Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared ...to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods. However, both methods face challenges in handling large genomes with many duplicated genes, especially in the presence of whole genome duplication.
In this paper, we present three simple yet powerful methods based on maximum-likelihood (ML) approaches that encode multiplicities of both gene adjacency and gene content information for phylogenetic reconstruction.
Extensive experiments on simulated data sets show that our new method achieves the most accurate phylogenies compared to existing approaches. We also evaluate our method on real whole-genome data from eleven mammals. The package is publicly accessible at http://www.geneorder.org .
Our new encoding schemes successfully incorporate the multiplicity information of gene adjacencies and gene content into an ML framework, and show promising results in reconstruct phylogenies for whole-genome data in the presence of massive duplications.
Serum Klotho (S-Klotho) is a transmembrane protein holds pivotal roles in anti-aging. The Dietary Inflammation Index (DII), a meticulously dietary tool, quantifies the inflammatory potential of an ...individual's diet. The existing research strongly suggests that a low DII diet plays a significant role in delaying aging and reducing aging-related symptoms in males. Testosterone could potentially act as a mediating intermediary between DII and S-Klotho. However, this aspect remains unexplored. This study aims to investigate the potential causal link of testosterone between DII and S-Klotho in males.
We utilized data from National Health and Nutrition Examination Survey (NHANES) which focused on male participants from 2013-2016. Mediation analyses were used to investigate the effects of testosterone (TT), free testosterone (FT), and free androgen index (FAI) on the DII-S-Klotho relationship, using three modes adjusting for covariates.
Mediation analysis unveiled a significant inverse correlation between DII and S-Klotho levels (model 1: c = -14.78, p = 0.046). The interaction between DII and S-Klotho was modulated by TT in model 1 (ab = -1.36; 95% CI: -5.59, -0.55; p = 0.008), but lost significance after adjustments (model 2: ab = -0.39; 95% CI: -4.15, 1.66; p = 0.378; model 3: ab = -0.59; 95% CI: -4.08, 2.15; p = 0.442). For FT, the mediating impact was not statistically significant (model 1: ab = 0.43; 95% CI: -0.51, 5.44; p = 0.188; model 2: ab = 0.72; 95% CI: -0.26, 5.91; p = 0.136; model 3: ab = 0.84; 95% CI: -0.02, 8.06; p = 0.056). Conversely, FAI consistently influenced the DII-S-Klotho relationship (model 1: ab = 2.39; 95% CI: 0.69, 9.42; p = 0.002), maintaining significance after adjustments (model 2: ab = 3.2; 95% CI: 0.98, 11.72; p = 0.004; model 3: ab = 3.15; 95% CI: 0.89, 14.51; p = 0.026).
This study observed no mediating influence of TT or FT on the correlation between DII and S-Klotho after covariate control. Remarkably, FAI continued to significantly mediate the DII-S-Klotho connection even following covariate adjustment, although its significance in males warrants careful consideration.
Objective
To identify sex-related differences in the outcome of hospitalized patients with spontaneous intracerebral hemorrhage (SICH), and to identify potential causal pathways between sex and SICH ...outcome.
Methods
A total of 111,112 medical records of in-hospital patients with SICH were collected. Data- and expert-driven techniques were applied, such as a multivariate logistic regression model and causal mediation analysis. These analyses were used to determine the confounders and mediators, estimate the true effect of sex on the SICH outcome, and estimate the average causal mediation effect for each mediator.
Results
(1) Failure (disability or death) rates in women with SICH were significantly lower than in men with SICH. On the day of discharge, the odds ratio (
OR
) of failure between women and men was 0.9137 95% confidence interval (CI), 0.8879–0.9402, while the odds ratio at 90 days post-discharge was 0.9353 (95% confidence interval, 0.9121–0.9591). (2) The sex-related difference in SICH outcome decreased with increasing age and disappeared after 75 years. (3) Deep coma, brainstem hemorrhage, and an infratentorial hemorrhage volume of >10 ml accounted for 62.76% (
p
< 0.001), 33.46% (
p
< 0.001), and 11.56% (
p
< 0.001) of the overall effect on the day of discharge, and for 52.28% (
p
< 0.001), 27.65% (
p
< 0.001), and 10.86% (
p
< 0.001) of the overall effect at the 90-day post-discharge.
