Does social-norm messaging influence expected satiety and ideal portion-size selection?

A person's perception of how long a food will stave off hunger (expected satiety) and the ideal amount to consume (ideal portion size) are both influenced by food-to-mealtime norms. Here, we examine whether social norms can modulate this effect, in three experimental studies. In study 1 (n = 235) participants were exposed to a social norm suggesting most people enjoyed consuming pasta for breakfast. There was a main effect of food-to-mealtime congruence for expected satiety and ideal portion size (p < 0.001) - participants selected a smaller portion of pasta for breakfast (vs. lunch) - but there were no other main effects/interactions (p ≥ 0.15). Study 2 (n = 200) followed the same approach as study 1, but sought to examine whether the typical volume of food consumed at breakfast and lunch needed to be controlled. Again, there was a main effect of congruence (the same pattern) (p ≤ 0.02) but no other main effects/interactions (p ≥ 0.73). Study 3 (n = 208) followed the same approach as study 2, but the social-norm message was changed to suggest that most people who eat pasta for breakfast found it effectively reduced their hunger. Again, there was a main effect of congruence (the same pattern) (p < 0.001) but no other main effects/interaction (p ≥ 0.26). These studies provide further evidence for the food-to-mealtime effect, but do not provide any evidence that a single, simple social-norm statement can modulate expected satiety or ideal portion size, or interact with the food-to-mealtime effect.

Direct validation of dune instability theory.

Modern dune fields are valuable sources of information for the large-scale analysis of terrestrial and planetary environments and atmospheres, but their study relies on understanding the small-scale dynamics that constantly generate new dunes and reshape older ones. Here, we designed a landscape-scale experiment at the edge of the Gobi desert, China, to quantify the development of incipient dunes under the natural action of winds. High-resolution topographic data documenting 42 mo of bedform dynamics are examined to provide a spectral analysis of dune pattern formation. We identified two successive phases in the process of dune growth, from the initial flat sand bed to a meter-high periodic pattern. We focus on the initial phase, when the linear regime of dune instability applies, and measure the growth rate of dunes of different wavelengths. We identify the existence of a maximum growth rate, which readily explains the mechanism by which dunes select their size, leading to the prevalence of a 15-m wavelength pattern. We quantitatively compare our experimental results with the prediction of the dune instability theory using transport and flow parameters independently measured in the field. The remarkable agreement between theory and observations demonstrates that the linear regime of dune growth is permanently expressed on low-amplitude bed topography, before larger regular patterns and slip faces eventually emerge. Our experiment underpins existing theoretical models for the early development of eolian dunes, which can now be used to provide reliable insights into atmospheric and surface processes on Earth and other planetary bodies.

Intra- and inter-operator reliability of three-dimensional preoperative planning in total knee arthroplasty.

PURPOSE: To characterize the intra- and inter-operator reliability of a CT-based 3D preoperative planning software. MATERIALS AND METHODS: This study analyzed 30 CT scans of de-identified knees with osteoarthritis. For each scan, a case planner segmented the bones and pre-planned the TKA. Three orthopedic surgeons then reviewed each pre-planning three times at least one week apart, in a blinded manner. During the reviews, the surgeons modified the pre-plannings until they felt the plannings matched the objectives defined collegially at the beginning of the study. Reliability was assessed using the Intraclass Correlation Coefficient (ICC) and the Standard Error of Measurement (SEM). RESULTS: The intra- and inter-operator reliabilities for implant size selection were almost perfect (ICC between 0.97 and 0.99). Implants of same sizes were selected in 67.1-90.0% of cases. For implant placements, almost perfect intra- and inter-operator reliability was observed in all degrees-of-freedom (ICC between 0.81 and 1.00), except in flexion-extension for the femur (intra-operator ICC between: 0.76 and 0.99; inter-operator ICC of 0.61) and the tibia (intra-operator ICC between 0.12 and 1.00; inter-operator ICC of 0.03). All implant placements SEM were below 1.3 mm or 1.7°. CONCLUSIONS: This study showed high intra- and inter-operator reliability for implant size selection and, in most of the degrees-of-freedom, also for implant placements. Further research is needed to evaluate the benefit of developing more precise means of describing the objectives of the surgical planning as well as to evaluate the possibility and relevance of adding features in the planning software to assist the operators.

Vertical Differentiation of Microplastics Influenced by Thermal Stratification in a Deep Reservoir.

