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The dating of organic findings is a fundamental task for many scientific fields. Radiocarbon dating is currently the most commonly used method. For wood, dendrochronology is another state‐of‐the‐art method. Both methods suffer from systematic restrictions, leading to samples that have not yet been able to be dated. Molecular changes over time are reported for many materials under different preservation conditions. Many of them are intrinsically monotonous. These monotonous molecular decay (MD) patterns can be understood as clocks that start at the time when a given molecule was formed. Factors that influence these clocks include input material composition and preservation conditions. Different wood species, degrees of pyrolysis, and pretreatments lead to different prediction models. Preservation conditions might change the speed of a given clock and lead to different prediction models. Currently published models for predicting the age of wood, paper, and parchment depend on infrared spectroscopy. In contrast to radiocarbon dating, dating via MD does not comprise a single methodology. Some clocks may deliver less precise results than the others. Ultimately, developing a completely different, new dating strategy‐such as MD dating–will help to bring to light a treasure trove of information hidden in the darkness of organic findings., This review focuses on molecular changes over time. Having been discussed since the 1960s, the variety of molecular clocks includes the change in amino acids in the primary structure of a protein over time. Molecular decay (MD) has a mainly monotonous function, a prerequisite to serving as such a clock. In addition, such clocks need a defined starting point and a defined decay function. In contrast to the decay of alpha and beta emitters, MD is influenced by several environmental factors indicated by preservation conditions. The MD method has the potential to be used for different organic materials and different scientific fields.

Sodium alginate beads were used as a carrier to immobilize a previously reported extracellular xylanase from Bacillus subtilis Lucky9 expressed in Escherichia coli. The optimal pH and the activity of the immobilized enzyme were increased at optimal temperature compared with the free enzyme. Our results suggest that the immobilized xylanase has potential applications in the biobleaching industry., In the paper industry, chlorine is often used to treat the pulp for bleaching. After pulping, a large amount of xylan is present in the fiber. Xylanase can be used to degrade xylan in an eco‐friendly process called biobleaching, which can help minimize the usage of chlorine in the delignification process. However, a bottleneck in the adoption of biobleaching is the cost of xylanase and the requirement that xylanase be active and stable at extreme conditions. Here, we investigated whether using sodium alginate beads to immobilize an extracellular xylanase from Bacillus subtilis (Lucky9) can reduce the potential cost of enzyme usage. The optimal pH and the activity of the immobilized enzyme were increased at optimal temperature compared with the free enzyme. In addition, immobilized xylanase was shown to be more stable than free xylanase. The results of this study suggest that the immobilized xylanase has potential applications in the biobleaching industry.

Surface functionalization strategies of synthetic materials for regenerative medicine applications comprise the development of microenvironments that recapitulate the physical and biochemical cues of physiological extracellular matrices. In this context, material-driven fibronectin (FN) nanonetworks obtained from the adsorption of the protein on poly(ethyl acrylate) provide a robust system to control cell behavior, particularly to enhance differentiation. This study aims at augmenting the complexity of these fibrillar matrices by introducing vitronectin, a lower-molecular-weight multifunctional glycoprotein and main adhesive component of serum. A cooperative effect during co-adsorption of the proteins is observed, as the addition of vitronectin leads to increased fibronectin adsorption, improved fibril formation, and enhanced vitronectin exposure. The mobility of the protein at the material interface increases, and this, in turn, facilitates the reorganization of the adsorbed FN by cells. Furthermore, the interplay between interface mobility and engagement of vitronectin receptors controls the level of cell fusion and the degree of cell differentiation. Ultimately, this work reveals that substrate-induced protein interfaces resulting from the cooperative adsorption of fibronectin and vitronectin fine-tune cell behavior, as vitronectin micromanages the local properties of the microenvironment and consequently short-term cell response to the protein interface and higher order cellular functions such as differentiation.

This paper is the third in a five-part series on the clinical and translational science educational pipeline, and it focuses on strategies for enhancing graduate research education to improve skills for interdisciplinary team science. Although some of the most cutting edge science takes place at the borders between disciplines, it is widely perceived that advancements in clinical and translational science are hindered by the "siloed" efforts of researchers who are comfortable working in their separate domains, and reluctant to stray from their own discipline when conducting research. Without appropriate preparation for career success as members and leaders of interdisciplinary teams, talented scientists may choose to remain siloed or to leave careers in clinical and translational science all together, weakening the pipeline and depleting the future biomedical research workforce. To address this threat, it is critical to begin at what is perhaps the most formative moment for academics: graduate training. This paper focuses on designs for graduate education, and contrasts the methods and outcomes from traditional educational approaches with those skills perceived as essential for the workforce of the future, including the capacity for research collaboration that crosses disciplinary boundaries.

