bluuebunny/crossref_metadata_2025 huggingface dataset:
How Well Do Climate Models Reproduce North Atlantic Subtropical Mode Water?
Authors: Dong Shenfu , Kelly Kathryn A.
Published: June 2013

Formation and the subsequent evolution of the subtropical mode water (STMW) involve various dynamic and thermodynamic processes. Proper representation of mode water variability and contributions from various processes in climate models is important in order to predict future climate change under changing forcings. The North Atlantic STMW, often referred to as Eighteen Degree Water (EDW), in three coupled models, both with data assimilation [GFDL coupled data assimilation (GFDL CDA)] and without data assimilation [GFDL Climate Model, version 2.1 (GFDL CM2.1), and NCAR Community Climate System Model, version 3 (CCSM3)], is analyzed to evaluate how well EDW processes are simulated in those models and to examine whether data assimilation alters the model response to forcing. In comparison with estimates from observations, the data-assimilating model gives a better representation of the formation rate, the spatial distribution of EDW, and its thickness, with the largest EDW variability along the Gulf Stream (GS) path. The EDW formation rate in GFDL CM2.1 is very weak because of weak heat loss from the ocean in the model. Unlike the observed dominant southward movement of the EDW, the EDW in GFDL CM2.1 and CCSM3 moves eastward after formation in the excessively wide GS in the models. However, the GFDL CDA does not capture the observed thermal response of the overlying atmosphere to the ocean. Observations show a robust anticorrelation between the upper-ocean heat content and air–sea heat flux, with upper-ocean heat content leading air–sea heat flux by a few months. This anticorrelation is well captured by GFDL CM2.1 and CCSM3 but not by GFDL CDA. Only GFDL CM2.1 captures the observed anticorrelation between the upper-ocean heat content and EDW volume. This suggests that, although data assimilation corrects the readily observed variables, it degrades the model thermodynamic response to forcing.
Changing Job Access of the Poor: Effects of Spatial and Socioeconomic Transformations in Chicago, 1990–2010
Authors: Hu Lingqian
Published: June 2013

Research has shown that the job access of the poor has been declining because of two major reasons: the spatial distribution of employment and housing, and socioeconomic restructuring. This paper aims to untangle the effects of the two factors on poor job seekers’ access to jobs in the Chicago metropolitan area from 1990 to 2010. Using census tracts as the unit of analysis, this research examines the effects of these two factors on the growth and distribution of poor job seekers and their matching jobs, as well as the consequential changes in job demand, supply and job access across the study area. Results show that spatial changes have increased job accessibility for the poor while socioeconomic transformation has adversely affected it.
Backward march: the turnaround in public cultural policy in Brazil
Authors: Silveira Sergio Amadeu da , Machado Murilo Bansi , Savazoni Rodrigo Tarchiani
Published: June 2013

The article analyses the turnaround in guidelines occurring in public policies for culture in Brazil. This is placed in the context of the transition from the government of Luiz Inácio Lula da Silva to the Dilma Rousseff administration, including the end of the cycle of shared leadership between Ministers Gilberto Gil (2003–8) and Juca Ferreira (2008–10) and the beginning of Ana de Hollanda’s administration of the Ministry of Culture. The analysis starts with evaluation of the inaugural speeches of Ministers Gil and Ana de Hollanda as moments for the enunciation of their differing strategic perspectives. It focuses on the consequences of their contrasting views in three spheres: (1) creative economy; (2) copyright; (3) the Alive Culture program. The article concludes that, in a continuing government program, Brazil is undergoing a reversal of cultural policy with large-scale implications.
Open source and journalism: toward new frameworks for imagining news innovation
Authors: Lewis Seth C , Usher Nikki
Published: June 2013

Journalists and technologists increasingly are organizing and collaborating, both formally and informally, across major news organizations and via grassroots networks on an international scale. This intersection of so-called ‘hacks and hackers’ carries with it a shared interest in finding technological solutions for news, particularly through open-source software programming. This article critically evaluates the phenomenon of open source in journalism, offering a theoretical intervention for understanding this phenomenon and its potential implications for newswork. Building on the literature from computer science and journalism, we explore the concept of open source as both a structural framework of distributed development and a cultural framework of pro-social hacker ethics. We identify four values of open-source culture that connect with and depart from journalism—transparency, tinkering, iteration, and participation—and assess their opportunities for rethinking journalism innovation.
Susceptibility of BALB/c-nu/nu Mice and BALB/c Mice to Equine Herpesvirus 9 Infection
Authors: El-Nahass E. , El-Dakhly Kh. M. , El-Habashi N. , Anwar Sh. I. , Sakai H. , Hirata A. , Okada A. , Abo-Sakaya R. , Fukushi H. , Yanai T.
Published: June 2013

