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Comparison between European Medicines Agency and US Food and Drug Administration in Granting Accelerated Marketing Authorizations for Covid-19 Medicines and their Utilized Regulations. Ther Innov Regul Sci 2024; 58:79-113. [PMID: 37861859 PMCID: PMC10764419 DOI: 10.1007/s43441-023-00574-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 08/21/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Prompted by the Covid-19 pandemic and the need to ensure timely and safe access to medicines during a pandemic, the aim of this study was to compare and contrast the EU and US regulations, processes, and outcomes pertaining to the granting of accelerated Marketing Authorizations (MAs) for COVID-19 vaccines and treatments with a view to determining how effective these regulations were in delivering safe medicines in a timely manner. METHODS MAs for medicines approved for Covid-related indications in the first two pandemic years (March 2020-February 2022) were identified using the European Medicines Agency (EMA) and US Food and Drug Administration (FDA) websites. Authorization reports and utilized regulations were reviewed to determine and compare approval timelines, facilitated pathways, accepted clinical evidence, and effectiveness of the regulations by assessing them against time and safety standards. RESULTS By the end of February 2022, the EMA and FDA had granted 12 and 14 MAs, respectively. Two EU and two US approvals were issued in relation to new indications for already-approved treatments; the remaining ones were first-time approvals of novel vaccines and treatments. The median time to approval was 24 days for the EMA's conditional MAs and 36 days for the USFDA's Emergency Use Authorizations (EUA) for all Covid-19 medicines. This is compared with 23 and 28 days, respectively, specifically for first-time novel vaccines and treatments authorized by both USFDA and EMA. The USFDA and EMA differed markedly in terms of the time taken to approve new indications of already-approved treatment; the USFDA took 65 days for such approval, compared with 133 days for the EMA. Where MAs were issued by both authorities, USFDA approvals were issued before EMA approvals; applications for approval were submitted to the FDA before submission to the EMA. Three EU and two US MAs were based on data from two or more phase 3 clinical trials; the remaining ones were based on single trial data. Only six EU and four US trials had been completed by the time of authorization. This was in line with regulations. While the applicable regulations shared many similarities, there were marked differences. For instance, the EU's conditional MA regulation pertains only to first approvals of new treatments. It does not cover new indications of already-approved treatments. This contrasts with the US, where the EUA regulation applies to both types of applications, something that may have impacted approval timelines. Overall, both EU and US utilized regulations were considered to be effective. For most cases, utilizing such regulations for Covid-19 MAs resulted in faster approval timelines compared to standard MAs. They were flexible enough to manage the process of granting emergency approvals while maintaining strict requirements and allowing comprehensive reviews of the supporting evidence. CONCLUSION US and EU regulations were effective in ensuring timely accelerated market access to Covid-19 medicines during the pandemic without compromising the approval standards related to safety or efficacy. The population in both regions will receive comparable access to medicines during a pandemic if sponsors submit their applications to both authorities in parallel.
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Impact of different financial incentive structures on a web-based health survey: do timing and amount matter? CONNECTED HEALTH AND TELEMEDICINE 2023; 2:200006. [PMID: 37641713 PMCID: PMC10462406 DOI: 10.20517/chatmed.2023.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Aim Financial incentives improve response to electronic health surveys, yet little is known about how unconditional incentives (guaranteed regardless of survey completion), conditional incentives, and various combinations of incentives influence response rates. We compared electronic health survey completion with two different financial incentive structures. Methods We invited women aged 30-64 years enrolled in a U.S. healthcare system and overdue for Pap screening to complete a web-based survey after receiving a mailed human papillomavirus (HPV) self-sampling kit in a pragmatic trial. HPV kit returners (n = 272) and non-returners (n = 1,083) were allocated to one of two different incentive structures: (1) Unconditional: $5 pre-incentive only (n = 653); (2) Combined: $2 pre-incentive plus $10 post-incentive conditional on completion (n = 702). Chi-square tests evaluated whether survey completion differed by incentive structure within kit return groups or was modified by kit return status. For each incentive-by-kit status group, the cost-per-survey response was calculated as: ([number invited*pre-incentive amount] + [number responses*post-incentive amount]) / number responses. Results Overall, survey response was higher in kit returners vs. kit non-returners (42.6% vs. 11.0%, P < 0.01), and survey response was higher in the combined (20.1%) vs. unconditional (14.4%) incentive group (P = 0.01). Kit return status did not modify the association between incentive type and survey response (P = 0.52). Among respondents, time to survey completion did not differ by incentive type among either kit returners or non-returners. Among returners, the cost-per-survey response was similar between groups ($13.57 unconditional; $14.15 combined); among non-returners, the cost was greater in the unconditional ($57.78) versus the combined ($25.22) group. Conclusion A combined incentive can be cost-effective for increasing survey response in health services research, particularly in hard-to-reach populations.
