bluuebunny/crossref_metadata_2025 huggingface dataset:
UK population norms for the modified dental anxiety scale with percentile calculator: adult dental health survey 2009 results
Authors: Humphris Gerry , Crawford John R , Hill Kirsty , Gilbert Angela , Freeman Ruth
Published: June 2013

Background

A recent UK population survey of oral health included questions to assess dental anxiety to provide mean and prevalence estimates of this important psychological construct.

Methods

A two-stage cluster sample was used for the survey across England, Wales, and Northern Ireland. The survey took place between October-December 2009, and January-April 2010. All interviewers were trained on survey procedures. Within the 7,233 households sampled there were 13,509 adults who were asked to participate in the survey and 11,382 participated (84%).

Results

The scale was reliable and showed some evidence of unidimensionality. Estimated proportion of participants with high dental anxiety (cut-off score = 19) was 11.6%. Percentiles and confidence intervals were presented and can be estimated for individual patients across various age ranges and gender using an on-line tool.

Conclusions

The largest reported data set on the MDAS from a representative UK sample was presented. The scale’s psychometrics is supportive for the routine assessment of patient dental anxiety to compare against a number of major demographic groups categorised by age and sex. Practitioners within the UK have a resource to estimate the rarity of a particular patient’s level of dental anxiety, with confidence intervals, when using the on-line percentile calculator.
Spica prunellae promotes cancer cell apoptosis, inhibits cell proliferation and tumor angiogenesis in a mouse model of colorectal cancer via suppression of stat3 pathway
Authors: Lin Wei , Zheng Liangpu , Zhuang Qunchuan , Zhao Jinyan , Cao Zhiyun , Zeng Jianwei , Lin Shan , Xu Wei , Peng Jun
Published: June 2013

Background

Constitutive activation of STAT3 is one of the major oncogenic pathways involved in the development of various types of malignancies including colorectal cancer (CRC); and thus becomes a promising therapeutic target. Spica Prunellaehas long been used as an important component in many traditional Chinese medicine formulas to clinically treat CRC. Previously, we found thatSpica Prunellaeinhibits CRC cell growth through mitochondrion-mediated apoptosis. Furthermore, we demonstrated its anti-angiogenic activitiesin vivoandin vitro. To further elucidate the precise mechanism of the potential tumoricidal activity ofSpica Prunellae, using a CRC mouse xenograft model, in this study we evaluated its therapeutic efficacy against CRC and investigated the underlying molecular mechanisms.

Methods

CRC mouse xenograft model was generated by subcutaneous injection of human colon carcinoma HT-29 cells into nude mice. Animals were given intra-gastric administration with 6 g/kg of the ethanol extract ofSpica Prunellae(EESP) daily, 5 days a week for 16 days. Body weight and tumor growth were measured every two days. Tumor growthin vivowas determined by measuring the tumor volume and weight. HT-29 cell viability was examined by MTT assay. Cell apoptosis and proliferation in tumors from CRC xenograft mice was evaluated via immunohistochemical staining (IHS) for TUNEL and PCNA, and the intratumoral microvessel density (MVD) was examined by using IHS for the endothelial cell-specific marker CD31. The activation of STAT3 was evaluated by determining its phosphorylation level using IHS. The mRNA and protein expression of Bcl-2, Bax, Cyclin D1, VEGF-A and VEGFR2 was measured by RT-PCR and IHS, respectively.

Results

EESP treatment reduced tumor volume and tumor weight but had no effect on body weight change in CRC mice; decreased HT-29 cell viability in a dose-dependent manner, suggesting that EESP displays therapeutic efficacy against colon cancer growthin vivoandin vitro, without apparent toxicity. In addition, EESP significantly inhibited the phosphorylation of STAT3 in tumor tissues, indicating its suppressive action on the activation of STAT3 signaling. Consequently, the inhibitory effect of EESP on STAT3 activation resulted in an increase in the pro-apoptotic Bax/Bcl-2 ratio, decrease in the expression of the pro-proliferative Cyclin D1 and CDK4, as well as down-regulation of pro-angiogenic VEGF-A and VEGFR-2 expression. Finally, these molecular effects led to the induction of apoptosis, the inhibition of cell proliferation and tumor angiogenesis.

Conclusions

Spica Prunellaepossesses a broad range of anti-cancer activities due to its ability to affect STAT3 pathway, suggesting thatSpica Prunellaecould be a novel potent therapeutic agent for the treatment of CRC.
Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci
Authors: Sabri Suriana , Steen Jennifer A , Bongers Mareike , Nielsen Lars K , Vickers Claudia E
Published: June 2013

Background

Metabolic engineering projects often require integration of multiple genes in order to control the desired phenotype. However, this often requires iterative rounds of engineering because many current insertion approaches are limited by the size of the DNA that can be transferred onto the chromosome. Consequently, construction of highly engineered strains is very time-consuming. A lack of well-characterised insertion loci is also problematic.

