Machine Learning for Uncovering Biological Insights in Spatial Transcriptomics Data

Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed immunofluorescence and spatial transcriptomics (ST) provide exciting new opportunities to augment our fundamental understanding of these processes in health and disease. The large and complex datasets resulting from these techniques, particularly ST, have led to rapid development of innovative machine learning (ML) tools primarily based on deep learning techniques. These ML tools are now increasingly featured in integrated experimental and computational workflows to disentangle signals from noise in complex biological systems. However, it can be difficult to understand and balance the different implicit assumptions and methodologies of a rapidly expanding toolbox of analytical tools in ST. To address this, we summarize major ST analysis goals that ML can help address and current analysis trends. We also describe four major data science concepts and related heuristics that can help guide practitioners in their choices of the right tools for the right biological questions

CHEMICAL AND PHASE TRANSFORMATION FROM VANADIUM SULFIDE TO OXIDE VIA A NEW CHEMICAL ROUTE FOR THE SYNTHESIS OF Βʹ-LIXV2O5 AS A HIGH PERFORMANCE CATHODE

The used of rechargeable lithium ion batteries are so widely nowadays on consumer electronics especially portable devices such as cellphones, laptops and etc. The advancement of technology has created batteries with providing high energy density without memory effect and minimum the self-discharge on standby mode. Even with these features, researchers are still trying to improve the batteries with more energy density, low cost, better safety and high durability. The energy density improves with high operation voltage and high capacity. All these features came from one source, material. The resources for current commercial cathode material are decreasing and so new alternative cathode with high performance is needed to replace the commercial cathode in the future. The high temperature vanadium pentoxide phase, βʹ-LixV2O5, was synthesized via a new chemical synthesis involving the evolution of vanadium oxides from the 600°C heat treatment of the pure LiVS2 in air. By employing this method of synthesis, well-crystalized, rod-shaped βʹ-LixV2O5 particles 20 – 30 μm in length and 3 – 6 μm in width were obtained. Moreover, the surface of βʹ-LixV2O5 particles was found to be coated by an amorphous vanadium oxysulfide film (~20 nm in thickness). In contrast to a low temperature vanadium pentoxide phase (LixV2O5), the electrochemical intercalation of lithium into the βʹ-LixV2O5 was fully reversible where 0.0 < x < 2.0, and it delivered a capacity of 310 mAh/g at a current rate of 0.07 C between 1.5 V and 4 V. Good capacity retention of more than 88% was also observed after 50 cycles even at a higher current rate of 2 C

AQUEOUS LIQUID SOLUTIONS FOR LI-LIQUID BATTERY

poster abstractThe evolvement of Lithium-ion battery industries has begun to carry the industries to step in a new revolution. Consequently, high demand in high energy density batteries in many electronic and electrical appliances, espe-cially energy storage industries been emerged. This new type of batteries has been in extensive research, such as lithium-water battery. Lithium-water battery is a newly developed battery with lithium as the anode and water as the cathode. Lithium is known as one of the most reac-tive metals in periodic table. Therefore, rigorous reaction will be observed when lithium is reacted with water and hence potentially providing an ex-tremely high energy density. This rigorous reaction can be converted into electrical energy and can be stored in a cell. Lithium-water battery is novel and hence, there is no standardized design. In this presentation, lithium anode is separated from water by liquid electrolyte and a ceramic solid electrolyte. The glass-ceramic solid electro-lyte which has Li1.3Ti1.7Al0.3(PO4)3 composition plays an important role of the design of this lithium–water battery. The main purpose of the solid electro-lyte is to separate water from lithium, avoiding a dangerous exothermic re-action. Also, the presence of the super-ionic conductor ceramic can provide very high lithium ion conductivity. The different sizes of solid electrolytes were used in designing Li-liquid battery cell. The effect of the electrolyte size on the voltage of the cell was studied to optimize the cell design. Then, the aqueous solutions containing different chemicals were tested as the liquid cathodes, and their electro-chemical performance were compared to those of the pure DI water. Further results will be presented in the poster presentation

