IPad: ID-based public auditing for the outsourced data in the standard model

Cloud storage is an important cloud computing service, it allows data users to store and access their files anytime, from anywhere and with any device. To ensure the security of the outsourced data, it also must allow data user to periodically verify integrity of the data which was outsourced to an untrusted cloud server at a relatively low cost. To solve this problem, most recent auditing protocols are mainly based on the traditional-public key infrastructure. In this infrastructure, the auditor must validate the certificates of data user before auditing data integrity. Thus, it results in a large amount of computation cost and is not suitable to the multi-user setting. To overcome this problem, in this paper, we propose two efficient ID-based public auditing protocols for the outsourced data by combing Water’s signature and public auditing for the outsourced data. And the two protocols are provably secure in the standard security model. Especially, our optimized protocol has constant communication overhead and computation cost. To the best of our knowledge, it is the first ID-based auditing for data integrity in the standard security model. By comparison with Wang et al.’s scheme and Tan et al.’s scheme, our protocols have the large advantages over the other two schemes in terms of communication cost and computation cost. Simulation results show that our proposed ID-based auditing protocols are the most efficient among three schemes in terms of computation cost.     

Efficient chameleon hashing-based privacy-preserving auditing in cloud storage

Cloud storage is an important application service in cloud computing, it allows data users to store and access their files anytime, from anywhere and with any device. To ensure the security of the outsourced data, data user needs to periodically check data integrity. In some cases, the identity privacy of data user must be protected. However, in the existing preserving identity privacy protocols, data tag generation is mainly based on complex ring signature or group signature. It brings a heavy burden to data user. To ensure identity privacy of data user, in this paper we propose a novel identity privacy-preserving public auditing protocol by utilizing chameleon hash function. It can achieve the following properties: (1) the identity privacy of data user is preserved for cloud server; (2) the validity of the outsourced data is verified; (3) data privacy can be preserved for the auditor in auditing process; (4) computation cost to produce data tag is very low. Finally, we also show that our scheme is provably secure in the random oracle model, the security of the proposed scheme is related to the computational Diffie–Hellman problem and hash function problem.     

A Game Theoretical Analysis of the Mating Sign Behavior in the Honey Bee

Queens of the honey bee, Apis mellifera (L.), exhibit extreme polyandry, mating with up to 45 different males (drones). This increases the genetic diversity of their colonies, and consequently their fitness. After copulation, drones leave a mating sign in the genital opening of the queen which has been shown to promote additional mating of the queen. On one hand, this signing behavior is beneficial for the drone because it increases the genetic diversity of the resulting colony that is to perpetuate his genes. On the other hand, it decreases the proportion of the drone??s personal offspring among colony members which is reducing drone fitness. We analyze the adaptiveness and evolutionary stability of this drone??s behavior with a game-theoretical model. We find that theoretically both the strategy of leaving a mating sign and the strategy of not leaving a mating sign can be evolutionary stable, depending on natural parameters. However, the signing strategy is not favored for most scenarios, including the cases that are biologically plausible in reference to empirical data. We conclude that leaving a sign is not in the interest of the drone unless it serves biological functions other than increasing subsequent queen mating chances. Nevertheless, our analysis can also explain the prevalence of such a behavior of honey bee drones by a very low evolutionary pressure for an invasion of the nonsigning strategy.     

A novel privacy protection of permissioned blockchains with conditionally anonymous ring signature

With the rapid development of permissioned blockchains, the problem of privacy leakage within permissioned blockchains is increasingly serious. In this paper, for the privacy problem in permissioned blockchains, a novel privacy protection method has been put forward. In this novel method, the ring signature is used to protect the privacy of the user in permissioned blockchains. On the other hand, the unconditional anonymity of ring signature may be abused maliciously by the adversary. Conditional anonymity is considered to improve the ring signature. Therefore, based on conditionally anonymous ring signature, permissioned blockchains privacy protection scheme has also been laid down. Furthermore, the effects of smart contract for transaction flows are considered. The asynchronous signing transaction process is proposed. The security of the scheme has been formally reduced to the Discrete Logarithm assumption. The comparison with the state-of-the-art and simulation experiment have also demonstrated that the proposed scheme is efficient and practical.