Results

A series of knock-in/knock-out (KIKO) vectors was constructed for integration of large DNA sequences onto the E. coli chromosome at well-defined loci. The KIKO plasmids target three nonessential genes/operons as insertion sites: arsB (an arsenite transporter); lacZ (β-galactosidase); and rbsA-rbsR (a ribose metabolism operon). Two homologous ‘arms’ target each insertion locus; insertion is mediated by λ Red recombinase through these arms. Between the arms is a multiple cloning site for the introduction of exogenous sequences and an antibiotic resistance marker (either chloramphenicol or kanamycin) for selection of positive recombinants. The resistance marker can subsequently be removed by flippase-mediated recombination. The insertion cassette is flanked by hairpin loops to isolate it from the effects of external transcription at the integration locus. To characterize each target locus, a xylanase reporter gene (xynA) was integrated onto the chromosomes of E. coli strains W and K-12 using the KIKO vectors. Expression levels varied between loci, with the arsB locus consistently showing the highest level of expression. To demonstrate the simultaneous use of all three loci in one strain, xynA, green fluorescent protein (gfp) and a sucrose catabolic operon (cscAKB) were introduced into lacZ, arsB and rbsAR respectively, and shown to be functional.

Conclusions

The KIKO plasmids are a useful tool for efficient integration of large DNA fragments (including multiple genes and pathways) into E. coli. Chromosomal insertion provides stable expression without the need for continuous antibiotic selection. Three non-essential loci have been characterised as insertion loci; combinatorial insertion at all three loci can be performed in one strain. The largest insertion at a single site described here was 5.4 kb; we have used this method in other studies to insert a total of 7.3 kb at one locus and 11.3 kb across two loci. These vectors are particularly useful for integration of multigene cassettes for metabolic engineering applications.
Pathologic fracture does not influence prognosis in stage IIB osteosarcoma: a case–control study
Authors: Zuo Dongqing , Zheng Longpo , Sun Wei , Hua Yingqi , Cai Zhengdong
Published: June 2013

Objective

This study tested the implication of pathologic fractures on the prognosis in stage IIb osteosarcoma.

Methods

A single center retrospective evaluation of clinical management and oncologic outcome was conducted with 15 pathological fracture patients (M:F = 10:5; age: mean 23.2, range 12–42) and 50 non-fracture patients between April 2002 and December 2010. These stage IIB osteosarcoma patients were matched for age, tumor site (femur, tibia, and humerus), and osteosarcoma subtype (i.e., control patients with osteosarcoma in the same sites as the fracture patients). All osteosarcoma patients with pathological fractures underwent brace or cast immobilization, adjuvant chemotherapy, and limb salvage surgery or amputation. Musculoskeletal Tumor Society (MSTS) functional scores were assessed. The mean follow-up time was 34.7 months (range, 8–47 months).

Results

Following limb salvage surgery, no statistical differences were observed in major complications (fracture = 20.0%, control = 12.0%,P= 0.43) or local recurrence complications (fracture = 26.7%, control = 14.0%,P= 0.25). Overall 3-year survival rates of the fracture and control groups (66.7% and 75.3%, respectively) were not statistically different (P= 0.5190). Three-year disease-free survival rates of the fracture and control groups were 53.3% and 66.5%, respectively (P= 0.25).

Conclusions

Pathologic fracture was not a prognostic indicator of recurrence or overall survival in localized osteosarcoma patients. Limb salvage can be achieved by and maintaining adequate surgical margins and applying adjuvant chemotherapy.
Vaccinia virus expressing bone morphogenetic protein-4 in novel glioblastoma orthotopic models facilitates enhanced tumor regression and long-term survival
Authors: Duggal Rohit , Geissinger Ulrike , Zhang Qian , Aguilar Jason , Chen Nanhai G , Binda Elena , Vescovi Angelo L , Szalay Aladar A
Published: June 2013

Background

Glioblastoma multiforme (GBM) is one of the most aggressive forms of cancer with a high rate of recurrence. We propose a novel oncolytic vaccinia virus (VACV)-based therapy using expression of the bone morphogenetic protein (BMP)-4 for treating GBM and preventing recurrence.

Methods

We have utilized clinically relevant, orthotopic xenograft models of GBM based on tumor-biopsy derived, primary cancer stem cell (CSC) lines. One of the cell lines, after being transduced with a cDNA encoding firefly luciferase, could be used for real time tumor imaging. A VACV that expresses BMP-4 was constructed and utilized for infecting several primary glioma cultures besides conventional serum-grown glioma cell lines. This virus was also delivered intracranially upon implantation of the GBM CSCs in mice to determine effects on tumor growth.

