dataesr/scientific-paragraphs-categorization huggingface dataset:
The confidence intervals (CIs) of the risk estimates, obtained using calibrated data, were estimated using bootstrap sampling to take into account the uncertainty related to measurement error correction. Calibrated and uncalibrated data were used to estimate the association of meat consumption with mortality on a continuous scale. Results of the 24-hour recalls (mean, standard error of the mean) were also used to describe the FFQ-based intake categories of red meat, processed meat, and poultry. In our analysis, we considered cause-specific mortality in addition to overall mortality. Therefore, we fitted a competing risk model  [27]  which, however, resulted in similar associations as those observed in non-competing risk models for deaths from cancer, cardiovascular diseases, respiratory diseases, digestive diseases, and other diseases, and are not shown in the tables.
The population attributable risk (PAR), which describes the proportion of cases that would be prevented if everyone in the study population had the reference level of the exposure, was estimated based on the formula  [28] : PAR = P i (HR i-1) / 1 + P i (HR i-1) × 100, where HR i and P i are the multivariate adjusted relative risks and the prevalence, respectively, in the study population for the i th exposure category (processed meat consumption 20+ g/day); I = 0: reference group (processed meat 0 to 19 g/day). All analyses were conducted using SAS version 9. 1 (SAS Institute, Cary, North Carolina).
Acknowledgements The work described in this article was carried out with the financial support of  Europe Against Cancer Program of the European Commission (SANCO) ;  Deutsche Krebshilfe, Deutsches Krebsforschungszentrum ,  German Federal Ministry of Education and Research ;  Danish Cancer Society; Health Research Fund (FIS)  of the  Spanish Ministry of Health, Spanish Regional Governments of Andalucia, Asturias, Basque Country, Murcia and Navarra ;  ISCIII RCESP exp. C03/09 , Spain;  Cancer Research UK; Medical Research Council ,  United Kingdom ;  Stroke Association, United Kingdom ;  British Heart Foundation ;  Department of Health, United Kingdom ;  Food Standards Agency ,  United Kingdom ;  Wellcome Trust ,  United Kingdom ; the  Hellenic Health Foundation  and the  Stavros Niarchos Foundation ;  Italian Association for Research on Cancer (AIRC) ;  Italian National Research Council ,  Fondazione-Istituto Banco Napoli, Italy ;  Dutch Ministry of Public Health, Welfare and Sports (VWS) ,  Netherlands Cancer Registry (NKR) ,  LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland) ,  World Cancer Research Fund (WCRF) ,  Statistics Netherlands  (The Netherlands);  Swedish Cancer Society; Swedish Scientific Council; Regional Government of Skåne, Sweden ; Nordforsk the  Norwegian Cancer Society ;  French League against Cancer (LNCC) ;  National Institute for Health and Medical Research (INSERM), France ;  Mutuelle Générale de l'Education Nationale (MGEN), France ;  3M  Co, France;  Gustave Roussy Institute (IGR) , France; and  General Councils of France.
THT (Thioflavine T ) fluorescence assay Aliquots of monomeric or oligomeric Aß were diluted to the appropriate final concentration (20 µM or 30 µM) in PBS. Each sample had a total volume of 100 µL and contained 20 µM thioflavin T dye. All kinetics measurements were carried out at 30 °C in 96-well plates. Data were recorded using a POLARstar Omega reader (BGM). Data points were recorded in cycles using the bottom-reading mode. A single cycle consisted of 10 s of orbital shaking (600 rpm) before fluorescence measurement, which was taken as the average of 10 flashes every 6 min. The dye was excited at 440 nm, and the fluorescence signal was recorded at 480 nm. For cross-seeding assays, nucleation seeds were prepared from fibers obtained during the kinetics measurement described above. A 100 µL aliquot of each sample was sonicated for 5 min (output 5 and 50 % duty cycle).
