bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial community in packed bed bioreactor involved in nitrate remediation from low level radioactive waste
Authors: Mishra Madhusmita , Jain Savita , Thakur Ashoke Ranjan , RayChaudhuri Shaon
Published: May 2013

Nitrate is the second largest contaminant of agriculture soil after pesticides. It also is a major pollutant from nuclear and metallurgical operations. Conventional methods for nitrate removal suffers from high cost and complexity leaving bioremediation as a viable alternative strategy. A pilot plant of 2.5 m3/day capacity has been functioning since 2005 based on microbial consortia treating actual effluent from nuclear power plant having pH of 7–8.5 (optimum) with N:C ratio of 1:1.7. The maximum biodegradable nitrate concentration of 3000 ppm could be reduced to below permissible limit (44.2 ppm) within 24 h in presence of sodium acetate as carbon source. Culture independent analysis (16S rDNA based) revealed clones having closest identity with uncultured bacterium, Pseudomonas stutzeri and Azoarcus sp. The existence of dissimilatory pathway of nitrate reduction in the community DNA is indicated by presence of nirS and nirK gene. Though the microbial mass was developed using municipal sewage, absence of Mycobacterium sp was confirmed using PCR. The understanding of the molecular identification of the consortium would help in developing the preservation strategy of the microbial mass for replication and perpetuation of the system.
Characterization of a virulent bacteriophage LK1 specific for Citrobacter freundii isolated from sewage water
Authors: Chaudhry Waqas Nasir , Haq Irshad Ul , Andleeb Saadia , Qadri Ishtiaq
Published: May 2013

Citrobacter freundii is a worldwide emerging nosocomial pathogen with escalating incidence of multidrug resistance. Citrobacter freundii exists in natural environment, especially in health care settings and is difficult to eradicate. Phage therapy is considered as an alternative way of controlling bacterial infections and contaminations. In this study, we have described isolation and characterization of a virulent bacteriophage LK1 capable of specifically infecting Citrobacter freundii. A virulent bacteriophage LK1, specific for Citrobacter freundii was isolated from sewage water sample. TEM showed that phage Lk1 has an icosahedral head 70 nm in diameter and short tail of 17 nm, and can be classified as a member of the Podoviridae family. Restriction analysis indicated that phage LK1 was a dsDNA virus with an approximate genome size of 20–23 kb. Proteomic pattern generated by SDS PAGE using purified LK1 phage particles, revealed three major and six minor protein bands with molecular weight ranging from 25 to 80 kDa. Adsorption rate of LK1 relative to the host bacterium was also determined which showed significant improvement in adsorption with the addition of CaCl2. In a single step growth experiment, LK1 exhibited a latent period of 24 min and burst size of 801 particle/cell. Moreover, pH and thermal stability of phage LK1 demonstrated a pH range of 5.0–6.0 and phage viability decreased to 0% at 65 °C. When LK1 was used to infect six other clinically isolated pathogenic strains, it showed relatively narrow host range. LK1 was capable of eliciting efficient lysis of Citrobacter freundii, revealing its potential as a non‐toxic sanitizer for controlling Citrobacter freundii infection and contamination in both hospital and other public environments.
Mariner‐based transposon mutagenesis for Bacteroides species
Authors: Ichimura Minoru , Uchida Keiko , Nakayama‐Imaohji Haruyuki , Hirakawa Hideki , Tada Tomoyo , Morita Hidetoshi , Yasutomo Koji , Okazaki Katsuichiro , Kuwahara Tomomi
Published: May 2013

Bacteroides is one of the most predominant groups of human gut microbiota. Recent metagenomic analyses and studies on gnotobiotic mice demonstrated the tight association of Bacteroides with epithelial function, the gut immune system and systemic metabolism in the host. The mariner family transposon shows relatively low target site specificity and has hosts ranging from prokaryotes to eukaryotes. Thereby, random mutagenesis using the mariner family transposon is expected to identify key molecules for human‐Bacteroides symbiosis. In this study, we constructed the plasmid pMI07 to deliver the gene cassette (ermF/ITR), which harbors the erythromycin resistant marker (ermF) and the inverted repeat sequences (ITRs) recognized by Himar1 transposase, to Bacteroides via electrotransformation. pMI07 successfully delivered ermF/ITR to the Bacteroides genomes and generated thousands of insertion mutants/μg of pMI07 in B. thetaiotaomicron, B. fragilis, B. ovatus, and also, although to a lesser extent, B. vulgatus. Analyses of the ermF/ITR insertion sites in B. thetaiotaomicron and B. vulgatus revealed that the cassette targeted the dinucleotide TA and integrated into the genomes in an unbiased manner. The data reported here will provide useful information for transposon mutagenesis in Bacteroides species, which will enable identification of the genes responsible for their unique phenotypes.
Antifungal attributes of siderophore produced by the Pseudomonas aeruginosa JAS‐25
Authors: Sulochana Mudgulkar Bhimsen , Jayachandra Sharanappa Yaradoddi , Kumar Subhash Katti Anil , Dayanand Agsar
Published: May 2013

