Summary
Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample‐size‐ and coverage‐based integrations of ...rarefaction (interpolation) and extrapolation (prediction) of Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages.
We briefly review the conceptual background of Hill numbers along with two approaches to standardization. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity). Two types of biodiversity data are allowed: individual‐based abundance data and sampling‐unit‐based incidence data.
Several applications of the iNEXT packages are reviewed: (i) Non‐asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage.
Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.
There have been intense debates about the decomposition of regional diversity (gamma) into its within-community component (alpha) and between-community component (beta). Although a recent
Ecology
...Forum achieved consensus in the use of "numbers equivalents" (Hill numbers) as the proper choice of diversity measure, three related major issues were still left unresolved. (1) What is the precise meaning of the "independence" or "statistical independence" of alpha diversity and beta diversity? (2) Which partitioning (additive vs. multiplicative) should be used for a given application? (3) What is the proper formula for alpha diversity, as there are two formulas in the literature? This paper proposes a possible resolution to each of these issues. For the first issue, we clarify the definitions of "independence" and "statistical independence" from two perspectives so that confusion about this issue can be cleared up. We also discuss the causes of dependence, so that the dependence relationship between any two diversity components in both partitioning schemes can be rigorously justified by theory and also intuitively understood by simulation. For the second issue, both multiplicative and additive beta diversities based on Hill numbers are useful measures and quantify different aspects of communities. However, neither can be directly applied to compare relative compositional similarity or differentiation across multiple regions with different numbers of communities because multiplicative beta diversity depends on the number of communities, and additive beta diversity additionally depends on alpha (equivalently, on gamma). Such dependences should be removed. We propose transformations to remove these dependences, and we show that the transformed multiplicative beta and additive beta both lead to the same classes of measures, which are always in a range of 0, 1 and thus can be used to compare relative similarity or differentiation among communities across multiple regions. These similarity measures include multiple-community generalizations of the Sørenson, Jaccard, Horn, and Morisita-Horn measures. For the third issue, we present some observations including a finding about which alpha formula produces independent alpha and beta components. These may help to resolve the choice of a proper formula for alpha diversity. Some related issues are also briefly discussed.
The relationship between tuberculosis (TB) and subsequent chronic kidney disease (CKD) remains unclear. Therefore, we examined the risk of CKD among patients with TB in a nationwide study.
We ...conducted a retrospective cohort study using data from the National Health Insurance system of Taiwan. The cohort included 8735 patients who were newly diagnosed with TB. Patients were recruited between 1998 and 2002, and the date of diagnosis was defined as the index date. Each patient was randomly matched with four people from the general population without TB, according to age, gender and the index year. The occurrence of CKD was followed up until the end of 2011. The relative risks of CKD were estimated using the Cox proportional hazard model after adjusting for age, gender, index year and comorbidities.
The overall incidence of CKD was 1.27-fold greater in the TB cohort than in the non-TB cohort. The adjusted hazard ratio (HR) of CKD associated with TB was higher in women (1.72; 95% confidence interval CI: 1.33-2.22), those aged <50 years (1.67; 95% CI: 1.15-2.41) and those without comorbidities (1.39; 95% CI: 1.06-1.83). In addition, patients with more comorbidities among hypertension, diabetes and hyperlipidemia have a greater risk of developing CKD in both cohorts, and the adjusted HRs were higher in the TB cohort than in the non-TB cohort.
TB patients had a significantly higher risk of developing CKD than the general population. The detailed mechanisms need further investigation.