This study aimed to clarify the timing and infectivity of equine herpesvirus 9 (EHV-9) infection in BALB/c-nu/nu mice and their immunocompetent counterpart (BALB/c). Following intranasal inoculation with 105 PFU of EHV-9, specimens from 8 mice per group were collected at different times postinoculation (PI) and assessed using histopathology, immunohistochemistry for viral antigen, and quantitative real-time polymerase chain reaction for ORF30 gene expression. In BALB/c-nu/nu mice, EHV-9 antigen was abundant in olfactory epithelia of all inoculated animals, and in the olfactory bulb of 1 animal. In contrast, only 1 BALB/c mouse per time point had rhinitis, with mild to moderate immunopositivity starting from 12 to 48 h PI, followed by a gradual virus clearance at 72 h PI. Statistically, significant differences were noted in the immunohistochemistry reactions between the 2 mouse strains, indicating that BALB/c-nu/nu is more susceptible to infection. Relative expression levels of ORF30 gene in olfactory epithelia were significantly different between the 2 groups, with the exception of 12 h PI, when BALB/c-nu/nu animals showed dramatic increases in ORF30 gene expression level until 48 h PI, followed by a decline in expression level until the end of experiment. In contrast, the expression level in brains showed no differences between mouse strain except at 96 h PI. In both strains, the highest messenger RNA expression was detected at 48 h PI, followed by a decline in BALB/c mice, proving a rapid clearance of virus in BALB/c and a gradual slowing down of the increased expression levels in BALB/c-nu/nu.
Comparison on intracochlear disturbances between drilling a manual and robotic cochleostomy
Authors: Assadi Masoud Z , Du Xinli , Dalton James , Henshaw Scott , Coulson Chris J , Reid Andrew P , Proops David W , Brett Peter N
Published: June 2013

During cochlear implantation, hearing preservation is a concern. Minimizing disturbances to the cochlea and protection of the underlying endosteal membrane during the formation of a cochleostomy are considered important factors. The robotic micro-drill system tested in this article is the first example of an autonomous surgical drill successfully producing a cochleostomy, which keeps the underlying endosteal membrane intact. This study compares induced disturbances within the cochlea during formation of cochleostomy using the robotic micro-drill with that of conventional manual drilling. The disturbance of the endosteal membrane is measured using a Microscope Scanning Vibrometer at a third window, produced in the cochlea. Results show that the highest velocity amplitude measured was associated with manual drilling technique. The robotic micro-drill technique produced only about 1% of the peak velocity amplitude seen in manual drilling and exhibited much more uniform behaviour, while keeping the underlying membrane intact. The technique applied when using the robotic drill could be a major step in reducing the trauma to the cochlea, by reducing disturbance levels.
Basic financial services: A new service of general economic interest?
Authors: Gómez-Barroso José Luis , Marbán-Flores Raquel
Published: June 2013

In July 2011, the European Commission released a Recommendation on access to a basic payment account. The contents of this Recommendation (where Member States are required to establish universal service obligations) imply that the Commission considers that services facilitating basic access to the financial system meet the requirements to be classified of general interest. This paper discusses this possibility after studying the phenomenon of the unbanked in the European Union and, more generally, in developed countries.
Towards an index of private pension provision
Authors: De Deken Johan
Published: June 2013

Privatization entails a number of quite different aspects that overlap only to some extent: (1) responsibility in provision; (2) possibilities of exit from statutory plans; (3) the transfer of the administration and management of schemes from public bodies acting in a unitary non-competitive administrative environment to private sector actors acting in a more fragmented competitive market based environment; (4) the transfer of the risks of retirement from the collective to the individual; and (5) the ‘recommodification’ and ‘financialization’ of retirement risks. The paper develops a compound index of private pension provision based on a number of quantifiable variables (theoretical replacement rates of public plans, assets of funded pension schemes, private pension expenditure and coverage by private pension plans) that tries to tap into these different aspects. It can be used to empirically categorize the extent to which Organisation for Economic Co-operation and Development (OECD) countries have privatized their pension provision.
Modeling of a hybrid semi-active/passive vibration control technique
Authors: Mohammadi S , Hatam S , Khodayari A
Published: June 2013

