dataesr/scientific-paragraphs-categorization huggingface dataset:
Data collection For all CMA drugs, we matched HTA reports based on the first approved indication in the CMA provided by the EMA. When products are approved for multiple indications or for an indication for which multiple comparator treatments exist, some HTA bodies split these into separate recommendations, either within the same dossier (France and Germany) or in a separate dossier (England and Scotland). In these cases, all recommendations were included separately. Basic product information was gathered from the EMA website, including therapeutic category, dates of CMA and possible SMA, orphan status, and type and amount of pivotal studies. For each HTA jurisdiction, data were collected on the overall reimbursement recommendations, outcomes of REAs, and outcomes of CEAs. Reasons for negative decisions or restrictions were collected, as well as decision and publication dates.
Data categorization and analysis Studies were categorized as uncontrolled when they did not include an active comparator or placebo arm (e. g. , single-arm trials and doseranging studies). In line with previous research we categorized HTA recommendations into positive, positive with restrictions (called restricted), or negative. 19 Furthermore, we collected the outcomes of the REA, the CEA for those countries that include CEA, and the overall recommendation separately. In France and Germany, REA assessments will result in one of multiple categories that have different consequences for price setting and negotiations, depending on the level of added benefit that the drug provides. We used sensitivity analysis to assess whether a different categorization mechanism would have led to different conclusions (primary categorization is provided in Figure  S1  and categorization for sensitivity analyses in Figure  S2 ).
We used four different statistical software packages: deltaCT, geNorm, NormFinder and BestKeeper. We report optimized reference gene pair combinations for studying development (early whole embryos), brains at later stages (metamorphosis and adult), and thyroid signalling. These reference gene pairs are suitable for studying different aspects of X. laevis development and organogenesis. Several features make the African clawed frog, Xenopus laevis, an outstanding tool in biomedical research and vertebrate development. Since the 1930s, they have been used by doctors as a simple test for pregnancy. Egg production in female frogs is stimulated by the chorionic gonadotropin hormone found in pregnant woman's urine. Biologists have utilized this same method to induce female frogs to lay eggs and then fertilise in vitro for synchronised development 1.
In this study, we used the recent RNA-seq data from Session et al. , to identify the most stably expressed genes during X. laevis development  3. Their expression stability was further validated using RT-qPCR. We used four statistical algorithms, delta-CT  16  , geNorm  17  , BestKeeper  18  and NormFinder  19. According to their stability, we identified the best reference genes candidates during different stages of X. laevis development. We further identified and validated the reference gene candidates for stage NF48 X. laevis brains when studying thyroid hormone signalling and its disruption.
RNA concentrations were determined using a spectrophotometer (NanoDrop ThermoScientific, Rockford, IL) and RNA quality verified using BioAnalyzer (Agilent) where we only used samples with RNA Integrity Number (RIN) >7. 5. 500 ng of RNA was used for reverse transcription using a High Capacity cDNA RT kit (Applied BioSystem, Foster City, CA) using manufacturer's instructions in a total 20 µl reaction. The random primers used ensure that the first strand synthesis includes total RNA, including mRNA and rRNA. The cDNAs were stored at -20°C until use. Primer design. RT-qPCR primers for the novel candidate reference genes were designed using Primer3plus  23  (Supplementary table  1 ). Primers for eef1a1. S, odc1. L, dio1, dio2, dio3, thrα (tr-alpha), and thrβ (tr-beta) were used from previously published data  22, 24.
The primers were designed to target the exon-exon region where possible to avoid genomic DNA amplification. The specificity of each primer set was checked used Xenbase Blast  25  and by manual alignment of the small and large copy of both genes. Transcript information of genes was based on Xenopus laevis 9. 1 genome primary transcripts by JGI. Primers were ordered from Eurofins, Germany. Melting curves were analysed to ensure amplification specificity and null primer-dimer formation. Primer PCR efficiency was evaluated using serial dilutions of cDNA sample (1:10, 1:100, 1;1,000 & 1:10,000) in Expression Suite Software (Applied Biosystem). The amplification efficiency (E) of the primers are; clta. L (93. 599%), cfl1. S (102. 668%), mlf2. S (104. 01%), tm9sf4. L (93. 713%), lpcat3. S (121. 422%), slc35b1.