     

Detection of apoptosis by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling and acridine orange in Drosophila embryos and adult male gonads

In Drosophila, vast numbers of cells undergo apoptosis during normal development. In addition, excessive apoptosis can be induced in response to a variety of stress or injury paradigms, including DNA damage, oxidative stress, nutrient deprivation, unfolded proteins and mechanical tissue damage. Two of the most commonly used methods to label apoptotic cells in Drosophila are terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) for fixed tissues and acridine orange (AO) staining for live embryos or tissues. Here, we describe protocols for labeling apoptotic cells in Drosophila embryos and adult male gonads. Slightly modified protocols can also be applied for other Drosophila tissues. The AO protocol is quick, simple and allows real-time imaging of doomed cells in live tissues. However, it is difficult to combine with conventional counterstains or Ab labeling. On the other hand, this functionality is readily afforded by the TUNEL protocol, which permits the detection of apoptotic cells in fixed tissues. These staining procedures can be completed in 1-2 d.     

Adaptability in protein structures: structural dynamics and implications in ligand design

The basic framework of understanding the mechanisms of protein functions is achieved from the knowledge of their structures which can model the molecular recognition. Recent advancement in the structural biology has revealed that in spite of the availability of the structural data, it is nontrivial to predict the mechanism of the molecular recognition which progresses via situation-dependent structural adaptation. The mutual selectivity of protein–protein and protein–ligand interactions often depends on the modulations of conformations empowered by their inherent flexibility, which in turn regulates the function. The mechanism of a protein’s function, which used to be explained by the ideas of ‘lock and key’ has evolved today as the concept of ‘induced fit’ as well as the ‘population shift’ models. It is felt that the ‘dynamics’ is an essential feature to take into account for understanding the mechanism of protein’s function. The design principles of therapeutic molecules suffer from the problems of plasticity of the receptors whose binding conformations are accurately not predictable from the prior knowledge of a template structure. On the other hand, flexibility of the receptors provides the opportunity to improve the binding affinity of a ligand by suitable substitution that will maximize the binding by modulating the receptors surface. In this paper, we discuss with example how the protein’s flexibility is correlated with its functions in various systems, revealing the importance of its understanding and for making applications. We also highlight the methodological challenges to investigate it computationally and to account for the flexible nature of the molecules in drug design.     

鳞翅目成虫乙醇保存标本基因组DNA的提取及在微卫星研究中的应用

高质量的基因组DNA样品是分子生态学研究的先决条件。本研究目的在于探索从东方粘虫Pseudaletia separata (Walker)成虫自然种群的乙醇保存标本中分离高质量基因组DNA的有效方案。在2 mL微型离心管中进行4种提取方案的实验比较,结果发现采用传统的苯酚抽提方法的2种方案提取腹部中段组织的基因组DNA,样品合格率只有7.69%~40%。但是,如果在苯酚抽提以前加入高浓度盐和十六烷基三甲基溴化铵（CTAB）,就会使DNA样品合格率达到68.42%~95.28%,而且DNA平均产量达到5.59~10.04 mg/g,明显高于前者的2.83~5.78 mg/g （统计检验表明,在不同种群中差异显著或不显著）。研究结果还证明腹部组织比胸部组织更适宜提取DNA。对来自一个自然种群的99头东方粘虫DNA合格样品的统计分析表明,DNA提取总量（μg）与组织样品用量（mg）之间存在弱的正相关关系,平均DNA提取量（mg/g）与组织样品用量（mg）之间存在中度负相关关系。总之,在2 mL微型离心管中,用10~20 mg腹部组织,利用CTAB+苯酚抽提方法可以获得高纯度和高含量的基因组DNA样品。用该方案提取的基因组DNA能够顺利地进行微卫星位点的分离和基因分型。     

Response to “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues”

I found the research paper “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues” by Price ME and colleagues in the June 2012 issue of Epigenetics to be an interesting read, but it contains errors in regards to the use of the MethylFlash Methylated DNA Quantification Kit. The text contained in the “Global DNA Methylation” paragraph under the “Methods” section of the paper claims that the kit was used by “following the manufacturer’s protocol.” I find that this is quite misleading to the reader as we have identified, based on the original electronic publication ahead of print, that the steps had not been correctly carried out.