Microplastics (MPs) are an emerging environmental concern. However, vertical transport of MPs remains unclear, particularly in deep reservoirs with thermal stratification (TS). In this study, the vertical variation in MP organization, stability, migration, and the driving factors of the profile in a deep reservoir were comprehensively explored. This is the first observation that TS interfaces in a deep reservoir act as a buffer area to retard MP subsidence, especially at the interface between the epilimnion and the metalimnion. Interestingly, there was a size-selection phenomenon for MP sinking. In particular, the high accumulation of large-sized MPs (LMPs; >300 µm) indicated that LMPs were more susceptible to dramatic changes in water density at the TS interfaces. Furthermore, simultaneous analysis of water parameters and MP surface characteristics showed that the drivers of MP deposition were biological to abiotic transitions during different layers, which were influenced by algae and metals. Specifically, scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy and microscopic Fourier transform infrared analyses implied that the occurrence of metals on the MP surface can promote MP deposition in the hypolimnion. Our findings demonstrated that TS significantly influenced the MP fate in deep reservoirs, and the hotspot of MP exposure risk for vulnerable benthic organisms on the reservoir floor deserves more attention.

Predicting post-operative vault and optimal implantable collamer lens size using machine learning based on various ophthalmic device combinations.

BACKGROUND: Implantable Collamer Lens (ICL) surgery has been proven to be a safe, effective, and predictable method for correcting myopia and myopic astigmatism. However, predicting the vault and ideal ICL size remains technically challenging. Despite the growing use of artificial intelligence (AI) in ophthalmology, no AI studies have provided available choices of different instruments and combinations for further vault and size predictions. This study aimed to fill this gap and predict post-operative vault and appropriate ICL size utilizing the comparison of numerous AI algorithms, stacking ensemble learning, and data from various ophthalmic devices and combinations. RESULTS: This retrospective and cross-sectional study included 1941 eyes of 1941 patients from Zhongshan Ophthalmic Center. For both vault prediction and ICL size selection, the combination containing Pentacam, Sirius, and UBM demonstrated the best results in test sets [R2 = 0.499 (95% CI 0.470-0.528), mean absolute error = 130.655 (95% CI 128.949-132.111), accuracy = 0.895 (95% CI 0.883-0.907), AUC = 0.928 (95% CI 0.916-0.941)]. Sulcus-to-sulcus (STS), a parameter from UBM, ranked among the top five significant contributors to both post-operative vault and optimal ICL size prediction, consistently outperforming white-to-white (WTW). Moreover, dual-device combinations or single-device parameters could also effectively predict vault and ideal ICL size, and excellent ICL selection prediction was achievable using only UBM parameters. CONCLUSIONS: Strategies based on multiple machine learning algorithms for different ophthalmic devices and combinations are applicable for vault predicting and ICL sizing, potentially improving the safety of the ICL implantation. Moreover, our findings emphasize the crucial role of UBM in the perioperative period of ICL surgery, as it provides key STS measurements that outperformed WTW measurements in predicting post-operative vault and optimal ICL size, highlighting its potential to enhance ICL implantation safety and accuracy.

Subjective socioeconomic disadvantage is indirectly associated with food portion selection through perceived disruption of personal resources during a nationwide COVID-19 stay-at-home order.

In addition to its public health implications, the global COVID-19 pandemic has also produced significant disruptions to individuals' socioeconomic resources and opportunities. Prior research has suggested that low subjective socioeconomic status (SSES) may stimulate appetite and motivate increased energy intake. Here, we tested whether individuals experiencing lower levels of SSES (SSES disadvantage) during a nationwide stay-at-home order for COVID-19 exhibited preferences for larger food portion sizes through perceived disruptions to personal financial and material resources. Data was collected near the conclusion of a nationwide partial lockdown (Singapore's "Circuit-Breaker" from April to June 2020). Participants (N = 295) completed an online survey involving a measure of SSES, the Coronavirus Impacts Questionnaire, and a food portion selection task where participants estimated the portion size they prefer to consume for a range of common foods. SSES disadvantage was associated with selection of smaller average portion sizes. Yet, a significant indirect effect of coronavirus impact was observed in this relationship, such that participants experiencing greater SSES disadvantage selected larger portion sizes through the effect of greater perceived impacts of COVID-19 to one's financial/material resources (controlling for one's actual level of income). These findings further support the idea that perceived deprivation and insecurity of important resources (financial, social, material) may influence intentions to consume greater amounts of energy. Consequently, systematic societal disruptions to such resources may reinforce and perpetuate potentially obesogenic eating behaviors of populations that are especially vulnerable to such shocks (i.e., people experiencing SSES disadvantage).

