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Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
This study pushes our understanding of research reliability by reproducing and replicating claims from 110 papers in leading economic and political science journals. The analysis involves computational reproducibility checks and robustness assessments. It reveals several patterns. First, we uncover a high rate of fully computationally reproducible results (over 85%). Second, excluding minor issues like missing packages or broken pathways, we uncover coding errors for about 25% of studies, with some studies containing multiple errors. Third, we test the robustness of the results to 5,511 re-analyses. We find a robustness reproducibility of about 70%. Robustness reproducibility rates are relatively higher for re-analyses that introduce new data and lower for re-analyses that change the sample or the definition of the dependent variable. Fourth, 52% of re-analysis effect size estimates are smaller than the original published estimates and the average statistical significance of a re-analysis is 77% of the original. Lastly, we rely on six teams of researchers working independently to answer eight additional research questions on the determinants of robustness reproducibility. Most teams find a negative relationship between replicators' experience and reproducibility, while finding no relationship between reproducibility and the provision of intermediate or even raw data combined with the necessary cleaning codes.
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association signals (129 of which are novel). We used structural equation modeling to decompose the contributions of direct fetal and indirect maternal genetic effects, then applied Mendelian randomization to illuminate causal pathways. For example, both indirect maternal and direct fetal genetic effects drive the observational relationship between lower birth weight and higher later blood pressure: maternal blood pressure-raising alleles reduce offspring birth weight, but only direct fetal effects of these alleles, once inherited, increase later offspring blood pressure. Using maternal birth weight-lowering genotypes to proxy for an adverse intrauterine environment provided no evidence that it causally raises offspring blood pressure, indicating that the inverse birth weight-blood pressure association is attributable to genetic effects, and not to intrauterine programming.
Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.
Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.
Background: Physicians and therapists are also consulted to give judgments on working ability. Ability to work cannot simply be derived from the patient’s symptom status but from the illness-related capacity impairments in relation to the work demands. A structured assessment of capacity impairments has been evaluated and applied internationally: the Mini-ICF-APP Social Functioning Scale. It is currently unclear whether a free-text clinical report (i.e., usual clinical practice: clinical exploration according to clinical standards, but without a standardized documentation form, instead a text is written) and a structured capacity assessment correspond to the overall work ability judgment, i.e., the decision whether a patient is “fit for work” or “unfit for work.” Objectives: This investigation assessed, for the first time, whether usual clinical judgment and the additional structured capacity rating support the work ability decision. Methods: A total of 100 medical reports from patients in a psychotherapy hospital were excerpted for psychopathological symptoms and capacity disorders using a checklist. Additionally, a structured assessment of capacity disorders was documented on the Mini-ICF-APP rating for all patients. Results: In the free-text clinical medical report, endurance, flexibility, and contacts to others were the things mainly reported as impaired. This was similar to the structured Mini-ICF-APP rating. However, other capacity impairments were also reported in the Mini-ICF-APP, i.e., adherence to rules and regulations, planning and structuring, assertiveness, and group integration. When the free-text clinical report and the structured Mini-ICF-APP rating were compared, there was a higher rate of stated impairments covering all capacity dimensions in the Mini-ICF-APP rating. Conclusions: The free-text report in the medical report shows the differences between patients who are fit for work and those who are not, and thus speak for the validity of work ability decisions. However, optimization is possible in terms of depth and differentiation of capacity impairment description by adhering to the standard set by the Mini-ICF-APP.
Second harmonic generation (SHG) microscopy is employed to study changes in crystalline organization due to altered gene expression and hydration in barley starch granules. SHG intensity and susceptibility ratio values (R'(SHG)) are obtained using reduced Stokes-Mueller polarimetric microscopy. The maximum R'(SHG) values occur at moderate moisture indicating the narrowest orientation distribution of nonlinear dipoles from the cylindrical axis of glucan helices. The maximum SHG intensity occurs at the highest moisture and amylopectin content. These results support the hypothesis that SHG is caused by ordered hydrogen and hydroxyl bond networks which increase with hydration of starch granules. (C) 2015 Optical Society of America
Structuring overmany length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, showhow Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature's demonstration of howcrystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials.
The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop between MONOPTEROS-(ARF5)dependent auxin signalling and auxin transport. This MONOPTEROS dependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.