Results

We found that the VACV that overexpresses BMP-4 demonstrated heightened replication and cytotoxic activity in GBM CSC cultures with a broad spectrum of activity across several different patient-biopsy cultures. Intracranial inoculation of mice with this virus resulted in a tumor size equal to or below that at the time of injection. This resulted in survival of 100% of the treated mice up to 84 days post inoculation, significantly superior to that of a VACV lacking BMP-4 expression. When mice with a higher tumor burden were injected with the VACV lacking BMP-4, 80% of the mice showed tumor recurrence. In contrast, no recurrence was seen when mice were injected with the VACV expressing BMP-4, possibly due to induction of differentiation in the CSC population and subsequently serving as a better host for VACV infection and oncolysis. This lack of recurrence resulted in superior survival in the BMP-4 VACV treated group.

Conclusions

Based on these findings we propose a novel VACV therapy for treating GBM, which would allow tumor specific production of drugs in the future in combination with BMPs which would simultaneously control tumor maintenance and facilitate CSC differentiation, respectively, thereby causing sustained tumor regression without recurrence.
INI1/hSNF5-interaction defective HIV-1 IN mutants exhibit impaired particle morphology, reverse transcription and integration in vivo
Authors: Mathew Sheeba , Nguyen Minh , Wu Xuhong , Pal Achintya , Shah Vaibhav B , Prasad Vinayaka R , Aiken Christopher , Kalpana Ganjam V
Published: June 2013

Background

Retroviral integrase catalyzes integration of viral DNA into the host genome. Integrase interactor (INI)1/hSNF5 is a host factor that binds to HIV-1 IN within the context of Gag-Pol and is specifically incorporated into HIV-1 virions during assembly. Previous studies have indicated that INI1/hSNF5 is required for late events in vivo and for integration in vitro. To determine the effects of disrupting the IN-INI1 interaction on the assembly and infectivity of HIV-1 particles, we isolated mutants of IN that are defective for binding to INI1/hSNF5 and tested their effects on HIV-1 replication.

Results

A reverse yeast two-hybrid system was used to identify INI1-interaction defective IN mutants (IID-IN). Since protein-protein interactions depend on the surface residues, the IID-IN mutants that showed high surface accessibility on IN crystal structures (K71R, K111E, Q137R, D202G, and S147G) were selected for further study. In vitro interaction studies demonstrated that IID-IN mutants exhibit variable degrees of interaction with INI1. The mutations were engineered into HIV-1NL4-3 and HIV-Luc viruses and tested for their effects on virus replication. HIV-1 harboring IID-IN mutations were defective for replication in both multi- and single-round infection assays. The infectivity defects were correlated to the degree of INI1 interaction of the IID-IN mutants. Highly defective IID-IN mutants were blocked at early and late reverse transcription, whereas partially defective IID-IN mutants proceeded through reverse transcription and nuclear localization, but were partially impaired for integration. Electron microscopic analysis of mutant particles indicated that highly interaction-defective IID-IN mutants produced morphologically aberrant virions, whereas the partially defective mutants produced normal virions. All of the IID-IN mutant particles exhibited normal capsid stability and reverse transcriptase activity in vitro.

Conclusions

Our results demonstrate that a severe defect in IN-INI1 interaction is associated with production of defective particles and a subsequent defect in post-entry events. A partial defect in IN-INI1 interaction leads to production of normal virions that are partially impaired for early events including integration. Our studies suggest that proper interaction of INI1 with IN within Gag-Pol is necessary for proper HIV-1 morphogenesis and integration.
Cognitive function and number of teeth in a community-dwelling population in Japan
Authors: Saito Yuki , Sugawara Norio , Yasui-Furukori Norio , Takahashi Ippei , Nakaji Shigeyuki , Kimura Hiroto
Published: June 2013

Background

It has been reported that oral health is poor in elderly populations and is associated with poor cognition and dementia. The objective of this study was to examine the association between tooth loss and cognitive function in a community-dwelling population in Japan.

Methods

We examined the association between tooth loss and cognitive function in 462 Japanese community-dwelling individuals. The Mini-Mental State Examination (MMSE) was employed to measure global cognitive status. A multiple logistic regression analysis, with both crude and adjusted conditions for confounding factors, was used to assess the relationship between poor cognition and the number of remaining teeth.

Results

The overall prevalence of poor cognition (MMSE ≤ 23) in this study population was 5.6%. Subjects with poor cognition were significantly older, less educated, scored lower in intellectual activity, and had fewer remaining teeth than those with normal cognition. According to the multiple logistic regression analysis, a lower number of teeth (0–10) was found to be a significant independent risk factor (OR = 20.21, 95% confidence interval = 2.20 to 185.47) of cognitive impairment.

Conclusions

This cross-sectional study on a Japanese community-dwelling population revealed relationships between tooth loss and cognitive function. However, the interpretation of our results was hampered by a lack of data, including socioeconomic status and longitudinal observations. Future research exploring tooth loss and cognitive function is warranted.
Medicinal plants from swidden fallows and sacred forest of the Karen and the Lawa in Thailand
Authors: Junsongduang Auemporn , Balslev Henrik , Inta Angkhana , Jampeetong Arunothai , Wangpakapattanawong Prasit
Published: June 2013

Background

Many ecosystem services provided by forests are important for the livelihoods of indigenous people. Sacred forests are used for traditional practices by the ethnic minorities in northern Thailand and they protect these forests that are important for their culture and daily life. Swidden fallow fields are a dominant feature of the agricultural farming landscapes in the region. In this study we evaluate and compare the importance of swidden fallow fields and sacred forests as providers of medicinal plants among the Karen and Lawa ethnic minorities in northern Thailand.