Small study effects occur when smaller studies show different, often larger, treatment effects than large ones, which may threaten the validity of systematic reviews and meta-analyses. The most well-known reasons for small study effects include publication bias, outcome reporting bias, and clinical heterogeneity. Methods to account for small study effects in univariate meta-analysis have been extensively studied. However, detecting small study effects in a multivariate meta-analysis setting remains an untouched research area. One of the complications is that different types of selection processes can be involved in the reporting of multivariate outcomes. For example, some studies may be completely unpublished while others may selectively report multiple outcomes. In this paper, we propose a score test as an overall test of small study effects in multivariate meta-analysis. Two detailed case studies are given to demonstrate the advantage of the proposed test over various naive applications of univariate tests in practice. Through simulation studies, the proposed test is found to retain nominal Type I error rates with considerable power in moderate sample size settings. Finally, we also evaluate the concordance between the proposed tests with the naive application of univariate tests by evaluating 44 systematic reviews with multiple outcomes from the Cochrane Database.

Pragmatic clinical trials (PCTs) have an established presence in clinical research and yet have only recently garnered attention within the landscape of genomic medicine. Using the PRagmatic‐Explanatory Continuum Indicator Summary 2 (PRECIS‐2) as a framework, this paper illustrates the application of PCT principles to The Integrating Pharmacogenetics In Clinical Care (I‐PICC) Study, a trial of pharmacogenetic testing prior to statin initiation for cardiovascular disease prevention in primary care. The trial achieved high engagement with providers (85% enrolled of those approached) and enrolled a representative sample of participants for which statin therapy would be recommended. The I‐PICC Study has a high level of pragmatism, which should enhance the generalizability of its findings. The PRECIS‐2 may be useful in the design and evaluation of PCTs of genomic medicine interventions, contributing to the generation of evidence that can bridge the gap between genomics innovation and clinical adoption.

Meeting children's vitamin A (VA) needs remains a policy priority. Doing so efficiently is a fiscal imperative and protecting at‐risk children during policy transitions is a moral imperative. Using the Micronutrient Intervention Modeling tool and data for Cameroon, we predict the impacts and costs of alternative VA intervention programs, identify the least‐cost strategy for meeting targets nationally, and compare it to a business‐as‐usual (BAU) strategy over 10 years. BAU programs effectively cover ∼12.8 million (m) child‐years (CY) and cost ∼$30.1 m; ∼US$2.34 per CY effectively covered. Improving the VA‐fortified oil program, implementing a VA‐fortified bouillon cube program, and periodic VA supplements (VAS) in the North macroregion for 3 years effectively cover ∼13.1 m CY at a cost of ∼US$9.5 m, or ∼US$0.71 per CY effectively covered. The tool then identifies a sequence of subnational policy choices leading from the BAU toward the more efficient strategy, while addressing VA‐attributable mortality concerns. By year 4, fortification programs are predicted to eliminate inadequate VA intake in the South and Cities macroregions, but not the North, where VAS should continue until additional delivery platforms are implemented. This modeling approach offers a concrete example of the strategic use of data to follow the Global Alliance for VA framework and do so efficiently., The objectives of this paper are to apply the Micronutrient Intervention Modeling tool to: update the model with a revised set of vitamin A (VA) intervention programs and data to support them, and identify concrete subnational policy pathways (sequences of VA program modifications) in Cameroon, which are guided by the Global Alliance for Vitamin A framework.

