bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Spatio-Temporal Attributes Index Based Query for Wireless Sensor Networks
Authors: Wu Weiguo , Chen Heng , Wu Yong , Liu Yi
Published: January 2009

Wireless sensor networks (WSNs) are envisioned to consist of hundreds to thousands of wireless sensor nodes. The operator doesn't interest in the data sensed by a specific sensor node generally, on the contrary, he pays more attention to the data gathered from a specific area in granted time. One crucial problem is how to process the great deal of data and respond to the query request.

We propose a novel query processing based data attributes, called Spatio-Temporal Attributes R-tree based Query (STARQ). Consider the similarity of data collected by a sensor node and its neighboring nodes, partial clustering algorithm is used to form a storage cluster. Partial clustering algorithm is implemented in two phases. First phase is the beginning of partial clustering, in which an object occurs. In second phase, a certain node (e.g., resumes from failure) senses an existed object. The method provided in this paper aims to obtain the neighboring nodes firstly, and judges whether existing a storage cluster that conforms to metadata of the sensor node or not. If the relevant storage cluster does not exist, first phase works, otherwise second phase. If failed in first phase, partial clustering algorithm is called again after a random time. If there are more than one relevant storage cluster in second phase, exercises a sort algorithm which is in descending order according to the storage node's capability weight, and tries to join a storage cluster in turn.

R-tree [ 1 ] is an approximately balanced search tree that is widely used to handle spatial data in traditional database systems. Motivated by the unique characteristic of R-tree, a Saptio-Temporal Attributes R-tree (STAR) is built on the top of storage clusters. Objects in STAR are not restricted to the geographical rectangles and could be any abstract ranges of arbitrary attributes. A top-down approach that achieves energy efficiency is adopted to locate the corresponding storage nodes, which transmit the relevant data back to the operator.

We compare STARQ with Directed Diffusion [ 2 ] and GHT [ 3 ] in NS-2. To measure the performance of these protocols, we consider two metrics: interval of query and the size of network. The simulation results show that STARQ has better performance with different query intervals and network size.
Scheme of Combined Marker Based Watershed for Infrared Image Segmentation
Authors: Bai Xiangzhi , Zhou Fugen , Xie Yongchun , Jin Ting
Published: January 2009

To segment infrared dim target, a combined marker based watershed algorithm is proposed, analysed, and verified.
Improving WSN Base Station Survivability with Rejuvenation Technology
Authors: Xin He , Xiaolin Gui , Wei Wei
Published: January 2009

The conventional security technology for WSN is mainly focused on improvement to the system's anti-invasion ability; however, seldom concerns how the system should go on providing external services after the invasion and failure, leading to the system's low survivability. In addition, base station is a keyport for WSN. Therefore, software rejuvenation technology is introduced into the construction of a survival model for WSN base station, in order to improve the overall WSN survival performance.

The model includes the monitor, the analysis unit, the rejuvenation operation unit, the evaluation unit, strategy Database, etc. Its operation principles are as follows: first, the monitor can gets context information of the system recourses through agents (software sensors), and makes prompt examination and data collecting. Then, the analysis unit will make policy on the collected data, and judge the existence cause and harm degree of abnormal resource consumption by means of knowledge provided by strategies database, in order to perform the rejuvenation operation in time. When the rejuvenation occurs, it is necessary to clear the internal status (e.g., trash recycling, refreshing operation system tables, reinitializing internal data construction etc., adopting different operations in the presence of different strategies), to cut off exterior malicious links, to release system resources, and to restore system performance. Besides, when the rejuvenation operation is performed, the reconfiguration operation can also be adopted in order that patches are put on according to the system loophole, to avoid wrong reappearance caused by system interior drawbacks or the continuous occurrence of the same exterior attacks. Finally, according to the restored system performance, an evaluation of the original strategy which influenced the operation this time should be made and recorded in the strategies database by the evaluation unit, making the frame model adjust itself to a varied environment. Thus, the uninterrupted services can be provided by the system in face of attack or failure by the model, which monitors system performance to predict the rejuvenation interval and performs rejuvenation operation.

Otherwise, the model is described by using the Semi-Markov Process and it is discovered that the detection probability of the system compromised state is the key parameter of improving the model's survivability by analyzing the model's stable health state probability. Too convienient for simulation, the base station survival model is described with Stochastic reward network and the experimental results gained by simulation tool SPNP show that the system detection probability is in inverse proportion of the failure probability. According to thought of rejuvenation technology, the failure probability can be reduced significantly by improving system detection probability so as to enhance the survivability of the system, and further improve the overall survival performance of WSN.
Privacy-Preserving Hierarchical-k-Means Clustering on Horizontally Partitioned Data
Authors: Xue Anrong , Jiang Dongjie , Ju Shiguang , Chen Weihe , Ma Handa
Published: January 2009

Privacy preserving mining of distributed data is an important direction for data mining, and privacy preserving clustering is one of the main researches. Privacy-preserving data mining techniques enable knowledge discovery without requiring disclosure of private data. The existing privacy preserving algorithms mainly concentrated on association rules and classification, only few algorithms on privacy preserving clustering, and these algorithms mainly concentrated on centralized and vertically partitioned data. So we proposed privacy preserving hierarchical k-means clustering algorithm on horizontally partitioned data, denoted as HPPHKC.