Methods

We made plant inventories in swidden fallow fields of three different ages (1–2, 3–4, 5–6 years old) and in sacred forests around two villages using a replicated stratified design of vegetation plots. Subsequently we interviewed the villagers, using semi-structured questionnaires, to assess the medicinal use of the species encountered in the vegetation survey.

Results

We registered a total of 365 species in 244 genera and 82 families. Of these 72(19%) species in 60(24%) genera and 32(39%) families had medicinal uses. Although the sacred forest overall housed more species than the swidden fallow fields, about equal numbers of medicinal plants were derived from the forest and the fallows. This in turn means that a higher proportion (48% and 34%) of the species in the relatively species poor fallows were used for medicinal purposes than the proportion of medicinal plants from the sacred forest which accounted for 17–22%. Of the 32 medicinal plant families Euphorbiaceae and Lauraceae had most used species in the Karen and Lawa villages respectively.

Conclusion

Sacred forest are important for providing medicinal plant species to the Karen and Lawa communities in northern Thailand, but the swidden fallows around the villages are equally important in terms of absolute numbers of medicinal plant species, and more important if counted as proportion of the total number of species in a habitat. This points to the importance of secondary vegetation as provider of medicinal plants around rural villages as seen elsewhere in the tropics.
Integrated pharmacokinetics/pharmacodynamics parameters-based dosing guidelines of enrofloxacin in grass carp Ctenopharyngodon idella to minimize selection of drug resistance
Authors: Xu Lijuan , Wang Hao , Yang Xianle , Lu Liqun
Published: June 2013

Background

Antibiotic resistance has become a serious global problem and is steadily increasing worldwide in almost every bacterial species treated with antibiotics. In aquaculture, the therapeutic options for the treatment of A. hydrophila infection were only limited to several antibiotics, which contributed for the fast-speed emergence of drug tolerance. Accordingly, the aim of this study was to establish a medication regimen to prevent drug resistant bacteria. To determine a rational therapeutic guideline, integrated pharmacodynamics and pharmacokinetics parameters were based to predict dose and dosage interval of enrofloxacin in grass carp Ctenopharyngodon idella infected by a field-isolated A. hydrophila strain.

Results

The pathogenic A. hydrophila strain (AH10) in grass carp was identified and found to be sensitive to enrofloxacin. The mutant selection window (MSW) of enrofloxacin on isolate AH10 was determined to be 0.5 - 3 μg/mL based on the mutant prevention concentration (MPC) and minimum inhibitory concentration (MIC) value. By using high-performance liquid chromatography (HPLC) system, the Pharmacokinetic (PK) parameters of enrofloxacin and its metabolite ciprofloxacin in grass carp were monitored after a single oral gavage of 10, 20, 30 μg enrofloxacin per g body weight. Dosing of 30 μg/g resulted in serum maximum concentration (Cmax) of 7.151 μg/mL, and concentration in serum was above MPC till 24 h post the single dose. Once-daily dosing of 30 μg/g was determined to be the rational choice for controlling AH10 infection and preventing mutant selection in grass carp. Data of mean residue time (MRT) and body clearance (CLz) indicated that both enrofloxacin and its metabolite ciprofloxacin present similar eliminating rate and pattern in serum, muscle and liver. A withdraw time of more than 32 d was suggested based on the drug eliminating rate and pharmacokinetic model described by a polyexponential equation.

Conclusions

Based on integrated PK/PD parameters (AUC/MIC, Cmax/MIC, and T>MPC), the results of this study established a principle, for the first time, on drawing accurate dosing guideline for pharmacotherapy against A. hydrophila strain (AH10) for prevention of drug-resistant mutants. Our approach in combining PK data with PD parameters (including MPC and MSW) was the new effort in aquaculture to face the challenge of drug resistance by drawing a specific dosage guideline of antibiotics.
Temporary organ displacement coupled with image-guided, intensity-modulated radiotherapy for paraspinal tumors
Authors: Katsoulakis Evangelia , Solomon Stephen B , Maybody Majid , Housman Douglas , Niyazov Greg , Riaz Nadeem , Lovelock Michael , Spratt Daniel E , Erinjeri Joseph P , Thornton Raymond H , Yamada Yoshiya
Published: June 2013

Background

To investigate the feasibility and dosimetric improvements of a novel technique to temporarily displace critical structures in the pelvis and abdomen from tumor during high-dose radiotherapy.