Data analysis. The RNA-seq data set was obtained from Sessions et al. , 2016  3. Average TPM (transcript per million) value of the 14 developmental stages of individual gene was calculated. Standard deviation (SD) between the 14 developmental stages of each individual genes was then calculated. The genes were then ranked from least deviation, among the 14 developmental stages, to highest. Only genes which had an average value of more than 50 TPM were selected (see Supplementary Dataset 1 & 2, and Fig. 1 ). The Heatmap, box plots, and line graphs were generated using GraphPad Prism 7. 0. Relative concentrations of cDNA for analysing relative changes in gene expression were calculated using 2 -ΔΔCt method  32.
Acknowledgements We thank  Gérard Benisti  for excellent animal care. We further thank  Dr Nicolas Pollet  and the European Amphibian Club 2017, Rennes for their insightful comments and feedback regarding our analysis. This work was supported by grants from  Centre National de la Recherche Scientifique (CNRS) ,  Muséum National d'Histoire Naturelle (MNHN) , and  European Union  contract  DEVCOM_GA N°607142.
Introduction: Transmission rate of HIV from mother to child transmission (MTCT) is reducing in many countries. While it is the case in Cameroon, risk factors should be identified to further reduce this transmission. We aimed to evaluate the risk factors associated with MTCT HIV in Cameroon from 2004 to 2013. Materials and methods: We conducted a retrospective study based on early infant diagnosis results as well as the clinical data collected from their mothers. Data collected from 2004 to 2013 were analyzed using Stata software and the Pearson's chi-square and Fisher's exact tests. Results: A total of 15,233 HIV infected mothers and their 15,404 exposed infants aged 6 weeks to 18 months were recruited. Mean age of infants was 16. 7 weeks, and 34. 8% were breastfed. Mean age of mothers was 27.
P42 PrEP in the CeGIDD of the Departemental Council 13: local data (June 2016-January 2018) Introduction: This retrospective study assesses the impact of Pre-Exposure Prophylaxis/HIV in patients included in the free centers of extra-hospital screening and Diagnosis information on CD13, examining HIV seroconversions, treatment tolerance and the prevalence of sexually transmitted diseases (Syphilis, Chlamydiae, Lymphogranuloma Venereal, hepatitis). Materials and methods: The ANSM order of June 07, 2016, authorizes extra-hospital CeGIDD to prescribe the association Emtricitabine/Fumarate of Tenofovir Disoproxil in HIV PrEP. This analysis covered a period of 20 months, from June 2016 to January 2018. 228 individuals were included, for which a compendium of behavioral and epidemiological data was carried out.
To detect nuclear AR, cells were suspended in ice cold extraction buffer (320 mM sucrose, 5 mM MgCl 2 , 10 mM HEPES, 1% Triton X-100, pH 7. 4) for 15 min to isolate nuclei. GLUT1 surface was monitored as a function of binding to the envelope glycoprotein of the human lymphotropic virus (HTVL) HTLV was fused to EGFP (H RBD EGFP, Metafora Biosystems, Montpellier, France), and it was added to cells at a concentration 1:10 in PBS with 2%FBS as previously reported  [20]. All samples were analyzed in a Cytomics FC500 flow cytometer (Beckman Coulter), and data analysis was performed by using FlowJo and Kaluza software.
Detection of intracellular ROS levels Cells were collected by trypsinization and washed twice with PBS. The number of cells was adjusted to 5×10 5 /sample. Total ROS levels were measured incubating cells with 1 μM H2DCFDA (Bioquochem SL, Llanera, Spain) for 15 min at 37 °C. Mitochondrial O 2. -was measured by using MitoSOX (Fisher Scientific, Madrid, Spain). Cells were stained with 5 μM MitoSOX at 37 °C for 15 min. Cells were analyzed using a Cytomics FC500 flow cytometer after staining. and data analysis was performed by using Kaluza software.
Funding PGM thanks support to " Formación del Personal Universitario " grant from  Ministerio de Educación, Cultura y Deporte ,  Gobierno de España  ( AP2012-4924 ) and IUOPA. DH is supported by  Fundacion ONCE , SK by  CNRS  and  NT  by  INSERM. This work was supported by  Ministerio de Economía y Competitividad ,  Gobierno de España , cofunded by  FEDER  ( MINECO-17-BFU2016-79139-R ).