The complexity on k-means clustering algorithm is only O(n), so most existing privacy preserving clustering algorithms are concentrated on k-means and based on two parties and the trusted third party, these algorithms have the drawbacks of inaccurate results because of choosing initial clustering centers randomly and applying to multi-party difficult and revealing privacy because of depending on the third party excessively. By introduction of three protocols for secure multi-party computation: distance computation, cluster center computation, and standardization and combination of the merits of hierarchical and k-means clustering, we presented a privacy-preserving hierarchical-k-means clustering algorithm on horizontally partitioned data for semi-honest parties using some secure multi-party computation protocols. The algorithm uses the security protocol mentioned above to achieve the protection of the privacy data, and uses the hierarchical clustering algorithm to obtain k cluster centers, then uses the k-means clustering algorithm to obtain the final k clusters. We introduce the clustering feature and the clustering feature tree, which are used to summarize the cluster representations. A clustering feature (CF) is a three-dimensional vector summarizing information about clusters of objects. The ith clustering feature is CFi = (cni,cci,cpi), where cni is the number of th clusters, denoted as the size of th cluster, cci is the center of the cni objects, and cpi is the pointer of the list of cni objects. The algorithm has two phases: the first phase, every object can be as a cluster, a secure computation protocol is used to compute the dissimilarity matrix and the most similar clusters will be merged. This process is repeated until we get the assigned clusters number k and get k clustering centers. In the second phase, the semi-honest third party and all data involved parties use the k-means algorithm refine the results of the first phase and get the final clustering results. Finally, we give the proof of security of the algorithm and analysis of communication costs, and we show that our scheme is secure and complete with good efficiency.
Architecture Design of P2PSIP System
Authors: Ji Yang , Zhang Chunhong , Li Lichun , Wang Yao , Tao Mao
Published: January 2009

P2PSIP (Peer-to-Peer Session Initiation Protocol) is proposed to construct fully distributed signaling architecture for multimedia communication systems. Instead of centralized SIP servers, P2PSIP overlays utilize distributed and dynamic nodes to support location and storage services. So far various design alternatives of overlay architectures have been proposed to describe the mechanism about how the user nodes are connected together to form an application layer topology.

However, there appears to have been little research work on comprehensively comparing the performance properties of various P2PSIP architectures, and no study has been made to investigate how to select appropriate overlay architecture according to application requirements. In this paper, we investigate various P2PSIP architectures and compare their features mainly from the perspective of application performance. The query latency of overlay and call setup delay of SIP sessions are modeled as significant performance considerations for selection of suitable architecture for different usage scenarios.

First, we comprehensively analyze implementations of P2PSIP architecture. Four typical P2PSIP architectures are described in detail: pure DHT, DHT-based SIP server farm, P2PSIP overlay formed by super nodes, and hierarchical P2PSIP overlay. Furthermore, we classify the nodes into peer and client according to their roles in the architecture. Then the performance model of query latency and call setup delay for P2PSIP overlay architectures is proposed. Several parameters to present features of the overlay architectures are defined. The analysis primarily focuses on the impact of possibility of packet loss caused by link error or network congestion and churn of overlay. Finally, an event-driven chord-based simulation to evaluate query latency and call setup delay for different P2PSIP architectures is developed.

An analytical model and simulation showed that the average call setup delay is less than ten seconds for all the architectures, which could satisfy the requirements of multimedia session establishments in most cases. We advocate that the super node or hierarchical architecture might be appropriate options rather than pure DHT in terms of latency performance in heterogeneous network environments. The server farm approach is good at management as well as performance, which might be the best option for systems supported by service providers.
Clustering Routing Based Maximizing Lifetime for Wireless Sensor Networks
Authors: Sun Yanjing , Gu Xiangping
Published: January 2009

Distinguished from traditional wireless networks, sensor networks are characterized with severe power, computation, and memory constraints. Due to strict energy constraint, innovative techniques that improve energy efficiency to prolong the network lifetime are highly required.

Many solutions and algorithms for overcoming the problem depend on decomposing the network into a number of administrative entities called clusters. The structure imposed by clustering makes it somewhat easier to manage the problem introduced by the complexity of large-scale WSNs. Hierarchical (clustering) mechanisms are especially effective in increasing network scalability and reducing energy depletion, which have been extensively exploited.

