
4; Thermo Scientific). Database search was performed against the Rhipicephalus or Hyalomma (12,465 and 5709 entries in November 2015, respectively) Uniprot protein databases. The following constraints were used for the searches: tryptic cleavage after Arg and Lys, up to two missed cleavage sites, and tolerances of 10 ppm for precursor ions and 0. 8 Da for MS/MS fragment ions, and the searches were performed allowing optional methionine oxidation and cysteine carbamidomethylation. Searches were performed against a decoy database in an integrated decoy approach. A false discovery rate (FDR) < 0. 01 was considered as a condition for successful peptide assignments and at least 2 peptides per protein was the condition for successful protein identification (Supporting information Data Set 1). Functional annotations for identified proteins were assigned using the Blast2GO software (version 3; http://www.
FUNDING Part of this research was supported by the  European Union   FP7   ANTIGONE  project number  278976. L. M-H was supported by the  University of Castilla La Mancha  ( UCLM, Spain ) fellowship. M. V and I. G. FM were supported by the  Research Plan of UCLM. F. R-F was supported by the ' Ramón y Cajal' program  of the  Spanish Ministry of Economy and Competitiveness.
Search Strategy We searched MEDLINE via PubMed, Cochrane, and EMBASE electronic databases to identify articles published from January 1, 2014 to August 31, 2016 that described the analysis of gait quality by using inertial sensors in healthy older adults or people with any pathology. Searches were not limited to neurological patients so as to compare with other types of gait disorders. The search involved the key words "Gait" with "inertial measurement unit, " "IMU, " "inertial sensor, " "accelerometer" or "gyrometer. ".
Inclusion Criteria We included articles of studies of humans that investigated gait with IMUs, computed parameters to quantify gait, included at least one group of ill or older people, and compared at least 2 cohorts of participants. We excluded articles of studies that quantified other activities (such as standing or running) or assessed general physical activity (step count or walking bout length); focused on walking segmentation or event detection (U-turn, freezing of gait); assessed gait from raw data or used IMUs as a feedback tool; or included only people younger than 65 years. The PRISMA guidelines were used to select articles.
Automatic detection involved use of industrial software (BTS G-STUDIO R and Locometrix R in 3 studies each, and Poseidon R , Mobility Lab R and EMG Works R in 1 study each), self-designed algorithms (9 studies) or previously described models and algorithms (30 studies). At least 2 studies used several algorithms. In total, 6 studies used the inverted pendulum modelbased algorithm developed by  Zijlstra and Hof (2003) , which has been found accurate for non-disabled adults and children as.