dataesr/scientific-paragraphs-categorization huggingface dataset:
05 months when combined with six cycles of chemotherapy  [56]. It is important to note, however, that bevacizumab is contraindicated for treatment of patients with SqCLC due to a heightened risk of life-threatening pulmonary hemorrhage in this patient population  [3, 57]. Ramucirumab, a mAb directed against VEGF receptor 2, has subsequently been approved for use in combination with docetaxel for the treatment of patients with metastatic platinumresistant NSCLC, including SqCLC. Ramucirumab has been shown to be effective as second-line therapy, improving both OS and PFS. In the phase III REVEL study (NCT01168973), ramucirumab 10 mg/kgþdocetaxel 75 mg/m 2 every 3 weeks resulted in a median (95% CI) OS of 10. 5  (9. 5-11. 2) months compared with 9. 1 (8. 4-10. 0) months with placeboþdocetaxel  [58].
Acknowledgements The concept of predictive biomarkers for EGFR-directed mAbs addressed in this article were originally discussed at a meeting convened by  Eli Lilly and Company  that covered topics for physician education on SqCLC, for which participants, including some of the authors on this publication, received an honorarium. This publication was developed separately from the meeting, and the authors received no payment in relation to the development of this publication. The authors would like to thank  Charlene Rivera, PhD  and  Rob Kite, BSc  (Hons), at  Complete HealthVizion  for assistance with writing and revising the draft manuscript on the basis of detailed feedback from all authors. Primary responsibility for the opinions, conclusions, and interpretation of data lay with the authors, and all authors approved the final version of the manuscript.
clinical trial. The INSPIRE trial (NCT00982111) further assessed the role of histology on the efficacy of necitumumab by comparing first-line necitumumab plus pemetrexed and cisplatin chemotherapy versus pemetrexed and cisplatin chemotherapy alone for the treatment of patients with advanced non- [32]mous NSCLC (i. e. adenocarcinoma, large-cell carcinoma, and other non-squamous histology)[32]. In contrast to the findings from SQUIRE, no significant differences were observed in OS between the two cohorts in the INSPIRE clinical setting. Median OS was 11. 3 months in the necitumumab plus pemetrexed and cisplatin group versus 11. 5 months in the pemetrexed and cisplatin group [HR ¼ 1. 01 (95% CI 0. 84-1. 21); P ¼ 0. 96]. In addition, there were no significant differences in OS between treatment groups in high and low EGFR protein expression groups (H-score !200 and <200, respectively).
Introduction: By 2020, 90% of all people diagnosed with HIV should receive long-term combination antiretroviral therapy (ART). In sub-Saharan Africa, this target is threatened by loss to follow-up in ART programmes. The proportion of people retained on ART long-term cannot be easily determined, because individuals classified as lost to follow-up, may have selftransferred to another HIV treatment programme, or may have died. We describe retention on ART in sub-Saharan Africa, first based on observed data as recorded in the clinic databases, and second adjusted for undocumented deaths and selftransfers. Methods: We analysed data from HIV-infected adults and children initiating ART between 2009 and 2014 at a sub-Saharan African HIV treatment programme participating in the International epidemiology Databases to Evaluate AIDS (IeDEA).
| Data sources The International epidemiology Databases to Evaluate AIDS (IeDEA) is a global consortium of HIV cohort studies. We included all HIV treatment cohorts that participate in IeDEA Central Africa, East Africa, Southern Africa, and West Africa  [17]. Fifty-seven cohorts from 22 countries contributed data, including 3 cohorts from Burundi, 2 from the Democratic Republic of the Congo, 10 from Rwanda (Central African region); 2 cohorts from Kenya, 1 from Tanzania, 4 from Uganda (East Africa); 1 cohort from Lesotho, 2 from Malawi, 1 from Mozambique, 7 from South Africa, 1 from Zambia and 2 from Zimbabwe (Southern Africa); 1 cohort from Benin, 2 from Burkina Faso, 8 from Côte d'Ivoire, 1 from Ghana, 1 from Guinea, 1 from Guinea-Bissau, 2 from Mali, 2 from Nigeria, 2 from Senegal and 1 from Togo (West Africa).
