PDBsum1 : A standalone program for generating PDBsum analyses

PDBsum1 is a standalone set of programs to perform the same structural analyses as provided by the PDBsum web server (https://www.ebi.ac.uk/pdbsum). The server has pages for every entry in the Protein Data Bank (PDB) and can also process user‐uploaded PDB files, returning a password‐protected set of pages that are retained for around 3 months. The standalone version described here allows for in‐house processing and indefinite retention of the results. All data files and images are pre‐generated, rather than on‐the‐fly as in the web version, so can be easily accessed. The program runs on Linux, Windows, and mac operating systems and is freely available for academic use at https://www.ebi.ac.uk/thornton-srv/software/PDBsum1.     

Molecular Analysis of the Interaction between Staphylococcal Virulence Factor Sbi-IV and Complement C3d

Staphylococcus aureus expresses numerous virulence factors that aid in immune evasion. The four-domain staphylococcal immunoglobulin binding (Sbi) protein interacts with complement component 3 (C3) and its thioester domain (C3d)-containing fragments. Recent structural data suggested two possible modes of binding of Sbi domain IV (Sbi-IV) to C3d, but the physiological binding mode remains unclear. We used a computational approach to provide insight into the C3d-Sbi-IV interaction. Molecular dynamics (MD) simulations showed that the first binding mode (PDB code 2WY8) is more robust than the second (PDB code 2WY7), with more persistent polar and nonpolar interactions, as well as conserved interfacial solvent accessible surface area. Brownian dynamics and steered MD simulations revealed that the first binding mode has faster association kinetics and maintains more stable intermolecular interactions compared to the second binding mode. In light of available experimental and structural data, our data confirm that the first binding mode represents Sbi-IV interaction with C3d (and C3) in a physiological context. Although the second binding mode is inherently less stable, we suggest a possible physiological role. Both binding sites may serve as a template for structure-based design of novel complement therapeutics.     

Transvenous vagus nerve stimulation does not modulate the innate immune response during experimental human endotoxemia: a randomized controlled study

IntroductionVagus nerve stimulation (VNS) exerts beneficial anti-inflammatory effects in various animal models of inflammation, including collagen-induced arthritis, and is implicated in representing a novel therapy for rheumatoid arthritis. However, evidence of anti-inflammatory effects of VNS in humans is very scarce. Transvenous VNS (tVNS) is a newly developed and less invasive method to stimulate the vagus nerve. In the present study, we determined whether tVNS is a feasible and safe procedure and investigated its putative anti-inflammatory effects during experimental human endotoxemia.MethodsWe performed a randomized double-blind sham-controlled study in healthy male volunteers. A stimulation catheter was inserted in the left internal jugular vein at spinal level C5–C7, adjacent to the vagus nerve. In the tVNS group (n = 10), stimulation was continuously performed for 30 minutes (0–10 V, 1 ms, 20 Hz), starting 10 minutes before intravenous administration of 2 ng kg⁻¹Escherichia coli lipopolysaccharide (LPS). Sham-instrumented subjects (n = 10) received no electrical stimulation.ResultsNo serious adverse events occurred throughout the study. In the tVNS group, stimulation of the vagus nerve was achieved as indicated by laryngeal vibration. Endotoxemia resulted in fever, flu-like symptoms, and hemodynamic changes that were unaffected by tVNS. Furthermore, plasma levels of inflammatory cytokines increased sharply during endotoxemia, but responses were similar between groups. Finally, cytokine production by leukocytes stimulated with LPS ex vivo, as well as neutrophil phagocytosis capacity, were not influenced by tVNS.ConclusionstVNS is feasible and safe, but does not modulate the innate immune response in humans in vivo during experimental human endotoxemia.

Trial registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01944228","term_id":"NCT01944228"}}NCT01944228. Registered 12 September 2013.     