Analyses of psychometric and endocrine data Global affect between blocks was averaged per condition (technical exclusion, social exclusion, inclusion) and subjected to a repeatedmeasures ANOVA, with the within-subject factor Condition (technical exclusion, social exclusion, inclusion) and the between-subjects factors Sex (male, female) and Order (first, second). Positive affect was determined as the mean value for the positive items and negative affect for negative items on the PANAS, respectively. As negative affect scores and all ESR scales (anger, disgust, fear, happiness, sadness, surprise) deviated from normal distribution, these scores were log-transformed. As the disgust ratings were still substantially skewed after transformation (for T1 sk = 1. 44, and for T2, sk = 6. 67), this scale was excluded from further analyses.
Data from the other scales were subjected to separate repeated-measures ANOVAs, with the within-subject factor Time (T1, T2) and the between-subjects factors Sex (male, female) and Order (first, second). Correcting for the number of comparisons yielded effects with p <. 007 regarding changes in affect (PANAS, ESR) to be considered significant. Changes in affect (positive, negative, anger) were calculated by subtracting values at T1 from values at T2. Cortisol levels at T1 could not be determined for one (female) participant. Hormone levels were log-transformed to correct for nonnormal distributions and subjected to three repeated-measures ANOVAs for cortisol, testosterone and progesterone, respectively, with the within-subject factor Time (T1, T2, T3) and the between-subjects factors Sex (male, female) and Order (first, second).
For these, only significant effects of Task or Time are reported in Section 3. 3. Moreover, to delineate whether order effects were attributable to task-related effects or general fatigue, we selected the PANAS items reverse-coding for fatigue, i. e. , attentive and active, and subjected the log-transformed scores to two analogous AN-OVAs (Time x Sex x Task). For the ANOVAs, within-subject effects are reported with partial eta squared as an indication of effect size. Whenever the assumption of sphericity was violated, Greenhouse-Geisser corrected p-values are reported. The α-level was set at p <. 05. Statistical testing was performed with the Statistical Package for the Social Sciences (IBM SPSS 20).
Image acquisition and processing Functional and anatomical data were acquired on a 3T TIM Trio scanner (Siemens Medical Solutions, Erlangen, Germany) equipped with the manufacturer's 32-channel head coil. Head motion was restricted with foam padding and a tape spanning from the head coil over the subject's nose to provide movement feedback. Stimuli were projected onto a screen, which participants viewed via a mirror mounted on the head coil. We recorded 23 interleaved slices with a gradient-echo EPI-sequence with distortion correction and the following BOLD imaging parameters: TE/TR = 38/1800 ms, flip angle = 90°, voxel size = 1. 5 × 1. 5 × 3 mm, bandwidth = 1446 Hz/pixel, slice thickness = 3 mm plus 1. 8 mm slice gap. At the beginning of the MR session, a high-resolution anatomical image using an MPRAGE sequence (3-D Magnetization Prepared Rapid Gradient Echo) was acquired with 160 sagittal slices, TR = 2300 ms, TE = 4.
21 ms, 1 × 1 × 1. 1 mm resolution, flip angle 9°, and inversion time 900 ms. Preprocessing and analyses of the imaging data was performed with statistical parametric mapping (SPM8, Wellcome Department of Imaging Neuroscience, London) implemented in Matlab (Mathworks Inc. , Sherborn, MA, USA) using standard algorithms and parameters unless specified differently. Images were realigned to correct for head movement, slice-time corrected, spatially normalized to MNI (Montreal Neurological Institute) stereotactic space using unified segmentation and finally smoothed with an 8 mm 3 full-width-at-half-maximum Gaussian kernel. In the GLM-analysis, the three experimental conditions (technical exclusion, social exclusion, inclusion) were modeled block-wise as three task-relevant regressors convolved with the canonical hemodynamic response function.
Rather than exclusion-specific changes, the overall decline likely reflects the diurnal profile of cortisol, which was evident in the data based on the entire session including both fMRI tasks. This observation ties in with fatigue emerging in the course of the session, irrespective of the order of tasks. Moreover, the adjustment to the potentially stressful MR environment may also play a role. While self-reported fear ratings were higher when Cyberball was the first task, possibly indicating stress, we did not systematically assess the perceived stress of the scanning experience and therefore cannot draw conclusions regarding these possible cortisol changes. Interestingly, however, we observed different hormonal patterns in males and females. In females, cortisol levels decreased from before to immediately after Cyberball, whereas in males, this decline was delayed.