In Central Africa and West Africa most participating sites were urban regional, provincial, or university hospitals. In East and Southern Africa they were health centres, district hospitals and regional, provincial, and university hospital from urban and rural settings. The number of patients ranged from 42 patients in the Nyarugunga clinic in Rwanda, to almost 230,000 patients at the Centre for Infectious Disease Research in Zambia (CIDRZ). Data are collected during routine care at ART initiation and at each follow-up visit, including socio-demographic information, date of ART start, type of ART, and (where available) CD4 counts and viral load measurements. Regional IeDEA data centres sent de-identified data to the University of Bern, Switzerland for cleaning and analysis.
| Outcomes For the analyses of the data as recorded in the clinical databases, outcomes were retention on ART, loss to follow-up, and death. Outcomes were mutually exclusive. For the definition of loss to follow-up, we calculated a patient's next appointment date as the last visit date plus a patient's most recent gap between two consecutive visits that was in accordance with the visit schedule of the clinic. We then classified patients more than 90 days late for their next clinic appointment who did not return to care during the study period as lost to follow-up on the day of the first missed appointment. In the adjusted analyses, outcomes were retention on ART, death, and stopping ART. We assumed that patients recorded as lost to follow-up by a treatment programme who were not classified as self-transfer or unrecorded death were alive and had stopped ART.
| Statistical analyses We used descriptive statistics to describe patient's characteristics at initiation of ART, stratified by IeDEA region. We used survival analysis methods to analyse time to loss to follow-up, stopping ART and death. We followed patients from ART initiation for a maximum of 5 years, censoring follow-up time of patients who transferred to another clinic or programme that was not covered by IeDEA on the date of transfer. Individuals retained on ART were censored 90 days before database closure, when they ceased to be at risk of loss to follow-up. We used the Kaplan-Meier estimator to calculate the cumulative probability of retention on ART and the Aalen-Johansen estimator to calculate the cumulative incidences of documented death or loss to follow-up and stopping ART. Death and loss to follow-up or stopping ART were competing risks  [18].
W LTF = 1 À p dead À p transfer , Figure  1  shows cumulative retention, loss to follow-up, and mortality based on the data recorded in the clinics' databases (panel A), and cumulative retention, stopping ART, and mortality from the adjusted analysis that take unobserved deaths and transfers among patients lost to follow-up into account (panel B). As expected, retention and mortality were higher in the adjusted analysis. Overall, cumulative retention declined from 76. 8% (95% CI 76. 7 to 77. 0) at year 1 to 52. 1% (51. 9 to 52. 3) at year 5 in the crude analysis, and from 83. 1% (83. 0 to 83. 2) to 66. 6% (66. 4 to 68. 8) in the adjusted analysis. Cumulative mortality increased from 3. 5% (3. 5 to 3. 6) in year 1 to 6. 0% (6. 0 to 6. 1) in year 5 in the crude analysis and from 8. 4% (8. 3 to 8.
We analysed data from over 500,000 HIV-infected children and adults who initiated ART in 22 countries in sub-Saharan Africa. We adjusted for unrecorded deaths and silent transfers among persons lost to follow-up and found that retention on ART was considerably higher in the adjusted analysis. We found that an estimated 19% of people who initiated ART had stopped ART by 5 years. Cumulative mortality was 15% at 5 years, substantially higher in the adjusted analysis than the analysis based on recorded deaths. The sensitivity analyses showed that estimates for ART outcomes were sensitive to the choice of adjustment parameters. Our study has important implications for monitoring outcomes of the scale-up of ART in sub-Saharan Africa in general, and particularly monitoring progress towards the 90-90-90 targets.