Siderophores produced by Pseudomonas sp. play a vital role in controlling several plant diseases. Public concern about chemical pesticides has fostered an interest to seek alternative control strategies. Production of siderophore by Pseudomonas aeruginosa JAS‐25 in King B medium was estimated at 400 nm and was partially purified by gel filtration chromatography using Sephadex G 25. Antifungal activity and inhibition of spore germination was studied against the phytopathogens like Fusarium oxysporum f. sp. ciceri, Fusarium udum, and Aspergillus niger by well plate assay and microphotographic method. Zone of inhibition of 3.0 cm was observed for F. udum and A. niger, proving it as potential biocontrol agent against phytopathogens. Partial 16S rRNA sequence analysis showed that the isolate JAS‐25 exhibited 99% homology with P. aeruginosa and could be of novel species and the sequence of the strain was deposited in Genbank with the accession number JX104229.
Kinetics of heavy metal inhibition of 1,2‐dichloroethane biodegradation in co‐contaminated water
Authors: Arjoon Ashmita , Olaniran Ademola Olufolahan , Pillay Balakrishna
Published: May 2013

Sites co‐contaminated with heavy metals and 1,2‐DCA may pose a greater challenge for bioremediation, as the heavy metals could inhibit the activities of microbes involved in biodegradation. Therefore, this study was undertaken to quantitatively assess the effects of heavy metals (arsenic, cadmium, mercury, and lead) on 1,2‐DCA biodegradation in co‐contaminated water. The minimum inhibitory concentrations (MICs) and concentrations of the heavy metals that caused half‐life doubling (HLDs) of 1,2‐DCA as well as the degradation rate coefficient (k1) and half‐life (t½) of 1,2‐DCA were measured and used to predict the toxicity of the heavy metals in the water microcosms. An increase in heavy metal concentration resulted in a progressive increase in the t½ and relative t½ and a decrease in k1. The MICs and HLDs of the heavy metals were found to vary, depending on the heavy metals type. In addition, the presence of heavy metals was shown to inhibit 1,2‐DCA biodegradation in a dose‐dependent manner, with the following order of decreasing inhibitory effect: Hg2+ > As3+ > Cd2+ > Pb2+. Findings from this study have significant implications for the development of bioremediation strategies for effective degradation of 1,2‐DCA and other related compounds in wastewater co‐contaminated with heavy metals.
Rhamnolipid biosurfactant against Fusarium sacchari—the causal organism of pokkah boeng disease of sugarcane
Authors: Goswami Debahuti , Handique Pratap Jyoti , Deka Suresh
Published: May 2013

Pokkah boeng disease on sugarcane caused by the fungus Fusarium sacchari results considerable damage to the crop leading to top rot, the most serious and advanced stage of pokkah boeng, where the growing point is killed and the entire top of the plant dies. In the present study, the effect of rhamnolipid biosurfactant as an antifungal agent against F. sacchari to control pokkah boeng disease was investigated. On the basis of surface tension reduction, 12 bacterial isolates were selected as potent biosurfactant producers and eight of them showed antagonistic effect against F. sacchari. Among the eight, the isolate DS9 was found as the effective inhibitor of the fungus in vitro which was further evaluated using its biosurfactant present in whole culture, cell‐free culture supernatant and crude biosurfactant at various concentrations. Reductions of fungal growths were found more with crude biosurfactant. By sequencing 16S rRNA, DS9 was identified as P. aeruginosa and the produced biosurfactant was characterized as rhamnolipid by Liquid Chromatography‐Mass Spectrometry (LC‐MS) analysis. The rhamnolipid biosurfactant inhibits phytopathogenic fungi F. sacchari and therefore seems to be a good biocontrol agent to control pokkah boeng disease of sugarcane.
Essential role of calcium in the infection process of broad‐spectrum methicillin‐resistant Staphylococcus aureus bacteriophage
Authors: Chhibber Sanjay , Kaur Tarsem , Kaur Sandeep
Published: May 2013

Phage therapy presents an alternative therapeutic option in treating infections caused by methicillin‐resistant Staphylococcus aureus (MRSA) strains not responding to antibiotic therapy. However, it is essential to study the role of external factors that may influence the yield and potency of phage preparations intended for use in various in vitro and in vivo studies. The present study focuses on the effects of calcium in the entire infection process of a broad‐spectrum lytic bacteriophage: MR‐10. The presence of calcium increased the adsorption rate of the phage and also participated in the process of penetration of the phage genome into the host cytoplasm. A final concentration of 5 mM of calcium ions supplemented in soft agar during the phage titration process significantly increased the phage titer. Hence, incorporation of such divalent cations during the isolation of lytic phages active against MRSA strains and during the preparation of high‐titer active phage preparations would definitely increase the isolation frequency and the final phage yield. This will contribute towards more effective phage preparations for use in treatments against MRSA infections.
Viewing the Strategy‐Performance Relationship Through a Reputational Lens: A Longitudinal Study of Leading Retailers
Authors: Brown D. Michael , Whysall Paul
Published: May 2013

Corporate reputation is a complex concept, involving several related but separate dimensions being a hybrid intangible asset that is managed internally but largely assessed externally by different audiences/stakeholders.
The Relationship Between Contextual Factors, Psychological Contract, and Change Outcomes
Authors: Massingham Peter
Published: May 2013

The contextual factors that combine to create the individual's emotional and cognitive states are often more important in understanding response to profound change than psychological relationship within the firm's organization.
PTSD Symptomatology and Hazardous Drinking as Risk Factors for Sexual Assault Revictimization: Examination in European American and African American Women
Authors: Littleton Heather , Ullman Sarah E.
Published: May 2013