The number of new infections per day is a key quantity for effective epidemic management. It can be estimated relatively directly by testing of random population samples. Without such direct epidemiological measurement, other approaches are required to infer whether the number of new cases is likely to be increasing or decreasing: for example, estimating the pathogen effective reproduction number, R, using data gathered from the clinical response to the disease. For Covid-19 (SARS-CoV-2) such R estimation is heavily dependent on modelling assumptions, because the available clinical case data are opportunistic observational data subject to severe temporal confounding. Given this difficulty it is useful to retrospectively reconstruct the time course of infections from the least compromised available data, using minimal prior assumptions. A Bayesian inverse problem approach applied to UK data on first wave Covid-19 deaths and the disease duration distribution suggests that fatal infections were in decline before full UK lockdown (24 March 2020), and that fatal infections in Sweden started to decline only a day or two later. An analysis of UK data using the model of Flaxman et al. (2020, Nature 584) gives the same result under relaxation of its prior assumptions on R, suggesting an enhanced role for non pharmaceutical interventions (NPIs) short of full lock down in the UK context. Similar patterns appear to have occurred in the subsequent two lockdowns. Estimates from the main UK Covid statistical surveillance surveys, available since original publication, support these results. Replication code for the paper is available in the supporting information of doi/10.1111/biom.13462., Comment: Gives the location of the replication code and corrects an accidental deletion in the first line of the conclusions

We propose a novel response‐adaptive randomization procedure for multi‐armed trials with continuous outcomes that are assumed to be normally distributed. Our proposed rule is non‐myopic, and oriented toward a patient benefit objective, yet maintains computational feasibility. We derive our response‐adaptive algorithm based on the Gittins index for the multi‐armed bandit problem, as a modification of the method first introduced in Villar et al. (Biometrics, 71, pp. 969‐978). The resulting procedure can be implemented under the assumption of both known or unknown variance. We illustrate the proposed procedure by simulations in the context of phase II cancer trials. Our results show that, in a multi‐armed setting, there are efficiency and patient benefit gains of using a response‐adaptive allocation procedure with a continuous endpoint instead of a binary one. These gains persist even if an anticipated low rate of missing data due to deaths, dropouts, or complete responses is imputed online through a procedure first introduced in this paper. Additionally, we discuss how there are response‐adaptive designs that outperform the traditional equal randomized design both in terms of efficiency and patient benefit measures in the multi‐armed trial context.

G protein–coupled receptors (GPCRs) are encoded by over 800 genes in the human genome. Motivated by different scientific rationales, the two classification systems that are mainly in use, the ABC and GRAFS systems, organize GPCRs according to their pharmacological features and phylogenetic relations, respectively. Within those systems, adhesion GPCRs (aGPCRs) constitute a group of over 30 mammalian homologs, most of which are still orphans with undefined activating signals and signal transduction properties. Previous efforts have further subdivided mammalian aGPCRs into nine subfamilies to indicate phylogenetic relationships. However, this subclassification scheme has shortcomings and inconsistencies that require attention. Here, we have reassessed the phylogenetic relationships of aGPCRs from vertebrate and invertebrate species. Our findings confirm that secretin receptor–like GPCRs most probably emerged from ancestral aGPCRs. We show that reassignment of several aGPCRs to families essentially requires input from functional data. Our analyses establish the need for introducing novel aGPCR subfamilies due to aGPCR sequences from invertebrate species that are not readily assignable to any existing subfamily. We conclude that the current classification systems ought to be updated to consider an unambiguous taxonomy of a hierarchically organized classification and pharmacological properties, and to accommodate phylogenetic affiliations between aGPCR genes within mammals and across the animal kingdom., The classification of adhesion G protein–coupled receptors (aGPCRs) into nine subfamilies according to existing systems for classifying GPCRs suffers from various shortcomings. This paper reassesses the phylogenetic relationships of aGPCRs from vertebrates and invertebrates and shows that reassignment of several aGPCRs to families essentially requires input from functional data, and that there is a need to introduce novel aGPCR subfamilies due to invertebrate aGPCRs that are not readily assignable to any existing subfamily.

The recently enacted Prescription Drug User Fee Act (PDUFA) VI includes in its performance goals "enhancing regulatory science and expediting drug development." The key elements in "enhancing regulatory decision tools to support drug development and review" include "advancing model-informed drug development (MIDD)." This paper describes (i) the US Food and Drug Administration (FDA) Office of Clinical Pharmacology's continuing efforts in developing quantitative clinical pharmacology models (disease, drug, and clinical trial models) to advance MIDD, (ii) how emerging novel tools, such as organ-on-a-chip technologies or microphysiological systems, can provide new insights into physiology and disease mechanisms, biomarker identification and evaluation, and elucidation of mechanisms of adverse drug reactions, and (iii) how the single organ or linked organ microphysiological systems can provide critical system parameters for improved physiologically-based pharmacokinetic and pharmacodynamic evaluations. Continuous public-private partnerships are critical to advance this field and in the application of these new technologies in drug development and regulatory review.