Our analysis has several limitations. We implemented WHO's definition of loss to follow-up and only consider the last recorded status of patients at closure of database. Patients with transient treatment interruptions who returned to care were considered as retained throughout follow-up. Therefore, our analysis does not take into account transient treatment interruptions and retention estimates reflect the final status of patients at database closure  [20]. Our analysis therefore may overestimate retention. Transient treatment interruption could be taken into account as intermediate states in multistate models, but heterogeneity of data makes it difficult to implement such analysis in multi-cohort studies  [21, 22]. Overall, 40% of people living with HIV were classified as lost to follow-up in the clinical databases of the ART programmes.
These patients may have discontinued ART, selftransferred to another programme, or died but their true outcomes are unknown. Unrecorded deaths can be ascertained and mortality estimates corrected by tracing patients lost to followup or by linking the clinical databases to the vital registry  [23, 24]. We used inverse probability weighting to adjust for undocumented mortality and self-transfers, based on the best available data from a meta-analysis of tracing or linkage studies performed in sub-Saharan Africa  [11]. We assumed that the pooled estimates from the meta-analysis were applicable to the IeDEA data in all regions. The meta-analysis included tracing studies from several countries in the East and Southern African IeDEA regions, but only a few tracing studies from the West and Central African IeDEA regions were available.
The pseudorapidity distributions of dijets as functions of their average transverse momentum (p ave T ) are measured in proton-lead (pPb) and proton-proton (pp) collisions. The data samples were collected by the CMS experiment at the CERN LHC, at a nucleon-nucleon center-of-mass energy of 5. 02 TeV. A significant modification of the pPb spectra with respect to the pp spectra is observed in all p ave T intervals investigated. The ratios of the pPb and pp distributions are compared to next-to-leading order perturbative quantum chromodynamics calculations with unbound nucleon and nuclear parton distribution functions (PDFs). These results give the first evidence that the gluon PDF at large Bjorken x in lead ions is strongly suppressed with respect to the PDF in unbound nucleons.
1 Relativistic heavy ion collisions aim to study the properties of the quark-gluon plasma (QGP)  [1] [2] [3] [4] , a deconfined state of quarks and gluons expected by quantum chromodynamics (QCD)  [5]  to exist for very high temperatures and energy densities. These studies are often performed by investigating changes in observables, such as jets and hadron spectra, in going from protonproton (pp) to heavy-ion collisions. The changes can be attributed to both initial-state effects (e. g. , different parton distribution functions (PDFs) for heavy nuclei than for nucleons) and final-state effects due to the creation of the QGP  [6, 7]. Knowledge of the nuclear parton distribution functions (nPDFs) in heavy nuclei is thus crucial in extracting QGP properties from experimental data. While the quark nPDF of lead ions (Pb) is well understood from deep inelastic scattering data  [8] , the gluon nPDF, which is particularly important for perturbative QCD (pQCD) calculations at the CERN LHC energies, is not well constrained.
In contrast to what is observed in head-on PbPb collisions, where QGP-induced gluon emission in the final state significantly alters the energy balance between the two highest-p T jets  [28] [29] [30] [31] , no significant dijet p T imbalance is observed in pPb data with respect to simulated pp distributions  [26]. Moreover, measurements of inclusive jet  [32] [33] [34] [35]  and inclusive charged-particle p T spectra  [36] [37] [38]  also show no sign of modification at high p T compared to pp data. The relatively small or negligible final-state effects in pPb collisions support the idea of using jets as probes for the nuclear PDF studies. Recent theoretical calculations suggest that the dijet pseudorapidity (η dijet = (η 1 + η 2 )/2) distribution in pPb collisions provides strong constraints on the gluon nPDFs  [39] [40] [41] [42]  because of the small experimental and theoretical uncertainties  [39].
In the pPb data sample, there is a 3% probability to have at least one additional interaction in the same bunch crossing (pileup). A pileup filter is employed  [47] , which rejects more than 90% of the pileup events and removes 0. 01% of the events without pileup. The filter uses the longitudinal and transverse distance between the leading vertex (the vertex with the highest number of associated tracks) and the vertex with the second largest number of associated tracks as criteria for identifying and removing pileup events. In the pp analysis, the pileup rejection procedure is not applied because of the significantly lower pileup rate (about a factor of three compared to pPb). Offline, jet reconstruction is performed using the CMS particle-flow (PF) algorithm  [48]. By combining information from all subdetector systems, the PF algorithm attempts to identify all stable particles in an event, classifying them as electrons, muons, photons, as well as charged and neutral hadrons.