A sexual victimization history is a risk factor for experiencing further sexual victimization. Posttraumatic stress disorder (PTSD) symptoms have been posited as predictors of revictimization through multiple pathways, including through their association with risk recognition and alcohol use. There is, however, limited longitudinal research examining these revictimization risk factors, including the extent to which they predict risk for forcible rape (rape involving threat or force) and incapacitated rape (rape of a victim incapacitated by substances). Additionally, there is no research evaluating ethnic differences in revictimization risk pathways. The current study examined PTSD symptoms and hazardous drinking as predictors of new forcible and incapacitated rape over 1 year in a community sample of European American (n = 217) and African American (n = 272) sexual assault victims (M = 34 years; 84% high school education or above). We hypothesized that PTSD symptoms would predict both types of revictimization and hazardous drinking would predict incapacitated rape. Results supported that PTSD symptoms predicted both types of rape (forcible rape, β = .34; incapacitated rape, β = .20), and hazardous drinking predicted incapacitated rape (β = .24). PTSD symptoms predicted hazardous drinking in African American women only (β = .20). Thus, there is a need to evaluate risk pathways for specific types of victimization among diverse samples.
The Co‐Occurrence of Major Depressive Disorder Among Individuals With Posttraumatic Stress Disorder: A Meta‐Analysis
Authors: Rytwinski Nina K. , Scur Michael D. , Feeny Norah C. , Youngstrom Eric A.
Published: May 2013

Although co‐occurring posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) is associated with greater distress, impairment, and health care utilization than PTSD alone, the magnitude of this problem is uncertain. This meta‐analysis aimed to estimate the mean prevalence of current MDD co‐occurrence among individuals with PTSD and examine potential moderating variables (U.S. nationality, gender, trauma type, military service, referral type) that may influence the rate of PTSD and MDD co‐occurrence. Meta‐analytic findings (k = 57 studies; N = 6,670 participants) revealed that 52%, 95% confidence interval [48, 56], of individuals with current PTSD had co‐occurring MDD. When outliers were removed, military samples and interpersonal traumas demonstrated higher rates of MDD among individuals with PTSD than civilian samples and natural disasters, respectively. U.S. nationality, gender, and referral type did not significantly account for differences in co‐occurrence rates. This high co‐occurrence rate accentuates the importance of routinely assessing MDD among individuals with PTSD and continuing research into the association between these disorders.
Attachment, Social Cognition, and Posttraumatic Stress Symptoms in a Traumatized, Urban Population: Evidence for the Mediating Role of Object Relations
Authors: Ortigo Kile M. , Westen Drew , DeFife Jared A. , Bradley Bekh
Published: May 2013

Research has linked multiple risk and resiliency factors to developing posttraumatic stress disorder (PTSD). One potentially important construct for understanding connections between trauma and PTSD is attachment. Although relationships between attachment and risk for PTSD have been described theoretically, limited research has addressed these relationships empirically. Furthermore, aspects of object relations overlap with attachment and PTSD, but have not been adequately incorporated in empirical research. One proposed pathway between attachment and PTSD involves the mediating role of object relations, particularly views of self and others. Present data were from a larger study investigating environmental and genetic risk factors for PTSD in an impoverished, primarily African American sample seeking care at a public urban hospital. Correlations indicated that adult attachment (with the exception of dismissing) and object relations relate to childhood traumas, (|r|s = .19–.29), adult traumas (|r|s = .14–.20), and self‐reported PTSD symptoms (|r|s = .20–.36). Analyses also found support for mediational roles of object relations in relationships between attachment and PTSD symptoms (Model R2 range = .136–.160). These data have theoretical, clinical, and research implications for understanding how particular aspects of attachment, specifically its effects on object relations, may protect against or predispose one to develop PTSD.
L'harmonisation de la Notion D'originalite en Droit D'auteur
Authors: Berthold Nicolas
Published: May 2013

S'il est un concept qui peut être qualifié de fondamental en droit d'auteur, c'est sans nul doute celui d'originalité. Si une œuvre est dénuée d'originalité, elle ne fera l'objet d'aucune protection par le droit d'auteur. Or, cette notion n'a jamais été définie de manière générale par le législateur européen, de sorte que la jurisprudence et la doctrine se sont divisées quant à l'interprétation à lui donner. Finalement, la Cour de Justice de l'Union Européenne (CJUE) s'est saisie du problème pour donner à cette notion une définition conforme à la conception subjective traditionnelle. Si cette définition eut normalement dû sonner le glas des interprétations divergentes, il est malheureusement apparu qu'en Belgique, postérieurement à cette décision de la Cour de Justice, la plus haute juridiction nationale a rendu une décision qui prend le contrepied de cette définition.
Protection of Industrial Design in the United States and in the EU: Different Concepts or Different Labels?
Authors: Schickl Lena
Published: May 2013

Industrial designs matter. It is undisputed that design is crucial for the success of a product. That is why companies are using intellectual property laws in an effort to protect their industrial design. This article will describe how intellectual property laws can protect design and compare the design protection regime in the United States and the EU. The comparison will show that design protection is significantly different in the United States and the EU. Within the EU, further harmonization is needed in order to provide for a strong coherent design protection. The paper will point out that the ubiquitous requirement of non‐functionality outside the realm of utility patent law in the United States is no longer appropriate in a world where the most successful designs purposefully combine functional and aesthetic elements.
A Relook at Sui Generis Software Protection Through the Prism of Multi—Licensing
Authors: Vasudeva Vikrant Narayan
Published: May 2013

