The pipeline project:Pre-publication independent replications of a single laboratory's research pipeline

This crowdsourced project introduces a collaborative approach to improving the reproducibility of scientific research, in which findings are replicated in qualified independent laboratories before (rather than after) they are published. Our goal is to establish a non-adversarial replication process with highly informative final results. To illustrate the Pre-Publication Independent Replication (PPIR) approach, 25 research groups conducted replications of all ten moral judgment effects which the last author and his collaborators had "in the pipeline" as of August 2014. Six findings replicated according to all replication criteria, one finding replicated but with a significantly smaller effect size than the original, one finding replicated consistently in the original culture but not outside of it, and two findings failed to find support. In total, 40% of the original findings failed at least one major replication criterion. Potential ways to implement and incentivize pre-publication independent replication on a large scale are discussed. (C) 2015 The Authors. Published by Elsevier Inc.</p

Data from a pre-publication independent replication initiative examining ten moral judgement effects

We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative, 25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable, unreliable, and culturally moderated findings. Unlike any previous replication project, this dataset includes the data from not only the replications but also from the original studies, creating a unique corpus that researchers can use to better understand reproducibility and irreproducibility in science

The pipeline project: Pre-publication independent replications of a single laboratory's research pipeline

This crowdsourced project introduces a collaborative approach to improving the reproducibility of scientific research, in which findings are replicated in qualified independent laboratories before (rather than after) they are published. Our goal is to establish a non-adversarial replication process with highly informative final results. To illustrate the Pre-Publication Independent Replication (PPIR) approach, 25 research groups conducted replications of all ten moral judgment effects which the last author and his collaborators had “in the pipeline” as of August 2014. Six findings replicated according to all replication criteria, one finding replicated but with a significantly smaller effect size than the original, one finding replicated consistently in the original culture but not outside of it, and two findings failed to find support. In total, 40% of the original findings failed at least one major replication criterion. Potential ways to implement and incentivize pre-publication independent replication on a large scale are discussed

Data from a pre-publication independent replication initiative examining ten moral judgement effects

We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative, 25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable, unreliable, and culturally moderated findings. Unlike any previous replication project, this dataset includes the data from not only the replications but also from the original studies, creating a unique corpus that researchers can use to better understand reproducibility and irreproducibility in science.Link_to_subscribed_fulltex

The pipeline project: Pre-publication independent replications of a single laboratory's research pipeline

© 2015 The Authors This crowdsourced project introduces a collaborative approach to improving the reproducibility of scientific research, in which findings are replicated in qualified independent laboratories before (rather than after) they are published. Our goal is to establish a non-adversarial replication process with highly informative final results. To illustrate the Pre-Publication Independent Replication (PPIR) approach, 25 research groups conducted replications of all ten moral judgment effects which the last author and his collaborators had âin the pipelineâ as of August 2014. Six findings replicated according to all replication criteria, one finding replicated but with a significantly smaller effect size than the original, one finding replicated consistently in the original culture but not outside of it, and two findings failed to find support. In total, 40% of the original findings failed at least one major replication criterion. Potential ways to implement and incentivize pre-publication independent replication on a large scale are discussed.Link_to_subscribed_fulltex

Characterization of monocyte gene expression in HIV-1 infected individuals

Monocytes/macrophages (M/M) are primary HIV-1 infection targets; they support virus replication and serve as HIV-1 reservoirs. Unlike CD4 T cells that progressively diminish over the course of infection, M/M pools are not observed to be depleted. M/M in HIV-1 infected individuals also exhibit functional impairment. A majority of the observations of HIV-1 mediated M/M modulation have been made in vitro models and a single report to date has studied circulating HIV-1 monocyte gene modulation. Understanding modulation in the peripheral monocyte pool is important as it also allows us to make inferences of modulation that may occur in tissue macrophages (derived from circulating monocytes) which are not easily accessible for in vivo studies and that are ultimate targets of HIV-1 infection. We have characterized gene expression in circulating monocytes in asymptomatic and chronically infected HIV-1 subjects. We have identified gene signatures associated with TNF, CD40/CD40L, ERK/MAPKinase, G-protein signaling and PPAR and p53 transcription that would support dysregulation of major monocyte functions including inflammatory response, lipid metabolism and survival. The gene signatures persist upon repeat sampling. We present via gene network analysis pathways of chronic immune activation - including TNF, IL6 and CD40/CD40L - in association with the observed dysregulation of lipid metabolism (via PPARG inhibition) and apoptosis resistance (via p53 inhibition, activation of ERK/MAPK). We identify inflammatory, selected lipid and apoptosis related genes associated with TNF signaling networks to be shared with other non-HIV macrophage activation programs and the p53 network related apoptosis genes to be associated specifically with HIV-1 monocyte/macrophages. We identify functional consequences of constitutive gene modulation as an increased modulation in inflammation, lipid and survival gene expression following acute TLR2 stimulation of HIV monocytes and as an increased HIV-1 monocyte apoptosis resistance as compared to uninfected monocytes and to increased apoptosis in infected CD4 T cells. Further, by replicating the observations of monocyte apoptotic resistance in Sooty mangabeys (having high virus replication and minimal immune activation [2]) we infer that HIV-1 binding independent of immune activation can induce apoptosis resistance in monocytes, and further indicate monocyte apoptosis regulation to be an evolutionarily conserved feature of lentiviral pathogenesis

