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.

The score-goldilocks design for phase 3 clinical trials.

In this paper, we propose a new Bayesian adaptive design, score-goldilocks design, which has the same algorithmic idea as goldilocks design. The score-goldilocks design leads to a uniform formula for calculating the probability of trial success for different endpoint trials by using the normal approximation. The simulation results show that the score-goldilocks design is not only very similar to the goldilocks design in terms of operating characteristics such as type 1 error, power, average sample size, probability of stop for futility, and probability of early stop for success, but also greatly saves the calculation time and improves the operation efficiency.

Does size-selective harvesting erode adaptive potential to thermal stress?

Overharvesting is a serious threat to many fish populations. High mortality and directional selection on body size can cause evolutionary change in exploited populations via selection for a specific phenotype and a potential reduction in phenotypic diversity. Whether the loss of phenotypic diversity that accompanies directional selection impairs response to environmental stress is not known. To address this question, we exposed three zebrafish selection lines to thermal stress. Two lines had experienced directional selection for (1) large and (2) small body size, and one was (3) subject to random removal of individuals with respect to body size (i.e. line with no directional selection). Selection lines were exposed to three temperatures (elevated, 34°C; ambient, 28°C; low, 22°C) to determine the response to an environmental stressor (thermal stress). We assessed differences among selection lines in their life history (growth and reproduction), physiological traits (metabolic rate and critical thermal max) and behaviour (activity and feeding behaviour) when reared at different temperatures. Lines experiencing directional selection (i.e. size selected) showed reduced growth rate and a shift in average phenotype in response to lower or elevated thermal stress compared with fish from the random-selected line. Our data indicate that populations exposed to directional selection can have a more limited capacity to respond to thermal stress compared with fish that experience a comparable reduction in population size (but without directional selection). Future studies should aim to understand the impacts of environmental stressors on natural fish stocks.

Transcatheter aortic valve replacement in the treatment of bicuspid aortic stenosis with "down-size" interventional valves: procedural and mid-term follow-up.

Background: Due to the influence of anatomical structure, replacing the bicuspid valve using transcatheter aortic valve replacement (TAVR) would increase the risk of perivalvular leakage and conduction block, affecting the hemodynamic effect of the interventional valve. In this study, for bicuspid and tricuspid valves, we implemented different valve selection strategies to explore the safety and effectiveness of TAVR in the treatment of bicuspid aortic stenosis with "down-size" interventional valves using the VenusA-valve system. Methods: The operation was performed with the VenusA-valve via transfemoral approach. The selected valves were appropriately sized based on the results of transthoracic echocardiography (TTE), contrast-enhanced computed tomography (CT), and the morphology of intraoperative pre-dilation balloons. For tricuspid valve cases, the VenusA valve is usually larger than the annulus diameter, whereas the "down-size" approach was adopted for bicuspid aortic valve (BAV) cases. The shape of the pre-dilation balloon allowed further sizing of the annulus diameter by the degree of lumbar constriction of the balloon, aiding in intervention valve size selection, particularly in cases of BAVs. Results: A total of 65 patients underwent TAVR for aortic stenosis with VenusA-valve systems. Of these, 29 cases had a BAV and 36 cases had a tricuspid aortic valve (TAV). The distribution of VenusA-valve sizes differed between TAV and BAV cases (P=0.007). Furthermore, there was a significant decrease in the average mean gradient in TAV patients from 54.7 to 12.2 mmHg (P<0.001), and in BAV patients from 61.6 to 14.3 mmHg (P<0.001). The percentage of paravalvular leakage greater than mild was 6.90% in the BAVs and 5.56% in the TAVs at procedural outcomes (P=0.955). The mean follow-up period was 22.23 months (range, 12 to 39 months). The proportion of New York Heart Association (NYHA) class III/IV decreased from 78.5% preoperatively to 11.3% at the last follow-up (P<0.001). A total of 27 patients with TAV and 19 patients with BAV underwent TTE at 1-year follow-up after operation. There was no significant contrast in the average pressure difference between TAVs and BAVs at 1-year follow-up (11.9 vs. 14.3 mmHg, P=0.18). Conclusions: The VenusA-valve for TAVR produced positive clinical outcomes and valve functionality in both BAVs and TAVs. In the case of BAVs, selecting a smaller interventional valve size was deemed viable.

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.

Optimizing ddRAD sequencing for population genomic studies with ddgRADer.

Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.

A Novel Filtration Membrane for Clustered Circulating Tumor Cell Extraction: A Prospective Feasibility Study.

BACKGROUND/AIM: Circulating tumor cells (CTCs) have garnered attention as biomarkers for therapeutic response and prognosis in malignant neoplasms. Nonetheless, existing literature predominantly relies on surrogate markers of tumor cells or focuses on single-cell CTC, failing to adequately address the challenge of detecting cluster-forming CTCs, which bear considerable prognostic implications. This prospective study aims to validate the efficacy of a novel filtration membrane, namely Soft Micro Pore Filter (S-MPF®), for rare cell recovery in detecting CTCs through the analysis of clinical samples. PATIENTS AND METHODS: Patients with confirmed lung cancer or highly suspected lung cancer based on specific criteria (solid tumor size >2.0 cm, serum carcinoembryonic level >7.5 ng/ml, maximum standard uptake value derived from fluorodeoxyglucose-position emission tomography >2.9) were included in the study. CTCs were extracted from preoperative peripheral arterial blood samples using S-MPF®, and the validity of the filtration system was positively verified. RESULTS: Out of the 25 enrolled patients, 23 had lung cancer. CTC positivity was observed in 17 cases (73.9%), whereas cluster CTC positivity was observed in 16 cases (69.6%), with a median count of two clusters. Single CTC positivity was observed in 11 cases (52.1%), with a median count of one cell. CONCLUSION: The utilization of the newly developed S-MPF® filtration membrane exhibited a high rate of CTC identification, demonstrating its suitability for clinical applications.