In this paper a new hybrid vibration damping technique as a combination of the semi-active pulse switching technique and passive constrained layer damping is proposed as an effective vibration control method for all frequency ranges. The semi-active pulse switching technique is an effective method to damp any type of vibrations with no need for external energy sources. However, its performance in high-frequency ranges decreases. In addition, passive techniques are not so effective in low-frequency ranges, but have significant effects in high-frequency ranges. The proposed hybrid damping technique as a combination of these two control methods is a new effective control technique for all frequency ranges. It covers the weakness of the semi-active method and provides significant damping in both low and high-frequency vibrations.
Aspergillosis in Cats
Authors: Hartmann Katrin , Lloret Albert , Pennisi Maria Grazia , Ferrer Lluis , Addie Diane , Belák Sándor , Boucraut-Baralon Corine , Egberink Herman , Frymus Tadeusz , Gruffydd-Jones Tim , Hosie Margaret J , Lutz Hans , Marsilio Fulvio , Möstl Karin , Radford Alan D , Thiry Etienne , Truyen Uwe , Horzinek Marian C
Published: June 2013

Overview:

Aspergillosis is a sporadic mycosis that occurs worldwide in mammals and birds and leads to a usually chronic, and only rarely acute, disease that mainly affects the nasal cavity and sinuses.

Infection:

Aspergillus species infections are commonly associated with predisposing local or systemic factors. Local disease can spread and involve the central nervous system or the lungs. Some Aspergillus species can also disseminate, causing systemic infections. In contrast to dogs, in which (nasal) aspergillosis is relatively common, aspergillosis is rare in cats, but considered an emerging infection.

Clinical signs:

There are two clinical forms of aspergillosis in cats, the sinonasal form (characterised by signs of chronic nasal infection) and the newly emerging, more invasive sino-orbital form (characterised by signs of orbital and surrounding tissue invasion). Sino-orbital involvement has been described now in approximately half of the reported cases.

Disease management:

Treatment should consist of local and systemic antifungal therapy.
Taming the shame: Policing excretions and body fluids in advertisements for hygiene products
Authors: Kama Amit , Barak-Brandes Sigal
Published: June 2013

Despite recent burgeoning interest in the body as a culturally constructed project, little research attention is paid to bodily excretions (sweat, urine, faeces, menstrual blood, saliva, mucus, skin oil) and their social implications. The present study addresses this lacuna. Since advertising for hygiene products reflects prevailing ideas regarding the body and the regulation of its excretions, this research focused on two questions: what messages are conveyed by advertisements for products that regulate excretions, and how is shame constituted? The study analysed 159 adverts published in Israeli newspapers. The results indicate that shame or regulation of the body’s orifices and waste do not constitute a frame for promoting hygiene products: cleaning one’s body for hygienic purposes is covert, and adverts reflect a hedonistic cult of the self. This apotheosis of the body implies that pampering oneself requires constant investment, including the purchase of products that serve a hygienic purpose only incidentally.
Smoking behavior and sociodemographic differences among young people: Further evidence from southern Sweden based on public health survey data
Authors: Ekman Björn , Khalife Jade , Moussa Kontie , Emmelin Maria
Published: June 2013

Aims: Tobacco-smoking behaviours of young people between the age of 18 and 25 years are less understood than those of middle-aged people. The aim of this study is to contribute to improved knowledge of some of the factors that are associated with smoking and cessation among young people. Methods: We use the most recently available public health survey data from the southern region of Skåne in Sweden to analyze these factors. The survey is a cross-sectional study with a total sample size of 28,198 individuals with 2801 in the age category of interest. We apply statistical measures of association between smoking and gender and also model the relationship between smoking and smoking cessation and the role of a set of sociodemographic determinants by means of logistic regression to estimate odds ratios. Results: The findings include significant differences between the younger age group and the older group with respect to the odds of smoking and method of cessation. We also find differences between young women and men with regard to smoking prevalence, intensity and cessation methods. In particular, young women attempt to quit smoking by means of unassisted methods to a significantly higher extent than do young men. Conclusions: There are significant differences between young people and older individuals with respect to a range of smoking behaviours. There are also strong gender effects within the group of young people. Policy development and anti-smoking interventions need to take such differences into consideration for improved effectiveness.
Life course socioeconomic position and mortality: A population register-based study from Sweden
Authors: Padyab Mojgan , Malmberg Gunnar , Norberg Margareta , Blomstedt Yulia
Published: June 2013