We propose and evaluate an energy efficient clustering scheme based on LEACH (low energy adoptive clustering hierarchy), that is, LEACH-Energy Distance (LEACH-ED). In LEACH-ED, cluster heads are elected by a probability based on the ratio between residual energy of node and the total current energy of all of the sensor nodes in the network. In addition, it also considers the distance of any two cluster heads to uniform the clustering, namely, if the distance between some node and an existing cluster head in the round less than the distance threshold, the node cannot be elected as a cluster head. The method uses two different sorts of nodes which are called special node and normal node.

Assume that special nodes are uniformly distributed in the interested area. In the algorithm, it sets a distance threshold [Formula: see text], where S is the acreage of interested filed, N is the number of sensor nodes in the entire network, and p is the desired percentage of cluster heads in each round. Each node generates a random probability p at the beginning of a new round and computes the threshold value (T(n)). In case of p < pt, the node is selected as a cluster head. The algorithm should consider the distance threshold between the sensor nodes and existing cluster heads while other cluster heads are selected.

Compared with the classical clustering algorithm LEACH and extended LEACH, it makes uniform the clustering and balances the network load by considering the residual energy of nodes and the restrained factor of distances between two cluster heads, so that extends the network's lifetime. Meanwhile, it also takes the acreage of area and the number of nodes into account and analyzes their impact on the performance of the networks.

The simulation results show that LEACH-ED greatly prolongs the network lifetime compared with LEACH and LEACH-C.
Effective Reformulation for Resource Allocation in Computational Grid
Authors: Dong Xiaoshe , Mei Yiduo , Ma Siyuan , Gong Guannan , Zhu Zhengdong
Published: January 2009

Grid enables resource sharing and dynamic allocation of computational resources. It is a great challenge to make numerous resources available on-demand to guarantee the Quality-of-Service for jobs. This paper presents a two-stage optimization model for resource allocation in grid. Job constraints are classified into mandatory constraints and negotiated constraints. In the first stage, a preprocessing procedure such as resource discovery deals with the mandatory constraints. This has been fulfilled as our previous work. In the second stage, negotiated constraints are treated as Knapsack Problem-based optimization problem. Centralized scheduling and decentralized scheduling have been considered in this paper. This work is fulfilled as part of the Constellation Model for grid resource management.

We formulate centralized scheduling as Multi-Constraint Multiple Knapsack Problem (MCMKP). In centralized scheduling, jobs are submitted to a global job queue. A global scheduler assigns each job to a proper grid site according to the scheduling strategy. The scheduling is done periodically (e.g. daily or weekly).

We formulate decentralized scheduling as Multi-Dimensional Knapsack Problem (MDKP). In decentralized scheduling, jobs are submitted to local job queues. Allocation decisions are made by local schedulers individually. Jobs that can not be executed immediately are sent to a global waiting queue. When local scheduling is initialized, a local scheduler can select jobs from both the local job queue and the global waiting queue.

Objectives of both centralized scheduling and decentralized scheduling are to optimize the utility defined by a grid economy approach. The defined utility makes the trade-offs between user-concerned metrics and system-concerned metrics. Heuristic algorithms such as Very Large-Scale Neighborhood Search proposed by R. K. Ahuja and C. B. Cunha [2005] can be used to solve the combinatorial optimization problem.

We implemented a prototype of the Constellation Model. Genetic algorithms for constrained optimization which is proposed by S. Venkatraman and G. G. Yen [2005] have been implemented to solve the above optimization problems. Experimental results show that, performance metrics such as gained utility, response rate, and resource utilization are improved and resources are allocated in an optimal way.
A Novel Algorithm Applied to Task Scheduling in Grid Computing
Authors: Wang Wei , Luo Daisheng , Shu Wanneng , Fang Yong
Published: January 2009

In this paper a novel optimal scheduling model and its algorithm are developed for task scheduling problems. A novel annealing-inspired genetic algorithm is applied to solve the scheduling model. The effectiveness of the algorithm is shown for a number of test problems and performance comparisons with the genetic algorithm, simulated annealing are also discussed.
Selling News: Behind the Content of Cable and Broadcast Morning Shows
Authors: Cleary Johanna , Adams-Bloom Terry
Published: January 2009

Through content analysis of the three broadcast networks and two leading cable news channels, this study's authors (1) examine how promotional content fits into the overall lineup of the morning news shows, (2) evaluate ownership patterns as they relate to this content, and (3) examine the policy implications of news decisions related to promotional content. The study identifies clear differences in the practices of the broadcast versus cable morning news programs.
USP9X Enhances the Polarity and Self-Renewal of Embryonic Stem Cell-derived Neural Progenitors
Authors: Jolly Lachlan A. , Taylor Verdon , Wood Stephen A.
Published: January 2009