Debate has been raging since the 1960s regarding intellectual property and software protection, primarily focusing on its accommodation within existing traditional intellectual property structures or sui generis approaches. Eventually, software protection was accommodated within a range of intellectual property rights, contract law and technological measures. However, several occurrences in the past three decades highlight developing fissures in the mode of software protection; certain other developments highlight increasing acceptance and ease in implementing sui generis protection. Correspondingly, the open source software licensing structure has emerged with a novel and extremely successful adaptation of intellectual property law. It has led to emergence of the multi‐licensing scheme, where software is licensed under two or more licensing structures—one of which is open source and the other “proprietary.” The multi‐licensing scheme reveals several similarities to various sui generis software protection proposals. Perhaps this is an indication of and validation that the industry has evolved to such an extent that there is a need to rethink the mode of software protection. Based on this premise, this article attempts to develop a proposal for a sui generis Model Software Law.
Diagnosis of laryngotracheal stenosis from routine pulmonary physiology using the expiratory disproportion index
Authors: Nouraei S. A. Reza , Nouraei S. Mahmoud , Patel Anil , Murphy Kevin , Giussani Dino A. , Koury Elias F. , Brown James M. , George P. Jeremy , Cummins Andrew C. , Sandhu Guri S.
Published: May 2013

Objective/Hypothesis

The study's objective was to determine the utility of expiratory disproportion index (EDI), the ratio of forced expiratory volume in 1 second (FEV1) to peak expiratory flow rate (PEFR) (EDI = FEV1[L]/PEFR[L/s] × 100), in differentiating between laryngotracheal stenosis (LTS) and other respiratory diagnoses. LTS is an uncommon complication of mechanical ventilation or vasculitis or a manifestation of airway compression or malignancy. It frequently masquerades as asthma and evades timely diagnosis, causing prolonged morbidity and airway‐related mortality.

Study Design

Observational study.

Methods

We compared spirometry results of 9,357 healthy subjects and nonstenosis pulmonary patients with 217 cases of LTS. Bootstrap analysis, receiver‐operating characteristic (ROC) statistics, and Pearson correlation were used to assess the diagnostic utility of the EDI and its correlation with stenosis severity.

Results

Mean EDI values were 36 ± 7 in nonstenosis cases, 76 ± 17 in benign stenoses, and 69 ± 23 in tracheal cancer (P < .0001). A significant correlation existed between anatomic stenosis severity and EDI (P < .0001; R = 0.61). Area under the ROC curve was 0.98, and at a threshold of >50, EDI had a sensitivity of 95.9% and a specificity of 94.2% in differentiating between stenosis and nonstenosis cases.

Conclusions

EDI can reliably diagnose LTS using routine lung function data. Its simplicity and clinical utility, first recognized by Duncan Empey, are underpinned by a unique physiology whereby PEFR, being determined by total tracheobronchial tree resistance, falls disproportionately compared with FEV1, which is determined within small intrathoracic airways. EDI provides valuable information about the presence and extent of LTS particularly in nonspecialist clinical settings and its routine inclusion within standard lung function reports could prevent the prolonged morbidity and mortality that currently result from missed and delayed diagnoses.

Level of Evidence

3b. Laryngoscope, 123:3099–3104, 2013
The role of plasma Epstein‐Barr virus DNA in the management of recurrent nasopharyngeal carcinoma
Authors: Chan Jimmy Yu Wai , Wong Stanley Thian‐Sze
Published: May 2013

Objectives/Hypothesis

To study the role of plasma Epstein‐Barr virus (EBV) DNA in patients with recurrent nasopharyngeal carcinoma (NPC) after previous chemoradiation.

Study Design

Prospective.

Methods

Sixty patients with recurrent NPC were recruited, and their plasma EBV DNA was checked preoperatively, 1 week postoperatively, and 6 months thereafter. In a pilot group of 30 patients, further testing was performed at 60 minutes after tumor resection. The plasma EBV DNA level was correlated with tumor T classification, resection margin status, and subsequent relapse.

Results

The mean preoperative plasma EBV DNA reflected the tumor load (T1: 48 copies/mL, T2: 316 copies/mL, T3: 890 copies/mL, P = .03). It was significantly higher in patients with positive margins at the time of surgery (722 vs. 126 copies/mL, P = .02) and in those with subsequent systemic metastasis (668 vs. 92 copies/mL, P = .01). However, it failed to predict local recurrence after surgery. Postoperative plasma EBV DNA was undetectable in all patients with positive resection margins. Serial measurements were able to identify 87.5% of local recurrences and 100% of distance metastases.

Conclusions

In patients with recurrent NPC requiring salvage nasopharyngectomy, preoperative plasma EBV DNA identifies patients at high‐risk of subsequent distant failure after surgery. Serial measurements of plasma EBV DNA after surgery, especially for those with high preoperative levels, is crucial to allow early detection of local of distant failure. Laryngoscope, 124:126–130, 2014
Effect‐site concentration of remifentanil to prevent cough after laryngomicrosurgery
Authors: Chang Chul Ho , Lee Jong Wha , Choi Jong Rim , Shim Yon Hee
Published: May 2013

Objectives/Hypothesis

The aim of this study was to discover the optimal effect‐site concentration of remifentanil for cough prevention that does not delay awakening or cause respiratory depression during emergence from anesthesia with propofol and remifentanil in laryngomicrosurgery patients.

