dataesr/scientific-paragraphs-categorization huggingface dataset:
While the proportions of patients who met all criteria were small in both groups, those who met these criteria had better survival and clinical worsening-free survival than those who did not. 72 4] [75] [76]  A post hoc analysis applying these methods to the PATENT studies showed that with each of the models assessed, riociguat improved risk status at Week 12. 77  Achieving 1 or more low-risk criterion using the French noninvasive method or a low-risk status, according to the SPAHR/COMPERA T A B L E 1 (Continued) NCT00855465; Table  1 ). 43 A total of 261 patients were enrolled, and randomised to receive placebo (n = 88) or riociguat individually adjusted to a maximum of 2. 5 mg tid (n = 173). The study met its primary endpoint of change in 6MWD from baseline to Week 16, with a mean increase of +39 m in the maximum riociguat 2.
| CHEST-2 Of the 243 patients who completed CHEST-1, 237 (98%) entered the open-label CHEST-2 LTE (NCT00910429) and received riociguat adjusted as tolerated up to a maximum dose of 2. 5 mg tid. The improvement in 6MWD seen with riociguat in CHEST-1 was sustained at 2 years in both inoperable and persistent/recurrent patients, but was more pronounced in the inoperable group (Figure  4 ; Table  2 ). Patients treated with placebo in CHEST-1 also showed improvement in 6MWD after conversion to open-label treatment with riociguat in CHEST-2 (mean increase in 6MWD:C 36 ± 71 m). 44 Estimated 2-year survival was 93% (95% CI: 89-96), and the rates of clinical worsening-free survival were 86% (95% CI: 81-90) and 78% (95% CI: 73-83) at 1 and 2 years, respectively, assuming that patients who withdrew had experienced clinical worsening.
| Patient risk assessment in the CHEST studies Currently, there are no recommendations for risk assessment in CTEPH, and 1 tool may not be appropriate for all patients due to the differing treatment pathways for operable and inoperable patients. However, several abbreviated PAH risk assessment tools have been applied to several databases, including the CHEST study database, in exploratory post hoc analyses. 77, 84 Application of the French invasive, French noninvasive and Swedish COMPERA methods to the CHEST database showed that treatment with riociguat was found to improve.
| STUDIES OF SWITCHING TO RIOCIGUAT 7] [88] [89] [90]  One of the rationales for developing sGC stimulators for the treatment of PAH is that a PDE5i may not be as effective under conditions where endogenous cGMP production is reduced. 91 Some patients with PAH do not reach treatment goals on PDE5i therapy,  23, 24  raising the question of whether they may respond better to enhanced cGMP production via sGC stimulators rather than decreased cGMP metabolism via a PDE5i. RESPITE (NCT02007629) was a 24-week, uncontrolled, openlabel, phase IIIb pilot study to determine the safety and efficacy of replacing a PDE5i with riociguat in patients with PAH who failed to respond to treatment with a PDE5i (Table  1 ). 47, 48 Inclusion criteria FC and time to clinical worsening were observed with patients treated with riociguat compared with those receiving the PDE5i, and there were also trends toward greater improvements in 6MWD and NT-proBNP.
| FURTHER STUDIES IN PAH AND CTEPH The MOTION study (NCT02191137) was a prospective, multicentre, single-arm, open-label, phase IV study to assess the impact of riociguat on patient-reported outcomes in patients with PAH. 94 The primary endpoint was change from baseline to Week 24 in the LPH questionnaire, a 21-item, validated, disease-specific health-related quality of life assessment tool comprising physical (score 0-40) and emotional (score 0-25) domains; a reduction in score indicates an improvement in health-related quality of life. 95 The primary endpoint was met, with a mean ± SD change in LPH score from baseline to Week 24 of -5. 4 ± 27. 8 (n = 75, P =. 048; the minimally important difference that indicates a clinically meaningful improvement was estimated to be a change from baseline of 7).