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Introduction of loxP sites by electroporation in the mouse genome; a simple approach for conditional allele generation in complex targeting loci. BMC Biotechnol 2022; 22:14. [PMID: 35549895 PMCID: PMC9097428 DOI: 10.1186/s12896-022-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
Background The discovery of the CRISPR-Cas9 system and its applicability in mammalian embryos has revolutionized the way we generate genetically engineered animal models. To date, models harbouring conditional alleles (i.e. two loxP sites flanking an exon or a critical DNA sequence of interest) are amongst the most widely requested project type that are challenging to generate as they require simultaneous cleavage of the genome using two guides in order to properly integrate the repair template. An approach, using embryo sequential electroporation has been reported in the literature to successfully introduce loxP sites on the same allele. Here, we describe a modification of this sequential electroporation procedure that demonstrated the production of conditional allele mouse models for eight different genes via one of two possible strategies: either by consecutive sequential electroporation (strategy A) or non-consecutive sequential electroporation (strategy B). This latest strategy originated from using the by-product produced when using consecutive sequential electroporation (i.e. mice with a single targeted loxP site) to complete the project.
Results By using strategy A, we demonstrated successful generation of conditional allele models for three different genes (Icam1, Lox, and Sar1b), with targeting efficiencies varying between 5 and 13%. By using strategy B, we generated five conditional allele models (Loxl1, Pard6a, Pard6g, Clcf1, and Mapkapk5), with targeting efficiencies varying between 3 and 25%. Conclusion Our modified electroporation-based approach, involving one of the two alternative strategies, allowed the production of conditional allele models for eight different genes via two different possible paths. This reproducible method will serve as another reliable approach in addition to other well-established methodologies in the literature for conditional allele mouse model generation.
Supplementary Information The online version contains supplementary material available at 10.1186/s12896-022-00744-8.
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Conditional and tissue-specific approaches to dissect essential mechanisms in plant development. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102119. [PMID: 34653951 PMCID: PMC7612331 DOI: 10.1016/j.pbi.2021.102119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 05/19/2023]
Abstract
Reverse genetics approaches are routinely used to investigate gene function. However, mutations, especially in critical genes, can lead to pleiotropic effects as severe as lethality, thus limiting functional studies in specific contexts. Approaches that allow for modifications of genes or gene products in a specific spatial or temporal setting can overcome these limitations. The advent of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technologies has not only revolutionized targeted genome modification in plants but also enabled new possibilities for inducible and tissue-specific manipulation of gene functions at the DNA and RNA levels. In addition, novel approaches for the direct manipulation of target proteins have been introduced in plant systems. Here, we review the current development in tissue-specific and conditional manipulation approaches at the DNA, RNA, and protein levels.
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Processing Conditional Perfection in Promises and Threats: The Role of Negation, Clause Order and Incentive. JOURNAL OF PSYCHOLINGUISTIC RESEARCH 2021; 50:1557-1573. [PMID: 34331178 DOI: 10.1007/s10936-021-09794-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The paper reports on two experiments that investigate whether polarity, clause order and incentive influence derivation of Conditional Perfection in two types of inducements (promises and threats). Both experiments are designed as inference tasks, additionally measuring reaction times to inferences. The paper shows that the derivation of Conditional Perfection is endorsed in both types of inducements. However, the negative consequent bias (i.e. higher rates of Conditional Perfection in conditionals with a negative consequent than in conditionals with an affirmative consequent) and the double negation effect (i.e. slowdown of reaction times to Conditional Perfection with a double negation in a consequent) hold for threats, but not for promises. The paper also reveals a parallel double negation effect (i.e. facilitation of Conditional Perfection in conditionals with negation in both clauses) in threats, but not in promises. Last but not least, the paper demonstrates that the effect of clause order and incentive on the derivation of Conditional Perfection is rather moderate. The paper supports the view that the derivation of Conditional Perfection is not effortful (Van Tiel and Schaeken in Cogn Sci 41:1119-1154, 2016) and has some indirect arguments for treating Conditional Perfection and scalar implicatures as separate phenomena.