Characterization of monocyte gene expression in HIV-1 infected individuals

Monocytes/macrophages (M/M) are primary HIV-1 infection targets; they support virus replication and serve as HIV-1 reservoirs. Unlike CD4 T cells that progressively diminish over the course of infection, M/M pools are not observed to be depleted. M/M in HIV-1 infected individuals also exhibit functional impairment. A majority of the observations of HIV-1 mediated M/M modulation have been made in vitro models and a single report to date has studied circulating HIV-1 monocyte gene modulation. Understanding modulation in the peripheral monocyte pool is important as it also allows us to make inferences of modulation that may occur in tissue macrophages (derived from circulating monocytes) which are not easily accessible for in vivo studies and that are ultimate targets of HIV-1 infection. We have characterized gene expression in circulating monocytes in asymptomatic and chronically infected HIV-1 subjects. We have identified gene signatures associated with TNF, CD40/CD40L, ERK/MAPKinase, G-protein signaling and PPAR and p53 transcription that would support dysregulation of major monocyte functions including inflammatory response, lipid metabolism and survival. The gene signatures persist upon repeat sampling. We present via gene network analysis pathways of chronic immune activation - including TNF, IL6 and CD40/CD40L - in association with the observed dysregulation of lipid metabolism (via PPARG inhibition) and apoptosis resistance (via p53 inhibition, activation of ERK/MAPK). We identify inflammatory, selected lipid and apoptosis related genes associated with TNF signaling networks to be shared with other non-HIV macrophage activation programs and the p53 network related apoptosis genes to be associated specifically with HIV-1 monocyte/macrophages. We identify functional consequences of constitutive gene modulation as an increased modulation in inflammation, lipid and survival gene expression following acute TLR2 stimulation of HIV monocytes and as an increased HIV-1 monocyte apoptosis resistance as compared to uninfected monocytes and to increased apoptosis in infected CD4 T cells. Further, by replicating the observations of monocyte apoptotic resistance in Sooty mangabeys (having high virus replication and minimal immune activation [2]) we infer that HIV-1 binding independent of immune activation can induce apoptosis resistance in monocytes, and further indicate monocyte apoptosis regulation to be an evolutionarily conserved feature of lentiviral pathogenesis

Efficacy and safety of intraoperative intracameral mydriasis in manual small incision cataract surgery - A randomized controlled trial

Purpose: The purpose of this study is to assess the efficacy and safety of intracameral mydriatic solution, as compared to preoperative topical mydriatics, in patients undergoing manual small incision cataract surgery (MSICS) under peribulbar anesthesia. To assess the sustainability of intracameral mydriasis in MSICS by monitoring pupil size at specific junctures during the surgery. Methods: This trial recruited 127 patients, who underwent MSICS under peribulbar block. Mydriasis in topical group was achieved with preoperative topical dilating drops while patients in intracameral group were taken up for surgery without dilation, and mydriasis was achieved intraoperatively with intracameral solution. Pupil sizes were measured serially, at six different junctures during surgery. Time duration of surgery, any intraoperative complications and first postoperative day visual acuity, corneal edema score, and anterior chamber inflammation score were noted in all patients. Results: Mean pupil size just before peribulbar block was 7.3 mm in topical group and 3.3 mm in intracameral group (P < 0.001). Mean pupil size in intracameral group increased to 7.3 mm 30 s after injecting intracameral dilating solution. Mean pupil size in both groups progressively reduced, reaching 5.5 mm (topical group) and 6.2 mm (intracameral group) just before intraocular lens implantation (P = 0.001), and measured 5.1 mm and 5.5 mm, respectively, at the end of surgery (P = 0.048). On first postoperative day, there was no significant difference in distribution of corneal edema scores, AC inflammation scores, and in median logMAR visual acuity between the two groups. Conclusions: MSICS can be performed effectively and safely utilizing intracameral mydriatic solution, without the use of preoperative dilating drops. Trial registration: CTRI/2016/06/00703