Electronic health records are valuable for clinical and translational research. Institutions must protect patient privacy and comply with applicable regulations while allowing appropriate access to clinical data for research. The processes that investigators must follow to access clinical data can be substantially different at different institutions. In this paper, we describe the process developed at our institution that has been active for 5 years and was used to satisfy over 200 requests for access to identified clinical data, usually within 1 day for internal requests and 3 days for visiting researchers.

The incubation period and generation time are key characteristics in the analysis of infectious diseases. The commonly used contact‐tracing based estimation of incubation distribution is highly influenced by the individuals' judgment on the possible date of exposure, and might lead to significant errors. On the other hand, interval censoring based methods are able to utilize a much larger set of traveling data but may encounter biased sampling problems. The distribution of generation time is usually approximated by observed serial intervals. However, it may result in a biased estimation of generation time, especially when the disease is infectious during incubation. In this paper, the theory from renewal process is partially adopted by considering the incubation period as the inter‐arrival time, and the duration between departure from Wuhan and onset of symptoms as the mixture of forward time and inter‐arrival time with censored intervals. In addition, a consistent estimator for the distribution of generation time based on incubation period and serial interval is proposed for incubation‐infectious diseases. A real case application to the current outbreak of COVID‐19 is implemented. We find that the incubation period has a median of 8.50 days (95% CI: 7.22, 9.15). The basic reproduction number in the early phase of COVID‐19 outbreak based on the proposed generation time estimation is estimated to be 2.96 (95% CI: 2.15, 3.86). This article is protected by copyright. All rights reserved

There is growing appreciation that process improvement holds promise for improving quality and efficiency across the translational research continuum but frameworks for such programs are not often described. The purpose of this paper is to present a framework and case examples of a Research Process Improvement Program implemented at Tufts CTSI. To promote research process improvement, we developed online training seminars, workshops, and in‐person consultation models to describe core process improvement principles and methods, demonstrate the use of improvement tools, and illustrate the application of these methods in case examples. We implemented these methods, as well as relational coordination theory, with junior researchers, pilot funding awardees, our CTRC, and CTSI resource and service providers. The program focuses on capacity building to address common process problems and quality gaps that threaten the efficient, timely and successful completion of clinical and translational studies.

To counteract damage to our genomes, numerous endo‐ and exonucleases incise the DNA backbone to remove damaged and aberrant DNA structures. It is imperative that such incisions be very tightly controlled, as unwanted DNA breaks are a key source of genome instability. Two new papers in The EMBO Journal shed light on how the activity of one such nuclease—ERCC1‐XPF, an enzyme involved in various DNA repair pathways—is regulated to perform incision in the vicinity of DNA interstrand crosslinks.

Depression might be associated with accelerated cellular aging. However, does this result in an irreversible state or is the body able to slow down or recover from such a process? Telomeres are DNA-protein complexes that protect the ends of chromosomes and generally shorten with age; and therefore index cellular aging. The majority of studies indicate that persons with depression have shorter leukocyte telomeres than similarly aged non-depressed persons, which may contribute to the observed unfavorable somatic health outcomes in the depressed population. Some small-scale preliminary studies raise the possibility that behavioral or pharmacological interventions may either slow down or else reverse this accelerated telomere shortening, possibly through increasing the activity of the telomere-lengthening enzyme telomerase. This paper covers the current state of evidence in the relationship between depression and the telomere-telomerase system and debates whether depression-related cellular aging should be considered a reversible process or permanent damage.

Retraction of: The EMBO Journal DOI 10.15252/embj.201694284 | Published online 28.07.2016 The authors have requested retraction of the paper noting: ‘We found a mistake for the materials used …

Using peer learning strategies, seven experienced PBRNs working in collaborative teams articulated procedures for PBRN Research Good Practices (PRGPs). The PRGPs is a PBRN-specific resource to facilitate PBRN management and staff training, to promote adherence to study protocols, and to increase validity and generalizability of study findings. This paper describes the team science processes which culminated in the PRGPs. Skilled facilitators used team science strategies and methods from the Technology of Participation (ToP®), and the Consensus Workshop Method to support teams to codify diverse research expertise in practice-based research. The participatory nature of "sense-making" moved through identifiable stages. Lessons learned include (1) team input into the scope of the final outcome proved vital to project relevance; (2) PBRNs with diverse domains of research expertise contributed broad knowledge on each topic; and (3) ToP® structured facilitation techniques were critical for establishing trust and clarifying the "sense-making" process.