dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusion Sedimentary radionuclide profiles ( 234 Th and 210 Pb) have evidenced that significant contemporary particle dynamics take place on the SE Aquitanian margin in comparison with nearby margins, whereas the CFC experiences moderate and constant sedimentation, and thus could be considered as a quiescent canyon. The comparison of our data with the ECOFER data shows a striking similarity in mass fluxes in the deep reaches of the CFC, within a 16-year period. Short-lived events, like seasonal downward export of surface biological production, may leave a tiny imprint in the deposited layers, as revealed by the presence of 234 Th excess only at the water-sediment interface. In CFC, focusing of fine sediment is confined to the middle canyon at about 500-1500 m and likely related to intermediate and bottom nepheloid layers detached from the shelf and the upper slope.
Given the 3-5-year periodicity of dengue outbreaks  [3]  we estimated that at least one decade of data would be necessary to provide an accurate image of recent evolution of epidemiology. Furthermore, a 10 year period was determined to observe serotype distribution over time and through several epidemics. For convenience, we chose to start our review period on 1 January 2000 and set the cutoff as 23 February 2012, the date when we initiated this review. An additional rationale for selecting 1 January 2000 as the start date for this review, as opposed to an earlier date, was that we hypothesized that this would limit the bias that any differences in surveillance practices over time would have on the results.
Materials and Methods A Literature Review Group developed a protocol for this literature survey and analysis based on the preferred reporting items of systematic reviews and meta-analyses (PRISMA) guidelines  [22]. The protocol was registered on PROSPERO, an international database of prospectively registered systematic reviews in health and social care managed by the Centre for Reviews and Dissemination, University of York (18 May 2012; http://www. crd. york. ac. uk/ PROSPERO/display_record. asp?ID=CRD42012002292). We utilised an inclusive search strategy to find papers, theses, dissertations, reports and statistical tables, as well as official web sites and grey materials. The Literature Review Group defined the inclusion/ exclusion criteria and guided the search and selection process described below.
Search strategy and selection criteria Search strings for each database were designed with reference to the expanded Medical Subject Headings thesaurus, encompassing the terms 'dengue', 'epidemiology', and 'Philippines'. Different search string combinations were used for each electronic database with the aim of increasing the query's sensitivity and specificity. Only studies published in English between 1 January 2000 and 23 February 2012 were included. For databases that did not allow language and/or date limitations, references not meeting these criteria were deleted manually at the first review stage. No limits by sex, age and ethnicity of study participants or by study type were imposed, although single-case reports were excluded, as were studies that only reported data for the period before 1 January 2000.
Author Summary Dengue disease is a tropical and subtropical mosquitoborne viral illness and is a major health concern in the Philippines. To determine the dengue disease burden in the Philippines and identify gaps and future research needs, we conducted a literature analysis and review to describe the epidemiology of dengue disease. We used well-defined methods to search and identify relevant research conducted between 2000 and 2011. This longterm review highlights an increase in the reported incidence of dengue disease in the Philippines. The rising incidence of dengue disease may be related to a growing population, increasing urbanization, improvements in surveillance, and the limited success of vector control measures. Gaps in the epidemiological information available in the Philippines during the period 2000-2011 include comprehensive national and regional data that describe the proportion of severe dengue disease, including hospitalizations and mortality, and incidence data per 100,000 population.
More comprehensive data are also needed for age, serotype, and seroprevalence on both national and regional levels. The data presented enable the observation of epidemiological characteristics, both within and across years. Such assessments are essential at national and regional levels to improve both preparedness and response activities relating to dengue disease outbreaks. After removing duplicate citations, the Literature Review Group reviewed the titles and abstracts and identified those for which the full text was retrieved. A second review was performed on the full text to make the final selection of relevant articles to include. Studies were reviewed by the Literature Review Group to ensure they complied with the search inclusion and exclusion criteria. In particular, publications of duplicate data sets were excluded, unless the articles were reporting different outcome measures.
