Nevin Manimala

Integr Comp Biol. 2022 Apr 22:icac015. doi: 10.1093/icb/icac015. Online ahead of print.

ABSTRACT

Arboreal animals must learn to modulate their movements to overcome the challenges posed by the complexity of their heterogeneous environment, reduce performance failure, and survive. Anolis lizards are remarkable in the apparent ease with which they conquer this heterogeneity, demonstrating an impressive ability to modulate their locomotor behavior to maintain stable locomotion on widely disparate surfaces. Significant progress has been made towards understanding the impact of substrate structure on the behavioral plasticity of arboreal species, but it is unclear whether the same strategies employed to shift between substrates in one context can be employed to shift between those same substrates in a new context. Is the kinematic shift between broad and narrow perches achieved in a similar way on different inclines? Do all species within an ecomorph make similar adjustments? Here, we analyze the limb movements of two trunk-crown Anolis ecomorphs, A. carolinensis and A. evermanni, running on 6 different surfaces (3 inclinations × 2 perch diameters), from the perspective of Transfer Learning. Transfer learning is that field of machine learning which aims at exploiting the knowledge gained from one task to improve generalization about another, related task. In our setting, we use transfer learning to show that the strategies employed to improve locomotor stability on narrow perches are transferred across environments with different inclines. Further, behaviors used on vertical inclines are shared, and thus transfer well, across perch diameters whereas the relationship between horizontal and intermediate inclines change on different perch diameters, leading to lower transfer learning of shallow inclines across perch diameters. Interestingly, the best incline for transfer of behavior differs between limbs: forelimb models learn best from the vertical incline and hind limb models learn best from horizontal and intermediate inclines. Finally, our results suggest both that subtle differences exist in how A. carolinensis and A. evermanni adjust their behaviors in typical trunk-crown environments and that they may have converged on similar strategies for modulating forelimb behavior on vertical surfaces and hind limb behavior on shallow surfaces. The transfer of behavior is analogous to phenotypic plasticity, which likely plays a key role in the rapid adaptive evolution characteristic of Anolis lizards. This work is an example of how modern statistical methodology can provide an interesting perspective on new biological questions, such as on the role and nuances of behavioral plasticity and the key behaviors that help shape the versatility and rapid evolution of Anolis lizards.

PMID:35451476 | DOI:10.1093/icb/icac015

G3 (Bethesda). 2022 Apr 22:jkac094. doi: 10.1093/g3journal/jkac094. Online ahead of print.

ABSTRACT

By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. We show that many of the events show a relative rate of duplicate gene loss prior to the first post-polyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate post-polyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with two distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (RGL; alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is therefore possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass RGL barriers.

PMID:35451464 | DOI:10.1093/g3journal/jkac094

Bioinformatics. 2022 Apr 22:btac288. doi: 10.1093/bioinformatics/btac288. Online ahead of print.

ABSTRACT

MOTIVATION: Elucidating the topology of gene regulatory networks (GRNs) from large single-cell RNA sequencing (scRNAseq) datasets, while effectively capturing its inherent cell-cycle heterogeneity and dropouts, is currently one of the most pressing problems in computational systems biology. Recently, graph learning (GL) approaches based on graph signal processing (GSP) have been developed to infer graph topology from signals defined on graphs. However, existing GL methods are not suitable for learning signed graphs, a characteristic feature of GRNs, which are capable of accounting for both activating and inhibitory relationships in the gene network. They are also incapable of handling high proportion of zero values present in the single cell datasets.

RESULTS: To this end, we propose a novel signed GL approach, scSGL, that learns GRNs based on the assumption of smoothness and non-smoothness of gene expressions over activating and inhibitory edges, respectively. scSGL is then extended with kernels to account for non-linearity of co-expression and for effective handling of highly occurring zero values. The proposed approach is formulated as a non-convex optimization problem and solved using an efficient ADMM framework. Performance assessment using simulated datasets demonstrates the superior performance of kernelized scSGL over existing state of the art methods in GRN recovery. The performance of scSGL is further investigated using human and mouse embryonic datasets.

AVAILABILITY AND IMPLEMENTATION: The scSGL code and analysis scripts are available on https://github.com/Single-Cell-Graph-Learning/scSGL.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35451460 | DOI:10.1093/bioinformatics/btac288

Medicine (Baltimore). 2022 Mar 11;101(10):e29034. doi: 10.1097/MD.0000000000029034.

ABSTRACT

BACKGROUND: There is currently no pooled data in the literature to support whether additional facet joint block results in better clinical analgesia after percutaneous kyphoplasty. We assessed the existing evidence on the safety and efficacy of facet joint block in the treatment of patients with thoracolumbar compression fractures undergoing percutaneous kyphoplasty based on qualified trials.

METHODS: We will search PubMed, Springer, ScienceDirect, Wanfang, and Cochrane Library databases through April, 2022. Cohort studies focusing on assessing and comparing the effect of facet joint block and control group will be included. The studies are screened and evaluated by 2 reviewers independently for eligibility. The following outcome measures must be showed: pain scores, Oswestry Disability Index, satisfaction, and complications observed within both groups from baseline to the end of follow-up period. Review Manager software (v 5.3; Cochrane Collaboration) is used for the meta-analysis. A P value of <.05 is considered to be statistically significant. Two independent reviewers will assess the risk of bias of the included studies at study level.