95 CE (NCT02634203) was a multicentre, randomised, controlled trial comparing riociguat with BPA in 105 newly diagnosed patients with inoperable CTEPH and PVR >320 dynÁsÁcm -5. 96 The primary endpoint was PVR at Week 26, expressed as a percentage of the baseline PVR, with secondary endpoints including changes from baseline in 6MWD, Borg dyspnoea index, WHO FC and NT-proBNP, as well as time to clinical worsening and safety. After 26 weeks, PVR was significantly improved with BPA (41% of baseline) compared with riociguat (68% of baseline; P <. 0001), although there was no improvement in 6MWD with BPA vs riociguat at Week 26 (+50 vs +44 m, respectively). BPA was also associated with significant improvements in Borg dyspnoea index, WHO FC, NT-proBNP and a number of haemodynamic parameters, compared with riociguat.
| RIOCIGUAT IN WHO GROUP 2 AND 3 PH In addition to the treatment of PAH and CTEPH, several studies have examined the safety and efficacy of riociguat in the treatment of PH due to chronic heart and lung disease. The phase II LEPHT study (NCT01065454) investigated the safety and efficacy of riociguat in 201 patients with PH and heart failure with reduced ejection fraction (≤40%). 49 The primary endpoint, change from baseline to Week 16 in mPAP, was not met. In addition, although significant increases were observed in cardiac index and stroke volume index, with significant decreases in PVR and SVR in the riociguat treatment group, no significant difference was seen in 6MWD. 49 In the smaller DILATE study (NCT01172756) in 39 patients with PH associated with heart failure with preserved ejection fraction, no change was seen in the primary endpoint of peak decrease in mPAP from baseline to 6 hours between 11 patients treated with placebo and 10 patients given 2 mg of riociguat.
50   The RISE-IIP study (NCT02138825) was a phase II, 26-week, multinational, randomised, double-blind, placebo-controlled trial that examined the safety and efficacy of riociguat in 147 patients with PH associated with idiopathic interstitial pneumonias (PH-IIP), a subgroup of ILD (Table  1 ). RISE-IIP was terminated on the recommendation of the independent Data Monitoring Committee due to increased rates of mortality and SAEs among patients receiving riociguat vs placebo, and no evidence of a positive risk:benefit ratio. 54 This resulted in the contraindication of riociguat in patients with PH-IIP. 60, 61 Future studies in PH-IIP could consider the use of centralised evaluation of baseline high-resolution computed tomography data to better detect these patients.
| RIOCIGUAT IN OTHER CONDITIONS There is a significant unmet need in patients with diffuse cutaneous systemic sclerosis (dcSSc) for therapies that can halt or slow disease progression. As riociguat was shown to possess antifibrotic properties in preclinical studies,  99, 100, 58  the safety and efficacy of riociguat for the treatment of dcSSc were investigated in RISE-SSc (NCT02283762), a 52-week, randomised, double-blind, placebo-controlled, phase II study in 121 patients (Table  1 ). 55 The primary efficacy endpoint, mean change in modified Rodnan skin score (an assessment of skin fibrosis) at Week 52, was not met at predefined significance (P <. 05). The small size of the study and a higher than expected skin fibrosis regression rate in the placebo arm may have resulted in decreased sensitivity for change in modified Rodnan skin score, potentially explaining the lack of a significant result.
The DIGIT study (NCT01926847) assessed the safety, efficacy and pharmacokinetics of riociguat (single dose, 2 mg) in 20 patients with primary and secondary Raynaud's phenomenon (Table  1 ). Riociguat improved digital blood flow in 40% of patients at room temperature and 60% of patients under conditions of cold exposure. 53 ociguat has also been investigated in cystic fibrosis (CF) based on the observation that activity of the CF transmembrane conductance regulator (CFTR) protein, a transmembrane chloride channel, is modulated by accumulation of cGMP. 102 In a mouse model of CF involving the ΔF508 CFTR mutation, the PDE5i sildenafil has been shown to increase CFTR function,  103.
40, 43 At 2 years, the exposure-adjusted frequency of common AEs was generally lower in the LTE studies, compared with PATENT-1 or CHEST-1. 40, 41, 43, 45 sults from RESPITE  47  and EXPosurE RegisTry riociguat in patients with PH (EXPERT; NCT02092818; a phase IV, prospective, noninterventional cohort study [registry] to investigate the longterm safety of riociguat in clinical practice),  105, 106  and observations in other studies  49, 50   The planned enrolment of at least 20 patients on ERA therapy is ongoing. Additionally, while conventional individual endpoints in PH trials, such as 6MWD and WHO FC, can provide valuable insight into the benefit of treatment for patients, there is a growing recognition that the impacts of these conditions are often multifaceted, and a more holistic approach incorporates different factors and endpoints being assessed together.
