Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

Sequencing-based spatial transcriptomics (ST) methods allow unbiased capturing of RNA molecules at barcoded spots, charting the distribution and localization of cell types and transcripts across a tissue. While the coarse resolution of these techniques is considered a disadvantage, we argue that the inherent proximity of transcriptomes captured on spots can be leveraged to reconstruct cellular networks. To this end, we developed ISCHIA (Identifying Spatial Co-occurrence in Healthy and InflAmed tissues), a computational framework to analyze the spatial co-occurrence of cell types and transcript species within spots. Co-occurrence analysis is complementary to differential gene expression, as it does not depend on the abundance of a given cell type or on the transcript expression levels, but rather on their spatial association in the tissue. We applied ISCHIA to analyze co-occurrence of cell types, ligands and receptors in a Visium dataset of human ulcerative colitis patients, and validated our findings at single-cell resolution on matched hybridization-based data. We uncover inflammation-induced cellular networks involving M cell and fibroblasts, as well as ligand-receptor interactions enriched in the inflamed human colon, and their associated gene signatures. Our results highlight the hypothesis-generating power and broad applicability of co-occurrence analysis on spatial transcriptomics data.

Comparative analysis of scheduling algorithms for radio resource allocation in future communication networks

BACKGROUND

Wireless links are fast becoming the key communication mode. However, as compared to the wired link, their characteristics make the traffic prone to time- and location-dependent signal attenuation, noise, fading, and interference that result in time varying channel capacities and link error rate. Scheduling algorithms play an important role in wireless links to guarantee quality of service (QoS) parameters such as throughput, delay, jitter, fairness and packet loss rate. The scheduler has vital importance in current as well as future cellular communications since it assigns resource block (RB) to different users for transmission. Scheduling algorithm makes a decision based on the information of link state, number of sessions, reserved rates and status of the session queues. The information required by a scheduler implemented in the base station can easily be collected from the downlink transmission.

METHODS

This paper reflects on the importance of schedulers for future wireless communications taking LTE-A networks as a case study. It compares the performance of four well-known scheduling algorithms including round robin (RR), best channel quality indicator (BCQI), proportional fair (PF), and fractional frequency reuse (FFR). The performance of these four algorithms is evaluated in terms of throughput, fairness index, spectral efficiency and overall effectiveness. System level simulations have been performed using a MATLAB based LTE-A Vienna downlink simulator.

RESULTS

The results show that the FFR scheduler is the best performer among the four tested algorithms. It also exhibits flexibility and adaptability for radio resource assignment.

Unique cellular network formation guided by heterostructures based on reduced graphene oxide - Ti3C2Tx MXene hydrogels

Two-dimensional (2D) materials remain highly interesting for assembling three-dimensional (3D) structures, amongst others, in the form of macroscopic hydrogels. Herein, we present a novel approach for inducing chemical inter-sheet crosslinks via an ethylenediamine mediated reaction between Ti₃C₂T_x and graphene oxide in order to obtain a reduced graphene oxide-MXene (rGO-MXene) hydrogel. The composite hydrogels are hydrophilic with a stiffness of ~20 kPa. They also possess a unique inter-connected porous architecture, which led to a hitherto unprecedented ability of human cells across three different types, epithelial adenocarcinoma, neuroblastoma and fibroblasts, to form inter-connected three-dimensional networks. The attachments of the cells to the rGO-MXene hydrogels were superior to those of the sole rGO-control gels. This phenomenon stems from the strong affinity of cellular protrusions (neurites, lamellipodia and filopodia) to grow and connect along architectural network paths within the rGO-MXene hydrogel, which could lead to advanced control over macroscopic formations of cellular networks for technologically relevant bioengineering applications, including tissue engineering and personalized diagnostic networks-on-chip. STATEMENT OF SIGNIFICANCE: Conventional hydrogels are made of interconnected polymeric fibres. Unlike conventional case, we used hydrothermal and chemical approach to form interconnected porous hydrogels made of two-dimensional flakes from graphene oxide and metal carbide from a new family of MXenes (Ti₃C₂T_x). This way, we formed three-dimensional porous hydrogels with unique porous architecture of well-suited chemical surfaces and stiffness. Cells from three different types cultured on these scaffolds formed extended three-dimensional networks - a feature of extended cellular proliferation and pre-requisite for formation of organoids. Considering the studied 2D materials typically constitute materials exhibiting enhanced supercapacitor performances, our study points towards better understanding of design of tissue engineering materials for the future bioengineering fields including personalized diagnostic networks-on-chip, such as artificial heart actuators.