Portions selected to stave off hunger are reduced when food is presented in an 'unusual' food-to-mealtime context: An implication for implicit satiety drivers.

Research suggests that the role of expected satiety in influencing portion-size selection is reduced when food is presented in unusual food-to-mealtime contexts; however, the underlying mechanism has not been explored. Other research has revealed that different implicit satiety drivers (e.g., to stop momentary hunger or obtain complete fullness) are associated with different perceived levels of stomach fullness, portion-size selections and can change on instruction. The current study explored whether changes in expected satiety and ideal portions in congruous vs incongruous contexts can be explained by changes in implicit satiety drivers. Another aim was to investigate a previous exploratory finding suggesting that portions selected to stave off hunger are reduced when foods are presented in unusual food-to-mealtime contexts. At two trials (breakfast/lunch), participants (n = 40) selected a portion of typical lunch (pasta) and breakfast (porridge) foods via a psychophysical computer-based method 1) to stave off hunger for 5 h, and 2) as an ideal portion. Participants also indicated their perceived level of stomach fullness associated with 1) each portion, and 2) five implicit satiety drivers. Results revealed that a smaller average portion was selected to stave off hunger in incongruous (vs congruous) food-to-mealtime contexts (531 ± 229 vs 575 ± 236 kcal) (p = 0.008). This suggests that expected satiety is influenced by momentary context; foods are perceived to be more satiating when consumed in unusual (vs usual) contexts. Results also showed that implicit satiety drivers are malleable in regard to the portion size associated with a perceived level of stomach fullness and that this can vary contextually. These findings provide initial evidence to explain the psychological mechanism underlying the contextual differences observed in portion-size selections. Future work should explore longer-term impacts of consuming foods in unusual contexts.

Does a Change in Device Design Alter Device Size Selection? A Comparison of Conventional and Occlutech Duct Occluder Designs.

AIM: The Occlutech duct occluder (ODO) with a novel design has been available for closure of patent ductus arteriosus (PDA) since 2011. Available data on initial experience with the ODO have shown that operators continue to choose device sizes based on their experience with conventional duct occluders (CDO). This study postulated that occlusion of the pulmonary arterial (PA) end of the ductus should achieve satisfactory PDA closure without additional complications. Accordingly, the size of the ODO was chosen such that the larger PA diameter in the new design exceeded the PA end of the ductus by 2-3 mm and 2-4 mm for normotensive and hypertensive ducts, respectively. It sought to examine the feasibility and safety of such an approach, and compared ODO and CDO devices with respect to device sizes deployed, to ascertain if the newer design had any advantages. METHODS: This prospective study enrolled 105 infants, children and a few adults with various duct morphologies and PA pressures for ductal closure using the ODO from 2018-2020. The control group consisted of 105 ducts closed with CDO. A comparison of the two groups with respect to duct diameter and implanted device sizes was performed using appropriate statistical software. RESULTS: The study found that 40% of the ducts had moderate-to-severe pulmonary hypertension. Most ducts measured between 3-4 mm in both groups. The mean weight of the subjects in both groups was 12 kg. Although there was no change in the way that duct occluders were chosen in both groups (2-3 mm over the pulmonary artery diameter), ODO could be significantly downsized in most ducts measuring between 2.5-6.4 mm in diameter (p<0.05). CONCLUSIONS: This study found successful closure of relatively larger PDA in infants and children using smaller ODO compared with CDO, without embolisation or aortic narrowing. It also demonstrated that a different device size selection technique may be safely employed with the ODO.

Problems of the Grid Size Selection in Differential Box-Counting (DBC) Methods and an Improvement Strategy.

The differential box-counting (DBC) method is useful for determining the fractal dimension of grayscale images. It is simple to learn and implement and has been extensively utilized. However, this approach has several problems, such as over- or undercounting the number of boxes due to inappropriate parameter choices, limiting the calculation accuracy. Many studies have been conducted to increase the algorithm's computational accuracy by improving the calculating parameters of the differential box-counting method. The grid size is a crucial parameter for the DBC method. Generally, there are two typical ways for selecting the grid size in relevant studies: consecutive integer and divisors of image size. However, both methods for grid size selection are problematic. The consecutive integer method cannot partition the image entirely and will result in the undercounting of boxes; the divisors of image size can partition the image completely. However, this method uses fewer grid sizes to compute fractal dimensions and has a relatively huge distance error (DE). To address the shortcomings of the above-mentioned two approaches, this research presents an improved grid size selection strategy. The improved method enhances computational accuracy by computing the discarded image edge areas in the consecutive integer method, allowing the original image information to be used as thoroughly as the divisor strategy. Based on fractional Brownian motion (FBM), Brodatz, and Aerials image sets, the accuracy of the three grid size selection techniques (consecutive integer method, divisors of image size method, and the improved algorithm) to compute the fractal dimension is then compared. The results reveal that, compared to the two prior techniques, the revised algorithm described in this study minimizes the distance error and increases the accuracy of the fractal dimension computation.