The effect of the remaining pileup events in pPb collisions is evaluated by comparing the results with and without the pileup filter. Those uncertainties are negligible compared to other sources. The total systematic uncertainties in η dijet and in the ratios of the pPb and pp spectra are evaluated by summing in quadrature over the contributions from the above sources. In the pPb/pp η dijet ratio measurements, the uncertainties due to the JES, jet energy resolution, and jet angular resolution are partially canceled and the total systematic uncertainties are between 2 and 20%, increasing from high-to low-p ave T values, and towards higher |η dijet | values. The measured η dijet spectra in pp collisions, shifted to match the range of the pPb data as described previously, and the corresponding pPb results, are available in Appendix A, which includes Refs.
19 to 0. 95, whereas the p-values for the DSSZ and nCTEQ15 nPDFs are never larger than 0. 015. This shows that, with a p-value cutoff of 0. 05, the data are incompatible with the DSSZ and nCTEQ15 nPDFs, but not incompatible with EPS09. This supports the interpretation of the RHIC pion data by the EPS09 nPDF, in which the modification of the pion spectra gives rise to the gluon EMC effect. The data also show smaller shadowing, antishadowing, and EMC effects than what is implemented in the nCTEQ15 PDF set. The results are consistent with EPPS16 with relaxed constraints (e. g. , more free parameters, increased error tolerance) on the nuclear PDF parametrization, which results in larger PDF uncertainties  [16]. The conclusions obtained from different p ave T intervals are similar, which provide important tests of the nuclear PDF at various Q 2 values.
Significant modifications of the η dijet distributions are observed in pPb data compared to the pp reference in all p ave T intervals, which show shadowing, antishadowing, and EMC effects in nuclear parton distribution functions. The ratios of the pPb and pp distributions are compared to next-to-leading order calculations with nucleon and nPDFs. Based on these comparisons, the results present the first evidence that the gluon PDF at large Bjorken x in lead ions is strongly suppressed with respect to that in unbound nucleons. The data are incompatible with predictions using nucleon PDFs or using nPDFs without large-x gluon suppression. Based on a statistical analysis, the EPS09 nPDF provides the best overall agreement with the data. This data can be used to place strong constraints on the next-generation of nPDFs, which are crucial for the understanding of high p T and high mass particle production at collider energies.
Acknowledgments We thank  Nestor Armesto ,  Paukkunen Hannu ,  Pia Zurita ,  Petja Paakkinen  and  Carlos Salgado  for the useful discussions and the NLO pQCD calculations with various nPDFs. We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centers and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES  and  CSF (Croatia) ;  RPF (Cyprus) ;  SENESCYT (Ecuador) ;  MoER ,  ERC IUT , and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  NKFIA (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  MSIP  and  NRF (Republic of Korea) ;  LAS (Lithuania) ;  MOE  and  UM (Malaysia) ;  BUAP ,  CINVESTAV ,  CONACYT ,  LNS ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI, CPAN, PCTI  and  FEDER (Spain) ;  Swiss Funding Agencies (Switzerland) ;  MST (Taipei) ; ThEPCenter, IPST, STAR, and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU  and  SFFR (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
, 2013). Numerous studies have shown that the GPS is an effective tool for characterizing the ionosphere through measuring the TEC, which represents the total number of electrons integrated along the path from the receiver to each GPS satellite  (Sethi et al. , 2001; Boutiouta and Belbachir, 2006; Chauhan and Singh, 2010; Ouattara et al. , 2011). Here, we present the vertical total electron content (VTEC) over Rabat (33. 998 • N, 6. 853 • W) obtained from the International GPS Geodynamics Service (IGS) network. The GPS data needed to determine the TEC are (1) data extracted from files stored in RINEX (Receiver INdependent EXchange) format, (2) data in IONEX format (IONosphere EXchange Format), (3) almanacs of the GPS satellite position and (4) the satellite clock biases. The procedure for extracting the TEC from GPS data is well documented in the literature  (Sardon et al.