STUDIES ON SULFHYDRYL GROUPS DURING CELL DIVISION OF SEA URCHIN EGG : III. —SH Groups of KCl-Soluble Proteins and Their Change during Cleavage

Sea urchin egg proteins extracted with KCl are mostly TCA-soluble and, conversely, those extracted with TCA are KCl-soluble. Both groups are water-insoluble and show fluctuations in—SH content during the division cycle. The fluctuation of the—SH groups of the KCl-soluble protein of the whole egg is due to a —SH—S—S— interchange within the freely reacting groups and not within the sluggish and masked —SH groups of the protein. The —SH content of the KCl-soluble protein of the egg cortex also fluctuates in a similar way.     

How reliable is internet-based self-reported identity,socio-demographic and obesity measures in European adults?

In e-health intervention studies, there are concerns about the reliability of internet-based, self-reported (SR) data and about the potential for identity fraud. This study introduced and tested a novel procedure for assessing the validity of internet-based, SR identity and validated anthropometric and demographic data via measurements performed face-to-face in a validation study (VS). Participants (n = 140) from seven European countries, participating in the Food4Me intervention study which aimed to test the efficacy of personalised nutrition approaches delivered via the internet, were invited to take part in the VS. Participants visited a research centre in each country within 2 weeks of providing SR data via the internet. Participants received detailed instructions on how to perform each measurement. Individual’s identity was checked visually and by repeated collection and analysis of buccal cell DNA for 33 genetic variants. Validation of identity using genomic information showed perfect concordance between SR and VS. Similar results were found for demographic data (age and sex verification). We observed strong intra-class correlation coefficients between SR and VS for anthropometric data (height 0.990, weight 0.994 and BMI 0.983). However, internet-based SR weight was under-reported (Δ −0.70 kg [−3.6 to 2.1], p < 0.0001) and, therefore, BMI was lower for SR data (Δ −0.29 kg m⁻² [−1.5 to 1.0], p < 0.0001). BMI classification was correct in 93 % of cases. We demonstrate the utility of genotype information for detection of possible identity fraud in e-health studies and confirm the reliability of internet-based, SR anthropometric and demographic data collected in the Food4Me study.Trial registration: {"type":"clinical-trial","attrs":{"text":"NCT01530139","term_id":"NCT01530139"}}NCT01530139 (http://clinicaltrials.gov/show/{"type":"clinical-trial","attrs":{"text":"NCT01530139","term_id":"NCT01530139"}}NCT01530139).

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-015-0476-0) contains supplementary material, which is available to authorized users.     

Hypothermia during Carotid Endarterectomy: A Safety Study

BackgroundCEA is associated with peri-operative risk of brain ischemia, due both to emboli production caused by manipulation of the plaque and to potentially noxious reduction of cerebral blood flow by carotid clamping. Mild hypothermia (34–35°C) is probably the most effective approach to protect brain from ischemic insult. It is therefore a substantial hypothesis that hypothermia lowers the risk of ischemic brain damage potentially associated with CEA. Purpose of the study is to test whether systemic endovascular cooling to a target of 34.5–35°C, initiated before and maintained during CEA, is feasible and safe.MethodsThe study was carried out in 7 consecutive patients referred to the Vascular Surgery Unit and judged eligible for CEA. Cooling was initiated 60–90 min before CEA, by endovascular approach (Zoll system). The target temperature was maintained during CEA, followed by passive, controlled rewarming (0.4°C/h). The whole procedure was carried out under anesthesia.ResultsAll the patients enrolled had no adverse events. Two patients exhibited a transient bradycardia (heart rate 30 beats/min). There were no significant differences in the clinical status, laboratory and physiological data measured before and after CEA.ConclusionsSystemic cooling to 34.5–35.0°C, initiated before and maintained during carotid clamping, is feasible and safe.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT02629653","term_id":"NCT02629653"}}NCT02629653     

2013 ASHG Awards and Addresses

Each year at the annual meeting of The American Society of Human Genetics (ASHG), addresses are given in honor of The Society and a number of award winners. A summary of each of these addresses is given below. On the following pages, we have printed the Presidential Address and the addresses for the William Allan Award, the Curt Stern Award, and the Victor A. McKusick Leadership Award. Webcasts of these addresses, as well as those of many other presentations, can be found at http://www.ashg.org.     