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.

Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.

Effects of size selection versus density dependence on life histories: A first experimental probe.

When prey experience size-based harvesting by predators, they are not only subject to selection due to larger individuals being preferentially harvested but also selection due to reductions in population density. Density-dependent selection represents one of the most basic interactions between ecology and evolution. Yet, the reduction in density associated with exploitation has not been tested as a possible driving force of observed evolutionary changes in populations harvested size-dependently. Using an artificial selection experiment with a mixture of Daphnia clones, we partition the evolutionary effects of size-based harvesting into the effects of removing large individuals and the effects of lowering the population density. We show that both size selection and density-dependent selection are significant drivers of life-history evolution. Importantly, these drivers affected different life-history traits with size-selective harvesting selecting for slower juvenile growth rates and a larger size at maturity, and low-density selecting for reduced reproductive output.

Annular and supra-annular structure assessments for transcatheter aortic valve replacement in patients with bicuspid aortic stenosis.

The clinical use indications for transcatheter aortic valve replacement (TAVR) for the treatment of severe symptomatic aortic stenosis (AS) have expanded from patients at high surgical risk to those at low risk based on the results of multiple large-scale randomized trials. However, patients with bicuspid AS have traditionally been excluded from clinical trials due to their unfavorable morphological characteristics. Bicuspid aortic valve (BAV) is the most frequent congenital heart disease, occurring in 1% to 2% of the total population and affects more than 20% of octogenarians undergoing isolated aortic valve replacement for AS. In recent years, TAVR in patients with bicuspid AS has been the focus of research, especially with respect to the standard of prosthesis size selection. Annulus-based prosthesis size selection using computed tomography (CT) is the standard sizing strategy for tricuspid AS, but no standard sizing for bicuspid AS has been developed thus far. According to Western TAVR experiences, transcatheter heart valve (THV) size selection for BAV patients should be based on the annular structure assessment by CT measurement, whereas Chinese experiences favor adopting the supra-annulus structure assessment for THV size selection. This article will review annular and supra-annular sizing for prosthesis size selection in patients with bicuspid AS before TAVR and discuss which has more favorable clinical outcomes.

Optimization of small RNA library preparation protocol from human urinary exosomes.

BACKGROUND: Sequencing of miRNAs isolated from exosomes has great potential to identify novel disease biomarkers, but exosomes have low amount of RNA, hindering adequate analysis and quantification. Here, we have assessed several steps in developing an optimized small RNA (sRNA) library preparation protocol for next-generation sequencing (NGS) miRNA analysis from urinary exosomes. METHODS: A total of 24 urinary exosome samples from donors were included in this study. RNA was extracted by column-based methods. The quality of extracted RNA was assessed by spectrophotometric quantification and Bioanalyzer software analysis. All libraries were prepared using the CleanTag small RNA library preparation protocol and the effect of our additional modifications on adapter-dimer presence, sequencing data and tagged small RNA library population was also analyzed. RESULTS: Our results show that good quality sequencing libraries can be prepared following our optimized small RNA library preparation protocol from urinary exosomes. When the size selection by gel purification step was included within the workflow, adapter-dimer was totally removed from cDNA libraries. Furthermore, the inclusion of this modification step within small RNA library protocol augmented the small RNA mapped reads, with an especially significant 37% increase in miRNA reads, and the gel purification step made no difference to the tagged miRNA population. CONCLUSIONS: This study provides researchers with an optimized small RNA library preparation workflow for next generation sequencing based exosome-associated miRNA analysis that yields a high amount of miRNA mapped reads without skewing the tagged miRNA population significantly.

Modified Goldilocks Design with strict type I error control in confirmatory clinical trials.