Methods

Between 2010 and 2012, 11 patients received high-dose image-guided intensity-modulated radiotherapy with temporary organ displacement (TOD) at our institution. In all cases, imaging revealed tumor abutting critical structures. An all-purpose drainage catheter was introduced between the gross tumor volume (GTV) and critical organs at risk (OAR) and infused with normal saline (NS) containing 5-10% iohexol. Radiation planning was performed with the displaced OARs and positional reproducibility was confirmed with cone-beam CT (CBCT). Patients were treated within 36 hours of catheter placement. Radiation plans were re-optimized using pre-TOD OARs to the same prescription and dosimetrically compared with post-TOD plans. A two-tailed permutation test was performed on each dosimetric measure.

Results

The bowel/rectum was displaced in six patients and kidney in four patients. One patient was excluded due to poor visualization of the OAR; thus 10 patients were analyzed. A mean of 229 ml (range, 80–1000) of NS 5-10% iohexol infusion resulted in OAR mean displacement of 17.5 mm (range, 7–32). The median dose prescribed was 2400 cGy in one fraction (range, 2100–3000 in 3 fractions). The mean GTV Dmin and PTV Dmin pre- and post-bowel TOD IG-IMRT dosimetry significantly increased from 1473 cGy to 2086 cGy (p=0.015) and 714 cGy to 1214 cGy (p=0.021), respectively. TOD increased mean PTV D95 by 27.14% of prescription (p=0.014) while the PTV D05 decreased by 9.2% (p=0.011). TOD of the bowel resulted in a 39% decrease in mean bowel Dmax (p=0.008) confirmed by CBCT. TOD of the kidney significantly decreased mean kidney dose and Dmax by 25% (0.022).

Conclusions

TOD was well tolerated, reproducible, and facilitated dose escalation to previously radioresistant tumors abutting critical structures while minimizing dose to OARs.
A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces
Authors: Xu Bin , Wei Xiaoming , Deng Lei , Guan Jihong , Zhou Shuigeng
Published: June 2013

Background

Hot spots are residues contributing the most of binding free energy yet accounting for a small portion of a protein interface. Experimental approaches to identify hot spots such as alanine scanning mutagenesis are expensive and time-consuming, while computational methods are emerging as effective alternatives to experimental approaches.

Results

In this study, we propose a semi-supervised boosting SVM, which is called sbSVM, to computationally predict hot spots at protein-protein interfaces by combining protein sequence and structure features. Here, feature selection is performed using random forests to avoid over-fitting. Due to the deficiency of positive samples, our approach samples useful unlabeled data iteratively to boost the performance of hot spots prediction. The performance evaluation of our method is carried out on a dataset generated from the ASEdb database for cross-validation and a dataset from the BID database for independent test. Furthermore, a balanced dataset with similar amounts of hot spots and non-hot spots (65 and 66 respectively) derived from the first training dataset is used to further validate our method. All results show that our method yields good sensitivity, accuracy and F1 score comparing with the existing methods.

Conclusion

Our method boosts prediction performance of hot spots by using unlabeled data to overcome the deficiency of available training data. Experimental results show that our approach is more effective than the traditional supervised algorithms and major existing hot spot prediction methods.
Cliques for the identification of gene signatures for colorectal cancer across population
Authors: Pradhan Meeta P , Nagulapalli Kshithija , Palakal Mathew J
Published: June 2013

Background

Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Studies have correlated risk of CRC development with dietary habits and environmental conditions. Gene signatures for any disease can identify the key biological processes, which is especially useful in studying cancer development. Such processes can be used to evaluate potential drug targets. Though recognition of CRC gene-signatures across populations is crucial to better understanding potential novel treatment options for CRC, it remains a challenging task.

Results

We developed a topological and biological feature-based network approach for identifying the gene signatures across populations. In this work, we propose a novel approach of using cliques to understand the variability within population. Cliques are more conserved and co-expressed, therefore allowing identification and comparison of cliques across a population which can help researchers study gene variations. Our study was based on four publicly available expression datasets belonging to four different populations across the world. We identified cliques of various sizes (0 to 7) across the four population networks. Cliques of size seven were further analyzed across populations for their commonality and uniqueness. Forty-nine common cliques of size seven were identified. These cliques were further analyzed based on their connectivity profiles. We found associations between the cliques and their connectivity profiles across networks. With these clique connectivity profiles (CCPs), we were able to identify the divergence among the populations, important biological processes (cell cycle, signal transduction, and cell differentiation), and related gene pathways. Therefore the genes identified in these cliques and their connectivity profiles can be defined as the gene-signatures across populations. In this work we demonstrate the power and effectiveness of cliques to study CRC across populations.

Conclusions

We developed a new approach where cliques and their connectivity profiles helped elucidate the variation and similarity in CRC gene profiles across four populations with unique dietary habits.
Detection of protein complexes from affinity purification/mass spectrometry data
Authors: Cai Bingjing , Wang Haiying , Zheng Huiru , Wang Hui
Published: June 2013

Background

Recent advances in molecular biology have led to the accumulation of large amounts of data on protein-protein interaction networks in different species. An important challenge for the analysis of these data is to extract functional modules such as protein complexes and biological processes from networks which are characterised by the present of a significant number of false positives. Various computational techniques have been applied in recent years. However, most of them treat protein interaction as binary. Co-complex relations derived from affinity purification/mass spectrometry (AP-MS) experiments have been largely ignored.