It is therefore clear that the toxicity of these new Aß alleles was not due to a change in protein concentration or localization but rather to other parameters, such as its autoassembly capacity. In many cases, multiple mutations can be found within a mutagenized Aß sequence. Interestingly, among the 135 single changes obtained, we never observed any mutations of V12, L34, or I31 (data not shown). This result could have been due to a non-random distribution of the mutations. Alternatively, it might indicate that these aminoacids are crucial for Aß toxicity and that their mutation would be counter-selected in our screen (this screen was based on the gain of toxicity of Aß). We tested this hypothesis and created point mutations at these three positions. Site-directed mutagenesis was performed using degenerate oligonucleotides for the different amino acids (V12, L34 and I31).
Discussion In this study, we analysed echocardiographic parameters in a model of LGMD2D, the sgcanull mouse. In our knowledge, no data were reported in the literature about heart function in sgca-null mice, using echocardiography. LGMD2D belongs to the group of muscular dystrophies which are histologically characterized by necrotic and regenerating fibers, increase in fiber size variation, fiber splitting and centrally located nuclei. LGMD2D is an autosomal recessive limb-girdle muscular dystrophy caused by mutations in the alpha-sarcoglycan gene. Clinically, LGMD2D is characterized by great variability, ranging from severe form with onset in the first decade of life and rapid progression, resembling Duchenne muscular dystrophy (DMD), to milder form with later onset and slower progression resembling to Becker muscular dystrophy (BMD).
Quickly establishing an appropriate individualized r-hGH dose by targeting a safe but efficacious IGF-I level would be clinically useful. Furthermore, a small number of patients still experience an inadequate growth response to a sufficient r-hGH dose, justifying treatment discontinuation. Identification of genomic markers that are predictive of an inadequate response to GH therapy could help detect these patients more quickly. Here we report original data from the PREDICT study (NCT00256126),  9, 10  investigating for the first time in a prospective study the association between genomic data (genetic polymorphisms and gene expression) and 1-month change in IGF-I (DIGF-I) following initiation of r-hGH treatment in children with GHD or Turner syndrome (TS). These two conditions are associated with significant short stature, and account for B50% of r-hGH prescriptions.
Study design The PREDICT study was a phase IV, multicenter, prospective, open-label, 1-month study to identify genomic markers associated with 1-month IGF-I generation in response to r-hGH therapy in GH treatment-naı ¨ve children with GHD or TS. This was an international study that recruited patients from centers in Argentina, Australia, Austria, Canada, Finland, France, Germany, Italy, Korea, Norway, Russia, Spain, Sweden, Taiwan and the United Kingdom. This study involved three stages. First, genes involved in growth and metabolism were identified by literature searches and selected for inclusion, based on advice from a panel of advisors (see Supplementary Table  S1  for a list of the candidate genes). Second, genotypes and gene expression data were assessed for their association with 1-month DIGF-I.
Genetic analysis Genotyping was performed on DNA extracted from whole blood using Illumina GoldenGate assays (Illumina, San Diego, CA, USA). In total, 1536 single-nucleotide polymorphisms (SNPs), located on 103 candidate genes, related to: (1) the GH-IGF-I axis; (2) bone and cell growth; and (3) glucose and lipid metabolism, were selected for genotyping. Of these, 1451 SNPs were genotyped successfully. Before analysis, genotyping data were filtered to remove SNPs with low minor allele frequency (o10%), those with a call rate o95%, and those showing significant deviation from the Hardy-Weinberg equilibrium using a Bonferroni correction for 1451 tests (except for X-linked SNPs in girls with TS and boys with GHD). After data cleaning, 1171 SNPs in GHD and 1182 SNPs in TS remained for analysis.
0 Arrays. Arrays were then scanned on an Affymetrix GeneChip 3000 7G scanner and assessed for quality against internal and hybridization controls. Processing and normalization of the raw gene expression data were performed on GHD and TS samples using a Robust Multi-array Average background correction modified for probe sequence with quantile normalization and median polish (Partek Genomics Suite, version 6. 3, St Louis, MO, USA). Confounding effects due to variations in cell populations and outliers were identified by cross validation using principal component analysis and iso-map multidimensional scaling (Qlucore Omics Explorer 2. 2, Qlucore, Lund, Sweden). A cut-off was set for the variable with the largest variance (s max ) to remove non-informative probes; this was set at 0. 05 (s/s max ) (Qlucore Omics Explorer 2.