The original text was the following: “DNA was hybridized to wells treated to have a high affinity for DNA. The wells were washed with a 5-mC-specific capture antibody followed by a detection antibody. The absorbance (or optical density) of each well was measured using a microplate spectrophotometer. Correlation of technical replicates was poor (r = 0.09, p = 0.72) using this kit.” However, the user guide of this kit clearly states that DNA is bound, not hybridized, to the strip wells and that the wells should be washed with the included Wash Buffer rather than a “5-mC-specific capture antibody.”

Therefore, it is not surprising that the result or correlation of replicates was poor and that the authors’ “results were variable” due to improper use of the kit. Based on our quality control tests and feedback from the vast amount of users of this popular kit, the variation between replicates should be less than 10% with R value > 0.9 (p < 0.01), assuming proper user performance according to the product manual.

I hope this helps to correct the misinformation presented in the paper as I feel that it is important to promote accuracy on behalf of the epigenetic research community. I also kindly encourage any users of an Epigentek product to work with our very knowledgeable technical support team should they have any difficulties.     

Improved coupling between proliferation-arrest and differentiation-induction in ML-1 human myeloblastic leukemia cells

Proliferation and differentiation are coupled in normal cells and are aberrant in leukemia cells. The studies reported here were aimed at more effectively coupling proliferation-arrest and differentiation-induction in a human myeloblastic leukemia cell line (ML-1). This was accomplished by using reduced serum conditions in conjunction with a differentiation-inducing agent: cells were first incubated in reduced serum [0.3% fetal bovine serum (FBS)] instead of standard conditions (7.5% FBS) and, second, exposed to 12-O-tetradecanoylphorbol-13-acetate (TPA). The effects of this protocol were as follows: first, cell proliferation was slowed and cells accumulated in G0/G1 phase of the cell cycle; this occurred with only a minimal decrease in viability [to approximately 88-92% (0.3% FBS) from greater than or equal to 96% (7.5% FBS)]. Second, the induction of differentiation was accelerated; this allowed the time of exposure to TPA to be decreased. Acceleration of induction was very pronounced when cells were maintained in 0.3% FBS both before and during exposure to TPA, with TPA at concentrations above the minimum sufficient for induction but below those causing significant cytotoxicity; as little as 1 hour of TPA exposure resulted in near-maximal induction (approximately 80%) with this protocol, compared to the greater than or equal to 1 day required with previous standard protocols. In sum, conditions that slow ML-1 cell proliferation (0.3% FBS) enhance TPA-induced differentiation, substantially narrowing the time frame of induction; these conditions should be useful for studying the molecular mechanisms that underlie the induction process.     

Multi-level on-demand access control for flexible data sharing in cloud

The exponential growth of data storage and sharing in cloud demands an efficient access control mechanism for flexible data sharing. Attribute-Based Encryption (ABE) is a promising cryptographic solution to share data among users in the cloud. But it suffers from user revocation, attribute revocation, forward secrecy and backward secrecy issues. Communication and computation overhead is more due to the linear variation in the size of ciphertext and the secret key with respect to the number of attributes. In this paper, we investigate an on-demand access control for flexible sharing of secure data among randomly selected users. It is a tunable access control mechanism for the flexible sharing of ciphertext classes in the cloud. It delegates the decryption rights of any set of ciphertext classes among the users only if their attributes are satisfied with the access policy associated with ciphertext and if they should possess a compact key corresponding to the intended set of ciphertext classes. It produces a constant size ciphertext and a compact secret key to efficiently utilize the storage space and reduce the communication cost. The compact key aggregates the power of secret keys used to encrypt the outsourced data. This method flexibly shares the ciphertext classes among the randomly selected users with a specific set of attributes. All other ciphertext classes outside the set remain confidential. It allows dynamic data updates by verifying the data manipulation privilege of users with the help of claim policy. The proposed scheme provides access control of varying granularity, at user-level, at file-level, and attribute-level. Granularity levels can be chosen based on applications and user demands. Hence, it is a multi-level, tunable access control over the shared data. It is very useful for secure data storage. This scheme tackles user revocation and attribute revocation problems so that, it allows the data owner to revoke a specific user or a group of users. It prevents forward and backward secrecy issues.

