NVB-tree: Failure-Atomic B+-tree for Persistent Memory

Department of Computer EngineeringEmerging non-volatile memory has opened new opportunities to re-design the entire system software stack and it is expected to break the boundaries between memory and storage devices to enable storage-less systems. Traditionally, B-tree has been used to organize data blocks in storage systems. However, B-tree is optimized for disk-based systems that read and write large blocks of data. When byte-addressable non-volatile memory replaces the block device storage systems, the byte-addressability of NVRAM makes it challenge to enforce the failure-atomicity of B-tree nodes. In this work, we present NVB-tree that addresses this challenge, reducing cache line flush overhead and avoiding expensive logging methods. NVB-tree is a hybrid tree that combines the binary search tree and the B+-tree, i.e., keys in each NVB-tree node are stored as a binary search tree so that it can benefit from the byte-addressability of binary search trees. We also present a logging-less split/merge scheme that guarantees failure-atomicity with 8-byte memory writes. Our performance study shows that NVB-tree outperforms the state-of-the-art persistent index - wB+-tree by a large margin.ope

Mixed cultures of Kimchi lactic acid bacteria show increased cell density and lactate productivity

This study was carried out to determine the characteristics of cell growth, lactate production and amino acid secretion among four kimchi lactic acid bacteria (Leuconostoc mesenteroides JEI, Leuconostoc kimchi 132, Lactobacillus sakei 171, and Weissella koreensis 521) alone and in selected mixtures. In solo culture, L. sakei 171 was superior in cell growth, lactate production and the release of amino acids to the extracellular medium. In contrast, W. koreensis 521 showed the least cell growth, lactate production and amino acid release among the tested bacteria. W. koreensis 521 consumed essential amino acids for growth, whereas L. sakei 171 released several of the essential amino acids important for the growth of W. koreensis 521. When we mixed L. sakei 171 and W. koreensis 521 at optimal concentrations, the obtained cell growth and lactic acid production were higher than those seen with either strain alone, presumably reflecting mutual effects between the two strains. Mixed culture of two kimchi lactobacilli on batch fermentation increased the cell density and lactic acid production with low nutrients consumption. These results suggest that mixed culturing of kimchi lactobacilli may be more effective than single culturing of kimchi lactic acid bacteria for improving lactic acid production.Keywords: Kimchi lactic acid bacteria, amino acid utilization, nutrients consumption.African Journal of BiotechnologyVol. 12(25), pp. 4000-400

Quantitative Screening of Cervical Cancers for Low-Resource Settings: Pilot Study of Smartphone-Based Endoscopic Visual Inspection After Acetic Acid Using Machine Learning Techniques

Background: Approximately 90% of global cervical cancer (CC) is mostly found in low- and middle-income countries. In most cases, CC can be detected early through routine screening programs, including a cytology-based test. However, it is logistically difficult to offer this program in low-resource settings due to limited resources and infrastructure, and few trained experts. A visual inspection following the application of acetic acid (VIA) has been widely promoted and is routinely recommended as a viable form of CC screening in resource-constrained countries. Digital images of the cervix have been acquired during VIA procedure with better quality assurance and visualization, leading to higher diagnostic accuracy and reduction of the variability of detection rate. However, a colposcope is bulky, expensive, electricity-dependent, and needs routine maintenance, and to confirm the grade of abnormality through its images, a specialist must be present. Recently, smartphone-based imaging systems have made a significant impact on the practice of medicine by offering a cost-effective, rapid, and noninvasive method of evaluation. Furthermore, computer-aided analyses, including image processing-based methods and machine learning techniques, have also shown great potential for a high impact on medicinal evaluations

Hepatic Cellular Distribution of Silica Nanoparticles by Surface Energy Modification

The cellular distribution of silica nanoparticles (NPs) in the liver is not well understood. Targeting specific cells is one of the most important issues in NP-based drug delivery to improve delivery efficacy. In this context, the present study analyzed the relative cellular distribution pattern of silica NPs in the liver, and the effect of surface energy modification on NPs. Hydrophobic NP surface modification enhanced NP delivery to the liver and liver sinusoid fFendothelial cells (LSECs). Conversely, hydrophilic NP surface modification was commensurate with targeting hepatic stellate cells (HSCs) rather than other cell types. There was no notable difference in NP delivery to Kupffer cells or hepatocytes, regardless of hydrophilic or hydrophobic NP surface modification, suggesting that both the targeting of hepatocytes and evasion of phagocytosis by Kupffer cells are not associated with surface energy modification of silica NPs. This study provides useful information to target specific cell types using silica NPs, as well as to understand the relationship between NP surface energy and the NP distribution pattern in the liver, thereby helping to establish strategies for cell targeting using various NPs. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.1