Dose-dense (DD) regimens of combination chemotherapy may produce superior clinical outcomes, but the basis for these effects are not completely clear. In this study, we assessed whether a DD ...combinatorial regimen of low-dose cisplatin and paclitaxel produces superior immune-mediated efficacy when compared with a maximum tolerated dose (MTD) regimen in treating platinum-resistant ovarian cancer as modeled in mice. Immune responses generated by the DD regimen were identified with regard to the immune cell subset responsible for the antitumor effects observed. The DD regimen was less toxic to the immune system, reduced immunosuppression by the tumor microenvironment, and triggered recruitment of macrophages and tumor-specific CD8(+) T-cell responses to tumors as determined by interleukin (IL)-2 and IFN-γ secretion. In this model, we found that the DD regimen exerted greater therapeutic effects than the MTD regimen, justifying its further clinical investigation. Fourteen patients with platinum-resistant relapse of ovarian cancer received DD chemotherapy consisting of weekly carboplatin (AUC2) and paclitaxel (60-80 mg/m(2)) as the third- or fourth-line treatment. Serum was collected over the course of treatment, and serial IFN-γ and IL-2 levels were used to determine CD8(+) T-cell activation. Of the four patients with disease control, three had serum levels of IL-2 and IFN-γ associated with cytotoxic CD8(+) T-cell activity. The therapeutic effect of the DD chemotherapy relied on the preservation of the immune system and the treatment-mediated promotion of tumor-specific immunity, especially the antitumor CD8(+) T-cell response. Because the DD regimen controlled drug-resistant disease through a novel immune mechanism, it may offer a fine strategy for salvage treatment.
Purpose
The objective of this retrospective study was to assess safety and comparative clinical effectiveness of laparoscopic inguinal hernia repair (LIHR) and robot-assisted inguinal hernia repair ...(RIHR) from multi-institutional experience in Taiwan.
Methods
Medical records from a total of eight hospitals were retrospectively collected and analyzed. Patients primarily diagnosed of inguinal hernia, recurrent inguinal hernia or incarceration groin hernia patients who either underwent laparoscopic or robot-assisted inguinal hernia repair between January 2018 and December 2022 were included in the study. Baseline characteristics, intra-operative and post-operative results were analyzed. To compare two cohorts, overlap weighting was employed to balance the significant inter-group differences. We also conducted subgroup analyses by state of a hernia (primary or recurrent/incarceration) and laterality (unilateral or bilateral) that indicated complexity of surgery.
Results
A total of 1,080 patients who underwent minimally invasive inguinal hernia repair from 8 hospitals across Taiwan were collected. Following the application of inclusion criteria, there were 279 patients received RIHR and 763 patients received LIHR. In the baseline analysis, RIHR was more often performed in recurrent/incarceration (RIHR 18.6% vs LIHR 10.3%,
p
= 0.001) and bilateral cases (RIHR 81.4 vs LIHR 58.3,
p
< 0.001). Suturing was dominant mesh fixation method in RIHR (RIHR 81% vs LIHR 35.8%,
p
< 0.001). More overweight patients were treated with RIHR (RIHR 58.8% vs LIHR 48.9%,
p
= 0.006). After overlap weighting, there were no significant difference in intraoperative and post-operative complications between RIHR and LIHR. Reoperation and prescription rates of pain medication (opioid) were significantly lower in RIHR than LIHR in overall group comparison (reoperation: RIHR 0% vs. LIHR 2.9%,
p
= 0.016) (Opioid prescription: RIHR 3.34 mg vs LIHR 10.82 mg,
p
= 0.001) while operation time was significantly longer in RIHR (OR time: RIHR 155.27 min vs LIHR 95.30 min, p < 0.001).
Conclusions
This real-world experience suggested that RIHR is a safe, and feasible option with comparable intra-operative and post-operative outcomes to LHIR. In our study, RIHR showed technical advantages in more complicated hernia cases with yielding to lower reoperation rates, and less opioid use.
Quantitative susceptibility mapping of the human brain has demonstrated strong potential in examining iron deposition, which may help in investigating possible brain pathology. This study assesses ...the reproducibility of quantitative susceptibility mapping across different imaging sites.