RESULTS: It is hypothesized that additional facet joint block is associated with better pain control.

CONCLUSIONS: This study expects to provide credible and scientific evidence for the efficacy and safety of facet joint block in the treatment of patients with thoracolumbar compression fractures undergoing percutaneous kyphoplasty.

REGISTRATION NUMBER: 10.17605/OSF.IO/ARY3C.

PMID:35451411 | DOI:10.1097/MD.0000000000029034

Medicine (Baltimore). 2022 Mar 11;101(10):e29021. doi: 10.1097/MD.0000000000029021.

ABSTRACT

Although glucocorticoids are commonly used for patients with acute respiratory distress syndrome in the intensive care unit, the exact attitudes of different intensive care unit (ICU) doctors about glucocorticoid usage are largely unknown. Herein, we investigated the practice of glucocorticoid application for acute respiratory distress syndrome (ARDS) by ICU doctors in China. Questionnaires were developed and sent to ICU doctors at 45 hospitals to perform statistics and analysis. ICU doctors with more working experience and professional titles had more knowledge of ARDS. Glucocorticoids were more likely to be used for ARDS caused by chemical inhalation. Doctors with longer working experience, better educational background, and higher professional titles used fewer glucocorticoids. In addition, 97.2%of the doctors considered using methylprednisolone or hydrocortisone first, 50.9% used glucocorticoids within 24hours of onset, and 37.1% insisted that steroid therapy should last 3 to 5days. Although ICU doctors with more working experience and professional titles have a better understanding of glucocorticoid use in ARDS, the majority of clinical practices and attitudes are similar among different doctors regardless of working experience, educational background, professional titles, or hospital grades.

PMID:35451401 | DOI:10.1097/MD.0000000000029021

Medicine (Baltimore). 2022 Mar 11;101(10):e28993. doi: 10.1097/MD.0000000000028993.

ABSTRACT

OBJECTIVE: The aim of this study was to find the optimum dosage of dexmedetomidine in Spinal Orthopedic Scoliosis Correction Surgery when used in combination with propofol and remifentanil in American Society of Anesthesiologists (ASA) III patients with severe scoliosis undergoing intraoperative wake-up test.

MATERIALS AND METHODS: We selected a total of 60 ASA III ≤40 years old patients who underwent Spinal Orthopedic Scoliosis Correction Surgery (SOSCS) and randomized them into groups A, B, and C. Group A was administered 0.2 μg/(kg·h) of dexmedetomidine, group B 0.3 μg/(kg·h), and group C 0.4 μg/(kg·h). The main parameters monitored were: wake-up time; wake-up quality; adverse effects that occur while the patient is awake; postoperative awareness of intraoperative wake-up test; heart rate (HR); mean arterial pressure (MAP); and oxygen saturation (SpO2). Values of these parameters were monitored at 7 timestamps separated by 5 minutes >30 minutes.

RESULTS: Group B had a higher MAP at 10 minutes before wake-up (P = .03) and at the moment of wake-up (P = .04) than group A. The Wake-up time of group A was 14.95 ± 7.42 minutes, group B was 14.7 ± 6.52 minutes, which was significantly shorter than that of group C 21.3 ± 10.02 minutes (P = .02). The wake-up quality was excellent. All other parameters had no significant statistical differences.

CONCLUSION: Doses of 0.2 to 0.3 μg/(kg·h) have shorter wake-up time and fewer hemodynamic fluctuations compared to 0.4 μg/(kg·h).

PMID:35451391 | DOI:10.1097/MD.0000000000028993

Medicine (Baltimore). 2022 Mar 11;101(10):e28982. doi: 10.1097/MD.0000000000028982.

ABSTRACT

BACKGROUND: Aromatase inhibitor-associated musculoskeletal symptoms (AIMSS) are among the most common prominent side effects in patients using aromatase inhibitors (AIs) for breast cancer. Muscle and joint pain, morning stiffness, arthritis, and bone loss are common clinical symptoms in individuals. Traditional Chinese medicine (TCM) has been demonstrated to be useful in the treatment of AIMSS in previous investigations, although the sample sizes were limited, and systematic reviews were inadequate. The effectiveness and safety of TCM in the treatment of AIMSS will be investigated in this study.

METHODS: Randomized controlled trials from January 2010 to October 2021 were limited to English or Chinese. We searched PubMed, EMBASE, Cochrane Library, Web of Science, Medline, China Biomedical Database (CBM), China National Knowledge Infrastructure (CNKI), Wanfang database, and the VIP database. Two researchers reviewed the literature and retrieved the data independently. Review Manager V5.3.was used to conduct the statistical analysis.

RESULTS: This systematic review and meta-analysis presents the most recent data on the use of TCM to treat AIMSS and offers a scientifically sound foundation for therapeutic practice. Upon completion, the findings will be submitted to a peer-reviewed journal.