We chose not to exclude articles and other data sources nor formally rank them on the basis of the quality of evidence. Indeed while it is recognized that assessing study quality can potentially add value to a literature review, the consensus of the Literature Review Group was that given the expected high proportion of surveillance data among the available data sources and the nature of surveillance data (passive reporting of clinicallysuspected dengue), such quality assessment would not add value in this case. As our primary objective was to describe the recent evolution of dengue, rather than to quantify disease in absolute terms, we therefore retained all available data sources. The selected data sources were collated and summarized using a data extraction instrument developed as a series of Excel (Microsoft Corp.
, Redmond, WA) spreadsheets. Data were extracted into the spreadsheets according to the following categories for analysis: incidence, age, sex and serotype distribution, serotype data, seroepidemiology or seasonality and environmental factors, by national or regional groups. Data from literature reviews of previously published peer-reviewed studies and pre-2000 data published within the search period were not extracted. The original data sources and the extraction tables were made available to all members of the Literature Review Group for review and analysis.
Amendment to protocol Additional data on dengue were provided by the Philippines DoH NEC on 28 May 2012  [23]. The NEC Library, formerly the Field Epidemiology Training Program (FETP) Library (http://nec. doh. gov. ph/index. php?option=com_content&view=article&id=43&Itemid= 58), established in 1989 under the FETP project of the DoH, contains reports of local infectious disease outbreaks submitted to them by FETP Fellows and by Regional Surveillance Units. The reports of dengue disease outbreaks that occurred between 1987 and 2011 were manually searched, and data were collated and summarized using the data extraction instrument. The NEC also provided data from the urban area of Quezon City, NCR, and the rural area of Rizal, Region IV-A. Data included the population numbers and the number of dengue disease cases by year (1999-2011) and by age (,1 year, 1-10 years, 11-20 years, 21-30 years, 31-40 years,.
National epidemiology Among the included sources, no complete and comparable data were found for the entire review period. The most complete datasets for the number of cases of dengue disease in the Philippines and the number of dengue-related deaths were reported by the DoH [5,  [25] [26] [27] [28] [29]  and the WHO  [6, 16, 20, 21, [30] [31] [32]  (Figures  3A  and 2B , Table  S2  and Table  S3 ), although a number of sources did report similar, but isolated, data during the survey period  [13, 33, 34 ]. An overall summary plot of these data would be of little value in identifying trends over time. Despite possible bias therefore it is useful to view the data made available during the review period from the WHO and DoH (Figures  3A  and 3B ). These data show that the reported number of dengue disease cases fluctuated throughout the review period, with an overall increase in cases observed over time (Figure  3A ).
There was a sharp rise in the number of cases in 2001  (23,   25, 29]. Possibly as a result of data extrapolation from incomplete submissions from some regions, the WHO data showed consistently higher numbers of cases than the DoH, but the same general pattern. A large increase in the number of cases was recorded in 2010, with 131,976 and 173,033 cases reported by the DoH and the WHO, respectively, compared with 56,545 and 57,819 cases, respectively, in 2009  [30] [31] [32] [33]. There were also a large number of cases reported by the DoH in 2011 (118,868)  [31]. Overall, the CFR ranged from 0. 5% to 1. 7% [5,  6, 16, 29, 30, 32]. There were 548 fatal cases in 2009 (CFR 0. 95%), increasing to 788-793 in 2010 (CFR 0. 60-0. 94%) [30, 32, 33]. Data on the severity of dengue disease cases were inconsistently reported over the review period.
Acknowledgments The authors take full responsibility for the content of this contribution and thank  Graham Joint  from  Communigen, Oxford  (supported by  Sanofi Pasteur)  for editorial assistance with preparation of the manuscript. Dr Mayan Lumandas , a Research Fellow and Consultant in Paediatric Infectious Diseases ( National Institute of Health, the Philippines ), manually searched the reports of dengue disease outbreaks that occurred between 2000 and 2011, provided by the  Philippines DoH NEC. Eric Tayag Head  of the  NEC  provided guidance on the effects of seasonality and environmental factors on dengue disease. The authors would like to thank  Gee Marsh  ( Sanofi Pasteur ) for provision of critical comments and suggestions on the drafts.