Goldilocks Design (GD) utilizes predictive probability to adaptively select a trial's sample size based on accumulating data. In order to control type I error at a desired level for a subset of the null space, extensive simulations at the study design stage are required to choose critical values, which is a challenge for this type of Bayesian adaptive design to be used for confirmatory trials. In this article, we propose a Modified Goldilocks Design (MGD) where type I error is analytically controlled over the entire null space. We do so by applying the conditional invariance principle and a combination test approach on [Formula: see text]-values that are obtained from independent cohorts of subjects. Simulation studies show that despite analytic control of type I error rate, the proposed MGD has similar power when compared with the original GD. We further apply it to an example trial with time-to-event endpoint in oncology.

Sequencing shorter cfDNA fragments improves the fetal DNA fraction in noninvasive prenatal testing.

BACKGROUND: Sequencing cell-free DNA in maternal plasma is an effective noninvasive prenatal testing technique that has been used in fetal aneuploidy screening worldwide. However, its clinical application is limited by the low fetal fraction (<4%) of cell-free DNA in many singleton pregnancies, which usually results in screen failures or no calls. In addition, dizygotic twin contributions of cell-free DNA into the maternal circulation can vary by 2-fold, complicating the quantitative diagnosis of fetal aneuploidy. OBJECTIVE: We performed semiconductor sequencing of shorter fragments (107-145 bp) of circulating cell-free DNA to improve the fetal DNA fraction at lower uniquely mapped reads (1-8.5 MB) to reduce the probability of no calls. STUDY DESIGN: We identified 2903 plasma samples from pregnant women, including 86 dizygotic twin pregnancy, that were collected at a single prenatal diagnostic center between October 2015 and July 2018. Size-selection noninvasive prenatal testing for fetal aneuploidy was applied to 2817 plasma samples (1409 male and 1408 female fetuses) and 86 dizygotic twins using noninvasive prenatal testing with and without size selection. Shorter fragment size was the key factor affecting fetal fraction in multivariable linear regression models as well as to validate the accuracy of the size selection for noninvasive prenatal testing. RESULTS: Analysis of 1409 male fetuses by multivariable linear regression showed that maternal age, body mass index, number of pregnancies, average cell-free DNA size, maternal plasma cell-free DNA concentration, library concentration, and multiple gestation were negatively correlated with fetal fraction. Conversely, gestational age and uniquely mapped reads were positively correlated with fetal fraction. Compared with ≤120 bp cell-free DNA fragments, mean fetal fraction differences were -3.57% (95% confidence interval, -5.95% to -1.19%), for 121-130 bp, -9.52% (95% confidence interval, -11.89% to -7.14%) for 131-140 bp, and -14.47% (95% confidence interval, -18.37% to -10.58%) for ≥141 bp (Ptrend < .0001). These results were statistically significant after multivariable adjustments in models for fetal fraction. Meanwhile, results from 86 dizygotic twins showed that the size selection increased the fetal fraction by ∼3.2-fold, with 98.8% of samples reaching a fetal fraction >10%. Improved detection accuracy was also achieved. CONCLUSION: Sequencing shorter cell-free DNA fragments is a reasonable strategy to reduce the probability of no calls results because of low fetal fraction and should be recommended to pregnant subjects.

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

BACKGROUND: RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. RESULTS: To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. CONCLUSIONS: For a given search space, the presented approach allows us to choose the best tile size and tile dimension in parallel tiled code implementing Nussinov's RNA folding. Experimental results, received on modern Intel multi-core processors, demonstrate that this code outperforms known closely related implementations when the length of RNA strands is bigger than 2500.

Population dynamics and development of the rhizocephalan Sacculina carcini, parasitic on the shore crab Carcinus maenas.

The ecologically important shore crab Carcinus maenas is commonly infected in its native range by the rhizocephalan Sacculina carcini. However, several aspects of this host-parasite interaction are poorly understood. Here, we analyse data from approximately 60000 Danish crabs to unravel factors governing infection patterns in time and space, and according to host sex and size. Female crabs were more frequently infected (12.6%) than males (7.9%). Sites with high salinity supported the highest infection prevalence. Infection prevalence peaked in summer (10 to 15%) and winter (20 to 35%) due in part to emergence of virginal externae in summer (main outbreak) and autumn (minor outbreak) preceded by peaks in crabs with lost externa (scars). Younger externae and scars dominated among males, whereas adult externae were most frequent among females. Infection prevalence increased with size in females but decreased in males, and modified (feminized) males showed lower scar frequency than unmodified ones. Modified males occurred frequently among the smaller size classes, whereas unmodified males dominated the larger size classes. Externa size was positively related to host size in both genders (same linear relationship). Molecular analyses suggested that hosts below 16 mm in carapace width do not become infected. Dissections of infected hosts revealed marked reduction of ovaries, whereas testes were unaffected by sacculinization. Our study demonstrates great spatio-temporal variation in infection prevalence mainly related to the parasite's life history. S. carcini appears capable of infecting all host sizes except the smallest. Owing to incomplete feminization of males, infections are rapidly lost from the larger and highly profitable male hosts.