I G U R E 3 Six-minute walking distance (6MWD) in PATENT-2. 41 (A) 6MWD in the overall population, and treatment-naïve and pretreated subgroups of PATENT-2. Graph shows mean ± standard error of the mean. (B) Kaplan-Meier analysis showing the association of 6MWD with survival based on median value at baseline. (C) Kaplan-Meier analysis showing the association of 6MWD with survival at follow-up. Reprinted with permission from Elsevier from Ghofrani et al. 41 method, at Week 12 of PATENT-1 conferred a significantly reduced risk of death or clinical worsening in PATENT-2. The REVEAL risk score (RRS) uses statistical modelling of validated parameters to assess the risk of 1-year mortality in patients with PAH. [78] [79] [80]  Post hoc assessment of the PATENT database found that RRS and risk strata between baseline and PATENT-1 Week 12 were significantly improved with riociguat treatment when compared with placebo.
Patients who had a greater number of low-risk criteria or a low-risk status at Week 16 of CHEST-1 had lower mortality and fewer clinical worsening events in CHEST-2. Application of the RRS to the CHEST database also showed that riociguat improved RRS compared with placebo from baseline to Week 16. Furthermore, RRS at baseline and at Week 16, and the change in RRS during CHEST-1, were associated with improved survival (HRs for a 1-point reduction in RRS: 0. 702, 0. 692 and 0. 682, respectively) and clinical worsening-free survival (HRs: 0. 697, 0. 719 and 0. 754, respectively) over 2 years in CHEST-2. 85.
Based on the results of the RESPITE study, a larger, multicentre, randomised, controlled24-week open-label study was conducted. The REPLACE study (NCT02891850) enrolled 226 patients with PAH who remained in WHO FC III with a 6MWD of 165-440 m despite treatment with stable doses of a PDE5i either alone or in combination with an ERA. 92  Patients were randomised to remain on their PDE5i or to switch to riociguat (2. 5 mg tid). Patients on concomitant ERA treatment prior to enrolment continued on this therapy throughout the study. The primary endpoint was clinical improvement at Week 24 defined as 2 of the following: ≥10%/≥30 m increase in 6MWD, WHO FC I/II, or ≥30% reduction in NT-proBNP in the absence of clinical worsening (death from any cause, hospitalisation for worsening PAH or disease progression).
Small open-label pilot studies in PH associated with ILD 51  and chronic obstructive pulmonary disease (COPD) 52  have also been conducted. In a pilot study of 23 patients with PH-COPD (NCT00640315), of whom 22 were evaluated for haemodynamics and lung function parameters, a single dose of riociguat 1 mg (10 patients) or 2. 5 mg (12 patients) given during right heart catheterisation acutely reduced mPAP and PVR, without a change in lung function or gas exchange. 52.
and preclinical data have indicated that riociguat may have a potential disease-modifying effect in CF by restoring chloride ion channel function (Bayer AG data on file). The Rio-CF (NCT0202170025) study was a randomised, double-blind, placebo-controlled, multicentre, phase II study investigating the safety and efficacy of riociguat in 21 patients with CF who were homozygous for the ΔF508 mutation. Following Part 1 of the study, the independent Data Safety Monitoring Board provided a positive recommendation for continuation; however, due to a shift in the treatment landscape for patients with homozygous ΔF508 CF 104 and difficulties adapting the study design, coupled with the limited efficacy seen in Part 1, Rio-CF was terminated.
have revealed no new safety signals compared with PATENT and CHEST, and AEs of special interest remain infrequent. Although most of the AEs were not serious, serious haemoptysis and pulmonary haemorrhage, including cases with fatal outcomes, have been observed in patients with CTEPH or PAH treated with riociguat. 61 These events may be driven by the significant vasodilator effect of riociguat on systemic vascular tone which could increase cardiac output resulting in greater blood flow through pulmonary capillaries. Due to the lack of selectivity for the pulmonary circulation, the dose of riociguat must be adjusted on a per-patient basis to ensure that excessive effects on lowering BP do not occur. 61 9 | FUTURE DIRECTIONS OF RIOCIGUATNew indications are being investigated in areas of unmet need: PATENT-CHILD (NCT2562235) is an ongoing open-label, single-arm, individual dose-titration study designed to assess the safety, tolerability, pharmacokinetics, pharmacodynamics and exploratory efficacy of riociguat plus standard of care (ERA and/or prostacyclin) in children and adolescents aged 6-17 years with PAH.
risk status from baseline to Week 16. 16 Patients who had a greater number of low-risk criteria or a low-risk status at Week 16 of CHEST-1 had lower mortality and fewer clinical worsening events in CHEST-2. Application of the RRS to the CHEST database also showed that riociguat improved RRS compared with placebo from baseline to Week 16. Furthermore, RRS at baseline and at Week 16, and the change in RRS during CHEST-1, were associated with improved survival (HRs for a 1-point reduction in RRS: 0. 702, 0. 692 and 0. 682, respectively) and clinical worsening-free survival (HRs: 0. 697, 0. 719 and 0. 754, respectively) over 2 years in CHEST-2. 85.