In particular, the power-spectrum now takes very similar scale invariant values on large and small scales, while on intermediate scales it is characterised by much larger amplitude and higher frequency superimposed oscillations. We also show that calculating non-Gaussianities in this model is a complicated but interesting task since all terms in the cubic action now contribute. Investigating whether the superimposed oscillations could fit to the Planck Cosmic Microwave Background (CMB) data (for instance by explaining the large scale Planck anomalies) with, at the same time, small non-Gaussianities remains an intriguing and open possibility.
This would require interfacing the numerical code used in this paper to calculate the power spectrum to a CMB code (typically the CAMB code  [47] ), and then in turn to a code allowing us to explore the corresponding parameter space (typically the COSMOMC code  [48] ). Moreover, we would also need to include in the analysis the constraints coming from the higher correlation functions (see below). Clearly, this is beyond the scope of the present article since, here, we mainly focus on the physical properties of the system rather than on data analysis. It is interesting, however, to have a broad idea about the physical values of the parameters. To this aim, we have represented in Fig. 9  the Planck "step model" best fit (solid blue line)  [1]  with the DBI-Starobinsky power spectrum (solid red line) with γ in ≃ 5 and A -≃ 0.
e. the fact that c S ≪ 1 enhancing the contribution coming from the discontinuity of V ′. From the observational point of view, given the Planck result, it is clear that the corresponding constraints on the parameters of the model will be very tight. On the other hand, we have seen that the amplitude of the superimposed oscillations can be large (or, at least, seems larger than in the CS-model), even if the parameters are relatively close to standard slow-roll inflation. As a consequence, a priori, it remains possible that non-negligible superimposed oscillations improve the fit to the CMB data (especially by matching the Planck anomalies) while, at the same time, equilateral non-Gaussianities remain within the observational bounds. We hope to address this issue in more detail in the near future.
Acknowledgements This work is partly supported by the  Polish Grants NCN  No  DEC-2011/01/D/ST2/02069 , by the  Joint Research Activity "Study of Strongly Interacting Matter " (acronym  HadronPhysics3 , Grant Agreement n. 283286) under the  Seventh Framework Programme  of the European Community, by the  GDR 3034 PH-QCD , the  ANR-12-MONU-0008-01  and the  COPIN-IN2P3  Agreement.
Phylogenetic analyses of influenza virus A and B sequences Cell culture isolates of influenza A/H3N2 (N = 4), influenza A(H1N1)pdm09 (N = 19) and influenza B2 (N = 11) viruses were obtained. Eight-segment genomic sequences were produced for Flu A/H3N2 isolates (GenBank accession numbers KF612026-KF612180) and Flu A/H3N2 isolates (GenBank accession numbers KF612181-KF612211). Partial sequences (segments HA, NA, NS, M) were produced for Flu B isolates (GenBank accession numbers KF612212-KF612267). The corresponding sequences were used for further phylogenetic analyses.
The data used in this analysis correspond to an integrated luminosity of 946 ± 33 pb -1 collected in 2011 at a centre-of-mass energy √ s = 7 TeV and 1985 ± 69 pb -1 collected in 2012 at √ s = 8 TeV. The two datasets are combined because the overall yields are low and the cross-sections are expected to be similar at the two energies. The J/ψ and ψ(2S) mesons are identified through their decays to two muons, while the χ c mesons are searched for in the decay channels χ c → J/ψ γ. The protons are only marginally deflected by the peripheral collision and remain undetected inside the beam pipe. Therefore, the signature for exclusive charmonium pairs is an event containing four muons, at most two photons, and no other activity. Beam-crossings with multiple proton interactions produce additional activity; in the 2011 (2012) data-taking period the average number of visible interactions per bunch crossing was 1.
Acknowledgements We thank  Lucian Harland-Lang  and  Valery Khoze  for many helpful discussions and for providing theoretical predictions. We express our gratitude to our colleagues in the CERN accelerator departments for the excellent performance of the LHC. We thank the technical and administrative staff at the LHCb institutes. We acknowledge support from  CERN  and from the national agencies:  CAPES ,  CNPq ,  FAPERJ  and  FINEP (Brazil) ;  NSFC (China) ;  CNRS/IN2P3  (France);  BMBF ,  DFG ,  HGF  and  MPG (Germany) ;  SFI (Ireland) ;  INFN (Italy) ;  FOM  and  NWO  (The Netherlands);  MNiSW  and  NCN (Poland) ;  MEN/IFA (Romania) ;  MinES  and  FANO (Russia) ;  MinECo (Spain) ;  SNSF  and  SER (Switzerland) ;  NASU (Ukraine) ;  STFC  ( United Kingdom );  NSF (USA). The Tier1 computing centres are supported by  IN2P3 (France) ,  KIT  and  BMBF (Germany) ,  INFN (Italy) ,  NWO  and SURF (The Netherlands),  PIC (Spain) ,  GridPP  ( United Kingdom ).