The substrate-specific deubiquitylating enzyme USP9X is a putative “stemness” gene expressed in many progenitor cell populations. To test its function in embryonic stem cell-derived neural progenitor/stem cells, we expressed USP9X from a Nestin promoter. Elevated USP9X levels resulted in two phenomena. First, it produced a dramatically altered cellular architecture wherein the majority (>80%) of neural progenitors was arranged into radial clusters. These progenitors expressed markers of radial glial cells and were highly polarized with adherens junction proteins (N-cadherin, β-catenin, and AF-6) and apical markers (Prominin1, atypical protein kinase C-ζ) as well as Notch, Numb, and USP9X itself, concentrated at the center. The cluster centers were also devoid of nuclei and so resembled the apical end-feet of radial progenitors in the neural tube. Second, USP9X overexpression caused a fivefold increase in the number of radial progenitors and neurons, in the absence of exogenous growth factors. 5-Bromo-2′-deoxyuridine labeling, as well as the examination of the brain lipid-binding protein:βIII-tubulin ratio, indicated that nestin-USP9X enhanced the self-renewal of radial progenitors but did not block their subsequent differentiation to neurons and astrocytes. nestin-USP9X radial progenitors reformed clusters after passage as single cells, whereas control cells did not, suggesting it aids the establishment of polarity. We propose that USP9X-induced polarization of these neural progenitors results in their radial arrangement, which provides an environment conducive for self-renewal.
KEA: kinase enrichment analysis
Authors: Lachmann Alexander , Ma'ayan Avi
Published: January 2009

Motivation: Multivariate experiments applied to mammalian cells often produce lists of proteins/genes altered under treatment versus control conditions. Such lists can be projected onto prior knowledge of kinase–substrate interactions to infer the list of kinases associated with a specific protein list. By computing how the proportion of kinases, associated with a specific list of proteins/genes, deviates from an expected distribution, we can rank kinases and kinase families based on the likelihood that these kinases are functionally associated with regulating the cell under specific experimental conditions. Such analysis can assist in producing hypotheses that can explain how the kinome is involved in the maintenance of different cellular states and can be manipulated to modulate cells towards a desired phenotype.

Summary: Kinase enrichment analysis (KEA) is a web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. The system draws from several available kinase–substrate databases to compute kinase enrichment probability based on the distribution of kinase–substrate proportions in the background kinase–substrate database compared with kinases found to be associated with an input list of genes/proteins.

Availability: The KEA system is freely available at http://amp.pharm.mssm.edu/lib/kea.jsp

Contact:  avi.maayan@mssm.edu
Parallelized prediction error estimation for evaluation of high-dimensional models
Authors: Porzelius Christine , Binder Harald , Schumacher Martin
Published: January 2009

Summary: There is a multitude of new techniques that promise to extract predictive information in bioinformatics applications. It has been recognized that a first step for validation of the resulting model fits should rely on proper use of resampling techniques. However, this advice is frequently not followed, potential reasons being difficulty of correct implementation and computational demand. This is addressed by the R package peperr, which is designed for reliable prediction error estimation through resampling, potentially accelerated by parallel execution on a compute cluster. Its interface allows easy connection to newly developed model fitting routines. Performance evaluation of the latter is furthermore guided by diagnostic plots, which helps to detect specific problems due to high-dimensional data structures.

Availability:  http://cran.r-project.org, http://www.imbi.uni-freiburg.de/parallel

Contact:  cp@fdm.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evaluation and Management of Neonatal Dysphagia: Impact of Pharyngoesophageal Motility Studies and Multidisciplinary Feeding Strategy
Authors: Jadcherla Sudarshan R , Stoner Erin , Gupta Alankar , Bates D Gregory , Fernandez Soledad , Di Lorenzo Carlo , Linscheid Thomas
Published: January 2009

Background and objectives:

Abnormal swallowing (dysphagia) among neonates is commonly evaluated using the videofluoroscopic swallow study (VSS). Radiological findings considered high risk for administration of oral feeding include nasopharyngeal reflux, laryngeal penetration, aspiration, or pooling. Our aims were to determine pharyngoesophageal motility correlates in neonates with dysphagia and the impact of multidisciplinary feeding strategy.

Methods:

Twenty dysphagic neonates (mean gestation ± standard deviation [SD] = 30.9 ± 4.9 weeks; median 31.1 weeks; range = 23.7–38.6 weeks) with abnormal VSS results were evaluated at 49.9 ± 16.5 weeks (median 41.36 weeks) postmenstrual age. The subjects underwent a swallow‐integrated pharyngoesophageal motility assessment of basal and adaptive swallowing reflexes using a micromanometry catheter and pneumohydraulic water perfusion system. Based on observations during the motility study, multidisciplinary feeding strategies were applied and included postural adaptation, sensory modification, hunger manipulation, and operant conditioning methods. To discriminate pharyngoesophageal manometry correlates between oral feeders and tube feeders, data were stratified based on the primary feeding method at discharge, oral feeding versus tube feeding.