Aims: Adverse social circumstances during one’s life course have been related to an increased risk of mortality. This article extends the literature by focusing on adversity at each phase of, and cumulatively at midlife in the Swedish population. Methods: Data on socioeconomic indicators from 1970, 1980 and 1990 were linked to death registrations from 2000 to 2009. Relative indices of inequalities were computed for socioeconomic indicators, in order to measure the cumulative impact of inequality on mortality. Results: A significant cumulative effect of being in the worst-off socioeconomic groups was found. For men, almost all indicators had a significant independent impact on risk of death. Among women, significant independent impacts were found for education in 1990 and for socioeconomic index in the 2 census years of 1970 and 1980. Conclusions: Being disadvantaged during a longer period in midlife has a significant negative impact on health. Policies targeted to reduce health inequality should focus on every stage of the midlife course.
The individualization of punishment: Sentencing in Slovenia
Authors: Plesničar Mojca M.
Published: June 2013

Sentencing issues are discussed at length in common law systems, but discussions infrequently include civil law systems. In an attempt to remedy this oversight somewhat, the article analyses the sentencing system in Slovenia, a fairly typical civil law country. The basis of the sentencing system is the concept of individualization of punishment, where proportionality is of the utmost importance and is set first by legislation determining sentencing ranges for specific offences and then by the judiciary aiming to narrow the ranges to an appropriate sentence in individual cases. The system is far from perfect, especially on the procedural side, but it offers a valid alternative to other sentencing solutions.
Juvenile adaptation to imprisonment: Feelings of safety, autonomy and well-being, and behaviour in prison
Authors: van der Laan André , Eichelsheim Veroni
Published: June 2013

Adaptation to imprisonment involves feelings of safety, autonomy, well-being, stress or misbehaviour among detained offenders. According to importation theory, characteristics such as previous experiences of imprisonment or psychiatric problems affect the adaptation of offenders to imprisonment; deprivation theory, in contrast, focuses on factors such as social interactions with peers or staff and fairness in procedures or in daily life encounters. In this study, adaptation to imprisonment and the relationship with importation and deprivation factors were investigated among 207 juvenile offenders incarcerated in Dutch juvenile correctional institutions. A cross -sectional multi-method design was used, including a survey, screening instruments, records and qualitative interviews. Controlling for importation characteristics, strong associations of adaptation to imprisonment were found with interactions with peers and staff, justice, daily activities and the number of juveniles in a group. The study provides valuable insight into the factors related to adaptation to imprisonment, which can help to improve safety in prison and, subsequently, could be useful in increasing the motivation of juveniles to participate in treatment programmes. The implications for theory and practice are discussed.
Field-regulated force by grafted polyelectrolytes
Authors: Seidel Christian , Budkov Yury A , Brilliantov Nikolay V
Published: June 2013

Generation of mechanical force regulated by external electric field is studied both theoretically and by molecular dynamics simulations. The force arises in deformable bodies linked to the free end of a grafted polyelectrolyte chain, which is exposed to an electric field that favours its adsorption. We consider a few target bodies with different force–deformation relations including (1) linear and (2) cubic dependences as well as (3) Hertzian-like force. Such force–deformation relations mimic the behaviour of (1) coiled and (2) stretched polymer chains, respectively, or (3) that of a squeezed colloidal particle. The magnitude of the arising force varies over a wide interval although the electric field alters within a relatively narrow range only. The predictions of our theory agree quantitatively well with the results of numerical simulations. Both cases of zero and finite electrical current are investigated, and we do not obtain substantial differences in the force generated. The phenomenon studied could possibly be utilised to design, for example, vice-like devices to fix nano-sized objects.
Headlines in Newspaper Editorials
Authors: Bonyadi Alireza , Samuel Moses
Published: June 2013

