We are witnessing a growing number of applications that involve both structured data and unstructured data. A simple example is academic citations : while the citation's content is unstructured text, the citation is associated with structured data such as author list, categories and publication time. To query such hybrid data, a natural approach is to combine structured queries with keyword search. Two fundamental problems arise for this unique marriage : (1) How to evaluate hybrid queries efficiently? (2) How to model relevance ranking? The second problem is especially difficult, because all the foundations of relevance ranking in information retrieval are built on unstructured text and no structures are considered. We present context-sensitive ranking, a ranking framework that integrates structured queries and relevance ranking. The key insight is that structured queries provide expressive search contexts. The ranking model collects keyword statistics in the contexts and feeds them into conventional ranking formulas to compute ranking scores. The query evaluation challenge is the computation of keyword statistics at runtime, which involves expensive online aggregations. At the core of our solution to overcome the efficiency issue is an innovative reduction from computing keyword statistics to answering aggregation queries. Many statistics, such as document frequency, require aggregations over the data space returned by the structured query. This is analogous to analytical queries in OLAP applications, which involve a large number of aggregations. We leverage and extend the materialized view research in OLAP to deliver algorithms and data structures that evaluate context-sensitive ranking efficiently

MOTIVATION: The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. RESULTS: We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads among isoforms efficiently. The weight represents the oversampling or undersampling of sequence reads and is estimated through a generalized Poisson model without any presumption on the bias sources and formats. WemIQ significantly improves the quantification of isoform and gene expression as well as the derived exon inclusion rates. It provides robust expression estimates across different laboratories and protocols, which is valuable for the integrative analysis of RNA-seq. For the recent single-cell RNA-seq data, WemIQ also provides the opportunity to distinguish bias heterogeneity from true biological heterogeneity and uncovers smaller cell-to-cell expression variability.

A traditional extensible processor with customized circuits achieves high performance at the cost of flexibility, while a dynamically extensible processor with reconfigurable fabric offers flexibility for instruction-set extensions (ISEs) but suffers from computational inefficiency. We introduce a novel architecture called Just-in-Time Customizable (JiTC) processor that reconciles the conflicting demands of performance and flexibility in extensible processors. Our key innovation is a multi-stage accelerator, called Specialized Functional Unit (SFU), that is tightly integrated in the processor pipeline. The SFU design is derived through a systematic study of a large range of representative embedded applications. The SFU can be reconfigured on per-cycle basis to support different application-specific instructions at near-ideal performance of an extensible processor. We also provide an automated compilation tool chain for JiTC processor. The experimental results confirm the efficiency and applicability of our approach. © 2013 IEEE.

Background

Service providers are often inadequately compliant with standard precaution protocols. This study used bottleneck analysis to identify the weakest link in standard precaution implementation and its associated challenges in hospitals.

Methods

Bottleneck analysis was conducted in 12 hospitals in Fujian Province, China. In each hospital, a focus group was organized among the key informants to illustrate the sequential steps of standard precaution implementation graphically. The level of difficulty and the specific challenges associated with each step were discussed.

Results

The sequential activities of standard precaution implementation generally start with making budget for personal protection equipment (PPE), followed by procurement, storage/inventory, in-hospital distribution, in-department distribution, usage/monitoring, and recycling of PPE. Service providers' improper use of PPE was the primary bottleneck. The reasons for improper use of PPE included high workload, time constraints, the sense of wearing PPE would interfere with clinical judgment, and various misconceptions. Making financial planning, recycling, and procurement of PPE were the secondary bottlenecks.

Conclusions

Bottleneck analysis is useful to illustrate workflow in healthcare systems and pinpoint constraints in standard precaution implementation. Institutional changes, including targeted provider training, adjustment of providers' workloads, and allocation of budget, are suggested strategies to address the identified bottlenecks in standard precaution.

The gene regulation underlying axon formation and its exclusiveness to neurons remains elusive. TRIM46 is postulated to determine axonal fate. We show Trim46 mRNA is expressed before axonogenesis, but TRIM46 protein level is inhibited by alternative splicing of two cassette exons coupled separately to stability controls of Trim46 mRNA and proteins, effectively inducing functional knockout of TRIM46 proteins. Exon 8 inclusion causes nonsense-mediated mRNA decay of Trim46 transcripts. PTBP2-mediated exon 10 skipping produces transcripts encoding unstable TRIM46 proteins. During axonogenesis, transcriptional activation, decreased exon 8 inclusion, and enhanced exon 10 inclusion converge to increase TRIM46 proteins, leading to its neural-specific expression. Genetic deletion of these exons alters TRIM46 protein levels and shows TRIM46 is instructive though not always required for AnkG localization nor a determinant of AnkG density. Therefore, two concurrently but independently regulated alternative exons orchestrate the temporal induction and tissue-specific expression of TRIM46 proteins to mediate axon formation.

A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.

Continuous neuronal survival is vital for mammals because mammalian brains have limited regeneration capability. After neurogenesis, suppression of apoptosis is needed to ensure a neurons long-term survival. Here we describe a robust genetic program that intrinsically attenuates apoptosis competence in neurons. Developmental downregulation of the splicing regulator PTBP1 in immature neurons allows neural-specific splicing of the evolutionarily conserved Bak1 microexon 5. Exon 5 inclusion triggers nonsense-mediated mRNA decay (NMD) and unproductive translation of Bak1 transcripts (N-Bak mRNA), leading to suppression of pro-apoptotic BAK1 proteins and allowing neurons to reduce apoptosis. Germline heterozygous ablation of exon 5 increases BAK1 proteins exclusively in the brain, inflates neuronal apoptosis, and leads to early postnatal mortality. Therefore, neural-specific exon 5 splicing and depletion of BAK1 proteins uniquely repress neuronal apoptosis. Although apoptosis is important for development, attenuation of apoptosis competence through neural-specific splicing of the Bak1 microexon is essential for neuronal and animal survival.

Background

Service providers are often inadequately compliant with standard precaution protocols. This study used bottleneck analysis to identify the weakest link in standard precaution implementation and its associated challenges in hospitals.

Methods

Bottleneck analysis was conducted in 12 hospitals in Fujian Province, China. In each hospital, a focus group was organized among the key informants to illustrate the sequential steps of standard precaution implementation graphically. The level of difficulty and the specific challenges associated with each step were discussed.

Results

The sequential activities of standard precaution implementation generally start with making budget for personal protection equipment (PPE), followed by procurement, storage/inventory, in-hospital distribution, in-department distribution, usage/monitoring, and recycling of PPE. Service providers' improper use of PPE was the primary bottleneck. The reasons for improper use of PPE included high workload, time constraints, the sense of wearing PPE would interfere with clinical judgment, and various misconceptions. Making financial planning, recycling, and procurement of PPE were the secondary bottlenecks.

Conclusions

Bottleneck analysis is useful to illustrate workflow in healthcare systems and pinpoint constraints in standard precaution implementation. Institutional changes, including targeted provider training, adjustment of providers' workloads, and allocation of budget, are suggested strategies to address the identified bottlenecks in standard precaution.

Synchrotron infrared hyperspectral microscopy is a label-free and non-invasive technique well suited for imaging of chemical events in situ. It can track the spatial and temporal distributions of molecules of interests in a specimen in its native state by the molecule’s characteristic vibrational modes. Despite tremendous progress made in recent years, IR hyperspectral imaging of chemical events in biomaterials in liquids remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. Here we report a multi-phase capillary-driven membrane device for label-free and real-time investigation of enzymatic deconstruction of algal cellulose purified from Cladophora aegagropila.