05; positive predictive value should be X40% and/or negative predictive value X90%. Gene expression profiles. Rank regression analysis was used to correlate change in baseline gene expression with 1-month DIGF-I (Figure  1 ). A paired t-test was used to compare gene expression changes over 1 month and analysis of variance was used to determine the differential baseline gene expression between quartile groups, both tests with age and gender as eliminated factors. False discovery-modified P-values (q) based on hypergeometric tests were also determined. Enriched gene functions and canonical biological pathways were identified with Ingenuity Pathways Analysis software (Ingenuity Systems, Redwood City, CA, USA) using Fisher's exact test. Network analysis. Analysis of inferred protein:protein interaction (PPI) networks was performed using Ingenuity Pathways Analysis software to increase confidence in the observations of differentially expressed genes by their correlation with biological pathways.
Gene expression changes over 1 month of treatment with r-hGH To support the use of gene expression profiling in whole blood as a valid model of GH action with sufficient sensitivity to detect direct and/or indirect GH-induced changes, gene expression in paired samples over 1 month of r-hGH treatment was evaluated. The expression of 5367 and 1850 probe sets in GHD and TS, respectively, with age and gender as confounding factors, changed significantly (t-test, Po0. 05), with 552 probe sets overlapping corresponding to 446 genes (Table  2 ). To establish the proportion of differentially expressed genes that were potentially regulated directly by GH, we compared the data by orthology with mouse genes identified as having STAT5 bound to putative regulatory elements by chromatin immunoprecipitation sequencing (ChIP:seq).
Integration of genetic and gene expression data Network analysis places the genes for which changes in expression were observed in the context of a model of all known PPIs, termed the interactome. The properties of these inferred networks can then be examined and correlated with biological function (Supplementary Figure  S2 ). CDK4 was found to carry SNPs associated with IGF-I response in both GHD and TS (Figure  4 ). To examine the biological function of the CDK4 SNPs, we generated inferred biological pathways using baseline gene expression significantly (Po0. 05) associated with carriage of different CDK4 alleles in low IGF-I responders. Parameters of network topology in these inferred pathways were calculated as markers of essential function. 22, 23 In children with GHD, changes were identified in MAPK-and GRB2/SOS-mediated signaling pathways (e.
29 Therefore, we have also used the analysis of PPI networks inferred from the data  30  and co-expression analysis  24  to increase confidence that the association with specific biological pathways is genuine. 31 ere, IGF-I generation at 1 month was found to be associated with polymorphisms in 5 genes in GHD and 13 genes in TS. Most of these genes are not involved in classic GH/IGF-I pathways. CDK4, a member of the early cell-cycle gene family and not known to be directly involved in response to GH, is the only common gene associated with IGF-I generation in the two cohorts of children. It is recognized that girls with TS received a higher dose of r-hGH than children with GHD, doses that were determined by standard clinical practice. Despite the dose discrepancy, the 1-month DIGF-I can be seen to overlap between GHD and TS, likely reflecting differences in sensitivity to r-hGH, yet the polymorphisms associated with this change in serum IGF-I differ.
Patients and Treatments Between 1992 and 2009, 22 patients (16 males/6 females) underwent a second Allo-HCT and were treated at the adult allogenic hematopoietic stem cell transplantation program at Institut Paoli-Calmettes, the Cancer Research Centre, at Marseille, France. Fourteen patients (64%) were re-transplanted for relapse, six patients (27%) were re-transplanted for GF, and two patients had both graft failure and disease progression. Patients' data were collected from a maintained database and by retrospective clinical chart review. The criteria for selection of patients for second transplant was good performance status, young age, availability of stem cells from the same or alternative donor, absence of chronic Graft Versus Host Disease (GVHD) and no alternative possible curative treatment.
Data collection In completing the template, informants were asked to adopt an evidence-based, comprehensive approach, by making use of the best data available and cooperating with organisations involved in the management of chronic disease. Where appropriate and necessary, additional information was gathered through interviews with key stakeholders and reviews of work in progress, such as pilot projects and committee reports. As it was beyond the scope of DISMEVAL to provide a complete inventory of chronic care management approaches being implemented in the included countries, key informants were asked to present a sample of approaches considered representative of a given health system in terms of the type and setting of delivery model, providers involved, key strategies employed, and population covered.