Effects of Sprint versus High-Intensity Aerobic Interval Training on Cross-Country Mountain Biking Performance: A Randomized Controlled Trial

Objectives

The current study compared the effects of high-intensity aerobic training (HIT) and sprint interval training (SIT) on mountain biking (MTB) race simulation performance and physiological variables, including peak power output (PPO), lactate threshold (LT) and onset of blood lactate accumulation (OBLA).

Methods

Sixteen mountain bikers (mean ± SD: age 32.1 ± 6.4 yr, body mass 69.2 ± 5.3 kg and VO_2max 63.4 ± 4.5 mL∙kg^-1∙min^-1) completed graded exercise and MTB performance tests before and after six weeks of training. The HIT (7–10 x [4–6 min—highest sustainable intensity / 4–6 min—CR100 10–15]) and SIT (8–12 x [30 s—all-out intensity / 4 min—CR100 10–15]) protocols were included in the participants’ regular training programs three times per week.

Results

Post-training analysis showed no significant differences between training modalities (HIT vs. SIT) in body mass, PPO, LT or OBLA (p = 0.30 to 0.94). The Cohen’s d effect size (ES) showed trivial to small effects on group factor (p = 0.00 to 0.56). The interaction between MTB race time and training modality was almost significant (p = 0.08), with a smaller ES in HIT vs. SIT training (ES = -0.43). A time main effect (pre- vs. post-phases) was observed in MTB race performance and in several physiological variables (p = 0.001 to 0.046). Co-variance analysis revealed that the HIT (p = 0.043) group had significantly better MTB race performance measures than the SIT group. Furthermore, magnitude-based inferences showed HIT to be of likely greater benefit (83.5%) with a lower probability of harmful effects (0.8%) compared to SIT.

Conclusion

The results of the current study suggest that six weeks of either HIT or SIT may be effective at increasing MTB race performance; however, HIT may be a preferable strategy.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01944865","term_id":"NCT01944865"}}NCT01944865     

The Salford Lung Study protocol: a pragmatic,randomised phase III real-world effectiveness trial in chronic obstructive pulmonary disease

Background

New treatments need to be evaluated in real-world clinical practice to account for co-morbidities, adherence and polypharmacy.

Methods

Patients with chronic obstructive pulmonary disease (COPD), ≥40 years old, with exacerbation in the previous 3 years are randomised 1:1 to once-daily fluticasone furoate 100 μg/vilanterol 25 μg in a novel dry-powder inhaler versus continuing their existing therapy. The primary endpoint is the mean annual rate of COPD exacerbations; an electronic medical record allows real-time collection and monitoring of endpoint and safety data.

Conclusions

The Salford Lung Study is the world’s first pragmatic randomised controlled trial of a pre-licensed medication in COPD.

Trial registration

Clinicaltrials.gov identifier {"type":"clinical-trial","attrs":{"text":"NCT01551758","term_id":"NCT01551758"}}NCT01551758.     

Nanoscale Distribution of Ryanodine Receptors and Caveolin-3 in Mouse Ventricular Myocytes: Dilation of T-Tubules near Junctions