Study Design

Prospective, randomized, controlled trial.

Methods

One hundred five patients were randomly assigned to maintain an effect‐site concentration (Ce) of remifentanil at a predetermined value of 1 (R1), 1.5 (R1.5), and 2 (R2) ng/mL during emergence. The incidence and grade (0, no coughing; 1, single cough; 2, more than one episode of nonsustained coughing; 3, sustained and repetitive coughing with head lift) of cough, emergence time, blood pressure (MAP), heart rate (HR), spontaneous respiratory rate, oxygen saturation, and postoperative nausea and vomiting (PONV) were recorded during emergence and recovery.

Results

The total number of patients with coughing during emergence was lower in groups R1.5 and R2 than in group R1. The cough grade during tracheal extubation was lower in groups R1.5 and R2 than in group R1. In group R2, emergence time was longer and postanesthesia care unit score was lower than in groups R1 and R1.5. Also in group R2, transient hypoventilation and PONV were more frequent compared to group R1. There were no differences in MAP and HR among the three groups during emergence and recovery.

Conclusions

Maintenance of remifentanil at Ce 1.5 and 2 ng/mL suppressed coughing without serious adverse events during emergence from anesthesia with propofol and remifentanil in patients undergoing laryngomicrosurgery.

Level of Evidence

1b Laryngoscope, 123:3105–3109, 2013
Effective embryoid body formation from induced pluripotent stem cells for regeneration of respiratory epithelium
Authors: Otsuki Koshi , Imaizumi Mitsuyoshi , Nomoto Yukio , Nomoto Mika , Wada Ikuo , Miyake Masao , Omori Koichi
Published: May 2013

Objectives/Hypothesis

We have previously demonstrated the potential use of induced pluripotent stem (iPS) cells for regeneration of respiratory epithelium by culturing embryoid bodies (EBs). The aim of the present study was to determine the most effective conditions for EB formation from iPS cells for regeneration of respiratory epithelium.

Study Design

Experimental study.

Methods

iPS cells cultured on a gelatin‐coated dish were seeded on low‐attachment plates for generating EBs. Under several conditions including the air–liquid interface (ALI) method, with varying cell numbers and suspension times, EBs were transferred to a gelatin‐coated dish supplemented with growth factors. The shape, size, aggregation, and adhesion of EBs for iPS cell differentiation were evaluated, and the cultured tissue was histologically examined.

Results

EBs appropriate for differentiation were observed using 1,000 cells after 5 days of suspension culture. Respiratory epithelium‐like tissue was histologically observed. The ciliary epithelium was confirmed immunohistologically.

Conclusions

Based on the varying suspension times and cell numbers with the ALI method, this study presented effective conditions for EB formation from iPS cells for regeneration of respiratory epithelium.

Level of Evidence

NA. Laryngoscope, 124:E8–E14, 2014
A four‐noded quadrilateral element for composite laminated plates/shells using the refined zigzag theory
Authors: Eijo A. , Oñate E. , Oller S.
Published: May 2013

A new bilinear four‐noded quadrilateral element (called quadrilateral linear refined zigzag) for the analysis of composite laminated and sandwich plates/shells based on the refined zigzag theory is presented. The element has seven kinematic variables per node. Shear locking is avoided by introducing an assumed linear shear strain field. The performance of the element is studied in several examples where the reference solution is the 3D finite element analysis using 20‐noded hexahedral elements. Copyright © 2013 John Wiley & Sons, Ltd.
Depressive symptoms after treatment in hepatocellular carcinoma survivors: prevalence, determinants, and impact on health‐related quality of life
Authors: Mikoshiba Naoko , Miyashita Mitsunori , Sakai Tomoko , Tateishi Ryosuke , Koike Kazuhiko
Published: May 2013

Objective

The purposes of this study were to investigate the prevalence and determinants of depressive symptoms among hepatocellular carcinoma (HCC) survivors and to evaluate the impact of depressive symptoms on health‐related quality of life (HRQOL).

Methods

A cross‐sectional study was conducted on 128 consecutive patients attending an outpatient clinic in Japan 1 year or more after curative treatment. To assess depressive symptoms and HRQOL, the participants were asked to complete the Center for Epidemiologic Studies Depressive Symptoms Scale, the European Organization for Research and Treatment of Cancer (EORTC) QLQ‐C30, and EORTC QLQ‐HCC18, respectively. Multiple logistic regression models were used to identify factors associated with depressive symptoms. EORTC QLQ‐C30 and EORTC QLQ‐HCC18 scores were compared between participants with and without depressive symptoms.

Results

The prevalence of depressive symptoms among the HCC survivors was 28.3%. The multiple logistic regression analysis revealed that the determinants of depressive symptoms included poor Karnofsky performance status (odds ratio [OR] = 4.59, 95% CI = 1.03–20.55, p = 0.04), poor liver function (OR = 3.22, 95% CI = 1.11–10.0, p = 0.03), living alone (OR = 6.87, 95% CI = 2.53–18.63, p = 0.0002), and unemployment (OR = 5.18, 95% CI = 1.73–15.54, p = 0.003). Survivors with depressive symptoms had poorer HRQOL in almost all domains compared with survivors with no depressive symptoms.