Results:

At discharge, 15 of 20 dysphagic neonates achieved oral feeding success, and the rest required chronic tube feeding. Pharyngoesophageal manometry correlates were significantly different (P < 0.05) between the primary oral feeders versus the chronic tube feeders for swallow frequency, swallow propagation, presence of adaptive peristaltic reflexes, oral feeding challenge test results, and upper esophageal sphincter tone. VSS results or disease characteristics had little effect on the feeding outcomes (P = NS).

Conclusions:

Swallow‐integrated esophageal motility studies permit prolonged evaluation of swallowing reflexes and responses to stimuli under controlled conditions at cribside. The dysfunctional neuromotor mechanisms may be responsible for neonatal dysphagia or its consequences. Manometry may be a better predictor than VSS in identifying patients who are likely to succeed in vigorous intervention programs.
Bone Mineral Content Deficits of the Spine and Whole Body in Children at Time of Diagnosis With Celiac Disease
Authors: Jatla Muralidhar , Zemel Babette S , Bierly Patricia , Verma Ritu
Published: January 2009

Background:

The aim of this study was to determine whether children with celiac disease (CD) have deficits in spine (SP) and whole body (WB) bone mineral content (BMC) at time of diagnosis, and whether the deficits are related to altered growth and body composition. The secondary aim was to examine the effect of histological grade on BMC.

Patients and Methods:

A retrospective study of children who had undergone a dual energy x‐ray absorptiometry scan at the time of diagnosis with CD between October 1, 2003, and June 15, 2006, were compared with a healthy reference sample of similar age and race from the same geographic region in the United States. SP and WB BMC were expressed as sex‐specific z scores relative to age and relative to height to assess differences in the CD group versus controls. Pearson correlation, t tests, and analysis of variance were performed to determine predictors of BMC.

Results:

Forty‐four children (mean age 10.6 ± 3.4 years; 77% female, 96% white) with CD were evaluated and compared with 338 healthy children. Children with CD were shorter than children of similar age and sex. SP and WB BMC for age z scores were significantly lower in the CD group compared with controls. When adjusted for height, significant deficits in WB BMC persisted in patients with CD. Low SP and WB BMC correlated with advanced histological grade in CD. Low body mass index correlated with low WB BMC in CD.

Conclusions:

Newly diagnosed children with CD may benefit from screening for low bone mineral content. Patients with low body mass index and those with advanced histological damage (Marsh grade IIIc) particularly may be at risk for osteopenia.
Dissociation Between Symptoms and Histological Severity in Pediatric Eosinophilic Esophagitis
Authors: Pentiuk Scott , Putnam Phillip E , Collins Margaret H , Rothenberg Marc E
Published: January 2009

Objectives:

The relation between patient symptoms and histological severity of eosinophilic esophagitis (EE) is not known. We created a pediatric EE symptom score (PEESS) and compared the results with histological findings in the esophagus.

Patients and Methods:

Subjects ages 3 to 18 years with a histological diagnosis of EE or their parent completed a survey rating the frequency and severity of their gastrointestinal symptoms. Scores ranged from 0 to 98. Eosinophil numbers in esophageal biopsy specimens were correlated with the PEESS.

Results:

A total of 49 subjects completed the PEESS. The symptom score did not correlate with the peak eosinophil count (r2 = 0.079). Newly diagnosed, untreated EE subjects (N = 15) had a mean score of 24.7 ± 16.4 with a modest correlation between the PEESS and the number of eosinophils in the distal esophagus (r2 = 0.37). The mean PEESS score in the 34 treated patients was lower than in untreated patients (15.6 ± 12.9; P = 0.046). The mean score for treated patients in histological remission was the same as for treated patients with active EE, regardless of treatment type. Abdominal pain was the most frequent and severe symptom reported. Among 20 of the 34 subjects (58.8%) in histological remission, 17 (85%) continued to report symptoms with a mean score of 17.4 ± 9.9 (range 1–38). Three children with active histological EE (10%) reported no symptoms.