A large meta-analysis found no increased risk of birth defects  [10] , despite the inclusion of two recent prospective studies that found an increased risk with first-trimester exposure to efavirenz  [11, 12]. The largest database for birth defects and ART today is the Antiretroviral Pregnancy Registry (APR), with 15,451 births included  [13]. To date, the only antiretrovirals (ARVs) for which use during the first trimester is associated with increased rates of overall birth defects in the APR compared with the general population (2. 8%) are nelfinavir (3. 9%) and didanosine (4. 6%); no association with specific birth defects was identified for these two drugs. Two other studies found an association between congenital heart defects (CHDs) and ART: zidovudine in one of these studies (adjusted odds ratio [AOR] = 2.
Methods The study was approved by the Hopital Cochin Institutional Review Board and the French computer database watchdog commission (Comission Nationale de l'Informatique et des Libertes). The French Perinatal Cohort (ANRS CO1/CO11) Since 1986, EPF has prospectively enrolled pregnant HIVinfected women delivering in 90 centers throughout France  [1]. In each participating maternity center, around 95% of all HIV-infected pregnant women were included, with informed consent. No specific recommendation for HIV treatment and obstetric care was made for women included in the cohort, but clinicians were encouraged to follow current French national guidelines, which include trimestrial prenatal ultrasound for all women, whatever their HIV status, and pediatric clinical and biological examinations at birth  and 1, 3, 6, 12, and 18-24 mo  for children exposed to maternal HIV  [4, 20].
Maternal variables included age, geographical origin, intravenous drug use (IDU), gravidity, parity, CD4 cell count, and HIV-1 viral load closest to the delivery, i. e. , the day of delivery or in the 7 d after delivery. Alcohol and tobacco use were recorded only after 2005, and data on concomitant medications were not available in the cohort. All ART combinations administered during pregnancy were recorded, with the dates when started and stopped. For each drug (called ''index drug''), exposure status was categorized as follows: (1) unexposed to the index drug, but exposed to other drugs (control group), (  2 ) exposed to the index drug since conception or the first trimester, or (3) exposed to the index drug only since the second or third trimester. Another categorization was used in sensitivity analyses concerning only first-trimester exposure: (1) unexposed to any ART in the first trimester, i.
A two-sided p,0. 05 was taken as indicating statistical significance. Data were analyzed using Stata 11. 0 software (Stata Corp)  [26]. No adjustment was used for multiple testing. For each ARV drug, we calculated the power to detect an association between overall birth defects and first-trimester exposure (compared with no exposure during pregnancy). Power to show an odds ratio (OR) of 1. 5 was. 85% for zidovudine, lamivudine, ritonavir, and lopinavir, and was. 70% for didanosine, stavudine, abacavir, tenofovir, and nevirapine (data shown in Table  2 ). For all these drugs, power was. 95% to detect an OR of 2.
Results The analysis was conducted in 13,124 live-born children, born between 1 January 1994 and 31 December 2010, among whom 42% (n = 5,388) were exposed to ART in the first trimester of pregnancy. PMTCT strategies varied over time, and the proportion of infants exposed to ART in the first trimester increased  from 19% in 1994-1996 to 52% in 2005-2010. The evolution in time of types of treatment and trimesters of exposure are presented in Table  3. The median maternal age was 31 y, most women were from sub-Saharan Africa (61%) and parous (62%), and very few were intravenous drug users (2%). Most women had a good immunovirological status (CD4$350 cells/ml and viral load ,400 copies/ml; Table  4 ). Data at birth was collected for the newborns of all women enrolled. Median followup of children was 19 mo (interquartile range 12-24 mo).