Plasmids pCaAct1-Sat1  (Lettner et al. 2010 ): This plasmid contains the SAT1 gene coding for nourseothricin resistance and was used for the PCR construction of the deletion cassette used to disrupt AFO1. p416GPDKanMx4: The KanMx4 ORF was amplified from the plasmid pAH3  (Bogengruber et al. 2003)  using the primers kanMX fwd and rev. The resulting linear DNA fragment was cloned into the vector p416GPD  (Mumberg et al. 1995 ) by using EcoRI and BamHI. pRS313 (addgene vector database) was used to clone the ATP3 alleles from strains C+ and C+afo1 -using the primers ATP3 fwd and ATP3rev. Basic features of this derivative of pBluescript are AmpR, HIS3 + , CEN6 ARS4 and lacZ_a. pRS313ATP3+ contained the WT ATP3+ yeast gene under its cognate promoter cloned BamHI/XhoI as described below. pRS313ATP3 G348T contained the ATP3 G348T suppressor allel under its cognate promoter cloned BamHI/XhoI from strain JS760-6D as described below.
Metabolic tests of C+ afo1 -and controls We next sought to define possible metabolic changes in the paradoxically fast growing respiratory-deficient strain C+ afo1 -. The strain was batch-grown in a bioreactor fermenter (see Materials & Methods), and the relevant metabolic parameters were monitored continuously and compared with two control strains, namely the C+ respiratory competent starting strain, and the congenic rho-zero petite strain obtained by ethidium bromide treatment and analyzed by DAPI staining. DAPI staining also showed that the C+ afo1 -strain was free of mitochondrial DNA (data not shown). As shown in Fig. 3 , the metabolomic and kinetic data surveying basic metabolism were compared between the mutant C+ afo1 -fast growing strain (green) and the two controls, C+ WT (blue) and C+ rho-zero (red).
In our case (ATP3 G348T ), this was indeed supported by the respiratory competence of strain JS760-6A (Fig. 4A ). To further explore this question, we mapped the predicted amino acid change onto the structure of yeast ATP synthase (  (Dautant et al. 2010) ; PDB ID 2WPD). This analysis showed that L116F lies at the interface between the Atp3 subunit ("rotor") and the Atp2 and Atp1 subunits ("stator") near the base of the Atp3 rotor (Fig. 6 ). The location of the amino acid, L116F, is highlighted in the structural model. The other suppressor mutations found in Atp3  (Vowinckel, under review)  are also located at the interface between the "rotor" and "stator" parts of the ATPase, although they were located at the C-terminal end of the Atp3 protein stalk, near the top in the structural model. The hypothesis which was first put forward and tested by the group of Clark-Walker  (Chen and Clark-Walker 2000)  and posits that all of the suppresssor mutations increase the ATPase activity, and, because more ATP is hydrolysed inside the mitochondria, possibly the mitochondrial membrane potential across the inner mitochondrial membrane is increased, caused by the change in charge separation across the inner mitochondrial membrane.
Replicative lifespans Finally, we wanted to check replicative lifespans in the newly made afo1 -and the suppressor mutations identified. Lifespans were determined by the microfluidics method (see Materials & Methods) in a tetrad of strains and controls in the BY4741 background and are presented in short form here. There was no significant change in the replicative lifespan due to afo1 -deletion mutation (data not shown). There seems to be a tendency to a short replicative lifespan in those members of the tetrad which carry the suppressor mutation. This result is at variance with our previous publication on the afo1 -mutant (Heeren et al.
ACKNOWLEDGEMENTS We are grateful to  M. M. Crane  for supplying the wafer molds for making the microfluidics devices for replicative lifespan measurements. The work presented here was supported by the grant  P26713  of the  Austrian Science Fund FWF  to M. B, by the grant  GM098629  from the  NIH  to P. J. C, by the grant  ANR-15-IDEX-01  to G. L. , by the  Institutional Research Concept   61388971  to J. H. and by the  WISS2025 Land Salzburg  project  P_147200_30  to  H. B. K. Additionally  this work was supported by the  Francis Crick Institute  which receives its core funding from  Cancer Research UK  ( FC001134 ), the  UK Medical Research Council  ( FC001134 ), and the  Wellcome Trust  ( FC001134 ), and received specific funding from the  ERC  ( StG26809 ) and  Wellcome Trust  ( IA200829/Z/16/Z ) to M.