Methods

This paper presents a new algorithm for detecting protein complexes from AP-MS data. The algorithm intends to detect groups of prey proteins that are significantly co-associated with the same set of bait proteins. We first construct AP-MS data as a bipartite network, where one set of nodes consists of bait proteins and the other set is composed of prey proteins. We then calculate pair-wise similarities of bait proteins based on the number of their commonly shared neighbours. A hierarchical clustering algorithm is employed to cluster bait proteins based on the similarities and thus a set of 'seed' clusters is obtained. Starting from these 'seed' clusters, an expansion process is developed to identify prey proteins which are significantly associated with the same set of bait proteins. Then, a set of complete protein complexes is derived. In application to two real AP-MS datasets, we validate biological significance of predicted protein complexes by using curated protein complexes and well-characterized cellular component annotation from Gene Ontology (GO). Several statistical metrics have been applied for evaluation.

Results

Experimental results show that, the proposed algorithm achieves significant improvement in detecting protein complexes from AP-MS data. In comparison to the well-known MCL algorithm, our algorithm improves the accuracy rate by about 20% in detecting protein complexes in both networks and increases the F-Measure value by about 50% in Krogan_2006 network. Greater precision and better accuracy have been achieved and the identified complexes are demonstrated to match well with existing curated protein complexes.

Conclusions

Our study highlights the significance of taking co-complex relations into account when extracting protein complexes from AP-MS data. The algorithm proposed in this paper can be easily extended to the analysis of other biological networks which can be conveniently represented by bipartite graphs such as drug-target networks.
Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum
Authors: Cai Hong , Hong Changjin , Gu Jianying , Lilburn Timothy G , Kuang Rui , Wang Yufeng
Published: June 2013

Background

Malaria causes over one million deaths annually, posing an enormous health and economic burden in endemic regions. The completion of genome sequencing of the causative agents, a group of parasites in the genusPlasmodium, revealed potential drug and vaccine candidates. However, genomics-driven target discovery has been significantly hampered by our limited knowledge of the cellular networks associated with parasite development and pathogenesis. In this paper, we propose an approach based on aligning neighborhood PPI subnetworks across species to identify network components in the malaria parasiteP. falciparum.

Results

Instead of only relying on sequence similarities to detect functional orthologs, our approach measures the conservation between the neighborhood subnetworks in protein-protein interaction (PPI) networks in two species,P. falciparumandE. coli. 1,082P. falciparumproteins were predicted as functional orthologs of known transcriptional regulators in theE. colinetwork, including general transcriptional regulators, parasite-specific transcriptional regulators in the ApiAP2 protein family, and other potential regulatory proteins. They are implicated in a variety of cellular processes involving chromatin remodeling, genome integrity, secretion, invasion, protein processing, and metabolism.

Conclusions

In this proof-of-concept study, we demonstrate that a subnetwork alignment approach can reveal previously uncharacterized members of the subnetworks, which opens new opportunities to identify potential therapeutic targets and provide new insights into parasite biology, pathogenesis and virulence. This approach can be extended to other systems, especially those with poor genome annotation and a paucity of knowledge about cellular networks.
Common plants as alternative analytical tools to monitor heavy metals in soil
Authors: Malizia Daniela , Giuliano Antonella , Ortaggi Giancarlo , Masotti Andrea
Published: June 2013

Background

Herbaceous plants are common vegetal species generally exposed, for a limited period of time, to bioavailable environmental pollutants. Heavy metals contamination is the most common form of environmental pollution. Herbaceous plants have never been used as natural bioindicators of environmental pollution, in particular to monitor the amount of heavy metals in soil. In this study, we aimed at assessing the usefulness of using three herbaceous plants (Plantago major L., Taraxacum officinale L. and Urtica dioica L.) and one leguminous (Trifolium pratense L.) as alternative indicators to evaluate soil pollution by heavy metals.

Results

We employed Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES) to assess the concentration of selected heavy metals (Cu, Zn, Mn, Pb, Cr and Pd) in soil and plants and we employed statistical analyses to describe the linear correlation between the accumulation of some heavy metals and selected vegetal species. We found that the leaves of Taraxacum officinale L. and Trifolium pratense L. can accumulate Cu in a linearly dependent manner with Urtica dioica L. representing the vegetal species accumulating the highest fraction of Pb.

Conclusions

In this study we demonstrated that common plants can be used as an alternative analytical tool for monitoring selected heavy metals in soil.
How effective are traditional methods of compositional analysis in providing an accurate material balance for a range of softwood derived residues?
Authors: Burkhardt Sabrina , Kumar Linoj , Chandra Richard , Saddler Jack
Published: June 2013

Background

Forest residues represent an abundant and sustainable source of biomass which could be used as a biorefinery feedstock. Due to the heterogeneity of forest residues, such as hog fuel and bark, one of the expected challenges is to obtain an accurate material balance of these feedstocks. Current compositional analytical methods have been standardised for more homogenous feedstocks such as white wood and agricultural residues. The described work assessed the accuracy of existing and modified methods on a variety of forest residues both before and after a typical pretreatment process.