We conducted super-resolution light microscopy (LM) imaging of the distribution of ryanodine receptors (RyRs) and caveolin-3 (CAV3) in mouse ventricular myocytes. Quantitative analysis of data at the surface sarcolemma showed that 4.8% of RyR labeling colocalized with CAV3 whereas 3.5% of CAV3 was in areas with RyR labeling. These values increased to 9.2 and 9.0%, respectively, in the interior of myocytes where CAV3 was widely expressed in the t-system but reduced in regions associated with junctional couplings. Electron microscopic (EM) tomography independently showed only few couplings with caveolae and little evidence for caveolar shapes on the t-system. Unexpectedly, both super-resolution LM and three-dimensional EM data (including serial block-face scanning EM) revealed significant increases in local t-system diameters in many regions associated with junctions. We suggest that this regional specialization helps reduce ionic accumulation and depletion in t-system lumen during excitation-contraction coupling to ensure effective local Ca²⁺ release. Our data demonstrate that super-resolution LM and volume EM techniques complementarily enhance information on subcellular structure at the nanoscale.The contraction of cardiac ventricular myocytes depends on the rapid cell-wide transient increase in intracellular [Ca²⁺] upon depolarization of the cell-membrane potential. The cardiac ryanodine receptor (RyR) (1), which is the intracellular Ca²⁺ release channel in the sarcoplasmic reticulum (SR), plays a central role in shaping Ca²⁺ transients. RyRs form clusters of various sizes (2,3) with the majority located within junctions between the SR and the surface membrane and its cytoplasmic extension, the transverse tubular (t-) system. It has been suggested that some RyR clusters are associated with caveolae, a specialized signaling microdomain of the surface membrane. Previous studies were complicated by the limited resolution of optical imaging methods of ∼250 nm, much larger than the nanometer scale of RyRs and caveolae. Accordingly, these studies report varying colocalization between RyRs and caveolin-3 (CAV3), a caveolar marker also expressed in the t-system (4,5).In this work, we investigated the relative distribution of CAV3 and RyRs in mouse ventricular myocytes both in the cytosol and near the cell surface with super-resolution fluorescence microscopy that achieves a resolution approaching 30 nm. Our data revealed unexpected local t-system swellings near junctional couplings, which was supported by two different three-dimensional electron microscopy (EM) modalities with <10-nm resolution: EM tomography and serial block-face scanning EM (SBFSEM).Super-resolution images of CAV3 and RyR labeling at the surface sarcolemma of mouse myocytes showed little overlap, suggesting that few RyRs were in couplings with caveolae (Fig. 1 A, for detailed methods, see the Supporting Material). Only ∼4.8% of RyR labeling was associated with CAV3 positive areas and ∼3.5% of CAV3 associated with RyR positive areas (n = 6 cells from three animals, Fig. 1 B, see also Table S1 in the Supporting Material), broadly consistent with previous data in rats (6). To support this finding, EM tomography was applied to mouse ventricular tissue that included a part of the surface sarcolemma, to our knowledge for the first time. Segmentation of peripheral couplings (containing RyR foot structures) and surface caveolae (∼60 nm in diameter and often interconnected) confirmed that the great majority of peripheral couplings were in regions devoid of caveolae (Fig. 1 C). A few junctional couplings containing feet were between caveolae and subsarcolemmal SR (Fig. 1 D, see also Fig. S1 and Movie S1 in the Supporting Material). We conducted a similar analysis in the cytosol where CAV3 expression occurs in the t-system (5) and RyRs are abundant in dyadic junctions between the t-system and SR terminal cisterns.Open in a separate windowFigure 1Colocalization of CAV3 and RyRs at the surface sarcolemma. (A) Super-resolution micrograph of the distribution of CAV3 (green) and RyRs (red) at the surface of a mouse cardiac myocyte. (B) Analysis of the association of CAV3 with RyRs. The fraction of RyR labeling within CAV3 positive areas was ∼4.8% (front data) whereas ∼3.5% of CAV3 was found in RyR-positive membrane areas. (C) Segmented EM tomogram containing a patch of surface sarcolemma (light blue) and associated caveolae (green) as well as peripheral couplings (red). (D) Detailed view of a region with abundant caveolae. (Arrows) Couplings with caveolae.As shown in Fig. 2 A, the spatial distribution of CAV3 and RyR clusters in super-resolution micrographs taken several microns below the surface sarcolemma is consistent with this view. The association of the two labels is slightly increased (as compared to the surface), according to distance analysis with 9% of CAV3 and 9.2% of RyR labeling associating with each other (Fig. 2 B, n = 6 cells from three