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Inferences from the negation of counterfactual and semifactual conditionals. Mem Cognit 2021; 50:1090-1102. [PMID: 34846638 PMCID: PMC8631256 DOI: 10.3758/s13421-021-01252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2021] [Indexed: 11/24/2022]
Abstract
Our goal was to study how people understand the negation of counterfactuals (such as “Antonio denied/said that it is false that if Messi had played, then Barcelona would have won”) and semifactuals (such as “Antonio denied that even if Messi had played, Barcelona would have won”). Previous studies have shown that participants negated basic conditionals using small-scope interpretations by endorsing a new conditional with the negated consequent, but also by making large-scope interpretations, endorsing a conjunction with the negated consequent. Three experiments showed that when participants were asked whether the negation of a counterfactual (Experiments 1 and 2) or semifactual (Experiment 3) conditional was followed by a new conditional, they made a small-scope interpretation, endorsing the same conditional with the negated consequent (e.g., “if/even if Messi had played, Barcelona would not have won”). However, they also accepted the conditional with the negated antecedent for semifactuals (e.g., “even if Messi had not played, Barcelona would have won”). When participants were asked whether the negation of a counterfactual or semifactual conditional is followed by a conjunction, they endorsed the conjunction with both the negated antecedent and the consequent (e.g., “Messi did not play and Barcelona did not win”), but again they accepted the conjunction with the negated antecedent only for semifactuals (e.g., “Messi did not play and Barcelona did win”). These results have implications for the main theories of reasoning.
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Deduction with uncertain conditionals (revised & simplified, with examples). Heliyon 2021; 7:e08328. [PMID: 34816036 PMCID: PMC8593440 DOI: 10.1016/j.heliyon.2021.e08328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/19/2021] [Accepted: 11/02/2021] [Indexed: 11/23/2022] Open
Abstract
Section 1 of this paper provides an introduction to this new “algebra of conditionals”, addresses various plausibility tests for such an algebra, provides a Venn diagram disproving a supposed counter-example, and answers various other objections raised in the literature about the efficacy of this algebraic extension of logic and conditional probability. Section 2 greatly simplifies the calculation of the implications of a set of conditional propositions or conditional events. These results depend on defining a deductive relation for conditionals (actually two have been found) with the property that the conjunction of two conditionals implies each of its components. That seemingly innocuous property assures that the deductively closed set implied by a finite set of n conditionals with respect to the deductive relation is implied by the single conditional formed by conjoining all n of them. The results are illustrated by solving several examples of deduction with several uncertain conditionals.
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PC-GAIN: Pseudo-label conditional generative adversarial imputation networks for incomplete data. Neural Netw 2021; 141:395-403. [PMID: 34139636 DOI: 10.1016/j.neunet.2021.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/24/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Datasets with missing values are very common in real world applications. GAIN, a recently proposed deep generative model for missing data imputation, has been proved to outperform many state-of-the-art methods. But GAIN only uses a reconstruction loss in the generator to minimize the imputation error of the non-missing part, ignoring the potential category information which can reflect the relationship between samples. In this paper, we propose a novel unsupervised missing data imputation method named PC-GAIN, which utilizes potential category information to further enhance the imputation power. Specifically, we first propose a pre-training procedure to learn potential category information contained in a subset of low-missing-rate data. Then an auxiliary classifier is determined using the synthetic pseudo-labels. Further, this classifier is incorporated into the generative adversarial framework to help the generator to yield higher quality imputation results. The proposed method can improve the imputation quality of GAIN significantly. Experimental results on various benchmark datasets show that our method is also superior to other baseline approaches. Our code is available at https://github.com/WYu-Feng/pc-gain.