For each approach, respondents described whether and how self-management support activities were implemented, according to the CCM-related Assessment of Chronic Illness Care (ACIC) survey  [34] ; that is, patient education, collaborative care planning, provision of selfmanagement tools, and structured follow-up. Principal data collection was carried out from June 2009 to December 2009, with sequential follow-up review untill July 2011 to complete missing data and clarify information.
Data analysis We used a general inductive approach to data analysis, in which emerging themes related to self-management support were identified through examination of the completed data template containing evidence from 13 countries. The data were analysed in detail by the lead author (AE) to identify key themes, which were discussed with and agreed by all coauthors. In total, three categories of themes were distinguished: (1) support mode and content ('what'); (2) support format and materials ('how'); and (3) support providers and locations ('who and where'). Data were then organised into a purposely built matrix comprising the three emerged categories of themes, which facilitated systematic cross-country comparison of selfmanagement support approaches in the 13 countries. For consistency, the same matrix was used to process and analyse the transcripts of the Dutch interviews concerning the implementation of self-management support in practice.
Acknowledgments This study was conducted with support from the DISMEVAL consortium. It draws on additional information from DISMEVAL partners and key informants who contributed information on approaches to chronic disease management in selected countries:  Fadila Farsi ,  Hélène Labrosse  (DISMEVAL partner,  Centre Anticancereux Leon Berard : cancer networks France),  Taavi Lai  ( Estonia, Latvia, Lithuania );  Péter Gaál  and  Márton Csere (Hungary) ;  Walter Ricciardi ,  Antonio G. De Belvis ,  Maria Lucia Specchia ,  TD Luca Valerio (Italy) ;  Liubove Murauskiene ,  Marija Veniute  (Lithuania); and  Isabelle Peytremann-Bridevaux ,  Bernard Burnand  and  Ignazio Cassis  (Switzerland); and was undertaken in cooperation with nine Dutch primary care groups:  Regionale Huisartsenzorg Maastricht/Heuvelland ,  Diabetes Zorgsysteem West-Friesland, Groninger Huisartsen Coöperatie, Huisartsenzorg Drenthe Medische Eerstelijns Ketenzorg, Eerstelijns Centrum Tiel ,  Coöperatie Zorgcirkels Woerden ,  Zorggroep Zwolle ,  Huisartsenketenzorg Arnhem ,  Cohesie Cure & Care.
To process the data, different programs were used: (i) the HierFstat package  [35]  in R  [36]  to compute the 95% confidence intervals of F is , (ii) the "binom. test" function in R to test the null hypothesis about the probability of success in Bernoulli's experiments, (iii) MicroChecker v. 2. 2. 3  [37]  to test the load of null alleles, (iv) Multilocus v1. 3b  [32]  for I A and ȓ d indices and to test the probabilities of repeated MLG and different MLG, (v) Populations (v. 1. 2. 30 © 1999, Olivier Langella, CNRS UPR9034) to build a general clustering analysis between all stocks using the Cavalli-Sforza and Edwards' chord genetic distances  [38] , and (vi) Fstat  [39]  for all other tests.
Between 1997 and 1998 a pilot study evaluating the impact of cyfluthrin impregnated bed nets on malaria transmission, was conducted in Mbandjock a semi urban locality with over 16,000 inhabitants. About 4,000 impregnated bed nets were distributed to the population and malaria transmission was monitored before and after bed net distribution to the population. This study presents the main results recorded and, discusses the possible lessons in relation to the recent nationwide distribution of LLINs to the population in Cameroon. This study also has the objective of presenting control activities that have taken place in the country and methods used in the past. Data from past control activities in Cameroon have been desperately lacking because the majority of these studies are not published.
Biting behavior Before bed net distribution, the human biting rate (HBR) varied from 1. 79 to 17. 3 bites/human/night in Mbandjock (Figure  2 ). The highest HBR (17. 3 bites/human/night) was recorded during the month of April 1997 and was closely associated to increased mosquito frequency in the districts of Bilingue (36 bites/human/night) and Gare (34. 75 bites/ human/night). In the districts of Membrat and Plateau, the average HBR during the same period varied from 1. 67   2 ). When the data was split into districts, Bilingue with >50 bites/human/night in April 1998 and Gare with >20 bites/human/night in May 1998 scored the highest HBR. A decrease of vector HBR was recorded from June to September 1998 in all districts. An. gambiae, the main species in Mbandjock was responsible for an average HBR of 6.