Conclusion
Men have a higher failure risk than women, which may be partially mediated by a higher risk for deep coma, brainstem hemorrhage, and an infratentorial hemorrhage volume of >10 ml. Future work should explore the biological mechanisms underlying this difference.
Cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL) is a hereditary cerebral small vascular disease caused by a homozygous mutation in the ...high-temperature requirement A serine peptidase 1 (
) gene. Cerebral microbleeds (CMBs) are increasingly being recognized as neuroimaging findings occurring with cerebrovascular disease and have different etiologies. Mild to moderate CMBs are not unusual in CARASIL, and they are observed to affect cortical and subcortical structures; in contrast, diffuse CMBs, especially in the cerebellum, are rare. In this case, we report a novel mutation of
in a 43-year-old woman whose imaging indicated multiple CMBs in all lobes, brain stem, and cerebellum. The amount and location of CMBs vary in CARASIL cases, and the potential cause is not fully understood. This study revealed that specific imaging findings of this patient may be related to a new genetic mutation.
In this article, Chinese German learners’ use of the prepositions um and in is analyzed in the context of conceptual metaphor theory using the CDLK corpus and Falko corpus. The study reveals that the ...error rate of the preposition in is significantly higher than that of the preposition um, which is ultimately due to the differences in cultural and conceptual systems between Germany and China. Chinese German learners use the spatial and temporal meanings of the prepositions more frequently, while they use the metaphorical meanings less frequently. Furthermore, there is no clear correlation between the learning time of Chinese German learners and the number of errors. The conclusions of this study could provide insights for improvements in teaching.
(Bi)harmonic field has wide applications in geometry processing. Traditionally, to locally control the influence region of a (bi)harmonic field, users usually need to determine the range of its ...support, regions with non-zero scalar values, by prescribing appropriate boundary conditions. However, this way is non-intuitive and inconvenient. We proposed localized quasi-(bi)harmonic field, which is achieved through a ℓ1-norm regularized convex optimization. It can conveniently control the local support of the scalar field while still keeping some nice properties of the (bi)harmonic field. We applied the localized quasi-(bi)harmonic field in applications such as shape deformation and shape merging, and the experiment results show its benefits.
We present a novel parallel algorithm for cloth simulation that exploits multiple GPUs for fast computation and the handling of very high resolution meshes. To accelerate implicit integration, we ...describe new parallel algorithms for sparse matrix-vector multiplication (SpMV) and for dynamic matrix assembly on a multi-GPU workstation. Our algorithms use a novel work queue generation scheme for a fat-tree GPU interconnect topology. Furthermore, we present a novel collision handling scheme that uses spatial hashing for discrete and continuous collision detection along with a non-linear impact zone solver. Our parallel schemes can distribute the computation and storage overhead among multiple GPUs and enable us to perform almost interactive simulation on complex cloth meshes, which can hardly be handled on a single GPU due to memory limitations. We have evaluated the performance with two multi-GPU workstations (with 4 and 8 GPUs, respectively) on cloth meshes with 0.5 -- 1.65M triangles. Our approach can reliably handle the collisions and generate vivid wrinkles and folds at 2 -- 5 fps, which is significantly faster than prior cloth simulation systems. We observe almost linear speedups with respect to the number of GPUs.