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Combination gene therapy for HIV using a conditional suicidal gene with CCR5 knockout. Virol J 2021; 18:31. [PMID: 33516234 PMCID: PMC7847599 DOI: 10.1186/s12985-021-01501-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene therapy approaches using hematopoietic stem cells to generate an HIV resistant immune system have been shown to be successful. The deletion of HIV co-receptor CCR5 remains a viable strategy although co-receptor switching to CXCR4 remains a major pitfall. To overcome this, we designed a dual gene therapy strategy that incorporates a conditional suicide gene and CCR5 knockout (KO) to overcome the limitations of CCR5 KO alone. METHODS A two-vector system was designed that included an integrating lentiviral vector that expresses a HIV Tat dependent Thymidine Kinase mutant SR39 (TK-SR39) and GFP reporter gene. The second non-integrating lentiviral (NIL) vector expresses a CCR5gRNA-CRISPR/Cas9 cassette and HIV Tat protein. RESULTS Transduction of cells sequentially with the integrating followed by the NIL vector allows for insertion of the conditional suicide gene, KO of CCR5 and transient expression of GFP to enrich the modified cells. We used this strategy to modify TZM cells and generate a cell line that was resistant to CCR5 tropic viruses while permitting infection of CXCR4 tropic viruses which could be controlled via treatment with Ganciclovir. CONCLUSIONS Our study demonstrates proof of principle that a combination gene therapy for HIV is a viable strategy and can overcome the limitation of editing CCR5 gene alone.
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Failure of SCS MR- Conditional Modes Due to High Impedance: A Review of Literature and Case Series. Pain Ther 2020; 10:729-737. [PMID: 33219927 PMCID: PMC8119585 DOI: 10.1007/s40122-020-00219-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/13/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction Magnetic resonance imaging (MRI) conditional modes are a novel feature for certain Food and Drug Administration (FDA)-approved spinal cord stimulation (SCS) devices. However, there is a paucity of literature around the limitation of MRI-conditional modes (“MRI safe”), specifically in clinical scenarios where urgent MRIs may be needed. One such limitation is load impedance, referring to the circuit’s resistance to the current being generated by the system. High impedance can limit the MRI-conditional mode capability, presenting potential harm to a patient undergoing an MRI or make an MRI unable to be completed. Methods Three cases were identified, and informed consent was obtained. All information was obtained via retrospective chart review. Results In this case series of three patients where MRI-conditional SCS systems were unable to be placed in “MRI safe” settings, preventing timely MRI study completion in the setting of high impedance, all three were required to undergo alternative imaging including CT scans, and two patients ultimately had the system explanted and one chose to be re-implanted after completion of scans. Conclusion This case series highlights the need for further investigation of impedance in SCS systems and potential limitations for future MRI usage. The review of literature of impedance in SCS shows both device- and physiologic-related etiologies for changes in impedance that warrant consideration by the implanting physician.
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The Role of Regulator-Imposed Post-Approval Studies in Health Technology Assessments for Conditionally Approved Drugs. Int J Health Policy Manag 2020; 11:642-650. [PMID: 33131224 PMCID: PMC9309934 DOI: 10.34172/ijhpm.2020.198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/04/2020] [Indexed: 11/09/2022] Open
Abstract
Background: The European Medicines Agency (EMA) aims to resolve uncertainties associated with conditionally approved drugs by imposing post-approval studies. Results from these studies may be relevant for health technology assessment (HTA) organizations. This study investigated the role of regulator-imposed post-approval studies within HTA. Methods: For all conditionally approved drugs up to December 2018, regulator-imposed post-approval studies were identified from EMA’s public assessment reports. The availability for and inclusion of study results in relative effectiveness (re)assessments were analyzed for 4 European HTA organizations: NICE (National Institute for Health and Care Excellence, England/Wales), HAS (Haute Autorité de Santé, France), ZIN (Zorginstituut Nederland, the Netherlands) and the European Network for Health Technology Assessment (EUnetHTA, Europe). When study results became available between an HTA organization’s initial assessment and reassessment, it was evaluated whether and how they affected the assessment and its outcome.
Results: For 36 conditionally approved drugs, 98 post-approval studies were imposed. In total, 81 initial relative effectiveness assessments (REAs) and 13 reassessments were available, with numbers of drugs (re)assessed varying greatly between jurisdictions. Study results were available for 16 initial REAs (20%) and included in 14 (88%), and available for 10 reassessments (77%) and included in all (100%). Five reassessments had an outcome different from the initial REA, with 4 (2 positive and 2 negative changes) relating directly to the new study results. Reassessments often cited the inability of post-approval studies to resolve the concerns reported in the initial REA.