What is the function of mitochondrial networks? A theoretical assessment of hypotheses and proposal for future research

Mitochondria can change their shape from discrete isolated organelles to a large continuous reticulum. The cellular advantages underlying these fused networks are still incompletely understood. In this paper, we describe and compare hypotheses regarding the function of mitochondrial networks. We use mathematical and physical tools both to investigate existing hypotheses and to generate new ones, and we suggest experimental and modelling strategies. Among the novel insights we underline from this work are the possibilities that (i) selective mitophagy is not required for quality control because selective fusion is sufficient; (ii) increased connectivity may have non-linear effects on the diffusion rate of proteins; and (iii) fused networks can act to dampen biochemical fluctuations. We hope to convey to the reader that quantitative approaches can drive advances in the understanding of the physiological advantage of these morphological changes

A novel ensemble artificial intelligence approach for gully erosion mapping in a semi-arid watershed (Iran)

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. In this study, we introduced a novel hybrid artificial intelligence approach of rotation forest (RF) as a Meta/ensemble classifier based on alternating decision tree (ADTree) as a base classifier called RF-ADTree in order to spatially predict gully erosion at Klocheh watershed of Kurdistan province, Iran. A total of 915 gully erosion locations along with 22 gully conditioning factors were used to construct a database. Some soft computing benchmark models (SCBM) including the ADTree, the Support Vector Machine by two kernel functions such as Polynomial and Radial Base Function (SVM-Polynomial and SVM-RBF), the Logistic Regression (LR), and the Naïve Bayes Multinomial Updatable (NBMU) models were used for comparison of the designed model. Results indicated that 19 conditioning factors were effective among which distance to river, geomorphology, land use, hydrological group, lithology and slope angle were the most remarkable factors for gully modeling process. Additionally, results of modeling concluded the RF-ADTree ensemble model could significantly improve (area under the curve (AUC) = 0.906) the prediction accuracy of the ADTree model (AUC = 0.882). The new proposed model had also the highest performance (AUC = 0.913) in comparison to the SVM-Polynomial model (AUC = 0.879), the SVM-RBF model (AUC = 0.867), the LR model (AUC = 0.75), the ADTree model (AUC = 0.861) and the NBMU model (AUC = 0.811)

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder—implications of a copy number variation involving DPP10

published_or_final_versio

Simvastatin inhibits the expression of inflammatory cytokines and cell adhesion molecules induced by LPS in human dental pulp cells

AimTo investigate the effect of simvastatin on lipopolysaccharide (LPS)‐stimulated inflammatory cytokines, cell adhesion molecules and nuclear factor‐κB (NF‐κB) transcription factors in human dental pulp cells (HDPCs).MethodologyThe effect of LPS and simvastatin on human dental pulp cell (HDPCs) viability was measured using a 3‐[4, 5‐dimethylthiazol‐2‐yl]‐2, 5 diphenyltetrazolium bromide (MTT) assay. The expression of inflammatory cytokines and cell adhesion molecules was evaluated by reverse‐transcription polymerase chain reaction (RT‐PCR), enzyme‐linked immunosorbent assay (ELISA) and Western blot analysis. NF‐κB transcription factors were evaluated by Western blot analysis. Statistical analysis was performed with analysis of variance (anova).ResultsThe viability of cells exposed to different concentrations of E. coli LPS, P. gingivalis LPS and simvastatin was not significantly different compared with that of control cells (P > 0.05). LPS significantly increased interleukin (IL)‐1β (P < 0.05) and IL‐6 mRNA expression (P < 0.05) and vascular cell adhesion molecule‐1 (VCAM‐1) (P < 0.05) and intercellular adhesion molecule‐1 (ICAM‐1) protein expression (P < 0.05) in HDPCs. Treatment with simvastatin significantly attenuated LPS‐stimulated production of IL‐1β, IL‐6, VCAM‐1 and ICAM‐1 (P < 0.05). Treatment with simvastatin decreased LPS‐induced expression of p65 and phosphorylation of IκB and also significantly decreased the phosphorylation of p65 and IκB in the cytoplasm and the level of p65 in the nucleus (P < 0.05).ConclusionsSimvastatin has a suppressing effect on LPS‐induced inflammatory cytokine, cell adhesion molecules and NF‐κB transcription factors in HDPCs. Therefore, simvastatin might be a useful candidate as a pulp‐capping agent in vital pulp therapy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136436/1/iej12635_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136436/2/iej12635.pd