animals). The similarity of manually traced t-system in EM tomograms (Fig. 2 C) and super-resolved CAV3 labeling suggested that CAV3 is widely distributed in the t-system except for regions where dyadic membrane junctions occur as CAV3 labeling was much weaker in regions with strong RyR labeling. It was notable that the t-system diameter appeared to increase at regions of strong RyR labeling (Fig. 2 D), broadly consistent with the behavior seen in tomograms (Fig. 2 C). This was confirmed by a quantitative analysis of t-tubule diameters in dyadic versus extradyadic regions on the basis of CAV3 and RyR labeling, with full-width at quarter-maximum mean diameters increasing from ∼150 nm distal to dyads, to ∼190 nm (using CAV3 signal only) or ∼280 nm (using CAV3 and RyR signal) near dyads (Fig. 2, G and H, see also Methods in the Supporting Material). The combined RyR and CAV3 signals seemed to be a better representation of the entire t-system lumen near junctions (see Fig. S2).Open in a separate windowFigure 2Distribution of CAV3 and RyRs in the cell interior. (A) Super-resolution micrograph of CAV3 (green) and RyR (red) distribution at t-system. (Arrow) Direction of longitudinal cell axis. (B) Distance analysis of the CAV3 and RyR association (N = 6 cells per group). (C) Segmented EM tomogram of a similar region with three-dimensional mesh models of t-system membrane (green) and dyadic couplings (red). (D) This image illustrates the tracing (white path) of t-tubules. The label distribution was extracted and linearized along the path (E) to calculate a mask that shows the full width at quarter-maximum diameter along tubules, CAV3 (green) and RyR (red) (F). (G) Histograms of local diameters extracted from traced t-tubules. (H) Mean diameters in junctional (dyad) and nonjunctional (ex-dyad) regions. See main text and the Supporting Material for details. ^**p < 0.01.Taken together, super-resolution imaging and EM tomography strongly support the presence of local t-system dilations in regions where the t-system opposes SR at dyads and such t-system bulges are connected by narrower tubule segments. Further support was provided by SBFSEM, another volume EM technique to study larger cell volumes (albeit at the expense of a slightly lower resolution). SBFSEM clearly showed local t-system dilations were regularly involved in the architecture of most (but not all) dyads (Fig. 3, see also Fig. S3 and Movie S2), as also observed in full three-dimensional super-resolution images (see Fig. S3 C).Open in a separate windowFigure 3Segmented SBFSEM data showing t-system dilations near dyadic junctions. (A) The overview shows t-system membranes (green) and jSR (red) in a mouse myocyte. (B, enlarged inset from panel A) Thin connecting tubules (arrows) and regular swellings in junctional regions at z-lines.Our data identify local dilations of the t-system associated with dyads in mouse cardiac myocytes. Frequent tubule distensions had been observed especially at the intersections of transverse and axial tubules (7), and constrictions were seen in rabbit myocytes although their relationship to dyads was unknown (8). The increased local t-system lumen near junctions may help reduce the predicted ionic accumulation/depletion during excitation-contraction coupling (9). Alternatively, it might simply be secondary to increasing local membrane area and allow the formation of large area junctions that harbor many RyRs. In connection with this point, it would be interesting to investigate the t-system near junctions in species that have larger average tubule diameters (e.g., human and rabbit (10)), or if this architecture changes in mouse heart failure models where t-tubule diameters are often increased.Most peripheral couplings were in regions void of surface caveolae, although a small number of RyR clusters were in junctional couplings between subsarcolemmal SR and caveolae as shown both by the low colocalization between CAV3 and RyRs as well as direct evidence from EM tomography. Similarly, a relatively small fraction of CAV3 colocalized with RyR clusters in the t-system although CAV3 was expressed widely in the t-system. A structural role of CAV3 in the t-system is still unclear—t-tubules in tomogram data did not reveal distinct caveolae shapes on the t-system membrane (see Fig. S4), although this might change in pathology (11). In any case, the t-system exhibits high curvature orthogonal to the tubule axis, which may be supported by CAV3 oligomerization. In addition, the presence of CAV3 in the t-system may be important for regulating other signaling systems (e.g., adrenergic signaling).Finally, our data demonstrate that complementary data from optical super-resolution and three-dimensional EM images assists data interpretation and reliability. We suggest that truly correlative optical and EM imaging approaches should provide further information and improve our knowledge of the basis of cardiac excitation-contraction coupling.     