This result of westward and equatorward winds during the magnetic storm is consistent with previous results obtained using ground-based Fabry-Perot interferometers  (Makela et al. , 2014; Zhang et al. , 2015). Xiong et al. (2015)  use the CHAMP zonal wind observations from 2001 to 2005 to investigate the global features of the disturbance winds during magnetically disturbed periods. They report that the disturbance zonal wind is mainly westward and increases with magnetic activity and latitude. Emmert et al. (2004)  report westward and equatorward nighttime disturbed winds at midlatitudes. Emmert et al. (2008)  present an empirical wind model (DWM07) representing average geospace-storminduced perturbations of upper thermospheric neutral winds. In constructing their model, they used data from the Wind Imaging Interferometer on board the Upper Atmosphere Research Satellite, the Wind and Temperature Spectrometer on board Dynamics Explorer 2, and seven ground-based FPIs.
The effect of the 27 February 2014 geomagnetic storm on the thermosphere and the ionosphere is discussed in this paper. Thermospheric winds were inferred from Fabry-Perot interferometer measurements deployed at Oukaïmeden Observatory (31. 206 • N, 7. 866 • W; 22. 84 • N magnetic). The ionospheric response of the storm was also analyzed using the VTEC data and a wide-angle imaging camera. The source of the geomagnetic and ionospheric storm was briefly investigated in Sect. 2. The zonal and meridional components of the winds were compared with their quiet-time climatology to study the effect of the storm on the wind dynamics. Traveling atmospheric disturbances were evident in the meridional windsthe first one coming from the Northern Hemisphere and the second one coming from the Southern Hemisphere.
We have observed a negative correlation between HmF2 and NmF2 during the passage of the TAD. The ionospheric response of the storm was also analyzed through the observation of equatorial plasma bubbles. We observe a reversal in the drift direction, which indicates a reversal of the background electric field direction due to the neutral wind disturbance dynamo. This is the first time that a case study of a geomagnetic storm has been achieved in north Africa by using Fabry-Perot interferometer data of the thermosphere. Additionally, this is the first coincident study of a storm using a ground-based FPI and an all-sky imager in this sector.
Acknowledgements. Work at the  University of Illinois , including for the deployment of the instrumentation to Morocco, was supported by  National Science Foundation CEDAR  grants  AGS 11-38998  and  AGS 14-52291  as well as by  NASA  grant  NNX14AD46G. The authors would like to thank the  Oukaïmeden Observatory  and its staff for their support and assistance to the FPI operations. The authors would like to thank  Christine Amory-Mazaudier  and  Rolland Fleury  for help in training schools and GPS data. The authors would like to thank all referees for help in evaluating this paper. The topical editor,  Petr Pisoft , thanks two anonymous referees for help in evaluating this paper.
Data availability. The LOS neutral wind data and camera images used in this study are freely available for use in the Madrigal database. Please contact Jonathan J. Makela (jmakela@illinois. edu) before using these data. The GPS data used in this study are freely available for use from the International GPS Geodynamics Service (IGS, 2018) (ftp://data-out. unavco. org/pub/rinex/obs/, last access: 6 July 2018) network. The Supplement related to this article is available online at https://doi. org/10. 5194/angeo-36-987-2018supplement.
Acknowledgements We thank  Daphna Fenel  and  Dr Guy Schoehn , from the  IBS/ UVHCI platform of the Partnership for Structural Biology in Grenoble (PSB/IBS)  for the Electron Microscopy. This work was supported by  Euronanomed   ENMII JTC2012  (project  2011-ERA-002-01-Dia-Amyl ) and the  French National Research Agency (ANR) :  ANR-12-RPIB Multimage. J. Pansieri  was granted by  FRM   DBS2013112844. The research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  (FP7/ 2007-2013 Grant agreement No. 320659 ).