HERFD-XANES Preparation of Hg reference compounds and bacterial samples Solid and liquid Hg reference compounds (including IHg and MeHg) were prepared as described in Supplementary Data 2 and analyzed by Hg HERFD-XANES spectroscopy to interpret spectra from experimental bacterial pellets. At the end of incubations with IHg and MeHg, BerOc1, and G200 cultures were centrifuged (4000 g, 30 min), rapidly rinsed once in fresh MM PF medium free of Hg, and twice in ultrapure water. After centrifugation (10000 g, 5 min), the bacterial pellet was collected and prepared as a frozen pellet in liquid N 2 and kept in LN 2 until measurements. Frozen bacterial pellets and Hg references were then transferred into a helium cryostat operating at 10K for measurements.
HERFD-XANES measurements Hg speciation was investigated using Hg L 3 -edge (12. 284 keV) HERFD-XANES spectroscopy on FAME-UHD beamline at ESRF (Grenoble, France). HERFD -XANES spectra were collected by selecting the Hg Lα1 (3d 5/2 = > 2p 3/2 ) fluorescence line using 5 spherically bent Si(111) crystal analyzers aligned in Bragg position  (Proux et al. , 2017). The diffracted intensity was measured with a Si drift detector (SDD). Calibration of the monochromator was done using a Se foil (maximum of the first derivative set at the Se K-edge position: 12. 658 keV). HERFD-XANES data treatment was performed using ATHENA software  (Ravel and Newville, 2005). Normalized HERFD-XANES spectra were treated by linear combination fitting (LCF) of Hg reference compounds spectra. The quality of the fit was estimated by the normalized sum-squared residual parameter NSS = (µ xanes -µ fit ) 2 / (µ xanes ) 2 in the energy range 12.
ACKNOWLEDGMENTS We thank  CDAPP (Communauté d'Agglomération Pau Pyrénées)  for  Marine Albertelli 's grant. We acknowledge  ESRF  for provision of beamline and  FAME-UHD  and  ID16B  staff for their help in collecting data. We are grateful for the assistance of  Sylvain Bohic  (ESRF and INSERM) in cryo-fixation for nano-XRF analysis. Microscopy Imaging was performed on the  Bordeaux Imaging Center , member of the  FranceBioImaging National Infrastructure  ( ANR-10-INBS-04 ).
Data analysis The Abraham solute descriptors (E, S, A, B, V) used for LSERs with Eq. (1) were extracted from an in-house database established from all available literature on the solvation parameter model (Tables  S1  and S2 ). The two additional descriptors for charges (D -and D + ) were calculated based on aqueous pKa values determined with Chemicalize program and apparent pH 5. See previous works for detailed description  [40]. The additional descriptors for flexibility (F) and globularity (G) were computed as previously described  [32, 33]. Multiple linear regressions (MLR) and discriminant analysis (DA) were performed using XLStat 19. 03. 44850 software (Addinsoft, New York, NY). The quality of the MLR fits was estimated using the adjusted determination coefficient (R 2 ), standard error in the estimate (SE) and Fisher F statistic.
As recommended by the ANSES (the French Agency for Food, Environmental and Occupational Health & Safety)  [7] , we therefore decided to set up and carry out another independent analysis with the objective to verify whether these published unexpected data could be confirmed or not. We thus considered a short series of 100 so far available identifiable EHS and/or MCS patients. Patients were randomly selected from the database used by the authors of the above publications to further analyze the results obtained by the use of UCTS in the patients. As depicted in Table  3 , we confirmed the previously reported data  [5, 6]  by showing that in comparison with normal individuals there is a decrease in MPI, whatever the categories of patients tested (EHS, MCS, or EHS/MCS)  [38]. We therefore consider that UCTS is an appropriate method to contribute to the diagnosis of EHS-and/or MCS-bearing patients.
Methods General practices in the University of Limerick, Education and Research Network  [20]  were invited to participate via email. Out of the 14 practices that responded, ten practices were selected as they were within 2 h travel from the university, had the capacity to host the researcher and used electronic health care records. The 10 practices that participated included a variety of practice sizes (small, medium, large) and types (urban, rural, mixed, teaching and non-teaching) (Table  1 ). This was a convenience sample but the participating practices were purposefully selected to be representative of Irish General Practice  [21]. Data collection was conducted in July and August 2019 according to a prespecified data extraction protocol designed by RD (Appendix). Data collection was supported in practices by DMC, who received a summer student research scholarship, and was supervised by RD.