ALMA observations of XID2028 XID2028 was observed during ALMA Cycle 3 with the 12 m array in Band 6 for a total time on source of 3. 5 hrs. The array included 38 antennas with a maximum baseline of 704 m. The phase centre of the dataset was set to the Hubble Space Telescope (HST) position of the QSO nucleus (RA=10:02:11. 29, DEC=+01:37:06. 67). The primary beam, corresponding to the field of view (FoV) of the observation, is ∼22. The conditions were overall good and only a small fraction of the data (∼15%) was excluded due to standard pipeline processing flagging. The spectral set-up covers a total bandwidth of 7. 5 GHz. For two spectral windows (SPWs) the correlator was set to frequency division mode (FDM) with a bandwidth of 1875 MHz and a channel spacing of 3. 9 MHz corresponding to a velocity resolution of ∼5 km/s, while two additional SPWs with 2 GHz bandwidth (time division mode; TDM) were used for continuum measurements.
We then estimated the continuum flux by fitting with a Gaussian function the visibilities of the continuum dataset (via the CASA task uvmodelfit). We measured a continuum flux of 142 µJy for a detection significance of 19σ when the visibility noise of 7. 5 µJy is considered. After deconvolving for the beam, the Gaussian fit returned a FWHM size of 0. 30 ±0. 05 for the continuum emitting region in the nucleus, which translates into an effective radius ∼ 1. 3 kpc. Coupling the information on the spatial extent observed in the dust continuum image and the SFR as inferred from the SED fit presented in Perna et al. 2015 (∼270 M yr -1 ; see also Appendix A. 1), we estimated a SFR surface density Σ SFR ∼ 25 +13 -17 M yr -1 kpc -2. This SFR surface density is significantly higher than that observed in normal star forming galaxies at z∼1.
2 ). However, the reduced χ 2 square is high (2. 27), which is likely due to the presence of deviations between the data and the Gaussian modelling (e. g. at -500 km s -1 < v < -150 km s -1 ; see also Section 6 for a more detailed discussion). We then estimated the line flux by fitting with a Gaussian function the visibilities of the continuum-subtracted dataset (using the CASA task uvmodelfit), in the same velocity range as above. We retrieve values for the total line flux (I CO(5-4) = 0. 77±0. 032 Jy km s -1 ), the spatial extent, (FWHM=0. 33±0. 02 ) and the line centroid (RA=10:02:11. 28, DEC=01:37:06. 64). The CO(5-4) and the dust continuum peak emission originate from the same region, at the phase centre position. Following  Solomon et al. (1997) , the measured CO(5-4) flux translates into a line luminosity of logL' CO(5-4) /(K km s -1 pc 2 )=9.
63±0. 05. From the observed far-infrared luminosity associated with the starburst (SB) component (logL IR =12. 47 erg s -1 ; integrated from 8 to 1000 µm), well constrained from the PACS/SPIRE dataset, following the analysis of L' CO(5-4) -L IR correlation in  Daddi et al. (2015)  we would expect logL' CO(5-4),L FIR =9. 95 K km s -1 pc 2. Although the observed value of the CO(5-4) line luminosity is still consistent within 2σ given the scatter of the correlation, it is in fact a factor of ∼2 lower than that expected on the basis of the SFR. Finally, we analysed the FDM spectral window centred at ∼240 GHz an tuned to observe the HCN(7-6) and HCO + (7-6) transitions. Both lines remain below the detection threshold and we can provide ∼ 3σ upper limits of 0. 07 Jy km s -1 for both transitions (assuming a FWHM=500 km s -1 ).
7±0. 35 Jy km s -1 , although it is consistent at about 1. 2σ with our previous measurement. The fact that a flux extraction in the PdBI CO(3-2) map with the parameters of the CO(5-4) detection returns a ∼2fold lower CO(3-2) flux is consistent with the older measurement being boosted by noise 3. XID2028 was observed in ALMA Band 3 as part of the programme 2015. 1. 00171. S (PI: E. Daddi) with a snapshot (4 min) observation, targeting the CO(2-1) transition. Using the spatial parameters obtained from our fit to the CO(5-4) data, and again consistently accounting for the 1. 1 beam of this ALMA dataset, we report a detection at ∼ 3σ with an integrated flux of I CO(2-1) =0. 35±0. 12 Jy km s -1 , which is consistent with the PdBI upper limit. XID2028 remains instead undetected in the continuum and has a 3 mm upper limit of 0.