In this study, the susceptibility values of 5 regions of interest in the human brain were measured on 9 healthy subjects following calibration by using phantom experiments. Each of the subjects was imaged 5 times on 1 scanner with the same procedure repeated on 3 different 3T systems so that both within-site and cross-site quantitative susceptibility mapping precision levels could be assessed. Two quantitative susceptibility mapping algorithms, similar in principle, one by using iterative regularization (iterative quantitative susceptibility mapping) and the other with analytic optimal solutions (deterministic quantitative susceptibility mapping), were implemented, and their performances were compared.
Results show that while deterministic quantitative susceptibility mapping had nearly 700 times faster computation speed, residual streaking artifacts seem to be more prominent compared with iterative quantitative susceptibility mapping. With quantitative susceptibility mapping, the putamen, globus pallidus, and caudate nucleus showed smaller imprecision on the order of 0.005 ppm, whereas the red nucleus and substantia nigra, closer to the skull base, had a somewhat larger imprecision of approximately 0.01 ppm. Cross-site errors were not significantly larger than within-site errors. Possible sources of estimation errors are discussed.
The reproducibility of quantitative susceptibility mapping in the human brain in vivo is regionally dependent, and the precision levels achieved with quantitative susceptibility mapping should allow longitudinal and multisite studies such as aging-related changes in brain tissue magnetic susceptibility.
Researchers have indicated that the collaborative problem‐solving space afforded by the collaborative systems significantly impact the problem‐solving process. However, recent investigations into ...collaborative simulations, which allow a group of students to jointly manipulate a problem in a shared problem space, have yielded divergent results regarding their effects on collaborative learning. Hence, this study analysed how students solved a physics problem using individual‐based and collaborative simulations to understand their effects on science learning. Multiple data sources including group discourse, problem‐solving activities, learning test scores, and questionnaire feedback were analysed. Lag sequential analysis on the data found that students using the two simulations collaborated with peers to solve the problem in significantly different patterns. The students using the collaborative simulations demonstrated active engagement in the collaborative activity; however, they did not transform discussions into workable problem‐solving activities. The students using the individual‐based simulation showed a lower level of collaboration engagement, starting with individual exploration of the problem with the simulation, followed by group reflection. The two groups also showed significant differences in their learning test scores. The findings and pedagogical suggestions are discussed in the hope of addressing critical activity design issues in using computer simulations for facilitating collaborative learning.
Lay Description
What is currently known about the subject matter?
Students tend to solve problems with simulations individually rather than collaboratively.
The free‐riding effect impedes student engagement in the collaborative process.
Collaborative simulations offer new affordances to better facilitate CPS processes.
What their paper adds to this?
Collaborative simulations strengthen interdependence and engagement in collaboration.
However, students did not show a significant enhancement in the learning tests.
They had difficulties transforming discussions into workable problem‐solving actions.
What the implications of study findings for practitioners?
Collaborative simulations can be applied to enhance collaborative engagement.
CPS activities should carefully leverage individual and collaborative learning.
Prompts that help students to closely relate their discussion to the simulation are needed.
Deep sequencing of 10,000 human genomes Telenti, Amalio; Pierce, Levi C. T.; Biggs, William H. ...
Proceedings of the National Academy of Sciences - PNAS,
10/2016, Letnik:
113, Številka:
42
Journal Article
Recenzirano
Odprti dostop
We report on the sequencing of 10,545 human genomes at 30×–40× coverage with an emphasis on quality metrics and novel variant and sequence discovery. We find that 84% of an individual human genome ...can be sequenced confidently. This high-confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. We present the distribution of over 150 million single-nucleotide variants in the coding and noncoding genome. Each newly sequenced genome contributes an average of 8,579 novel variants. In addition, each genome carries on average 0.7 Mb of sequence that is not found in the main build of the hg38 reference genome. The density of this catalog of variation allowed us to construct high-resolution profiles that define genomic sites that are highly intolerant of genetic variation. These results indicate that the data generated by deep genome sequencing is of the quality necessary for clinical use.
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