Conclusion: Results from regulator-imposed post-approval studies for conditionally approved drugs were not often used in REAs by HTA organizations, because they were often not yet available at the time of initial assessment and because reassessments were scarce. When available, results from post-approval studies were almost always used within HTA, and they have led to changes in conclusions about drugs’ relative effectiveness. Post-approval studies can be relevant within HTA but the current lack of alignment between regulators and HTA organizations limits their potential.
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Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein. Methods 2020; 191:87-94. [PMID: 32717290 DOI: 10.1016/j.ymeth.2020.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
Cre-loxP recombination system is a powerful tool for genome engineering. One of its applications is found in genetic mouse models that often require to induce Cre recombination in preimplantation embryos. Here, we describe a technically simple, affordable and highly efficient protocol for Cre protein delivery into mouse zygotes by electroporation. We show that electroporation based delivery of Cre has no negative impact on embryo survival and the method can be easily combined with in vitro fertilization resulting in a significantly faster generation of desired models. Lastly, we demonstrate that Cre protein electroporation is suitable for allelic conversion in primary cells derived from conditional mouse models.
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An operational approach to the execution of MR examinations in patients with CIED. Radiol Med 2020; 125:1311-1321. [PMID: 32367321 DOI: 10.1007/s11547-020-01206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 04/16/2020] [Indexed: 10/24/2022]
Abstract
In the context of the increasing spread of cardiac active implantable heart devices (CIEDs) in the population and of the wide diagnostic/therapeutic utility of magnetic resonance (MRI) examinations, the goal of this paper is to provide the experience of the Santa Maria Nuova Hospital of the USL Tuscany Center in Florence and to report an organizational proposal to perform, in the hospital settings, MRI examinations on patients carrying CIED. This report is intended to show the operational choices of a Radiology Department which organizes this activity in accordance with the new Italian regulatory framework in the field of safety of MR sites (Ministero della Salute in Decreto Ministeriale 10 agosto 2018 Determinazione degli standard di sicurezza e impiego per le apparecchiature a risonanza magnetica, 2018).
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A long-term conditional survival analysis for gastric cancer based on 7th and 8th TNM classification in Eastern and Western populations. Eur J Surg Oncol 2018; 44:1949-1954. [PMID: 30197165 DOI: 10.1016/j.ejso.2018.07.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/01/2018] [Accepted: 07/23/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND To compare the power to predict the 5-year conditional disease-specific survival (CS5) between the 7th and 8th editions of the TNM for gastric cancer (GC) patients. METHOD This retrospective study recruited 20,548 patients who underwent GC surgery from the databases of the Surveillance, Epidemiology, End Results and a center in Asia. The CS5 was evaluated with the 7th and 8th TNM classification. RESULTS A two-step model showed that at the 3-5th postoperative years, the 8th staging remained an independent risk factor, whereas there was no significant difference for 7th -edition staging. Further analysis of the ability to predict CS5 indicated that there were significant differences in the CS5 of 7th -edition stages IIb and IIIa at baseline and at the postoperative 1-4th years (all p < 0.05, Cohen's d > 0.5). However, the CS5 of the fifth year was similar between them (p = 0.307, Cohen's d = 0.35). Meanwhile, the results indicated that the 8th -edition staging could effectively determine the CS5 among stages Ⅰa, Ⅰb, Ⅱa, Ⅱb, Ⅲa, and Ⅲb at baseline and at the postoperative 1-5th years (all p < 0.05). However, neither the 7th - nor the 8th -edition staging could predict the CS5 for stages Ⅲb and Ⅲc from the postoperative third to fifth years (all p > 0.05). CONCLUSIONS For patients with stages IIB and IIIA GC, the 8th TNM has a higher discriminatory value than the 7th edition for CS5 after the postoperative fourth year. However, a more detailed classification system is still needed to predict conditional survival for GC.