Which Single Intervention Would Do the Most to Improve the Health of Those Living on Less Than $1 Per Day?

Background to the debate: PLoS Medicine is participating in the Council of Science Editors'' global theme issue on poverty and human development on October 22, 2007 (http://www.councilscienceeditors.org/globalthemeissue.cfm). Over 200 scientific and medical journals are taking part. For our theme issue, we asked a wide variety of commentators worldwide—including clinicians, medical researchers, health reporters, policy makers, health activists, and development experts—to name the single intervention that they think would improve the health of those living in poverty. We also asked four individuals living in poor, rural agricultural communities in the Santillana district, province of Huanta, Ayacucho, Peru to give us their response to the question, “What do you think would do the most to improve your health and the health of your family?” (The four community members were Severino Rojas Poma, Mercedes Vargas Soto, Julián De La Cruz Chahua, and Martín Rojas Poma). Our October 2007 Editorial discusses this debate further.     

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins

A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.     

Aclidinium bromide and formoterol fumarate as a fixed-dose combination in COPD: pooled analysis of symptoms and exacerbations from two six-month,multicentre, randomised studies (ACLIFORM and AUGMENT)

Background

The combination of aclidinium bromide, a long-acting anticholinergic, and formoterol fumarate, a long-acting beta₂-agonist (400/12 μg twice daily) achieves improvements in lung function greater than either monotherapy in patients with chronic obstructive pulmonary disease (COPD), and is approved in the European Union as a maintenance treatment. The effect of this combination on symptoms of COPD and exacerbations is less well established. We examined these outcomes in a pre-specified analysis of pooled data from two 24-week, double-blind, parallel-group, active- and placebo-controlled, multicentre, randomised Phase III studies (ACLIFORM and AUGMENT).

Methods

Patients ≥40 years with moderate to severe COPD (post-bronchodilator forced expiratory volume in 1 s [FEV₁]/forced vital capacity <70 % and FEV₁ ≥30 % but <80 % predicted normal) were randomised (ACLIFORM: 2:2:2:2:1; AUGMENT: 1:1:1:1:1) to twice-daily aclidinium/formoterol 400/12 μg or 400/6 μg, aclidinium 400 μg, formoterol 12 μg or placebo via Genuair™/Pressair®. Dyspnoea (Transition Dyspnoea Index; TDI), daily symptoms (EXAcerbations of Chronic pulmonary disease Tool [EXACT]-Respiratory Symptoms [E-RS] questionnaire), night-time and early-morning symptoms, exacerbations (Healthcare Resource Utilisation [HCRU] and EXACT definitions) and relief-medication use were assessed.

Results

The pooled intent-to-treat population included 3394 patients. Aclidinium/formoterol 400/12 μg significantly improved TDI focal score versus placebo and both monotherapies at Week 24 (all p < 0.05). Over 24 weeks, significant improvements in E-RS total score, overall night-time and early-morning symptom severity and limitation of early-morning activities were observed with aclidinium/formoterol 400/12 μg versus placebo and both monotherapies (all p < 0.05). The rate of moderate or severe HCRU exacerbations was significantly reduced with aclidinium/formoterol 400/12 μg compared with placebo (p < 0.05) but not monotherapies; the rate of EXACT-defined exacerbations was significantly reduced with aclidinium/formoterol 400/12 μg versus placebo (p < 0.01) and aclidinium (p < 0.05). Time to first HCRU or EXACT exacerbation was longer with aclidinium/formoterol 400/12 μg compared with placebo (all p < 0.05) but not the monotherapies. Relief-medication use was reduced with aclidinium/formoterol 400/12 μg versus placebo and aclidinium (p < 0.01).