     

Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium

Purpose  The Cancer Vaccine Consortium of the Cancer Research Institute (CVC-CRI) conducted a multicenter HLA-peptide multimer proficiency panel (MPP) with a group of 27 laboratories to assess the performance of the assay. Experimental design  Participants used commercially available HLA-peptide multimers and a well characterized common source of peripheral blood mononuclear cells (PBMC). The frequency of CD8+ T cells specific for two HLA-A2-restricted model antigens was measured by flow cytometry. The panel design allowed for participants to use their preferred staining reagents and locally established protocols for both cell labeling, data acquisition and analysis. Results  We observed significant differences in both the performance characteristics of the assay and the reported frequencies of specific T cells across laboratories. These results emphasize the need to identify the critical variables important for the observed variability to allow for harmonization of the technique across institutions. Conclusions  Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Voxel model of a rabbit: assessment of absorbed doses in organs after CT examination performed by two different protocols

The objective of this work was to assess absorbed doses in organs and tissues of a rabbit, following computed tomography (CT) examinations, using a dedicated 3D voxel model. Absorbed doses in relevant organs were calculated using the MCNP5 Monte Carlo software. Calculations were perfomed for two standard CT protocols, using tube voltages of 110 kVp and 130 kVp. Absorbed doses were calculated in 11 organs and tissues, i.e., skin, bones, brain, muscles, heart, lungs, liver, spleen, kidney, testicles, and fat tissue. The doses ranged from 15.3 to 28.3 mGy, and from 40.2 to 74.3 mGy, in the two investigated protocols. The organs that received the highest dose were bones and kidneys. In contrast, brain and spleen were organs that received the smallest doses. Doses in organs which are stretched along the body did not change significantly with distance. On the other hand, doses in organs which are localized in the body showed maximums and minimums. Using the voxel model, it is possible to calculate the dose distribution in the rabbit’s body after CT scans, and study the potential biological effects of CT doses in certain organs. The voxel model presented in this work can be used to calculated doses in all radiation experiments in which rabbits are used as experimental animals.

     

AIB-OR: Improving Onion Routing Circuit Construction Using Anonymous Identity-Based Cryptosystems

The rapid growth of Internet applications has made communication anonymity an increasingly important or even indispensable security requirement. Onion routing has been employed as an infrastructure for anonymous communication over a public network, which provides anonymous connections that are strongly resistant to both eavesdropping and traffic analysis. However, existing onion routing protocols usually exhibit poor performance due to repeated encryption operations. In this paper, we first present an improved anonymous multi-receiver identity-based encryption (AMRIBE) scheme, and an improved identity-based one-way anonymous key agreement (IBOWAKE) protocol. We then propose an efficient onion routing protocol named AIB-OR that provides provable security and strong anonymity. Our main approach is to use our improved AMRIBE scheme and improved IBOWAKE protocol in onion routing circuit construction. Compared with other onion routing protocols, AIB-OR provides high efficiency, scalability, strong anonymity and fault tolerance. Performance measurements from a prototype implementation show that our proposed AIB-OR can achieve high bandwidths and low latencies when deployed over the Internet.     

Skeletal muscle generated from induced pluripotent stem cells-induction and application

Human induced pluripotent stem cells(hiPS cells or hiPSCs) can be derived from cells of patients with severe muscle disease. If skeletal muscle induced from patientiPSCs shows disease-specific phenotypes, it can be useful for studying the disease pathogenesis and for drug development. On the other hand, human iPSCs from healthy donors or hereditary muscle diseaseiPSCs whose genomes are edited to express normal protein are expected to be a cell source for cell therapy. Several protocols for the derivation of skeletal muscle from human iPSCs have been reported to allow the development of efficient treatments for devastating muscle diseases. In 2017, the focus of research is shifting to another stage:(1) the establishment of mature myofibers that are suitable for study of the pathogenesis of muscle disease;(2) setting up a highthroughput drug screening system; and(3) the preparation of highly regenerative, non-oncogenic cells in large quantities for cell transplantation, etc.     