Size-controlled synthesis of phase separated protein condensates with interfacial protein cages

Phase separation of specific proteins into liquidic condensates is a key mechanism to form membrane-less organelles, which organize diverse cellular processes in space and time. These protein condensates hold immense potential as biomaterials that can contain specific sets of biomolecules with extremely high densities and dynamic liquid properties. Despite their appeal, methods to manipulate protein condensate materials remain largely unexplored. Here, we developed a one-pot assembly method to synthesize coalescence-free protein condensates from a few μm to 100 nm sizes with surface-stabilizing protein cages. We discovered that large protein cages (~30 nm), with precisely tuned interaction strengths to condensates, could effectively localize on condensate surfaces and block coalescence during phase separation. This approach proved applicable to diverse condensates with varying compositions and fluidities. Condensate sizes were concisely controlled by modulating condensate/cage ratios. In addition, we successfully visualized the 3D structures of intact protein condensates with interfacial cages with cryo-electron tomography (ET). Protein cages formed monolayer shells on protein condensates, where cages were slightly buried in condensates with contact angles lower than 90 degree. These cage-covered protein condensates maintained dynamic properties, including the capacity for selective material exchange or recruitment from the external environment

Self-assembly inside cellular organelles: Aspects of functions and various strategies for cancer therapy

Self-assembly generates three-dimensional architectures through the non-covalent interactions of building blocks of various sizes, ranging from nanometers to micrometers, and the assembled structures may have new functions that the building blocks do not have. Cell self-assembly has attracted considerable attention in cancer treatment because it can overcome the side effects of conventional chemotherapy and the low therapeutic effect on drug-resistant cells. In addition, the trigger in the building block reacts with the specific environment of the cancer, such as pH, ions, redox reactions, enzymes, or receptors, facilitating cancer-targeted therapy. However, the precise control of self-assembly for the construction of nanostructures is difficult in harsh intracellular environments. To overcome this challenge, various researchers have investigated intracellular self-assembly. In particular, the self-assembly in cellular organelles is of great interest. Compared with self-assembly in the cytoplasm of cells, organelle-targeting self-assembly has the advantage of being able to self-assemble without side effects under more stable conditions with a relatively low concentration of building blocks. In this mini-review, we discuss the latest research on self-assembly inside or near organelles for cancer treatment

EclipseMR: Distributed and Parallel Task Processing with Consistent Hashing

We present EclipseMR, a novel MapReduce framework prototype that efficiently utilizes a large distributed memory in cluster environments. EclipseMR consists of double-layered consistent hash rings - a decentralized DHT-based file system and an in-memory key-value store that employs consistent hashing. The in-memory key-value store in EclipseMR is designed not only to cache local data but also remote data as well so that globally popular data can be distributed across cluster servers and found by consistent hashing. In order to leverage large distributed memories and increase the cache hit ratio, we propose a locality-aware fair (LAF) job scheduler that works as the load balancer for the distributed in-memory caches. Based on hash keys, the LAF job scheduler predicts which servers have reusable data, and assigns tasks to the servers so that they can be reused. The LAF job scheduler makes its best efforts to strike a balance between data locality and load balance, which often conflict with each other. We evaluate EclipseMR by quantifying the performance effect of each component using several representative MapReduce applications and show EclipseMR is faster than Hadoop and Spark by a large margin for various applications

MOF ?? Biopolymer: Collaborative Combination of Metal-Organic Framework and Biopolymer for Advanced Anticancer Therapy

Metal???organic framework (MOF) nanoparticles with high porosity and greater tunability have emerged as new drug delivery vehicles. However, premature drug release still remains a challenge in the MOF delivery system. Here, we report an enzyme-responsive, polymer-coated MOF gatekeeper system using hyaluronic acid (HA) and PCN-224 nanoMOF. The external surface of nanoMOF can be stably covered by HA through multivalent coordination bonding between the Zr cluster and carboxylic acid of HA, which acts as a gatekeeper. HA allows selective accumulation of drug carriers in CD44 overexpressed cancer cells and enzyme-responsive drug release in the cancer cell environment. In particular, inherent characteristics of PCN-224, which is used as a drug carrier, facilitates the transfer of the drug to cancer cells more stably and allows photodynamic therapy. This HA-PCN system enables a dual chemo and photodynamic therapy to enhance the cancer therapy effect