A method for improving the accuracy of non-invasive prenatal screening by cell-free foetal DNA size selection.

Background Non-invasive prenatal screening (NIPS) using cell-free foetal DNA (cfDNA) has been widely used for identifying common foetal aneuploidies (e.g. trisomy 21 (T21), trisomy (T18) and trisomy 13 (T13)) in clinical practice. The sensitivity and specificity of NIPS exceeds 99%, but the positive prediction value (PPV) is approximately 70% (combined T21, T18 and T13). Thus, some 30% of pregnant women who have positive NIPS results are eventually identified as normal by amniocentesis. These women therefore must undertake needless invasive tests and risk miscarrying healthy babies because of false positive NIPS results. Methods In order to achieve higher accuracy, we amended the standard NIPS (s-NIPS) protocol with an additional cfDNA size selecting step in agarose-electrophoresis. The advantage of the new method (named e-NIPS) was validated by comparing the results of e-NIPS and s-NIPS using 114 retrospective cases selected from 15,930 cases. Results Our results showed that the foetal cfDNA fraction can be enriched significantly by a size selection step. With this modification, all 98 negative cases and 9 of 11 false positive cases of s-NIPS were correctly identified by e-NIPS, resulting in an increased PPV from 71% to 77%. Additionally, a simulation test showed that e-NIPS is more reliable than s-NIPS, especially when the foetal cfDNA concentration and sequencing coverage are low. Conclusion cfDNA size selection is an important step in improving the accuracy of non-invasive prenatal screening for chromosomal abnormalities.

Rapid, broad-scale gene expression evolution in experimentally harvested fish populations.

Gene expression changes potentially play an important role in adaptive evolution under human-induced selection pressures, but this has been challenging to demonstrate in natural populations. Fishing exhibits strong selection pressure against large body size, thus potentially inducing evolutionary changes in life history and other traits that may be slowly reversible once fishing ceases. However, there is a lack of convincing examples regarding the speed and magnitude of fisheries-induced evolution, and thus, the relevant underlying molecular-level effects remain elusive. We use wild-origin zebrafish (Danio rerio) as a model for harvest-induced evolution. We experimentally demonstrate broad-scale gene expression changes induced by just five generations of size-selective harvesting, and limited genetic convergence following the cessation of harvesting. We also demonstrate significant allele frequency changes in genes that were differentially expressed after five generations of size-selective harvesting. We further show that nine generations of captive breeding induced substantial gene expression changes in control stocks likely due to inadvertent selection in the captive environment. The large extent and rapid pace of the gene expression changes caused by both harvest-induced selection and captive breeding emphasizes the need for evolutionary enlightened management towards sustainable fisheries.

Differential foraging preferences on seed size by rodents result in higher dispersal success of medium-sized seeds.

Rodent preference for scatter-hoarding large seeds has been widely considered to favor the evolution of large seeds. Previous studies supporting this conclusion were primarily based on observations at earlier stages of seed dispersal, or on a limited sample of successfully established seedlings. Because seed dispersal comprises multiple dispersal stages, we hypothesized that differential foraging preference on seed size by animal dispersers at different dispersal stages would ultimately result in medium-sized seeds having the highest dispersal success rates. In this study, by tracking a large number of seeds for 5 yr, we investigated the effects of seed size on seed fates from seed removal to seedling establishment of a dominant plant Pittosporopsis kerrii (Icacinaceae) dispersed by scatter-hoarding rodents in tropical forest in southwest China. We found that small seeds had a lower survival rate at the early dispersal stage where more small seeds were predated at seed stations and after removal; large seeds had a lower survival rate at the late dispersal stage, more large seeds were recovered, predated after being cached, or larder-hoarded. Medium-sized seeds experienced the highest dispersal success. Our study suggests that differential foraging preferences by scatter-hoarding rodents at different stages of seed dispersal could result in conflicting selective pressures on seed size and higher dispersal success of medium-sized seeds.