Conclusions:

Children with untreated EE had a higher PEESS than treated subjects. Symptoms persisted in 85% of EE patients despite histological resolution and 10% with active EE reported no symptoms. Our data indicate a dissociation between symptoms and histology in pediatric EE.
Role of the Innate Immune System in the Pathogenesis of Inflammatory Bowel Disease
Authors: van Lierop Pieter PE , Samsom Janneke N , Escher Johanna C , Nieuwenhuis Edward ES
Published: January 2009

Crohn disease and ulcerative colitis are chronic inflammatory diseases of the intestinal tract commonly denoted as inflammatory bowel diseases. It has been proposed that these diseases result from aberrant mucosal immune responses to nonpathogenic microbial residents of the intestines. Recently, it was established that continuous interactions between the innate and the adaptive intestinal immune cells and the microbiota are directly involved in maintaining the physiological noninflammatory state of the intestinal mucosa. In light of the complexity of this mucosal homeostasis, it is astonishing that the inflammatory bowel diseases are relatively rare. Recently, altered functions of the innate immune system have been identified. As such, both hyperresponsiveness and hyporesponsiveness of innate cells have been implicated in the pathogenesis of inflammatory bowel diseases.
Alteration of Canalicular Transporters in a Mouse Model of Total Parenteral Nutrition
Authors: Tazuke Yuko , Teitelbaum Daniel H
Published: January 2009

Objectives:

Parenteral nutrition–associated liver disease (PNALD) is a major problem with prolonged total parenteral nutrition (TPN) administration. Our laboratory previously demonstrated significant changes in the expression of multidrug resistance genes (MDRs) 1 and 2, hepatocyte transporters, in a TPN mouse model. The present study hypothesized that these changes would lead to functional changes in the liver, and would contribute to the development of liver dysfunction.

Materials and Methods:

Mice received either intravenous saline and standard chow or TPN with or without intravenous lipids. Functional assays were performed after 7 days of infusion.

Results:

TPN with lipids led to a significant increase in serum bile acid levels, consistent with an early state of PNALD. Use of TPN without lipids prevented an elevation in bile acid levels. In both TPN groups, MDR2 expression was significantly (68%) lower than controls and bile phosphatidylcholine content, a functional measure of MDR2, was 40% less than controls. MDR1 expression in the TPN with lipid group was 31% higher than controls, whereas in the TPN without lipids mice there was no significant change. Hepatocyte extrusion of rhodamine dye, a measure of MDR1 function, declined only in the TPN with lipid group. Peroxisome proliferator–activated receptor‐α expression decreased in both TPN groups. Fenofibrate given with TPN resulted in an increased expression of MDR1 and MDR2, and functionally increased hepatocyte rhodamine extrusion and presence of bile phosphatidylcholine in the TPN with lipid group.

Conclusions:

The study shows that TPN led to alterations in the function of MDR1‐ and MDR2‐expressed proteins. The changes help in the understanding of the mechanisms leading to PNALD, and suggest that fibrate administration may palliate these changes.
A Randomized Placebo‐controlled Comparison of 2 Prebiotic/Probiotic Combinations in Preterm Infants: Impact on Weight Gain, Intestinal Microbiota, and Fecal Short‐chain Fatty Acids
Authors: Underwood Mark A , Salzman Nita H , Bennett Stephen H , Barman Melissa , Mills David A , Marcobal Angela , Tancredi Daniel J , Bevins Charles L , Sherman Michael P
Published: January 2009

Objective:

To compare the effect of 2 prebiotic/probiotic products on weight gain, stool microbiota, and stool short‐chain fatty acid (SCFA) content of premature infants.

Patients and Methods:

This randomized, blinded, placebo‐controlled trial included 90 premature infants treated with either a dietary supplement containing 2 lactobacillus species plus fructooligosaccharides (CUL, Culturelle, ConAgra, Omaha, NE), a supplement containing several species of lactobacilli and bifidobacteria plus fructooligosaccharides (PBP, ProBioPlus DDS, UAS Laboratories, Eden Prairie, MN), or placebo (a dilute preparation of Pregestamil formula) twice daily for 28 days or until discharge if earlier. The primary outcome was weight gain. Secondary outcomes were stool bacterial analysis by culture and 16S rDNA quantitative polymerase chain reaction and stool SCFA content measured by high performance liquid chromatography.

Results:

Both prebiotic/probiotic combinations contained more bacterial species than noted on the label. No significant effect on infant growth of either prebiotic/probiotic supplement was observed. By cultures, 64% of infants receiving PBP became colonized with bifidobacteria, compared with 18% of infants receiving CUL and 27% of infants receiving placebo (chi‐square, P = 0.064). No differences were noted between groups in colonization rates for lactobacilli, Gram‐negative enteric bacteria, or staphylococci. By 16S rDNA polymerase chain reaction analysis, the bifidobacteria content in the stools of the infants receiving PBP was higher than in the infants receiving CUL or placebo (Kruskal‐Wallis, P = 0.011). No significant differences in stool SCFA content were detected between groups. No adverse reactions were noted.