Conclusions

This study suggests that after treatment, many HCC survivors experience depressive symptoms that are strongly associated with poorer HRQOL. Copyright © 2013 John Wiley & Sons, Ltd.
Brassinin Induces Apoptosis in PC‐3 Human Prostate Cancer Cells through the Suppression of PI3K/Akt/mTOR/S6K1 Signaling Cascades
Authors: Kim Sung‐Moo , Park Jeong Ha , Kim Ki Dong , Nam Dongwoo , Shim Bum Sang , Kim Sung‐Hoon , Ahn Kyoo Seok , Choi Seung‐Hoon , Ahn Kwang Seok
Published: May 2013

The oncogenic PI3K/Akt/mammalian target of rapamycin (mTOR) signaling axis and its downstream effector, the ribosomal protein S6 kinase 1 (S6K1) play a key role in mediating cell survival in various tumor cells. Here, we investigated the effects of brassinin (BSN), a phytoalexin first identified as a constituent of cabbage, on the PI3K/Akt/mTOR/S6K1 activation, cellular proliferation, and apoptosis in PC‐3 human prostate cancer. BSN exerted a significant dose‐dependent cytotoxicity and reduced constitutive phosphorylation of Akt against androgen‐independent PC‐3 cells as compared to androgen‐dependent LNCaP cells. Moreover, knockdown of androgen receptor (AR) by small interfering RNA enhanced the potential effect of BSN on induction of apoptosis in LNCaP cells. BSN clearly suppressed the constitutive activation of PI3K/Akt/mTOR/S6K1 signaling cascade, which correlated with the induction of apoptosis as characterized by accumulation of cells in subG1 phase, positive Annexin V binding, TUNEL staining, loss of mitochondrial membrane potential, down‐regulation of antiapoptotic and proliferative proteins, activation of caspase‐3, and cleavage of PARP. Additionally, BSN could block broad‐spectrum inhibition of PI3K/Akt/mTOR/S6K1 axes, and aberrant Akt activation by pcDNA3‐myr‐HA‐Akt1 plasmid could not prevent the observed suppressive effect of BSN on constitutive mTOR activation. Finally, overexpression of Bcl‐2 also attenuated BSN‐mediated apoptosis in PC‐3 cells. Taken together, our findings suggest that BSN can interfere with multiple signaling cascades involved in tumorigenesis and might be provided as a potential therapeutic candidate for both the prevention and treatment of prostate cancer. Copyright © 2013 John Wiley & Sons, Ltd.
Improved Lipid Profile in Hyperlipidemic Patients Taking Vaccinium arctostaphylos Fruit Hydroalcoholic Extract: A Randomized Double‐Blind Placebo‐Controlled Clinical Trial
Authors: Kianbakht S. , Abasi B. , Hashem Dabaghian Fataneh
Published: May 2013

Dyslipidemia is a common contributory cause of cardiovascular disease. Vaccinium arctostaphylos L. (Caucasian whortleberry) fruit is rich of anthocyanins. Anthocyanins may exert cardioprotective effects by various mechanisms such as favorably modulating dyslipidemia. Therefore, in this randomized double‐blind placebo‐controlled clinical trial with hyperlipidemic (hypercholesterolemic and/or hypertriglyceridemic) patients aged 20–60 years, the effects of taking a standardized whortleberry fruit hydroalcoholic extract (one 350 mg capsule every 8 h for 2 months) on fasting blood levels of lipids, creatinine and liver enzymes including SGOT and SGPT were evaluated in 40 patients and compared with the placebo group (n = 40). The extract lowered the blood levels of total cholesterol (P < 0.001), triglyceride (P = 0.002) and low‐density lipoprotein cholesterol (LDL‐C) (P = 0.002), but increased the blood high‐density lipoprotein cholesterol (HDL‐C) levels (P < 0.001) without any significant effects on the blood levels of SGOT, SGPT and creatinine (P > 0.05) compared with the placebo group at the endpoint. Whortleberry reduced total cholesterol, triglyceride and LDL‐C 27.6%, 19.2% and 26.3%, respectively, but increased HDL‐C 37.5% compared with baseline. No adverse effects were reported. Short‐term treatment with whortleberry fruit appears safe and improves lipid profile in hyperlipidemic patients. Copyright © 2013 John Wiley & Sons, Ltd.
Conditions under which CNOP sensitivity is valid for tropical cyclone adaptive observations
Authors: Qin Xiaohao , Duan Wansuo , Mu Mu
Published: May 2013

To determine whether profound improvements in tropical cyclone (TC) forecasting are achievable by deploying dropwindsondes according to conditional nonlinear optimal perturbation (CNOP) sensitivity, observing system simulated experiments (OSSEs) were conducted on 20 TCs that developed over the western North Pacific during 2010 using Mesoscale Model 5 and its 3DVar assimilation system. Of the 20 cases, 13 showed neutral or improved track forecasts of between 0% and 51.2%. Eliminating initial errors within the CNOP pattern, which are related to either the storm directly or the surrounding regimes indirectly, reduced the subsequent track forecast errors. The remaining 7 TCs showed deterioration in the accuracy of the track forecasts over the 48 h forecast period. Accurate forecasts made without adaptive observations, a low sensitivity of forecast errors to initial errors, or major forecast errors associated with regimes other than the TC, can lead to a decline in the accuracy of TC track forecasts.