We present a Bayesian inference scheme for scaled Brownian motion, and investigate its performance on synthetic data for parameter estimation and model selection in a combined inference with fractional Brownian motion. We include the possibility of measurement noise in both models. We find that for trajectories of a few hundred time points the procedure is able to resolve well the true model and parameters. Using the prior of the synthetic data generation process also for the inference, the approach is optimal based on decision theory. We include a comparison with inference using a prior different from the data generating one.
Acid sphingomyelinase mediates murine acute lung injury following transfusion of aged platelets
(2017)
Pulmonary complications from stored blood products are the leading cause of mortality related to transfusion. Transfusion-related acute lung injury is mediated by antibodies or bioactive mediators, yet underlying mechanisms are incompletely understood. Sphingolipids such as ceramide regulate lung injury, and their composition changes as a function of time in stored blood. Here, we tested the hypothesis that aged platelets may induce lung injury via a sphingolipid-mediated mechanism. To assess this hypothesis, a two-hit mouse model was devised. Recipient mice were treated with 2 mg/kg intraperitoneal lipopolysaccharide (priming) 2 h before transfusion of 10 ml/kg stored (1-5 days) platelets treated with or without addition of acid sphingomyelinase inhibitor ARC39 or platelets from acid sphingomyelinase-deficient mice, which both reduce ceramide formation. Transfused mice were examined for signs of pulmonary neutrophil accumulation, endothelial barrier dysfunction, and histological evidence of lung injury. Sphingolipid profiles in stored platelets were analyzed by mass spectrophotometry. Transfusion of aged platelets into primed mice induced characteristic features of lung injury, which increased in severity as a function of storage time. Ceramide accumulated in platelets during storage, but this was attenuated by ARC39 or in acid sphingomyelinase-deficient platelets. Compared with wild-type platelets, transfusion of ARC39-treated or acid sphingomyelinase-deficient aged platelets alleviated lung injury. Aged platelets elicit lung injury in primed recipient mice, which can be alleviated by pharmacological inhibition or genetic deletion of acid sphingomyelinase. Interventions targeting sphingolipid formation represent a promising strategy to increase the safety and longevity of stored blood products.
Recently, glasses, a subset of amorphous solids, have gained attention in various fields, such as polymer chemistry, optical fibers, and pharmaceuticals. One of their characteristic features, the glass transition temperature (T-g) which is absent in 100% crystalline materials, influences several material properties, such as free volume, enthalpy, viscosity, thermodynamic transitions, molecular motions, physical stability, mechanical properties, etc. In addition to T-g, there may be several other temperaturedependent transitions known as sub-T-g transitions (or beta-, gamma-, and delta-relaxations) which are identified by specific analytical techniques. The study of T-g and sub-T-g transitions occurring in amorphous solids has gained much attention because of its importance in understanding molecular kinetics, and it requires the combination of conventional and novel characterization techniques. In the present study, three different analytical techniques [modulated differential scanning calorimetry (mDSC), dynamic mechanical analysis (DMA), and dielectric relaxation spectroscopy (DRS)] were used to perform comprehensive qualitative/quantitative characterization of molecular relaxations, miscibility, and molecular interactions present in an amorphous polymer (PVPVA), a model drug (indomethacin, IND), and IND/PVPVA-based amorphous solid dispersions (ASDs). This is the first ever reported DMA study on PVPVA in its powder form, which avoids the contribution of solvent to the mechanical properties when a selfstanding polymer film is used. A good correlation between the techniques in determining the T-g value of PVPVA, IND, and IND/ PVPVA-based ASDs is established, and the negligible difference (within 10 degrees C) is attributed to the different material properties assessed in each technique. However, the overall T-g behavior, the decrease in T-g with increase in drug loading in ASDs, is universally observed in all the above-mentioned techniques, which reveals their complementarity. DMA and DRS techniques are used to study the different sub-T-g transitions present in PVPVA, amorphous IND, and IND/PVPVA-based ASDs because these transitions are normally too weak or too broad for mDSC to detect. For IND/PVPVA-based ASDs, both techniques show a shift of sub-T-g transitions (or secondary relaxation peaks) toward the high-temperature region from -140 to -45 degrees C. Thus, this paper outlines the usage of different solid-state characterization techniques in understanding the different molecular dynamics present in the polymer, drug, and their interactions in ASDs with the integrated information obtained from individual techniques.