Results

When “traditional” pulp and paper methods were used, the total amount of material that could be quantified in each of the six softwood-derived residues ranged from 88% to 96%. It was apparent that the extractives present in the substrate were most influential in limiting the accuracy of a more representative material balance. This was particularly evident when trying to determine the lignin content, due to the incomplete removal of the extractives, even after a two stage water-ethanol extraction. Residual extractives likely precipitated with the acid insoluble lignin during analysis, contributing to an overestimation of the lignin content. Despite the minor dissolution of hemicellulosic sugars, extraction with mild alkali removed most of the extractives from the bark and improved the raw material mass closure to 95% in comparison to the 88% value obtained after water-ethanol extraction. After pretreatment, the extent of extractive removal and their reaction/precipitation with lignin was heavily dependent on the pretreatment conditions used. The selective removal of extractives and their quantification after a pretreatment proved to be even more challenging. Regardless of the amount of extractives that were originally present, the analytical methods could be refined to provide reproducible quantification of the carbohydrates present in both the starting material and after pretreatment.

Conclusion

Despite the challenges resulting from the heterogeneity of the initial biomass substrates a reasonable summative mass closure could be obtained before and after steam pretreatment. However, method revision and optimisation was required, particularly the effective removal of extractives, to ensure that representative and reproducible values for the major lignin and carbohydrate components.
Exploratory benchtop study evaluating the use of surgical design and simulation in fibula free flap mandibular reconstruction
Authors: Logan Heather , Wolfaardt Johan , Boulanger Pierre , Hodgetts Bill , Seikaly Hadi
Published: June 2013

Background

Surgical design and simulation (SDS) is a useful tool to help surgeons visualize the anatomy of the patient and perform operative maneuvers on the computer before implementation in the operating room. While these technologies have many advantages, further evidence of their potential to improve outcomes is required. The present benchtop study was intended to identify if there is a difference in surgical outcome between free-hand surgery completed without virtual surgical planning (VSP) software and preoperatively planned surgery completed with the use of VSP software.

Methods

Five surgeons participated in the study. In Session A, participants were asked to do a free-hand reconstruction of a 3d printed mandible with a defect using a 3d printed fibula. Four weeks later, in Session B, the participants were asked to do the same reconstruction, but in this case using a preoperatively digitally designed surgical plan. Digital registration computer software, hard tissue measures and duration of the task were used to compare the outcome of the benchtop reconstructions.

Results

The study revealed that: (1) superimposed images produced in a computer aided design (CAD) software were effective in comparing pre and post-surgical outcomes, (2) there was a difference, based on hard tissue measures, in surgical outcome between the two scenarios and (3) there was no difference in the time it took to complete the sessions.

Conclusion

The study revealed that the participants were more consistent in the preoperatively digitally planned surgery than they were in the free hand surgery.
Modeling population growth in online social networks
Authors: Zhu Konglin , Li Wenzhong , Fu Xiaoming
Published: June 2013

Purpose

Online social networks (OSNs) are now among the most popular applications on the web offering platforms for people to interact, communicate and collaborate with others. The rapid development of OSNs provides opportunities for people’s daily communication, but also brings problems such as burst network traffic and overload of servers. Studying the population growth pattern in online social networks helps service providers to understand the people communication manners in OSNs and facilitate the management of network resources. In this paper, we propose a population growth model for OSNs based on the study of population distribution and growth in spatiotemporal scale-space.

Methods

We investigate the population growth in three data sets which are randomly sampled from the popular OSN web sites including Renren, Twitter and Gowalla. We find out that the number of population follows the power-law distribution over different geographic locations, and the population growth of a location fits a power function of time. An aggregated population growth model is conducted by integrating the population growth over geographic locations and time.

Results

We use the data sets to validate our population growth model. Extensive experiments also show that the proposed model fits the population growth of Facebook and Sina Weibo well. As an application, we use the model to predict the monthly population in three data sets. By comparing the predicted population with ground-truth values, the results show that our model can achieve a prediction accuracy between 86.14% and 99.89%.