Newspaper editorials constitute a part of media discourse, which is an extremely important field of research in intercultural rhetoric analysis and EFL (English as a foreign language)/ESL (English as a second language) studies. Specifically, certain features of editorial headlines and also their important role in monitoring and directing readers’ attention have made the interface between the linguistic analysis of newspaper editorial headlines and teaching of EFL as a relevant issue in language teaching. Through conducting a contrastive textual analysis of selected headlines, culled from the editorials of the English newspaper, The New York Times, and those of Persian newspaper, Tehran Times, the present study aimed at exploring the kind of textual and rhetorical strategies the two newspapers used for propagating their preferred ideologies. The results of the study indicated that headlines in the two papers presented a subjective attitude of the writers (newspapers) toward the topic. However, based on the analysis of the data, it became clear that there were certain differences between the two sets of headlines in terms of Presupposition, and certain Rhetorical devices.
Book Review: Gender and Green Governance
Authors: Elliott Carolyn
Published: June 2013

Bina Agarwal, Gender and Green Governance.Delhi: Oxford University Press. 2010. 488 pages. ₹ 625.
Retraction of “Issues of Landlessness, Contract and Corporate Farming,” by Amit Kumar Bose
Authors: Bose Amit Kumar
Published: June 2013

It has been brought to the publisher’s attention that the article “Issues of Landlessness, Contract and Corporate Farming,” by Amit Kumar Bose, published in the Journal of Land and Rural Studies (Volume 1, Issue 1) included substantial portions of text from an earlier article written by Prof. Sukhpal Singh, titled “Corporate Farming in India: Is it Must for Agricultural Development?” (IIMA working paper No. 2006-11-06). Huge chunks in pages 32 to 39 of the article are verbatim copying of Prof. Singh’s work, without adequate permission from him and adequate attribution. The Editors of LRS and the Publisher extend their sincere apology to Prof Singh for this failure to credit his work.

This article profiles the nature and extent of companies being involved in farming and examines its effect on the farmers in the Indian context. The article tries to explain how contract farming is a more preferred venture than corporate farming, in terms of farmers’ security, financial stability and small land holding viability.
The role of uPAR in epithelial-mesenchymal transition in small airway epithelium of patients with chronic obstructive pulmonary disease
Authors: Wang Qin , Wang Yunshan , Zhang Yi , Zhang Yuke , Xiao Wei
Published: June 2013

Background

Epithelial-mesenchymal transition (EMT) plays a crucial role in small airway fibrosis of patients with chronic obstructive pulmonary disease (COPD). Increasing evidence suggests that the urokinase plasminogen activator receptor (uPAR) is involved in the pathogenesis of COPD. Increased uPAR expression has been implicated in the promotion of EMT in numerous cancers; however the role of uPAR in EMT in small airway epithelial cells of patients with COPD remains unclear. In this study, we investigated the degree of EMT and uPAR expression in lung epithelium of COPD patients, and verified the effect of uPAR on cigarette smoke extract (CSE)-induced EMT in vitro.

Methods

The expression of EMT biomarkers and uPAR was assessed in lung epithelium specimens from non-smokers (n = 25), smokers (n = 25) and non-smokers with COPD (n = 10) and smokers with COPD (n = 18). The role of uPAR on CSE-induced EMT in human small airway epithelial cells (HSAEpiCs) was assessed by silencing uPAR expression in vitro.

Results

Markers of active EMT and uPAR expression were significantly increased in the small airway epithelium of patients with COPD compared with controls. We also observed a significant correlation between uPAR and vimentin expression in the small airway epithelium. In vitro, CSE-induced EMT in HSAEpiCs was associated with high expression of uPAR, and targeted silencing of uPAR using shRNA inhibited CSE-induced EMT. Finally, we demonstrate that the PI3K/Akt signaling pathway is required for uPAR-mediated EMT in HSAEpiCs.

Conclusions

A uPAR-dependent signaling pathway is required for CSE-induced EMT, which contributes to small airway fibrosis in COPD. We propose that increased uPAR expression in the small airway epithelium of patients with COPD participates in an active EMT process.
Rare inheritance of Leri-Weill Syndrome due to crossover of short stature Homeobox Gene (SHOX) Deletions between X and Y Chromosomes: a case report
Authors: Censani Marisa , Anyane-Yeboa Kwame , Wapner Ronald , Spiegel Erica , Guzman Edwin , Oberfield Sharon E
Published: June 2013

Background

Leri-Weill syndrome (LWS) is a genetic disorder caused by deletions or mutations in the SHOX gene or by deletions downstream of the gene and is classically characterized by short stature, mesomelic shortening of forearms and legs, and Madelung deformity. Correct identification of short stature homeobox-containing gene (SHOX) deficiency in children with growth problems is vital for appropriate initiation of growth hormone therapy.