Finally, from the observed SFR and gas mass, we can estimate the rate at which the gas is converted into stars, i. e. the gas depletion timescale (t depl =M gas /SFR). We inferred t depl ∼ 40-75 Myr using the CO and dust-fit derived gas masses, respectively. By comparing the gas depletion timescale and host galaxy prop-erties of XID2028 to that of normal star-forming galaxies (∼ 0. 5 -1. 5 Gyr;  Sargent et al. 2014 ), Brusa et al. (2015b)  proposed that, despite sitting on the MS, XID2028 is consuming its residual gas more rapidly than similar host galaxies at the same redshift. Our new analysis based on ALMA data further strengthens the significance of this result. The two values of the depletion timescale for XID2028 derived from the dust continuum and CO estimates in this work are plotted as red and green symbols in Fig.
Summary and conclusions We presented ALMA data of XID2028, a star forming-QSO system at high redshift (z∼ 1. 5), thought to be in the feedback phase. The presence of a massive outflow with significant impact on the host galaxy has been previously unveiled through NIR observations  (Perna et al. 2015; Cresci et al. 2015a) , and anomalous molecular gas content has been reported from the study of the CO(3-2) line transition  (Brusa et al. 2015b). With the new analysis at (sub)millimetre wavelengths, also informed by high-resolution near-infrared imaging obtained through LUCI@LBT and complete multiwavelength coverage in the framework of the COSMOS survey, we report the following results: • We detected compact (∼2. 5 kpc diameter) dust continuum emission at rest-frame ∼ 500µm, confined to a central region of the galaxy and coincident with a point source detected by HST (at ∼ 0.
The emission in the high velocity channels (including the red tail) can be interpreted as outflowing gas in opposite directions, as predicted in biconical outflow models. • We report that the blueshifted emission appears to be cospatial with the ionised outflow seen in SINFONI data (see Fig. 10 ). XID2028 may therefore represent a unique case beyond the local Universe with a spatially resolved outflow in the molecular and ionised phase, over the same spatial region, and therefore likely associated with the same outflow episode (different from, e. g. SDSSJ1356 reported in  Sun et al. 2014). With this assumption, we report a total mass outflow rate of Ṁtot ∼ 500 -800 M yr -1. To our knowledge, this is the first time that the measurement of total outflowing mass including the molecular and atomic components, in both the ionised and neutral phases, is attempted for a z∼ 1.
Acknowledgements. This paper makes use of the following ALMA data: ADS/JAO. ALMA#2015. 1. 00299. S (PI: Brusa), #2015. 1. 00137. S (PI:  Scoville), and #20015. 1. 00171. S (PI: Daddi). ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), NSC, and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. XID2028 is an interesting target from several perspectives (e. g. massive MS galaxy; bright FIR/Herschel source with substantial SFR), and as such, in addition to our deep dedicated follow-up, it has also been targeted independently by two different ALMA snapshot programmes as part of large samples (100+) of high-z galaxies. A careful scrutiny of the ALMA archive and an open collaboration with the PIs of the programmes allowed us to make the best use of ALMA data.
We thank the ARGOS team for obtaining the K-band imaging of XID2028 during a commissioning run. We gratefully thank the staff of the Italian ARC node for their support in data reduction. This research was finalised at the Munich Institute for Astro-and Particle Physics (MI-APP) of the DFG cluster of excellence "Origin and Structure of the Universe", during the programme "In & Out: What rules the galaxy baryon cycle?" (July 2017). MB, MP, and GL acknowledge support from the FP7 Career Integration Grant "eEASy" ("SMBH evolution through cosmic time: from current surveys to eROSITA-Euclid AGN Synergies", CIG 321913). EL is supported by a European Union COFUND/Durham Junior Research Fellowship (under EU grant agreement no. 609412). MTS was supported by a Royal Society Leverhulme Trust Senior Research Fellowship (LT150041).
2014) , while the stellar mass is a factor of 2 higher in the new fits. This highlights the uncertainty associated with the degeneracy of various components in SED fitting routines. In this work we consider as fiducial stellar mass value M =4. 5 × 10 11 M , also motivated by the fact that our LUCI imaging suggests a resolved host galaxy contribution to the K-band flux > 20% (see Section 3). In the unlikely case that the remaining 80% unresolved flux is entirely due to the central AGN, we conservatively assume as a lower limit of the stellar mass M = 2×10 11 M. We take into account of all uncertainties affecting SFR (SFR=240-280 M yr -1 ) and M (from 2×10 11 to 10 12 M ) in the error associated with the sSFR. We however note that the value of T dust is constrained by the Herschel and ALMA data points and does not depend on the details of the fit at shorter wavelengths.