Discussion The prevalence of birth defects in our study population was 4. 4% as assessed using the EUROCAT guidelines and 7% using the MACDP classification. This is higher than the rates reported in most large studies including patients exposed to ARV drugs, which were 1. 5% in the European Collaborative Study, published in 2005 and thus including different drugs than those used in more recent studies  [18] , 2. 8% in a recent study in the United Kingdom  [17] , and 2. 9% in the APR  [13]. The prevalence in our cohort is, however, consistent with that observed in smaller prospective studies, which all report higher rates, from 5. 3% to 8. 3%  [11, 12, 16, 27]. We hypothesize that studies involving few centers may have a higher level of reporting because of greater motivation of clinicians for the specific research program and more intensive data monitoring than in large multicenter cohort studies and registries.
The discrepancy may be due to differences between the populations included in the studies and the different methods used to diagnose birth defects. Additional large studies are therefore necessary to obtain more and better evidence on the potential harm of individual anti-HIV drugs to children exposed during pregnancy. So in this study, the authors conducted a large cohort study in France to assess the relationship between different antiretroviral drugs and specific birth defects. What Did the Researchers Do and Find? The researchers used a large national health database known as the French Perinatal Cohort that contains information on HIV-infected mothers who delivered infants in 90 centers throughout France. Pediatricians follow all children, whatever their HIV status, to two years of age, and health statistics are collected according to national health-care guidelines.
Results and discussion Antibodies against IL-10 Antibodies of the IgG isotype Sera of 20 healthy donors as well as 52 IBD patients were subjected to ELISA testing in search of anti-IL-10 IgG antibodies. Upon testing, eight out of 52 IBD patients (15%) showed OD values above a cut-off of μ + 3SD (Figure  1A ). Data were analyzed by t-test, comparing the Crohn's disease (CD) and ulcerative colitis (UC) groups both to the healthy control group. We found the CD group to exhibit significantly elevated levels of anti-IL-10 IgG antibodies, whereas the UC group testing resulted in a non-significant p-value (p = 0. 41). In our cohort, 18% of CD patients (7/38) had anti-IL-10 autoantibodies; this replicates the results of Ebert et al. [19] , who found 17% of CD patients to have anti-IL-10 IgG autoantibodies in the serum, thus validating our results in spite of a small sample size.
Acknowledgements This work has been supported by the  EC Marie-Curie  Grant  MEXT-CT-2006-042316 , as well as by funds from the  EU 7th  framework programme (FP7 2007-2013 No. 223293  and  FP7 2007-2013 EURO-PADnet HEALTH-F2-2008-201549 ), by the  German Federal Ministry of Education and Research  ( BMBF 01 EO 0803 ) and by  Marie Curie Actions CIG  (294253, EOG). The authors are responsible for the contents of this publication. The article processing charge was funded by the open access publication fund of the  Albert Ludwigs University Freiburg.
For ChIP-on-chip experiments, ChIP material was amplified and labeled as in  van Bakel et al. (2008). Each ChIP was compared to its reciprocally labeled input sample. For origin efficiencies, genomic DNA was harvested prior to DNA synthesis and during S phase after treatment with HU. Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) and hybridized to microarrays; dye-swap experiments were performed to reduce noise. All experiments used Agilent 4344k S. pombe arrays (60-mer oligos, $250 nt resolution). Details for the analysis of microarray data are provided in the Supplemental Experimental Procedures.
To determine origin efficiencies, cells were treated with hydroxyurea (HU) prior to S phase and harvested at time points when DNA replication is complete in the control samples without HU (data not shown). Genomic DNA was isolated and copy number determined using Agilent 4344k S. pombe arrays. x axis: chromosome coordinates; y axis: copy number. (F) Time course of meiotic progression of pat-114 diploids induced to undergo meiosis. Heat-fixed cells were stained with DAPI to detect nuclei, and the number of nuclei per cell was counted each hour to determine the kinetics of meiosis I and II after nitrogen depletion (ÀN) and in continuous nitrogen-rich conditions (+N) (n R 200). The time for the end of premeiotic S phase (t = 0) was determined by flow cytometry (see G). In both cases, most cells have proceeded through meiosis I around 2 hr and meiosis II around 3 hr after the completion of S phase.