Conclusions

Aclidinium/formoterol 400/12 μg significantly improves 24-hour symptom control compared with placebo, aclidinium and formoterol in patients with moderate to severe COPD. Furthermore, aclidinium/formoterol 400/12 μg reduces the frequency of exacerbations compared with placebo.

Trial registration

{"type":"clinical-trial","attrs":{"text":"NCT01462942","term_id":"NCT01462942"}}NCT01462942 and {"type":"clinical-trial","attrs":{"text":"NCT01437397","term_id":"NCT01437397"}}NCT01437397 (ClinicalTrials.gov)

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0250-2) contains supplementary material, which is available to authorized users.     

Golimumab in patients with active rheumatoid arthritis after treatment with tumor necrosis factor α inhibitors: findings with up to five years of treatment in the multicenter,randomized, double-blind,placebo-controlled,phase 3 GO-AFTER study

IntroductionThe aim of this study was to assess long-term golimumab therapy in rheumatoid arthritis (RA) patients who discontinued previous tumor necrosis factor-α (TNF)-inhibitor(s).MethodsPatients enrolled into this multicenter, randomized, double-blind, placebo-controlled study of active RA (≥4 tender, ≥4 swollen joints) received placebo (Group 1) or golimumab 50 mg (Group 2) or 100 mg (Group 3) injections every 4 weeks. Patients in Groups 1 and 2 with inadequate response at week 16 escaped to golimumab 50 and 100 mg, respectively. At week 24, Group 1 patients crossed-over to golimumab 50 mg, Group 2 continued golimumab 50/100 mg per escape status, and Group 3 maintained dosing. During the long-term-extension (LTE), golimumab 50 mg could be increased to 100 mg, and 100 mg could be decreased to 50 mg. Data through 5 years are reported for all patients (safety) and patients using methotrexate (efficacy, intention-to-treat (ITT) analysis with last-observation-carried-forward for missing data and non-responder imputation for unsatisfactory efficacy discontinuations).ResultsIn total, 459 of 461 randomized patients received the study agent, 304 of whom were methotrexate-treated and included in efficacy analyses. Through week 256, the proportions of methotrexate-treated patients achieving American-College-of-Rheumatology (ACR) responses were 37.6% to 47.0% for ACR20, 21.4% to 35.0% for ACR50, and 7.8% to 17.0% for ACR70 response across randomized groups. Golimumab safety through week 268 was generally consistent with that at week 24 and week 160 and other anti-TNF agents.ConclusionsIn some patients with active RA discontinuing previous TNF-antagonist therapy, golimumab safety and efficacy, assessed conservatively with ITT analyses, was confirmed through 5 years.

Trial registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00299546","term_id":"NCT00299546"}}NCT00299546. Registered 03 March 2006.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0516-6) contains supplementary material, which is available to authorized users.     

Involving society in science: Reflections on meaningful and impactful stakeholder engagement in fundamental research

Open Science calls for transparent science and involvement of various stakeholders. Here are examples of and advice for meaningful stakeholder engagement. Subject Categories: Economics, Law & Politics, History & Philosophy of Science