In this paper, we present a new framework for object recognition via weakly supervised metric and template learning, wherein the optimal metric and templates are jointly learned. Its advantages ...include high computational speed, and robustness against image noise and unbalanced training data. Specifically, considering the noise in the training data, our framework is formulated as a weakly supervised learning model in which images with higher reliability will contribute more to the training result. A latent structural SVM based Weakly Supervised Metric and Template Learning (WSMTL) method is designed to jointly learn the metric, the templates, and a weight vector. The weight vector is used to represent each image׳s reliability. With the learned metric and object templates, each testing sample is recognized via 1-NN searching within templates. Owing to the 1-NN searching scheme in the recognition phase, WSMTL is of great computational efficiency. We used CMU PIE database with synthesized noise to evaluate the robustness of WSMTL. Experimental results show that WSMTL is robust against noise and unbalanced training data. Moreover, we compared it with some state-of-the-art recognition methods on the public traffic sign dataset BTSC and human face database, i.e., Extended Yale-B. The comparison results demonstrate that our method outperforms the others in object recognition tasks.
In longitudinal cohort studies, it is often of interest to predict the risk of a terminal clinical event using longitudinal predictor data among subjects at risk by the time of the prediction. The ...at-risk population changes over time; so does the association between predictors and the outcome, as well as the accumulating longitudinal predictor history. The dynamic nature of this prediction problem has received increasing interest in the literature, but computation often poses a challenge. The widely used joint model of longitudinal and survival data often comes with intensive computation and excessive model fitting time, due to numerical optimization and the analytically intractable high-dimensional integral in the likelihood function. This problem is exacerbated when the model is fit to a large dataset or the model involves multiple longitudinal predictors with nonlinear trajectories. This challenge can be addressed from an algorithmic perspective, by a novel two-stage estimation procedure, and from a computing perspective, by Graphics Processing Unit (GPU) programming. The latter is implemented through PyTorch, an emerging deep learning framework. The numerical studies demonstrate that the proposed algorithm and software can substantially speed up the estimation of the joint model, particularly with large datasets. The numerical studies also concluded that accounting for nonlinearity in longitudinal predictor trajectories can improve the prediction accuracy in comparison to joint modeling that ignore nonlinearity.
The aim of the present study was to compare the short-term outcomes between spontaneous ventilation video-assisted thoracic surgery (SV-VATS) and mechanical ventilation video-assisted thoracic ...surgery (MV-VATS) in the elderly. All patients included in the present study underwent lobectomy, segmentectomy, or wedge resection and lymph node dissection.
A retrospective cohor.
The first affiliated hospital of Guangzhou Medical University, Guangzhou, China.
The present study included 799 elderly patients diagnosed with non-small-cell lung cancer undergoing SV-VATS or MV-VATS. After propensity score matching, 80 patients in the SV-VATS group and 80 patients in the MV-VATS group were analyzed.
Patients in the SV-VATS group received spontaneous-ventilation anesthesia, which was administered as follows: intravenous anesthesia + laryngeal mask airway + thoracic paravertebral block + visceral pleural surface anesthesia + thoracic vagus nerve block. Patients in the MV-VATS group received general endotracheal anesthesia. SV-VATS or MV-VATS was performed according to the preference of the patients.
There were no significant differences in anesthesia time (226.3 ± 79.8 v 238.5 ± 66.2 min; p = 0.44), surgery time (166.2 ± 102.6 v 170.1 ± 83.4 min; p = 0.66), and number of dissected lymph nodes (5.3 ± 7.5 v 4.4 ± 7.4; p = 0.23) between the two groups. There were significant differences in intraoperative bleeding (61.5 ± 165.1 v 82.2 ± 116.9 mL; p < 0.001). After surgery, the two groups were statistically comparable in terms of hospitalization (17.6 ± 7.6 v 17.2 ± 6.9 days; p = 0.95) and incidence of complications (7.5% v 13.8%; p = 0.20), while there were significant differences in chest tube duration (6.1 ± 3.3 v 4.5 ± 1.2 days; p < 0.001).
SV-VATS is feasible and as safe as MV-VATS, and it could be considered as an alternative treatment for the elderly.
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