Conclusions

With our proposed population growth model, people can estimate the population size of an online social network in a certain time period and it can also be used for population prediction for a future time.
Joint Optimization of Sampling and Control of Partially Observable Failing Systems
Authors: Kim Michael Jong , Makis Viliam
Published: June 2013

Stochastic control problems that arise in reliability and maintenance optimization typically assume that information used for decision-making is obtained according to a predetermined sampling schedule. In many real applications, however, there is a high sampling cost associated with collecting such data. It is therefore of equal importance to determine when information should be collected and to decide how this information should be utilized for maintenance decision-making. This type of joint optimization has been a long-standing problem in the operations research and maintenance optimization literature, and very few results regarding the structure of the optimal sampling and maintenance policy have been published. In this paper, we formulate and analyze the joint optimization of sampling and maintenance decision-making in the partially observable Markov decision process framework. We prove the optimality of a policy that is characterized by three critical thresholds, which have practical interpretation and give new insight into the value of condition-based maintenance programs in life-cycle asset management. Illustrative numerical comparisons are provided that show substantial cost savings over existing suboptimal policies.
The Impact of Size and Occupancy of Hospital on the Extent of Ambulance Diversion: Theory and Evidence
Authors: Allon Gad , Deo Sarang , Lin Wuqin
Published: June 2013

In recent years, growth in the demand for emergency medical services, along with decline in the number of hospitals with emergency departments (EDs), has raised concerns about the ability of the EDs to provide adequate service. Many EDs frequently report periods of overcrowding during which they are forced to divert incoming ambulances to neighboring hospitals, a phenomenon known as “ambulance diversion.” The objective of this paper is to study the impact of key operational characteristics of the hospitals such as the number of ED beds, the number of inpatient beds, and the utilization of inpatient beds on the extent to which hospitals go on ambulance diversion. We propose a simple queueing network model to describe the patient flow between the ED and the inpatient department. We analyze this network using two different approximations—diffusion and fluid—to derive two separate sets of measures for inpatient occupancy and ED size. We use these sets of measures to form hypotheses and test them by estimating a sample selection model using data on a cross section of hospitals from California. We find that the measures derived from the diffusion approximation provide better explanation of the data than those derived from the fluid approximation. For this model, we find that the fraction of time that the ED spends on diversion is decreasing in the spare capacity of the inpatient department and in the size of the ED, where both are appropriately normalized for the size of the inpatient department. In addition, controlling for these hospital-specific factors, we find that the fraction of time on diversion at a hospital increases with the number of hospitals in its neighborhood. We also find that certain hospitals, owing to their location, ownership, and trauma center status, are more likely to choose ambulance diversion to mitigate overcrowding than others.
Generational structuring of childhood images in television commercials
Authors: Lämsä Tiina
Published: June 2013

This article examines how images of childhood are displayed in generational relations in television commercials. The data comprise 104 commercials shown on Finnish television in winter 2005 (N = 174 child performers). Generational structuring is seen as a dynamic cultural process, where the concept of ‘adulthood’ is described through the concept of ‘childhood’ and the concept of ‘childhood’ is defined through the concept of ‘adulthood’. This notion is used to study the positions constructed for children in the audiovisual data and how these relate to other people present in the commercials. The most popular combinations in the commercials were the child as a fully independent agent in a child-centric construction, or the child as an authenticator complementing the family and adulthood. The images ranged from an obedient to a lively child, and mental activity, creativity, learning abilities and gendered stereotypes were contrasted with elements of neediness.
Young grandchildren and their grandparents: a secondary analysis of continuity and change across four birth cohorts
Authors: Gray Jane , Geraghty Ruth , Ralph David
Published: June 2013

This article examines the changing texture of intergenerational relationships in Ireland. Focusing on the young child as ‘anchor’ generation, we traced changes in the quality and significance of grandchild–grandparent relationships across four birth cohorts, through a secondary analysis of two major qualitative longitudinal datasets made available by the Irish Qualitative Data Archive. The article describes how we addressed the challenges associated with bringing these datasets into dialogue.
Book Reviews
Authors: Biggane Julia , Tedaldi Chiara , McCarthy Eamon , Vargas Marta del Moral , Raminger Kathrin , Reckling Tobias
Published: June 2013

The Truth About Spain! Mobilising British Public Opinion 1936–1939, Hugo García (2010) Brighton, Portland and Ontario: Sussex Academic Press, 337 pp., ISBN 978-1-84519-332-4 (hbk), £55

British News Media and The Spanish Civil War. Tomorrow May be Too Late, David Deacon (2008) Edinburgh: Edinburgh University Press, viii + 196 pp., ISBN 978-0-7486-2748-6 (hbk), £60.00

A Companion to Spanish Women’s Studies, Xon De Ros and Geraldine Hazbun (Eds) (2011) Woodbridge: Tamesis, 405 pp., ISBN 978-1-85566-224-7 (hbk), £65

Feminismos Y Antifeminismos, Ana Aguado and Teresa Mª Ortega (Eds) (2011) Valencia and Granada: PUV & Editorial Universidad de Granada, 362 pp., ISBN 978-84-370-7892-2 (pbk), €24.50.

Legacies Of War and Dictatorship in Contemporary Portugal and Spain, Alison Ribeiro De Menezes and Catherine O’leary (Eds) (2011) Oxford: Peter Lang (Iberian and Latin American Studies: The Arts, Literature and Identity, 1), xvii + 270 pp., ISBN 978-3-03911-872-4 (pbk); 978-3-0353-0198-4 (Ebook), £36.