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Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants. BMC Biol 2018; 16:70. [PMID: 29925374 PMCID: PMC6011369 DOI: 10.1186/s12915-018-0530-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/22/2023] Open
Abstract
Background Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method. Results We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. We observed that the use of lssDNA molecules as donors efficiently yielded founders bearing the conditional allele, with seven out of nine projects giving rise to modified alleles. However, rearranged alleles including nucleotide changes, indels, local rearrangements and additional integrations were also frequently generated by this method. Specifically, we found that alleles containing unexpected point mutations were found in three of the nine projects analyzed. Alleles originating from illegitimate repairs or partial integration of the donor were detected in eight projects. Furthermore, additional integrations of donor molecules were identified in four out of the seven projects analyzed by copy counting. This highlighted the requirement for a thorough allele validation by polymerase chain reaction, sequencing and copy counting of the mice generated through this method. We also demonstrated the feasibility of using lssDNA donors to generate thus far problematic point mutations distant from active CRISPR cutting sites by targeting two distinct genes (Gckr and Rims1). We propose a strategy to perform extensive quality control and validation of both types of mouse models generated using lssDNA donors. Conclusion lssDNA donors reproducibly generate conditional alleles and can be used to introduce point mutations away from CRISPR/Cas9 cutting sites in mice. However, our work demonstrates that thorough quality control of new models is essential prior to reliably experimenting with mice generated by this method. These advances in genome editing techniques shift the challenge of mutagenesis from generation to the validation of new mutant models. Electronic supplementary material The online version of this article (10.1186/s12915-018-0530-7) contains supplementary material, which is available to authorized users.
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Modulation of Myeloid Cell Function Using Conditional and Inducible Transgenic Approaches. Methods Mol Biol 2018; 1809:145-168. [PMID: 29987790 DOI: 10.1007/978-1-4939-8570-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transgenic mice have emerged as a central tool in the study of lung myeloid cells during homeostasis and disease. The use of Cre/Lox site-specific recombination allows for conditional deletion of a gene of interest in a spatially controlled manner. The basic Cre/Lox system can be further refined to include an inducible trigger, enabling conditional deletion of a gene of interest in a spatially and temporally controlled manner. Here we provide an overview of commercially available conditional and inducible conditional mouse strains that target lung myeloid cells and describe the appropriate breeding schemes and controls for transgenic animal systems that can be used to modulate myeloid cell function.
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Probability in reasoning: a developmental test on conditionals. Cognition 2015; 137:22-39. [PMID: 25590946 DOI: 10.1016/j.cognition.2014.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
Abstract
Probabilistic theories have been claimed to constitute a new paradigm for the psychology of reasoning. A key assumption of these theories is captured by what they call the Equation, the hypothesis that the meaning of the conditional is probabilistic in nature and that the probability of If p then q is the conditional probability, in such a way that P(if p then q)=P(q|p). Using the probabilistic truth-table task in which participants are required to evaluate the probability of If p then q sentences, the present study explored the pervasiveness of the Equation through ages (from early adolescence to adulthood), types of conditionals (basic, causal, and inducements) and contents. The results reveal that the Equation is a late developmental achievement only endorsed by a narrow majority of educated adults for certain types of conditionals depending on the content they involve. Age-related changes in evaluating the probability of all the conditionals studied closely mirror the development of truth-value judgements observed in previous studies with traditional truth-table tasks. We argue that our modified mental model theory can account for this development, and hence for the findings related with the probability task, which do not consequently support the probabilistic approach of human reasoning over alternative theories.
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Slc26a4-insufficiency causes fluctuating hearing loss and stria vascularis dysfunction. Neurobiol Dis 2014; 66:53-65. [PMID: 24561068 DOI: 10.1016/j.nbd.2014.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/03/2014] [Accepted: 02/10/2014] [Indexed: 12/13/2022] Open
Abstract
SLC26A4 mutations can cause a distinctive hearing loss phenotype with sudden drops and fluctuation in patients. Existing Slc26a4 mutant mouse lines have a profound loss of hearing and vestibular function, with severe inner ear malformations that do not model this human phenotype. In this study, we generated Slc26a4-insufficient mice by manipulation of doxycycline administration to a transgenic mouse line in which all Slc26a4 expression was under the control of doxycycline. Doxycycline was administered from conception to embryonic day 17.5, and then it was discontinued. Auditory brainstem response thresholds showed significant fluctuation of hearing loss from 1 through 3months of age. The endocochlear potential, which is required for inner ear sensory cell function, correlated with auditory brainstem response thresholds. We observed degeneration of stria vascularis intermediate cells, the cells that generate the endocochlear potential, but no other abnormalities within the cochlea. We conclude that fluctuations of hearing result from fluctuations of the endocochlear potential and stria vascularis dysfunction in Slc26a4-insufficient mouse ears. This model can now be used to test potential interventions to reduce or prevent sudden hearing loss or fluctuation in human patients. Our strategy to generate a hypomorphic mouse model utilizing the tet-on system will be applicable to other diseases in which a hypomorphic allele is needed to model the human phenotype.