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.

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.

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.

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.

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).

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.

A nano-magnetic size selective cfDNA extraction platform for liquid biopsy with enhanced precision.

As an emerging biomarker, cell-free DNA (cfDNA) carries crucial genetic information for the diagnosis of hereditary disease and cancer. However, test accuracy was severely compromised by the low abundance of cell-free DNA in peripheral blood, frequently diluted by genomic DNA released from white blood cells, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Herein we report a novel strategy for the efficient recovery of cfDNA with significant removal of genomic DNA contamination during the cfDNA extraction process, based on a nano-magnetic size selective cfDNA extraction platform. With this platform, over 90% cfDNA recovery rate was achieved with minimal genomic DNA contamination. For non-invasive prenatal testing, an increase of fetal fraction from 10.10% to 29.94% medially was observed in 11 maternal plasma samples, with two false-negative samples identified by the proposed workflow. Enrichment of cfDNA in plasma sample of cancer patient demonstrated âˆ¼ 100% increase of circulating tumor DNA (ctDNA) percentage by panel sequencing of specific mutation sites. The approach is simple, automatable and cost-efficient, can improve liquid biopsy precision and reduce sequencing depth through significant enrichment of target abundance. The nano-magnetic platform demonstrated its potential application in liquid biopsy, since it exhibited numerous advantages in avoiding false negative results, reducing sequencing cost, improving data quality, and rescuing contaminated samples.

ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs.

Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq protocol (ncRNAseq), allowing the capture and sequencing of mid-sized non-coding RNAs without detriment to the coverage of coding mRNAs. This protocol is coupled with a two-step alignment: a pre-alignment to a curated non-coding genome, passing only the non-mapping reads to a standard genomic alignment. ncRNAseq correctly assigns the highest read-numbers to established abundant non-coding RNAs and correctly identifies cytosolic and nuclear enrichment of known non-coding RNAs in two cell lines.

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.

From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube.

Liquid biopsies hold great promise for the management of cancer. Reliable liquid biopsy data depend on stable and reproducible pre-analytical protocols that comply with quality measures, irrespective of the sampling and processing site. We established a workflow for plasma preservation, followed by processing, cell-free nucleic acid isolation, quantification, and enrichment of potentially tumor-derived cell-free DNA and RNA. Employing the same input material for a direct comparison of different kits and protocols allowed us to formulate unbiased recommendations for sample collection, storage, and processing. The presented workflow integrates the stabilization in Norgen, PAX, or Streck tubes and subsequent parallel isolation of cell-free DNA and RNA with NucleoSnap and NucleoSpin. Qubit, Bioanalyzer, and TapeStation quantification and quality control steps were optimized for minimal sample use and high sensitivity and reproducibility. We show the efficiency of the proposed workflow by successful droplet digital PCR amplification of both cell-free DNA and RNA and by detection of tumor-specific alterations in low-coverage whole-genome sequencing and DNA methylation profiling of plasma-derived cell-free DNA. For the first time, we demonstrated successful parallel extraction of cell-free DNA and RNA from plasma samples. This workflow paves the road towards multi-layer genomic analysis from one single liquid biopsy sample.

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.

Development of a simplified and inexpensive RNA depletion method for plasmid DNA purification using size selection magnetic beads (SSMBs).

Plasmid DNA (pDNA) isolation from bacterial cells is one of the most common and critical steps in molecular cloning and biomedical research. Almost all pDNA purification involves disruption of bacteria, removal of membrane lipids, proteins and genomic DNA, purification of pDNA from bulk lysate, and concentration of pDNA for downstream applications. While many liquid-phase and solid-phase pDNA purification methods are used, the final pDNA preparations are usually contaminated with varied degrees of host RNA, which cannot be completely digested by RNase A. To develop a simple, cost-effective, and yet effective method for RNA depletion, we investigated whether commercially available size selection magnetic beads (SSMBs), such as Mag-Bind® TotalPure NGS Kit (or Mag-Bind), can completely deplete bacterial RNA in pDNA preparations. In this proof-of-principle study, we demonstrated that, compared with RNase A digestion and two commercial plasmid affinity purification kits, the SSMB method was highly efficient in depleting contaminating RNA from pDNA minipreps. Gene transfection and bacterial colony formation assays revealed that pDNA purified from SSMB method had superior quality and integrity to pDNA samples cleaned up by RNase A digestion and/or commercial plasmid purification kits. We further demonstrated that the SSMB method completely depleted contaminating RNA in large-scale pDNA samples. Furthermore, the Mag-bind-based SSMB method costs only 5-10% of most commercial plasmid purification kits on a per sample basis. Thus, the reported SSMB method can be a valuable and inexpensive tool for the removal of bacterial RNA for routine pDNA preparations.

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.