Cardiovascular Responses to Isometric Hand grip vs. Relaxed Hand Grip in Sustained Cycling Efforts

ABSTRACT: Canivel, RG, Wyatt, FB, and Baker, JS. Cardiovascular responses to isometric hand grip vs. relaxed hand grip in sustained cycling efforts. J Strength Cond Res 26(11): 3101-3105, 2012-Peripheral isometric contractions may lead to enhanced performance. Previous research using hand grip protocols indicates increased stabilization and peak power outputs. Research is lacking with the grip vs. no-grip protocol during sustained efforts. The purpose of this study is to determine cardiovascular reactions (i.e., heart rate [HR], blood pressure [BP], and rate pressure product [RPP]) during sustained cycling via an isometric and relaxed hand grip. Nine (n = 9) recreational cyclists participated in this study. After signing a medical and physical readiness questionnaire, the subjects were randomly assigned to 1 of 2 different protocols. Preexercising values of the HR (beats per minute), BP (miilimeters of mercury), height (centimeters), weight (kilograms), and age (years) were assessed before testing. A Monark bicycle ergometer was used for testing. Grip was substantiated through the use of a hand grip dynamometer at 20 kg of tension. Protocol 1 used an isometric "Hand Grip" scenario at 150 W for 20 minutes. Protocol 2 used a "Relaxed Hand Grip" at the same power and time. During the 20-minute exercise test, HR (POLAR), BP (stethoscope and sphygmomanometer), and calculated RPP (HR × systolic BP [SPB]/100) were recorded every minute. Statistical measures included mean and SDs between protocols, and dependent samples t-tests were used to examine differences between grip and no-grip protocols. At an alpha of ≤0.05, SBP did show a significant increase when using no grip, 161.4 (5.1) mm Hg vs. grip, 154.1 (6.6) mm Hg. However, rate pressure product and heart rate showed no significant differences between protocols. Our data suggested that the use of an isometric hand grip is transient and diminishes over time.     

Nuclei isolation protocols for flow cytometry allowing nuclear DNA content estimation in problematic microalgal groups

Microalgae are fundamentally important organisms for global ecosystem functioning with high potential in biotechnology and its applications. The knowledge of their nuclear DNA content has become a prerequisite for many areas of microalgal research. Due to common presence of various pigments, secondary metabolites and complex cell walls, the nuclear DNA content estimation using flow cytometry (FCM) is, however, often laborious or even impossible with the currently used protocols. In this study the performance of six nuclei isolation protocols was compared on various problematic microalgae using FCM. The nuclei isolation methods involved osmotic bursting of cells, razor blade chopping of fresh biomass and two newly introduced protocols, razor blade chopping of desiccated biomass and bead beating. These techniques also involved the use of two different nuclei isolation solutions, Otto I + II solutions, and LB01 buffer. Performance of the particular protocols differed greatly, depending on the used nuclei isolation solution and microalgal group. The most successful method was a newly adopted chopping of desiccated biomass in LB01 buffer. This method seems more appropriate for nuclei isolation in filamentous microalgae; on the other hand, bead beating appears to be more suitable for nuclei isolation in solitarily living algae. Using the optimal protocol for a given species, their nuclear DNA content was estimated, resulting in first DNA content estimates for four investigated taxa (Chlamydomonas noctigama, Gonyostomum semen, Microglena sp. and Stigeoclonium sp.). The estimated DNA content spanned from 0.15 to 32.52 pg.

     

An Efficient Two-Tier Causal Protocol for Mobile Distributed Systems

Causal ordering is a useful tool for mobile distributed systems (MDS) to reduce the non-determinism induced by three main aspects: host mobility, asynchronous execution, and unpredictable communication delays. Several causal protocols for MDS exist. Most of them, in order to reduce the overhead and the computational cost over wireless channels and mobile hosts (MH), ensure causal ordering at and according to the causal view of the Base Stations. Nevertheless, these protocols introduce certain disadvantage, such as unnecessary inhibition at the delivery of messages. In this paper, we present an efficient causal protocol for groupware that satisfies the MDS''s constraints, avoiding unnecessary inhibitions and ensuring the causal delivery based on the view of the MHs. One interesting aspect of our protocol is that it dynamically adapts the causal information attached to each message based on the number of messages with immediate dependency relation, and this is not directly proportional to the number of MHs.