ETHICS AND DISSEMINATION: As the systematic review protocol did not involve human subjects, ethical approval was not required.

PROSPERO REGISTRATION NUMBER: CRD42020192553.

PMID:35451389 | DOI:10.1097/MD.0000000000028982

Medicine (Baltimore). 2022 Mar 11;101(10):e28977. doi: 10.1097/MD.0000000000028977.

ABSTRACT

Heart rate variability (HRV) is an important cardiac health marker, with lower values indicating a reduction in vagal control of cardiac rhythm and decreasing significantly with advancing age. In this study, we evaluated the effects of strength exercises for the upper and lower limbs on cardiac autonomic modulation in elderly women.We registered 29 participants using a portable RS800CX heart rate monitor to record the RR intervals. For the collection of HRV data, the volunteers remained seated at rest for 10 minutes. After the rest period, the participants performed the exercises. Immediately after the exercise protocol, the subjects remained seated at rest for 30 minutes. HRV indices were analyzed in the following periods: rest, 0 to 10 minutes, 5 to 10 minutes, 10 to 20 minutes, and 20 to 30 minutes. Systolic arterial pressure and diastolic arterial pressure were measured in the following periods: rest, immediately after exercise, and 30 minutes after exercise.Regarding the mean of the RR intervals, heart rate, and indexes of the time and frequency domains surveyed, there were no statistically significant differences between the 4 moments in the protocols for upper and lower limbs. No significant differences were found in systolic and diastolic pressures between the 3 time points surveyed in the protocols for the upper and lower limbs.Resistance exercises performed with low-intensity loads and a greater number of repetitions did not promote significant variations in cardiac autonomic modulation and blood pressure levels, showing good safety in elderly women.

PMID:35451388 | DOI:10.1097/MD.0000000000028977

Environ Sci Pollut Res Int. 2022 Apr 22. doi: 10.1007/s11356-022-20166-5. Online ahead of print.

ABSTRACT

Pethoxamid is chloroacetamide herbicide. Pethoxamid is commonly used to kill different weeds in various crops. Pethoxamid can leach in the water and soil and can cause toxic effects to other non-target species. Current study is therefore aimed to perform the investigation of the cytotoxic and genotoxic effects of pethoxamid on Allium cepa cells.The root growth, mitotic index (MI), chromosomal aberrations (CAs), and DNA damage were assessed through root growth inhibition, A. cepa ana-telophase, and alkaline comet assays, respectively. Furthermore, molecular docking was performed to evaluate binding affinity of pethoxamid on DNA and very-long-chain fatty acid (VLCFA) synthases. In root growth inhibition test, onion root length was statistically significantly decreased in a concentration dependent manner. Concentration- and time-dependent decreases in MI were observed, whereas increase in CAs such as disturbed ana-telophase, chromosome laggards, stickiness, anaphase bridges, and DNA damage was caused by the pethoxamid on A. cepa root cells. Molecular docking revealed that pethoxamid binds selectively to GC-rich regions in the minor groove of the DNA structure and showed remarkable binding affinity against all synthases taking part in the sequential biosynthesis of VLCFAs. It was concluded that the pethoxamid-induced genotoxicity and cytotoxicity may be through multiple binding ability of this herbicide with DNA and VLCFA synthases.

PMID:35449332 | DOI:10.1007/s11356-022-20166-5

Environ Sci Pollut Res Int. 2022 Apr 21. doi: 10.1007/s11356-022-20227-9. Online ahead of print.

ABSTRACT

The assessment of the generalization of the strict hypertension definition in the 2017 ACC/AHA Hypertension Guideline from environmental condition remains sparse. The aims of this study are to investigate and compare the associations of ambient air pollution and traffic-related pollution (TRP) with hypertension defined by the different criteria. A total of 32,135 participants were recruited from the baseline survey of the CHCN-BTH in 2017. We defined hypertension as SBP/DBP ≥ 140/90 mmHg according to the hypertension guidelines in China, Japan, Europe and ISH (traditional criteria) and defined as SBP/DBP ≥ 130/80 mmHg according to the 2017 ACC/AHA Hypertension Guideline (strict criteria). A two-level generalized linear mixed models were applied to investigate the associations of air pollutants (i.e. PM_2.5, SO₂, NO₂) and TRP with blood pressure (BP) measures and hypertension. Stratified analyses and two-pollutant models were also performed. The stronger associations of air pollutants were found in the hypertension defined by the strict criteria than that defined by the traditional criteria. The ORs per an IQR increase in PM_2.5 were 1.17 (95% CI: 1.09, 1.25) for the strict criteria and 1.14 (95% CI: 1.06, 1.23) for the traditional criteria. The similar conditions were also observed for TRP. The above results were robust in both stratified analyses and two-pollutant models. Our study assessed the significance of the hypertension defined by the strict criteria from environmental aspect and called attention to the more adverse effects of air pollution and TRP on the earlier stage of hypertension.

PMID:35449329 | DOI:10.1007/s11356-022-20227-9