Effects of exercise treatment on functional outcome parameters in mid-portion achilles tendinopathy
(2023)
Exercise interventions are evident in the treatment of mid-portion Achilles tendinopathy (AT). However, there is still a lack of knowledge concerning the effect of different exercise treatments on improving a specific function (e.g., strength) in this population. Thus, this study aimed to systematically review the effect of exercise treatments on different functional outcomes in mid-portion AT. An electronic database of Pubmed, Web of Science, and Cochrane Central Register of Controlled Trials were searched from inception to 21 February 2023. Studies that investigated changes in plantar flexor function with exercise treatments were considered in mid-portion AT. Only randomized controlled trials (RCTs) and clinical controlled trials (CCTs) were included. Functional outcomes were classified by kinetic (e.g., strength), kinematic [e.g., ankle range of motion (ROM)], and sensorimotor (e.g., balance index) parameters. The types of exercise treatments were classified into eccentric, concentric, and combined (eccentric plus concentric) training modes. Quality assessment was appraised using the Physiotherapy Evidence Database scale for RCTs, and the Joanna Briggs Institute scale for CCTs. The search yielded 2,260 records, and a total of ten studies were included. Due to the heterogeneity of the included studies, a qualitative synthesis was performed. Eccentric training led to improvements in power outcomes (e.g., height of countermovement jump), and in strength outcomes (e.g., peak torque). Concentric training regimens showed moderate enhanced power outcomes. Moreover, one high-quality study showed an improvement in the balance index by eccentric training, whereas the application of concentric training did not. Combined training modalities did not lead to improvements in strength and power outcomes. Plantarflexion and dorsiflexion ROM measures did not show relevant changes by the exercise treatments. In conclusion, eccentric training is evident in improving strength outcomes in AT patients. Moreover, it shows moderate evidence improvements in power and the sensorimotor parameter "balance index". Concentric training presents moderate evidence in the power outcomes and can therefore be considered as an alternative to improve this function. Kinematic analysis of plantarflexion and dorsiflexion ROM might not be useful in AT people. This study expands the knowledge what types of exercise regimes should be considered to improve the functional outcomes in AT.
The growth of plant organs is under genetic control. Work in model species has identified a considerable number of genes that regulate different aspects of organ growth. This has led to an increasingly detailed knowledge about how the basic cellular processes underlying organ growth are controlled, and which factors determine when proliferation gives way to expansion, with this transition emerging as a critical decision point during primordium growth. Progress has been made in elucidating the genetic basis of allometric growth and the role of tissue polarity in shaping organs. We are also beginning to understand how the mechanisms that determine organ identity influence local growth behaviour to generate organs with characteristic sizes and shapes. Lastly, growth needs to be coordinated at several levels, for example between different cell layers and different regions within one organ, and the genetic basis for such coordination is being elucidated. However, despite these impressive advances, a number of basic questions are still not fully answered, for example, whether and how a growing primordium keeps track of its size. Answering these questions will likely depend on including additional approaches that are gaining in power and popularity, such as combined live imaging and modelling.
Achilles tendinopathy (AT) is a debilitating injury in athletes, especially for those engaged in repetitive stretch-shortening cycle activities. Clinical risk factors are numerous, but it has been suggested that altered biomechanics might be associated with AT. No systematic review has been conducted investigating these biomechanical alterations in specifically athletic populations. Therefore, the aim of this systematic review was to compare the lower-limb biomechanics of athletes with AT to athletically matched asymptomatic controls. Databases were searched for relevant studies investigating biomechanics during gait activities and other motor tasks such as hopping, isolated strength tasks, and reflex responses. Inclusion criteria for studies were an AT diagnosis in at least one group, cross-sectional or prospective data, at least one outcome comparing biomechanical data between an AT and healthy group, and athletic populations. Studies were excluded if patients had Achilles tendon rupture/surgery, participants reported injuries other than AT, and when only within-subject data was available.. Effect sizes (Cohen's d) with 95% confidence intervals were calculated for relevant outcomes. The initial search yielded 4,442 studies. After screening, twenty studies (775 total participants) were synthesised, reporting on a wide range of biomechanical outcomes. Females were under-represented and patients in the AT group were three years older on average. Biomechanical alterations were identified in some studies during running, hopping, jumping, strength tasks and reflex activity. Equally, several biomechanical variables studied were not associated with AT in included studies, indicating a conflicting picture. Kinematics in AT patients appeared to be altered in the lower limb, potentially indicating a pattern of “medial collapse”. Muscular activity of the calf and hips was different between groups, whereby AT patients exhibited greater calf electromyographic amplitudes despite lower plantar flexor strength. Overall, dynamic maximal strength of the plantar flexors, and isometric strength of the hips might be reduced in the AT group. This systematic review reports on several biomechanical alterations in athletes with AT. With further research, these factors could potentially form treatment targets for clinicians, although clinical approaches should take other contributing health factors into account. The studies included were of low quality, and currently no solid conclusions can be drawn.