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Abstract
The endolysosomal system and autophagy are essential components of macromolecular turnover in eukaryotic cells. The low-abundance signaling lipid PI(3,5)P2 is a key regulator of this pathway. Analysis of mouse models with defects in PI(3,5)P2 biosynthesis has revealed the unique dependence of the mammalian nervous system on this signaling pathway. This insight led to the discovery of the molecular basis for several human neurological disorders, including Charcot-Marie-Tooth disease and Yunis-Varon syndrome. Spontaneous mutants, conditional knockouts, transgenic lines, and gene-trap alleles of Fig4, Vac14, and Pikfyve (Fab1) in the mouse have provided novel information regarding the role of PI(3,5)P2in vivo. This review summarizes what has been learned from mouse models and highlights the utility of manipulating complex signaling pathways in vivo.
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The compatibility heuristic in non-categorical hypothetical reasoning: inferences between conditionals and disjunctions. Cogn Psychol 2013; 67:98-129. [PMID: 23968595 DOI: 10.1016/j.cogpsych.2013.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/30/2022]
Abstract
A new theory explains how people make hypothetical inferences from a premise consistent with several alternatives to a conclusion consistent with several alternatives. The key proposal is that people rely on a heuristic that identifies compatible possibilities. It is tested in 7 experiments that examine inferences between conditionals and disjunctions. Participants accepted inferences between conditionals and inclusive disjunctions when a compatible possibility was immediately available, in their binary judgments that a conclusion followed or not (Experiment 1a) and ternary judgments that included it was not possible to know (Experiment 1b). The compatibility effect was amplified when compatible possibilities were more readily available, e.g., for 'A only if B' conditionals (Experiment 2). It was eliminated when compatible possibilities were not available, e.g., for 'if and only if A B' bi-conditionals and exclusive disjunctions (Experiment 3). The compatibility heuristic occurs even for inferences based on implicit negation e.g., 'A or B, therefore if C D' (Experiment 4), and between universals 'All A's are B's' and disjunctions (Experiment 5a) and universals and conditionals (Experiment 5b). The implications of the results for alternative theories of the cognitive processes underlying hypothetical deductions are discussed.
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Glial A30P alpha-synuclein pathology segregates neurogenesis from anxiety-related behavior in conditional transgenic mice. Neurobiol Dis 2013; 59:38-51. [PMID: 23867236 DOI: 10.1016/j.nbd.2013.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/23/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Abstract
In Parkinson's disease (PD) patients, alpha-synuclein (α-syn) pathology advances in form of Lewy bodies and Lewy neurites throughout the brain. Clinically, PD is defined by motor symptoms that are predominantly attributed to the dopaminergic cell loss in the substantia nigra. However, motor deficits are frequently preceded by smell deficiency or neuropsychological symptoms, including increased anxiety and cognitive dysfunction. Accumulating evidence indicates that aggregation of α-syn impairs synaptic function and neurogenic capacity that may be associated with deficits in memory, learning and mood. Whether and how α-syn accumulation contributes to neuropathological events defining these earliest signs of PD is presently poorly understood. We used a tetracycline-suppressive (tet-off) transgenic mouse model that restricts overexpression of human A30P α-syn to neurons owing to usage of the neuron-specific CaMKIIα promoter. Abnormal accumulation of A30P correlated with a decreased survival of newly generated neurons in the hippocampus and olfactory bulb. Furthermore, when A30P α-syn expression was suppressed, we observed reduction of the human protein in neuronal soma. However, residual dox resistant A30P α-syn was detected in glial cells within the hippocampal neurogenic niche, concomitant with the failure to fully restore hippocampal neurogenesis. This finding is indicative to a potential spread of pathology from neuron to glia. In addition, mice expressing A30P α-syn show increased anxiety-related behavior that was reversed after dox treatment. This implies that glial A30P α-synucleinopathy within the dentate gyrus is part of a process leading to impaired hippocampal neuroplasticity, which is, however, not a sole critical event for circuits implicated in anxiety-related behavior.
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