The concepts of Open Science and Responsible Research and Innovation call for a more transparent and collaborative science, and more participation of citizens. The way to achieve this is through cooperation with different actors or “stakeholders”: individuals or organizations who can contribute to, or benefit from research, regardless of whether they are researchers themselves or not. Examples include funding agencies, citizens associations, patients, and policy makers (https://aquas.gencat.cat/web/.content/minisite/aquas/publicacions/2018/how_measure_engagement_research_saris1_aquas2018.pdf). Such cooperation is even more relevant in the current, challenging times—even apart from a global pandemic—when pseudo‐science, fake news, nihilist attitudes, and ideologies too often threaten social and technological progress enabled by science. Stakeholder engagement in research can inform and empower citizens, help render research more socially acceptable, and enable policies grounded on evidence‐based knowledge. Beyond, stakeholder engagement is also beneficial to researchers and to research itself. In a recent survey, the majority of scientists reported benefits from public engagement (Burns et al, 2021). This can include increased mutual trust and mutual learning, improved social relevance of research, and improved adoption of results and knowledge (Cottrell et al, 2014). Finally, stakeholder engagement is often regarded as an important factor to sustain public investment in the life sciences (Burns et al, 2021).

Stakeholder engagement in research can inform and empower citizens, help render research more socially acceptable and enable policies grounded on evidence‐based knowledge

Here, we discuss different levels of stakeholder engagement by way of example, presenting various activities organized by European research institutions. Based on these experiences, we propose ten reflection points that we believe should be considered by the institutions, the scientists, and the funding agencies to achieve meaningful and impactful stakeholder engagement.     

DECOMP: A PDB decomposition tool on the web

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi­monomer ligands, and the server also offers the preprocessed ligand­protein decomposition of the complete PDB for downloading (up to size: 5GB)

Availability

http://decomp.pitgroup.org     

Evaluation of coagulation activation after Rhinovirus infection in patients with asthma and healthy control subjects: an observational study

Background

Asthma exacerbations are frequently triggered by rhinovirus infections. Both asthma and respiratory tract infection can activate haemostasis. Therefore we hypothesized that experimental rhinovirus-16 infection and asthmatic airway inflammation act in synergy on the haemostatic balance.

Methods

28 patients (14 patients with mild allergic asthma and 14 healthy non-allergic controls) were infected with low-dose rhinovirus type 16. Venous plasma and bronchoalveolar lavage fluid (BAL fluid) were obtained before and 6 days after infection to evaluate markers of coagulation activation, thrombin-antithrombin complexes, von Willebrand factor, plasmin-antiplasmin complexes, plasminogen activator inhibitor type-1, endogenous thrombin potential and tissue factor-exposing microparticles by fibrin generation test, in plasma and/or BAL fluid. Data were analysed by nonparametric tests (Wilcoxon, Mann Whitney and Spearman correlation).

Results

13 patients with mild asthma (6 females, 19-29 y) and 11 healthy controls (10 females, 19-31 y) had a documented Rhinovirus-16 infection. Rhinovirus-16 challenge resulted in a shortening of the fibrin generation test in BAL fluid of asthma patients (t = -1: 706 s vs. t = 6: 498 s; p = 0.02), but not of controls (t = -1: 693 s vs. t = 6: 636 s; p = 0.65). The fold change in tissue factor-exposing microparticles in BAL fluid inversely correlated with the fold changes in eosinophil cationic protein and myeloperoxidase in BAL fluid after virus infection (r = -0.517 and -0.528 resp., both p = 0.01).Rhinovirus-16 challenge led to increased plasminogen activator inhibitor type-1 levels in plasma in patients with asthma (26.0 ng/mL vs. 11.5 ng/mL in healthy controls, p = 0.04). Rhinovirus-16 load in BAL showed a linear correlation with the fold change in endogenous thrombin potential, plasmin-antiplasmin complexes and plasminogen activator inhibitor type-1.

Conclusions

Experimental rhinovirus infection induces procoagulant changes in the airways of patients with asthma through increased activity of tissue factor-exposing microparticles. These microparticle-associated procoagulant changes are associated with both neutrophilic and eosinophilic inflammation. Systemic activation of haemostasis increases with Rhinoviral load.

Trial registration

This trial was registered at the Dutch trial registry (http://www.trialregister.nl): NTR1677.