Following analysis of the potential causes of inaccuracy in the track forecasts, we find that TC cases with profound positive effects on track forecasts often satisfy the following four conditions: (i) an inaccurate initial forecast without additional observation data; (ii) proper sensitivity of the forecast errors to the initial errors; (iii) a large proportion of the forecast errors fall within the verification region; and (iv) the TC system is the dominant regime in the verification region at verification time. Seven TCs satisfied these four conditions, and showed a mean reduction of 28.75% in track forecast errors over periods of 12–48 h. This result suggests that the TC cases satisfying these four conditions often show profound improvements on track forecast by dropwindsondes guided by CNOP sensitivity.
Automatic scaling of F layer from ionograms
Authors: Chen Ziwei , Wang Shun , Zhang Shunrong , Fang Guangyou , Wang Jinsong
Published: May 2013

The correct automatic scaling of ionograms is one of the fundamental first steps to obtain ionospheric information. In this paper, new algorithms are proposed to scale F layer traces and separate ordinary ray and extraordinary ray traces from ionograms automatically. The method is mainly based on mathematical morphology, graph theory, and the echo characteristics of the ionosphere. Digital ionogram data from the Chinese Academy of Sciences Digital Ionosonde, installed at Dulan (36°17′N, 98°5′E), were used to demonstrate the data processing procedures.
Range‐dependent Terrain Mapping and Multipath Planning using Cylindrical Coordinates for a Planetary Exploration Rover
Authors: Ishigami Genya , Otsuki Masatsugu , Kubota Takashi
Published: May 2013

This paper presents terrain mapping and path‐planning techniques that are key issues for autonomous mobility of a planetary exploration rover. In this work, a LIDAR (light detection and ranging) sensor is used to obtain geometric information on the terrain. A point cloud of the terrain feature provided from the LIDAR sensor is usually converted to a digital elevation map. A sector‐shaped reference grid for the conversion process is proposed in this paper, resulting in an elevation map with cylindrical coordinates termed as C2DEM. This conversion approach achieves a range‐dependent resolution for the terrain mapping: a detailed terrain representation near the rover and a sparse representation far from the rover. The path planning utilizes a cost function composed of terrain inclination, terrain roughness, and path length indices, each of which is subject to a weighting factor. The multipath planning developed in this paper first explores possible sets of weighting factors and generates multiple candidate paths. The most feasible path is then determined by a comparative evaluation between the candidate paths. Field experiments with a rover prototype at a Lunar/Martian analog site were performed to confirm the feasibility of the proposed techniques, including the range‐dependent terrain mapping with C2DEM and the multipath‐planning method.
SPATIAL AND TEMPORAL PATTERNS OF NITRIFICATION RATES IN FORESTED FLOODPLAIN WETLAND SOILS OF UPPER MISSISSIPPI RIVER POOL 8
Authors: Jicha T. M. , Johnson L. B. , Hill B. H. , Regal R. R. , Elonen C. M. , Pearson M. S.
Published: May 2013

Overbank flooding is thought to be a critical process controlling nitrogen retention and cycling. Yet, studies aimed at quantifying these effects, specifically nitrification, are relatively few. In this study, we investigated the effects of season and flood frequency on soil nitrification rates in forested floodplains of Upper Mississippi River, Pool 8. Samples were collected from three plots within each site in April, August and November 2006. Plots were equally divided among three flood frequency categories as follows: rare, moderate and frequent based on elevation and flood probability model. We found a significant difference in nitrification rates among flood frequency categories as follows: rare > moderate > frequent (F = 4.49, p < 0.01) and over season: spring > summer > autumn (F = 8.88, p < 0.01). Regression for all samples showed that elevation, NH4‐N, bulk density and soil temperature explained a moderate amount of variation in nitrification rates (R2 = 0.29, p < 0.01). Models for moderately flooded, spring, summer and autumn samples improved when analysed individually. The absence of a correlation between nitrification rates and hydrology limits our ability to predict rates based on hydrology alone. The model based on elevation and season allows us to estimate nitrification rates with moderate confidence (R2 = 0.27, p < 0.01). A rough calculation of forest floodplain nitrification rates suggests that 473 mt of NO3‐N are produced annually, about 0.5% of Pool 8 total annual NO3‐N budget. Copyright © 2013 John Wiley & Sons, Ltd.
EFFECTS OF GEOMORPHIC PROCESS DOMAINS ON RIVER ECOSYSTEMS: A COMPARISON OF FLOODPLAIN AND CONFINED VALLEY SEGMENTS
Authors: Bellmore J. R. , Baxter C. V.
Published: May 2013

