Anonymous, authentic, and accountable resource management based on the E-cash paradigm

The prevalence of digital information management in an open network has driven the need to maintain balance between anonymity, authenticity and accountability (AAA). Anonymity allows a principal to hide its identity from strangers before trust relationship is established. Authenticity ensures the correct identity is engaged in the transaction even though it is hidden. Accountability uncovers the hidden identity when misbehavior of the principal is detected. The objective of this research is to develop an AAA management framework for secure resource allocations. Most existing resource management schemes are designed to manage one or two of the AAA attributes. How to provide high strength protection to all attributes is an extremely challenging undertaking. Our study shows that the electronic cash (E-cash) paradigm provides some important knowledge bases for this purpose. Based on Chaum-Pederson’s general transferable E-cash model, we propose a timed-zero-knowledge proof (TZKP) protocol, which greatly reduces storage spaces and communication overheads for resource transfers, without compromising anonymity and accountability. Based on Eng-Okamoto’s general divisible E-cash model, we propose a hypercube-based divisibility framework, which provides a sophisticated and flexible way to partition a chunk of resources, with different trade-offs in anonymity protection and computational costs, when it is integrated with different sub-cube allocation schemes. Based on the E-cash based resource management framework, we propose a privacy preserving service oriented architecture (SOA), which allows the service providers and consumers to exchange services without leaking their sensitive data. Simulation results show that the secure resource management framework is highly practical for missioncritical applications in large scale distributed information systems

A Randomized Controlled Trial of Auricular Transcutaneous Electrical Nerve Stimulation for Managing Posthysterectomy Pain

Background. A patient- and assessor-blinded randomized controlled trial was conducted to examine the effectiveness of auricular transcutaneous electrical nerve stimulation (TENS) in relieving posthysterectomy pain. Method. Forty-eight women who had undergone a total abdominal hysterectomy were randomly assigned into three groups (n = 16 each) to receive either (i) auricular TENS to therapeutic points (the true TENS group), (ii) auricular TENS to inappropriate points (the sham TENS group), or (iii) 20 minutes of bed rest with no stimulation (the control group). The intervention was delivered about 24 hours after the operation. A visual analogue scale was used to assess pain while resting (VAS-rest) and upon huffing (VAS-huff) and coughing (VAS-cough), and the peak expiratory flow rate (PEFR) was assessed before and at 0, 15, and 30 minutes after the intervention. Result. As compared to the baseline, only the true TENS group reported a significant reduction in VAS-rest (P = .001), VAS-huff (P = .004), and VAS-cough (P = .001), while no significant reduction in any of the VAS scores was seen in the sham TENS group (all P > .05). In contrast, a small rising trend was observed in the VAS-rest and VAS-huff scores of the control group, while the VAS-cough score remained largely unchanged during the period of the study. A between-group comparison revealed that all three VAS scores of the true TENS group were significantly lower than those of the control group at 15 and 30 minutes after the intervention (all P < .02). No significant between-group difference was observed in PEFR at any point in time. Conclusion. A single session of auricular TENS applied at specific therapeutic points significantly reduced resting (VAS-rest) and movement-evoked pain (VAS-huff, VAS-cough), and the effects lasted for at least 30 minutes after the stimulation. The analgesic effects of auricular TENS appeared to be point specific and could not be attributed to the placebo effect alone. However, auricular TENS did not produce any significant improvement in the performance of PEFR

Local structural alignment of RNA with affine gap model

Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.The project is partially supported by the Seed Funding Programme for Basic Research (Project number: 200911159065) of the University of Hong Kong

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

A Gramaticalização do Verbo Ir e a Variação de Formas para Expressar o Futuro do Presente: uma Fotografia Capixaba

Esta pesquisa verifica o estágio do processo de gramaticalização do verbo IR, que tem assumido a função de auxiliar em construções perifrásticas para expressar tempo. Para isso, investiga-se a variação entre as formas sintética e perifrástica com IR para expressão do futuro do presente. Temos por hipótese que a forma perifrástica já atinge todos os gêneros das duas modalidades da língua, uma vez que já se especializou para codificar tempo. São examinados dois gêneros, tomando-os como prototípicos do continuun oral/escrito: entrevistas com informantes universitários e editoriais de jornal. Partindo de uma orientação teórica Funcionalista, num quadro mais geral, concebe-se a língua como flexível ao uso, passível de influências cognitivas, sociais e também individuais, embora haja nela forças que atuam no sentido de regularizar a estrutura. Seguindo algumas pesquisas que têm se mostrado frutíferas, o modelo funcionalista estará em diálogo com outro modelo que procura dar conta da heterogeneidade estruturada da língua e de seus processos de mudança: a Teoria Variacionista. Num quadro mais específico, os fundamentos que orientam a pesquisa são os da Gramaticalização. Os dados extraídos dos gêneros selecionados serão submetidos ao programa computacional GOLDVARB 2001 e, em seguida, interpretados à luz das teorias lingüísticas que fundamentam esta pesquisa

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.published_or_final_versio

Ad hoc influenza vaccination during years of significant antigenic drift in a tropical city with 2 seasonal peaks

We evaluated the acceptability of an additional ad hoc influenza vaccination among the health care professionals following seasons with significant antigenic drift. Self-administered, anonymous surveys were performed by hard copy questionnaires in public hospitals, and by an on-line platform available to all healthcare professionals, from April 1st to May 31st, 2015. A total of 1290 healthcare professionals completed the questionnaires, including doctors, nurses, and allied health professionals working in both the public and private systems. Only 31.8% of participating respondents expressed an intention to receive the additional vaccine, despite that the majority of them agreed or strongly agreed that it would bring benefit to the community (88.9%), save lives (86.7%), reduce medical expenses (76.3%), satisfy public expectation (82.8%), and increase awareness of vaccination (86.1%). However, a significant proportion expressed concern that the vaccine could disturb the normal immunization schedule (45.5%); felt uncertain what to do in the next vaccination round (66.0%); perceived that the summer peak might not occur (48.2%); and believed that the summer peak might not be of the same virus (83.5%). Furthermore, 27.8% of all respondents expected that the additional vaccination could weaken the efficacy of previous vaccinations; 51.3% was concerned about side effects; and 61.3% estimated that there would be a low uptake rate. If the supply of vaccine was limited, higher priority groups were considered to include the elderly aged ≥65 years with chronic medical conditions (89.2%), the elderly living in residential care homes (87.4%), and long-stay residents of institutions for the disabled (80.7%). The strongest factors associated with accepting the additional vaccine included immunization with influenza vaccines in the past 3 years, higher perceived risk of contracting influenza, and higher perceived severity of the disease impact. The acceptability to an additional ad hoc influenza vaccination was low among healthcare professionals. This could have a negative impact on such additional vaccination campaigns since healthcare professionals are a key driver for vaccine acceptance. The discordance in perceived risk and acceptance of vaccination regarding self versus public deserves further evaluation

Local structural alignment of RNA with affine gap model

BACKGROUND: Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. RESULTS: In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. CONCLUSIONS: Based on an experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.published_or_final_versio