Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa, Jaculus jaculus.

Vertebrate animals that run or jump across sparsely vegetated habitats, such as horses and jerboas, have reduced the number of distal limb bones, and many have lost most or all distal limb muscle. We previously showed that nascent muscles are present in the jerboa hindfoot at birth and that these myofibers are rapidly and completely lost soon after by a process that shares features with pathological skeletal muscle atrophy. Here, we apply an intra- and interspecies differential RNA-Seq approach, comparing jerboa and mouse muscles, to identify gene expression differences associated with the initiation and progression of jerboa hindfoot muscle loss. We show evidence for reduced hepatocyte growth factor and fibroblast growth factor signaling and an imbalance in nitric oxide signaling; all are pathways that are necessary for skeletal muscle development and regeneration. We also find evidence for phagosome formation, which hints at how myofibers may be removed by autophagy or by nonprofessional phagocytes without evidence for cell death or immune cell activation. Last, we show significant overlap between genes associated with jerboa hindfoot muscle loss and genes that are differentially expressed in a variety of human muscle pathologies and rodent models of muscle loss disorders. All together, these data provide molecular insight into the process of evolutionary and developmental muscle loss in jerboa hindfeet.

Compact machine learning model for the accurate prediction of first 24-hour survival of mechanically ventilated patients.

Background: The field of machine learning has been evolving and applied in medical applications. We utilised a public dataset, MIMIC-III, to develop compact models that can accurately predict the outcome of mechanically ventilated patients in the first 24 h of first-time hospital admission. Methods: 67 predictive features, grouped into 6 categories, were selected for the classification and prediction task. 4 tree-based algorithms (Decision Tree, Bagging, eXtreme Gradient Boosting and Random Forest), and 5 non-tree-based algorithms (Logistic Regression, K-Nearest Neighbour, Linear Discriminant Analysis, Support Vector Machine and Naïve Bayes), were employed to predict the outcome of 18,883 mechanically ventilated patients. 5 scenarios were crafted to mirror the target population as per existing literature. S1.1 reflected an imbalanced situation, with significantly fewer mortality cases than survival ones, and both the training and test sets played similar target class distributions. S1.2 and S2.2 featured balanced classes; however, instances from the majority class were removed from the test set and/or the training set. S1.3 and S 2.3 generated additional instances of the minority class via the Synthetic Minority Over-sampling Technique. Standard evaluation metrics were used to determine the best-performing models for each scenario. With the best performers, Autofeat, an automated feature engineering library, was used to eliminate less important features per scenario. Results: Tree-based models generally outperformed the non-tree-based ones. Moreover, XGB consistently yielded the highest AUC score (between 0.91 and 0.97), while exhibiting relatively high Sensitivity (between 0.58 and 0.88) on 4 scenarios (1.2, 2.2, 1.3, and 2.3). After reducing a significant number of predictors, the selected calibrated ML models were still able to achieve similar AUC and MCC scores across those scenarios. The calibration curves of the XGB and BG models, both prior to and post dimension reduction in Scenario 2.2, showed better alignment to the perfect calibration line than curves produced from other algorithms. Conclusion: This study demonstrated that dimension-reduced models can perform well and are able to retain the important features for the classification tasks. Deploying a compact machine learning model into production helps reduce costs in terms of computational resources and monitoring changes in input data over time.

Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus.

Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and we achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Increasing amphiphile concentrations induce rounding of droplets, prevent droplet fusion, and, at high concentrations, cause full dispersal of droplets. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that the addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of transcriptional cluster formation in biological cells using relatively simple DNA sequence-programmable nanostructures, opening novel ways to control the mesoscopic organization of synthetic nanomaterials.

A DNA Segregation Module for Synthetic Cells.

The bottom-up construction of an artificial cell requires the realization of synthetic cell division. Significant progress has been made toward reliable compartment division, yet mechanisms to segregate the DNA-encoded informational content are still in their infancy. Herein, droplets of DNA Y-motifs are formed by liquid-liquid phase separation. DNA droplet segregation is obtained by cleaving the linking component between two populations of DNA Y-motifs. In addition to enzymatic cleavage, photolabile sites are introduced for spatio-temporally controlled DNA segregation in bulk as well as in cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). Notably, the segregation process is slower in confinement than in bulk. The ionic strength of the solution and the nucleobase sequences are employed to regulate the segregation dynamics. The experimental results are corroborated in a lattice-based theoretical model which mimics the interactions between the DNA Y-motif populations. Altogether, engineered DNA droplets, reconstituted in GUVs, can represent a strategy toward a DNA segregation module within bottom-up assembled synthetic cells.

Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas.

Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.

Evolutionary loss of foot muscle during development with characteristics of atrophy and no evidence of cell death.

Many species that run or leap across sparsely vegetated habitats, including horses and deer, evolved the severe reduction or complete loss of foot muscles as skeletal elements elongated and digits were lost, and yet the developmental mechanisms remain unknown. Here, we report the natural loss of foot muscles in the bipedal jerboa, Jaculus jaculus. Although adults have no muscles in their feet, newborn animals have muscles that rapidly disappear soon after birth. We were surprised to find no evidence of apoptotic or necrotic cell death during stages of peak myofiber loss, countering well-supported assumptions of developmental tissue remodeling. We instead see hallmarks of muscle atrophy, including an ordered disassembly of the sarcomere associated with upregulation of the E3 ubiquitin ligases, MuRF1 and Atrogin-1. We propose that the natural loss of muscle, which remodeled foot anatomy during evolution and development, involves cellular mechanisms that are typically associated with disease or injury.

Changing While Staying the Same: Preservation of Structural Continuity During Limb Evolution by Developmental Integration.

More than 150 years since Charles Darwin published "On the Origin of Species", gradual evolution by natural selection is still not fully reconciled with the apparent sudden appearance of complex structures, such as the bat wing, with highly derived functions. This is in part because developmental genetics has not yet identified the number and types of mutations that accumulated to drive complex morphological evolution. Here, we consider the experimental manipulations in laboratory model systems that suggest tissue interdependence and mechanical responsiveness during limb development conceptually reduce the genetic complexity required to reshape the structure as a whole. It is an exciting time in the field of evolutionary developmental biology as emerging technical approaches in a variety of non-traditional laboratory species are on the verge of filling the gaps between theory and evidence to resolve this sesquicentennial debate.

Cost-effectiveness analysis of active management of third-stage labour in Vietnam.

Active management of the third stage of labour (AMTSL) using oxytocin substantially reduces postpartum haemorrhage (PPH), a leading cause of maternal mortality. An economic analysis of the use of AMTSL was conducted as part of an intervention study in Thanh Hoa Province, Vietnam. A spreadsheet was used to calculate various scenarios and estimate the costs and outcomes of the routine use of AMTSL with oxytocin in Uniject compared with oxytocin in ampoules, and AMTSL compared with no AMTSL. We estimated the health outcomes from probabilities that were generated from the effectiveness portion of the AMTSL intervention project. The study also estimates the costs of treating PPH and the net incremental costs of AMTSL (costs and savings); examines the impact of different scenarios of PPH rate and Uniject cost; and estimates the potential cost per PPH case and PPH death averted. The additional net cost per woman of providing AMTSL with ampoules was just US dollar 0.20 in the base case; using Uniject devices added only US dollar 0.08 more per woman to the ampoule cost. Varying the rate of PPH had the biggest effect; if the underlying PPH rate were 8%, the incremental cost of AMTSL drops to just US dollar 0.07 per woman with ampoules and the cost to avert a case of PPH is US dollar 2.10 with ampoules and US dollar 4.52 with Uniject. The low net incremental cost of AMTSL suggests that the introduction of AMTSL in primary-level facilities in Vietnam can reduce the incidence of PPH and benefit women's health without adding much to national health care costs.

Telithromycin: a novel agent for the treatment of community-acquired upper respiratory infections.

The ketolides are a new subclass of macrolides, and telithromycin is the first of these agents to be approved. Modifications to the basic macrolide structure result in enhanced activity against penicillin- and erythromycin resistant respiratory pathogens. It is therefore an option in the treatment of mild to moderate community-acquired respiratory infections, such as pneumonia, acute exacerbations of chronic bronchitis, pharyngitis/tonsillitis, and sinusitis. Telithromycin also offers the advantages of once-daily dosing and a shorter course of therapy in certain infections. Comparative clinical trials, although limited and involving only a small number of resistant organisms, showed the equivalence of telithromycin to existing therapies, although telithromycin generally had a higher frequency of mild to moderate gastrointestinal adverse effects. Further clinical and safety data, especially in patients with resistant organisms, are needed.