bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
KEA: kinase enrichment analysis
Authors: Lachmann Alexander , Ma'ayan Avi 
Published: January 2009

Abstract
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

Abstract
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

ABSTRACTBackground 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

ABSTRACTBackground: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

ABSTRACTObjectives: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

ABSTRACTCrohn 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

ABSTRACTObjectives: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.