Acknowledgements This paper is to pay homage to the regret memory of  Bernard Bouchité  who died a couple of years ago and who initiated this study. We thank  Mr Kenmegne Guy Rostand  and  Dr Parfait Awono Ambene  who helped with data registration in the database. This work was supported by  Bayer ,  IRD , and a  Wellcome Trust Intermediate Fellowship in Public Health and Tropical Medicine  ( WTO86423MA ) to ANC.
Background: To evaluate the public health efficacy of a community-based smoking cessation program (TABADO) among vocational school trainees (15 to 20 years old). Methods: This prospective, controlled, quasi-experimental study was conducted in eight vocational training centres (VTC) in France. The intervention group underwent the TABADO program, which included a general information session for all students and small-group sessions plus individual counselling and nicotine therapy, if needed, for volunteers in an enhanced program. The control group received no specific intervention other than the educational services usually available. The primary outcome was 30-day point prevalence abstinence at 12 months. Results: The mean age of the 1,814 students included was 16. 9 years (SD = 1. 0); 84. 7% were males.
A smoking cessation program called TABADO, based on these elements was developed by a multidisciplinary team in Nancy, France  [11]. This community-based program combines information sessions for all smokers and non-smokers, as well as medication and cognitive behavioural therapy for smokers who volunteer for the enhanced program. This program was designed to target a particularly vulnerable population, vocational school trainees, since 49. 9% of 17-year-old French students in apprenticeships are daily smokers, versus 28. 9% in the general population of the same age  [12]. This evaluation study was conducted in vocational training centres (VTCs) in the Lorraine region of France. That study's design has been described in detail elsewhere  [13]. The main objective of this study was to evaluate the efficacy of offering this community-based intervention as part of a comprehensive approach to prevention in a population of young trainees in VTCs.
Intervention The TABADO intervention combined a general program aimed at all participants, in the form of an information session on tobacco consumption, with a specific enhanced program undertaken by some smokers on a volunteer basis (identified here as "EP participants")  [11]. This volunteer contingent underwent two stages: 1) individual consultation with a team of physicians specialized in tobacco addiction who visited the VTC and provided personalized assistance with choosing nicotine replacement therapy (patches or gums), if needed; and 2) a small group approach, supervised by the same physicians, consisting of discussion sessions to share experiences, strengthen motivation and prevent relapse. Each group underwent four sessions spread over three months (to accommodate the 1:3 week training schedule described above); preceding those group sessions, individual counselling was also offered to each student.
Data collection Monitoring data for all students The program was implemented over two inclusion periods: the first beginning in February 2008, and the second in November 2008. In both cases, data collection began with a first visit, conducted within the same period for both intervention and control schools, during which all students completed an initial assessment questionnaire asking about smoking status, sociodemographic data, knowledge, attitudes and behaviour. A final questionnaire to evaluate smoking status was administered at 12 months and contained the items in the initial questionnaire plus items to assess changes in perception of health risks associated with smoking. The final questionnaire also included items to measure changes over time in tobacco consumption among smokers. Thus, it enabled an overall assessment of the efficacy of the intervention among the target population.
Clinical research assistants distributed and collected the questionnaires. The primary outcome was 30-day point prevalence abstinence at 12 months. The rate of abstinence was defined by the number of baseline smokers who had quit at 12 months relative to the total number of baseline smokers. Baseline smokers were defined as respondents who reported that they smoked at the time of the initial questionnaire (on the question: "Are you a smoker or non-smoker?"). Abstinence was defined as being a nonsmoker (i. e. , ex-smoker) at 12 months and having not smoked for at least one month before that point (data from two questions in the final survey: "Are you a smoker, non-smoker, or ex-smoker?" and "How long have you not been smoking?"). The validity of responses regarding smoking status in the questionnaire was ensured by measuring expired carbon monoxide concentrations in 140 students selected at random (the calculated sample size was 130, for 90% sensitivity, 5% precision and 5% alpha).