The role of Cx36 and Cx43 in 4‐aminopyridine‐induced rhythmic activity in the spinal nociceptive dorsal horn: an electrophysiological study in vitro

Connexin (Cx) proteins and gap junctions support the formation of neuronal and glial syncytia that are linked to different forms of rhythmic firing and oscillatory activity in the CNS. In this study, quantitative reverse transcription polymerase chain reaction (RT‐qPCR) was used to profile developmental expression of two specific Cx proteins, namely glial Cx43 and neuronal Cx36, in postnatal lumbar spinal cord aged 4, 7, and 14 days. Extracellular electrophysiology was used to determine the contribution of Cx36 and Cx43 to a previously described form of 4‐aminopyridine (4‐AP)‐induced 4–12 Hz rhythmic activity within substantia gelatinosa (SG) of rat neonatal dorsal horn (DH) in vitro. The involvement of Cx36 and Cx43 was probed pharmacologically using quinine, a specific uncoupler of Cx36 and the mimetic peptide blocker Gap 26 which targets Cx43. After establishment of 4–12 Hz rhythmic activity by 4‐AP (25 μmol/L), coapplication of quinine (250 μmol/L) reduced 4‐AP‐induced 4–12 Hz rhythmic activity (P < 0.05). Preincubation of spinal cord slices with Gap 26 (100 μmol/L), compromised the level of 4‐AP‐induced 4–12 Hz rhythmic activity in comparison with control slices preincubated in ACSF alone (P < 0.05). Conversely, the nonselective gap junction “opener” trimethylamine (TMA) enhanced 4–12 Hz rhythmic behavior (P < 0.05), further supporting a role for Cx proteins and gap junctions. These data have defined a physiological role for Cx36 and Cx43 in rhythmic firing in SG, a key nociceptive processing area of DH. The significance of these data in the context of pain and Cx proteins as a future analgesic drug target requires further study

Detection of regulator genes and eQTLs in gene networks

Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression levels of nearby genes (they are "expression quantitative trait loci" or eQTLs for short) and presumably play a gene regulatory role, affecting the status of molecular networks of interacting genes, proteins and metabolites. Computational systems biology approaches to reconstruct causal gene networks from large-scale omics data have therefore become essential to understand the structure of networks controlled by eQTLs together with other regulatory genes, and to generate detailed hypotheses about the molecular mechanisms that lead from genotype to phenotype. Here we review the main analytical methods and softwares to identify eQTLs and their associated genes, to reconstruct co-expression networks and modules, to reconstruct causal Bayesian gene and module networks, and to validate predicted networks in silico.Comment: minor revision with typos corrected; review article; 24 pages, 2 figure

A hybrid solid electrolyte for flexible solid-state sodium batteries

Development of Na-ion battery electrolyte with high-performance electrochemical properties and high safety is still challenging to achieve. In this study, we report on a NASICON (Na3Zr2Si2PO12)-based composite hybrid solid electrolyte (HSE) designed for use in a high safety solid-state sodium battery for the first time. The composite HSE design yields the required solid-state electrolyte properties for this application, including high ionic conductivity, a wide electrochemical window, and high thermal stability. The solid-state batteries of half-cell type exhibit an initial discharge capacity of 330 and 131 mA h g(-1) for a hard carbon anode and a NaFePO4 cathode at a 0.2C-rate of room temperature, respectively. Moreover, a pouch-type flexible solid-state full-cell comprising hard carbon/HSE/NaFePO4 exhibits a highly reversible electrochemical reaction, high specific capacity, and a good, stable cycle life with high flexibility.open0