The geomorphic template of streams and rivers exerts strong controls on the structure and function of aquatic ecosystems. However, relationships between stream geomorphology and ecosystem structure and function are not always clear and have not been investigated equally across spatial scales. In montane regions, rivers often alternate between canyon‐confined segments and unconfined floodplain segments. Yet, few studies have evaluated how this pattern influences aquatic ecosystems. Here, we compared five confined river segments to five paired floodplain segments in terms of allochthonous inputs, aquatic primary producer and invertebrate production, stream retentive capacity, and aquatic invertebrate community composition. We found that floodplains had a higher (up to 4×) retentive capacity, a greater richness (58%) of aquatic invertebrates, and a distinctly different invertebrate community, relative to confined segments. Contrary to our expectations, allochthonous inputs were approximately 2× greater for confined segments, and aquatic primary and invertebrate production exhibited no consistent differences between segment types. However, results did indicate that floodplains had greater overall community respiration than confined segments. Together, these findings suggest that floodplain and confined segments do indeed differ in terms of aquatic ecosystem structure and function but not entirely as expected. Confined segments had greater allochthonous inputs but a lower capacity to retain those inputs, whereas floodplains had a high capacity to retain transported organic matter and also a more diverse community of invertebrates and higher overall community respiration to ‘digest’ retained organic matter. If these findings are generalizable, then they would indicate that confined segments are sources for organic matter within river networks, whereas floodplains act as filters, removing and processing organic matter transported from upstream confined segments. Copyright © 2013 John Wiley & Sons, Ltd.
Flow field forecasting for univariate time series
Authors: Frey Micheal R. , Caudle Kyle A.
Published: May 2013

A statistical learning methodology, called ﬂow ﬁeld forecasting, is presented for predicting the future of a univariate time series. Flow ﬁeld forecasting draws information from an interpolated ﬂow ﬁeld of the observed time series to incrementally build a forecast. The time series need not have uniformly spaced observations. Included in the presentation are measures of assessment, a procedure for forecast updating as new data arrive and a performance comparison of ﬂow ﬁeld forecasting with other major forecasting techniques. © 2013 Wiley Periodicals, Inc. Statistical Analysis and Data Mining, 2013
Rank‐based principal stratum sensitivity analyses
Authors: Lu X. , Mehrotra D.V. , Shepherd B.E.
Published: May 2013

We describe rank‐based approaches to assess principal stratification treatment effects in studies where the outcome of interest is only well‐defined in a subgroup selected after randomization. Our methods are sensitivity analyses, in that estimands are identified by fixing a parameter and then we investigate the sensitivity of results by varying this parameter over a range of plausible values. We present three rank‐based test statistics and compare their performance through simulations, and provide recommendations. We also study three different bootstrap approaches for determining levels of significance. Finally, we apply our methods to two studies: an HIV vaccine trial and a prostate cancer prevention trial. Copyright © 2013 John Wiley & Sons, Ltd.
Self‐calibrated SAR ADC based on split capacitor DAC without the use of fractional‐value capacitor
Authors: Du Ling , Ning Ning , Zhang Jun , Yu Qi , Liu Yang
Published: May 2013

A successive approximation register analog‐to‐digital converter (SAR ADC) based on a split‐capacitor digital‐to‐analog converter (CDAC) with a split binary weighted capacitor array and C‐2C ladder is proposed. In present design, a unit split capacitor is used in the CDAC instead of the fractional‐value capacitor in the conventional configuration. The preset error induced by the unit split capacitor and the mismatch error of the upper bit CDAC are self‐calibrated. The calibration range and the impact of calibration DAC resolution on circuit linearity are studied to provide an optimum design guideline. Behavior simulation and post‐layout simulation are performed to verify the proposed calibration method. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Elimination of artifacts on aperture synthesis images using ultrasonic sensor's directivity and the ratio of intensity
Authors: Tachioka Yuuki , Hirano Takashi , Ishii Jun
Published: May 2013

Aperture synthesis images using a small number of ultrasonic sensors contain circular or elliptic artifacts. In this letter, to generate clear images less aﬀected by artifacts with the same number of sensors, we propose a method that eliminates these artifacts using sensor's directivity and the ratio of its intensity. The experiments of detecting a plate were performed in terms of estimation of the edge point and the inclination of the plate. Results show that the proposed method can achieve smaller errors than the conventional method. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Chemoinformatics applications of cluster analysis
Authors: MacCuish John David , MacCuish Norah Elizabeth
Published: May 2013

Chemoinformatics applications of cluster analysis over the past 35 years include chemical diversity for compound acquisition, analysis of HTS results for lead discovery, 2D and 3D chemical similarity searching for virtual screening, and hypothesis generation for lead hopping using molecular shape and pharmacophore descriptors. These applications still provide the majority of cluster analysis usage, but the advent of greater and greater computational resources has allowed researchers to tackle applications of ever increasing scale and complexity. In the past few years, a far broader array of clustering methods is now used—some entirely new, some common to other disciplines, and others modified to specific chemoinformatic applications. The chemoinformatic applications have also broadened to include greater biological information more commonly associated with bioinformatics. Indeed, clustering techniques, such as coclustering or self‐organizing trees, commonly found in bioinformatics, are beginning to find chemoinformatic application uses. Issues such as visualization and validation of clustering results continue to present challenging problems, especially given that the scale of many problems now attempted has increased enormously. Some new validation techniques have been introduced in the chemoinformatics literature that now allow for both a better understanding of the clustering results and help point to methods of greater efficacy. Effective validation and visualization of clustering results of large data sets has proven to be more problematic. WIREs Comput Mol Sci 2014, 4:34–48. doi: 10.1002/wcms.1152

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Computer and Information Science > Chemoinformatics