Conclusions:

Infants receiving PBP were more likely to become colonized with bifidobacteria. No significant differences in weight gain or stool SCFA content were detected.
Alternative Splicing Studies of the Reactive Oxygen Species Gene Network inPopulusReveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase
Authors: Srivastava Vaibhav , Srivastava Manoj Kumar , Chibani Kamel , Nilsson Robert , Rouhier Nicolas , Melzer Michael , Wingsle Gunnar
Published: January 2009

Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.
Ethylene Modulates the Role of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 in Cross Talk between Salicylate and Jasmonate Signaling
Authors: Leon-Reyes Antonio , Spoel Steven H. , De Lange Elvira S. , Abe Hiroshi , Kobayashi Masatomo , Tsuda Shinya , Millenaar Frank F. , Welschen Rob A.M. , Ritsema Tita , Pieterse Corné M.J.
Published: January 2009

The plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) play crucial roles in the signaling network that regulates induced defense responses against biotic stresses. Antagonism between SA and JA operates as a mechanism to fine-tune defenses that are activated in response to multiple attackers. In Arabidopsis (Arabidopsis thaliana), NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) was demonstrated to be required for SA-mediated suppression of JA-dependent defenses. Because ET is known to enhance SA/NPR1-dependent defense responses, we investigated the role of ET in the SA-JA signal interaction. Pharmacological experiments with gaseous ET and the ET precursor 1-aminocyclopropane-1-carboxylic acid showed that ET potentiated SA/NPR1-dependent PATHOGENESIS-RELATED1 transcription, while it rendered the antagonistic effect of SA on methyl jasmonate-induced PDF1.2 and VSP2 expression NPR1 independent. This overriding effect of ET on NPR1 function in SA-JA cross talk was absent in the npr1-1/ein2-1 double mutant, demonstrating that it is mediated via ET signaling. Abiotic and biotic induction of the ET response similarly abolished the NPR1 dependency of the SA-JA signal interaction. Furthermore, JA-dependent resistance against biotic attackers was antagonized by SA in an NPR1-dependent fashion only when the plant-attacker combination did not result in the production of high levels of endogenous ET. Hence, the interaction between ET and NPR1 plays an important modulating role in the fine tuning of the defense signaling network that is activated upon pathogen and insect attack. Our results suggest a model in which ET modulates the NPR1 dependency of SA-JA antagonism, possibly to compensate for enhanced allocation of NPR1 to function in SA-dependent activation of PR genes.
Molecular Modeling and Site-Directed Mutagenesis Reveal Essential Residues for Catalysis in a Prokaryote-Type Aspartate Aminotransferase
Authors: de la Torre Fernando , Moya-García Aurelio A. , Suárez María-Fernanda , Rodríguez-Caso Carlos , Cañas Rafael A. , Sánchez-Jiménez Francisca , Cánovas Francisco M.
Published: January 2009

We recently reported that aspartate (Asp) biosynthesis in plant chloroplasts is catalyzed by two different Asp aminotransferases (AAT): a previously characterized eukaryote type and a prokaryote type (PT-AAT) similar to bacterial and archaebacterial enzymes. The available molecular and kinetic data suggest that the eukaryote-type AAT is involved in the shuttling of reducing equivalents through the plastidic membrane, whereas the PT-AAT could be involved in the biosynthesis of the Asp-derived amino acids inside the organelle. In this work, a comparative modeling of the PT-AAT enzyme from Pinus pinaster (PpAAT) was performed using x-ray structures of a bacterial AAT (Thermus thermophilus; Protein Data Bank accession nos. 1BJW and 1BKG) as templates. We computed a three-dimensional folding model of this plant homodimeric enzyme that has been used to investigate the functional importance of key amino acid residues in its active center. The overall structure of the model is similar to the one described for other AAT enzymes, from eukaryotic and prokaryotic sources, with two equivalent active sites each formed by residues of both subunits of the homodimer. Moreover, PpAAT monomers folded into one large and one small domain. However, PpAAT enzyme showed unique structural and functional characteristics that have been specifically described in the AATs from the prokaryotes Phormidium lapideum and T. thermophilus, such as those involved in the recognition of the substrate side chain or the “open-to-closed” transition following substrate binding. These predicted characteristics have been substantiated by site-direct mutagenesis analyses, and several critical residues (valine-206, serine-207, glutamine-346, glutamate-210, and phenylalanine-450) were identified and functionally characterized. The reported data represent a valuable resource to understand the function of this enzyme in plant amino acid metabolism.
Time-resolved X-ray microscopy of nanoparticle aggregates under oscillatory shear
Authors: Auernhammer G. K. , Fauth K. , Ullrich B. , Zhao J. , Weigand M. , Vollmer D.
Published: January 2009

Of all the current detection techniques with nanometre resolution, only X-ray microscopy allows imaging of nanoparticles in suspension. Can it also be used to investigate structural dynamics? When studying the response to mechanical stimuli, the challenge lies in its application with a precision comparable with the spatial resolution. In the first shear experiments performed in an X-ray microscope, this has been accomplished by inserting a piezo actuator driven shear cell into the focal plane of a scanning transmission X-ray microscope. Thus shear-induced re-organization of magnetite nanoparticle aggregates could be demonstrated in suspension. As X-ray microscopy proves suitable for studying structural change, new prospects open up in physics at small length scales.
Distinguishing between two sympatricAcanthopagrusspecies from Dapeng Bay, Taiwan, using morphometric and genetic characters
Authors: Tseng M. C. , Jean C. T. , Tsai W. L. , Chen N. C.
Published: January 2009