Achilles tendinopathy (AT) is a debilitating injury in athletes, especially for those engaged in repetitive stretch-shortening cycle activities. Clinical risk factors are numerous, but it has been suggested that altered biomechanics might be associated with AT. No systematic review has been conducted investigating these biomechanical alterations in specifically athletic populations. Therefore, the aim of this systematic review was to compare the lower-limb biomechanics of athletes with AT to athletically matched asymptomatic controls. Databases were searched for relevant studies investigating biomechanics during gait activities and other motor tasks such as hopping, isolated strength tasks, and reflex responses. Inclusion criteria for studies were an AT diagnosis in at least one group, cross-sectional or prospective data, at least one outcome comparing biomechanical data between an AT and healthy group, and athletic populations. Studies were excluded if patients had Achilles tendon rupture/surgery, participants reported injuries other than AT, and when only within-subject data was available.. Effect sizes (Cohen's d) with 95% confidence intervals were calculated for relevant outcomes. The initial search yielded 4,442 studies. After screening, twenty studies (775 total participants) were synthesised, reporting on a wide range of biomechanical outcomes. Females were under-represented and patients in the AT group were three years older on average. Biomechanical alterations were identified in some studies during running, hopping, jumping, strength tasks and reflex activity. Equally, several biomechanical variables studied were not associated with AT in included studies, indicating a conflicting picture. Kinematics in AT patients appeared to be altered in the lower limb, potentially indicating a pattern of “medial collapse”. Muscular activity of the calf and hips was different between groups, whereby AT patients exhibited greater calf electromyographic amplitudes despite lower plantar flexor strength. Overall, dynamic maximal strength of the plantar flexors, and isometric strength of the hips might be reduced in the AT group. This systematic review reports on several biomechanical alterations in athletes with AT. With further research, these factors could potentially form treatment targets for clinicians, although clinical approaches should take other contributing health factors into account. The studies included were of low quality, and currently no solid conclusions can be drawn.
The bimolecular recombination characteristics of conjugated polymer poly[(4,4'-bis(2-ethylhexyl)dithieno[3,2-b:2',3'-d]silole)-2,6-diyl-alt-(2,5-bis 3-tetradecylthiophen-2-y1 thiazolo 5,4-d thiazole)-2,5diy1] (PDTSiTTz) blended with the fullerene series PC60BM, ICMA, ICBA, and ICTA have been investigated using microsecond and femtosecond transient absorption spectroscopy, in conjunction with electroluminescence measurements and ambient photoemission spectroscopy. The non-Langevin polymer PDTSiTTz allows an inspection of intrinsic bimolecular recombination rates uninhibited by diffusion, while the low oscillator strengths of fullerenes allow polymer features to dominate, and we compare our results to those of the well-known polymer Si-PCPDTBT. Using mu s-TAS, we have shown that the trap -limited decay dynamics of the PDTSiTTz polaron becomes progressively slower across the fullerene series, while those of Si-PCPDTBT are invariant. Electroluminescence measurements showed an unusual double peak in pristine PDTSiTTz, attributed to a low energy intragap charge transfer state, likely interchain in nature. Furthermore, while the pristine PDTSiTTz showed a broad, low-intensity density of states, the ICBA and ICTA blends presented a virtually identical DOS to Si-PCPDTBT and its blends. This has been attributed to a shift from a delocalized, interchain highest occupied molecular orbital (HOMO) in the pristine material to a dithienosilole-centered HOMO in the blends, likely a result of the bulky fullerenes increasing interchain separation. This HOMO localization had a side effect of progressively shifting the polymer HOMO to shallower energies, which was correlated with the observed decrease in bimolecular recombination rate and increased "trap" depth. However, since the density of tail states remained the same, this suggests that the traditional viewpoint of "trapping" being dominated by tail states may not encompass the full picture and that the breadth of the DOS may also have a strong influence on bimolecular recombination.