Morphometric and genetic data were used to compare two sympatric and morphologically similar species,Acanthopagrus berdaandAcanthopagrus taiwanensis, in Dapeng Bay, South‐western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochromeb(0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 forA. taiwanensisand 0·003 forA. berda). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 forA. taiwanensisand 0·637 ± 0·145 forA. berda. Nei’s unbiased measure of interspecific genetic distance (DS) was 1·334.FST(0·134) andRST(0·404) values indicated significant differentiation between species. An unrooted neighbour‐joining tree was constructed by allele‐sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species,A. taiwanensisandA. berda.
Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes
Authors: Valdez‐Moreno M. , Ivanova N. V. , Elías‐Gutiérrez M. , Contreras‐Balderas S. , Hebert P. D. N.
Published: January 2009

The freshwater fish fauna of Mexico and Guatemala is exceptionally diverse with >600 species, many endemic. In this study, patterns of sequence divergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average divergence among conspecific individuals was 0·45%, while congeneric taxa showed 5·1% divergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low divergence values (<2%), but nevertheless, clear barcode clusters were apparent in the Bramocharax–Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply divergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding diversity of this fauna.
Rodlet cell biometry: interspecific and intraspecific variability
Authors: Manera M. , Giari L. , Dezfuli B. S.
Published: January 2009

Intraspecific and interspecific variability in rodlet cell size in various tissues of several species of freshwater and marine fish were documented. Differences were attributed mainly to fish species, although tissue type contributed significantly, providing evidence for the presence of rodlet cell morphotypes.
Correlated trait responses to multiple selection pressures in larval amphibians reveal conflict avoidance strategies
Authors: GARCIA TIFFANY S. , PAOLETTI DAVID J. , BLAUSTEIN ANDREW R.
Published: January 2009

1. Larval amphibians frequently experience simultaneous, conflicting selection pressures from ultraviolet‐B (UV‐B) radiation and predation risk, two stressors that can select for opposing defence strategies. When both UV‐B and predators are present, individuals can reconcile potential conflicts by correlating particular trait responses (e.g. combining dark or light body colouration with increased or decreased activity rates to create an appropriate multiple stressor strategy). Optimal combinations of body colour and activity rate are predicted to change across an elevation gradient with increasing UV‐B exposure.

2. In this study, we tested how larval amphibians combine changes in body colouration and activity rates to create a correlated response to potentially conflicting selection pressures. We quantified activity and colour response in two amphibian species, the pacific treefrog (Hyla regilla) and the long‐toed salamander (Ambystoma macrodactylum), from both high and low elevation populations, and exposed individuals to both a common predator and naturally relevant levels of UV‐B.

3. Hyla regilla and A. macrodactylum individuals from low elevation populations responded with correlated response strategies while high elevation populations did not. Low elevation H. regilla coupled decreased activity rates to reduce predator detection with dark body colouration to screen out UV‐B. Low elevation A. macrodactylum adopted cryptic colouration when predators were present and decreased activity in response to UV‐B. Individuals from high elevation H. regilla and A. macrodactylum populations responded only with changes in activity and not colour change.

4. The observed population differences may reflect variation in selection strengths across an elevation gradient. High elevation habitats may require individuals to focus defence efforts on the greatest potential risk. Additionally, pigmentation changes may not be an adequate defence in these UV‐B intense habitats.
Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix
Authors: Kawai Yoshikazu , Daniel Richard A. , Errington Jeffery
Published: January 2009

The bacterial actin homologue MreB plays a key role in cell morphogenesis. In Bacillus subtilis MreB is essential under normal growth conditions and mreB mutants are defective in the control of cell diameter. However, the precise role of MreB is still unclear. Analysis of the lethal phenotypic consequences of mreB disruption revealed an unusual bulging phenotype that precedes cell death. A similar phenotype was seen in wild‐type cells at very low Mg2+ concentrations. We found that inactivation of the major bi‐functional penicillin‐binding protein (PBP) PBP1 of B. subtilis restored the viability of an mreB null mutant as well as preventing bulging in both mutant and wild‐type backgrounds. Bulging was associated with delocalization of PBP1. We show that the normal pattern of localization of PBP1 is dependent on MreB and that the proteins can physically interact using in vivo pull‐down and bacterial two‐hybrid approaches. Interactions between MreB and several other PBPs were also detected. Our results suggest that MreB filaments associate directly with the peptidoglycan biosynthetic machinery in B. subtilis as part of the mechanism that brings about controlled cell elongation.