Method

We report a phenotypically normal 23 day old male infant born to a father diagnosed with Leri-Weill syndrome at age 12 years with a documented SHOX deletion on his X chromosome. The patient’s fetal long bones had been found to be about three weeks delayed in growth on prenatal ultrasound during the second trimester.

Results

The infant underwent genetic evaluation at 23 days of life and was found to have a SHOX deletion on Yp11.32 identified using single nucleotide polymorphism microarray (SNP) analysis and confirmed by FISH using a SHOX gene probe.

Conclusion

We report the case of a male infant diagnosed with Leri-Weill syndrome with an unusual documented inheritance between father and son due to crossover between X and Y chromosomes duringpaternalmeiosis. Our case is the youngest patient in literature documented by FISH analysis to have an X to Y chromosome transfer and the first of these patients diagnosedpriorto onset of short stature or Madelung deformity. Our patient was identified prior to growth failure and can now be monitored for growth abnormalities with the ability to implement growth augmentation therapy without delay. Our case highlights the importance of advising affected SHOX patients of risks to future offspring and supports screening off-spring of parents carrying SHOX abnormalities regardless of sex.
Impact of Hepatitis C Virus (HCV) infection on biomolecular markers influencing the pathogenesis of bladder cancer
Authors: Hemmaid Kamel Z , Awadalla Amira , Elsawy Essam , Hussein Abdel-aziz M , Abdel-aziz Azza , Shokeir Ahmed A , El-Hefnawy Ahmed S , Abol-enein Hassan
Published: June 2013

Objective

The present study was designed to determine the possible impact of hepatitis C virus (HCV) infection on the expression of telomerase (TERT), retinoblastoma (RB1), E2F3, TP53, CDKN1A (p21) and fibroblast growth factor receptor- 3 (FGFR3) genes in patients with bladder cancer (BC).

Materials and methods

100 patients with bladder cancer (15 female and 85 male) were divided into 2 groups; Group I: 50 HCV negative subjects (age range 36–79), and Group II: 50 HCV positive subjects (age range 42–80). Expressions of the telomerase, retinoblastoma (Rb), E2F3, TP53 and FGFR3 genes were tested by immunohistochemistry and real time PCR in tumour tissues and healthy bladder tissues. Also, telomerase activity was assessed by telomeric repeats amplification protocol (TRAP).

Results

Bladder tumors associated with HCV infection were of high grade and invasive squamous cell carcinomas (SCCs). Expressions of hTERT, Rb, E2F3, TP53 and FGFR3 as well as telomerase activity were significantly higher in bladder tissues of HCV-infected patients compared with bladder tissues of non infected patients (p<0.05). On the contrary, CDKN1A (p21) expression was significantly lower in bladder tissues of HCV-infected patients compared to bladder tissues of non infected patients (p<0.05).

Conclusion

The expressions of hTERT, Rb, E2F3, TP53 and FGFR3 as well as the activity of telomerase were significantly high in malignant bladder tissues associated with HCV infection. On the other hand, CDKN1A (p21) expression was low in bladder tissues of HCV-infected subjects. Moreover, there was a positive correlation between HCV infection and expression of telomerase, E2F3, TP53 and FGFR3. There was a negative correlation between HCV infection and expression of Rb and p21.
Molecular analysis of appendiceal mucinous cystadenoma and rectal adenocarcinoma in a patient with urothelial carcinoma: a case report
Authors: Pulighe Fabio , Paliogiannis Panagiotis , Cossu Antonio , Palmieri Giuseppe , Colombino Maria , Scognamillo Fabrizio , Trignano Mario
Published: June 2013

Introduction

In this report, we present the case of a patient affected by appendiceal cystadenoma, a colorectal adenocarcinoma, and a concomitant bladder carcinoma, as well as the results of the molecular study of the most relevant mutational pathways involved in these tumors.

Case presentation

A 68-year-old Italian man was admitted to our unit complaining of macrohematuria, rectorrhagia, and rectal tenesmus for about 2 months. A colonoscopy showed the presence of a rectal lesion at 11cm from the anal margin; multiple biopsies were performed and a diagnosis of moderately differentiated adenocarcinoma was made. Abdominal ultrasonography and total body computed tomography performed subsequently to stage the rectal cancer showed the presence of two round nodules, interpreted as swollen lymph nodes of neoplastic origin, at the anterior aspect of the iliopsoas muscle and a budding lesion affecting the bladder. The patient underwent transurethral biopsy of the lesion in the right retrotrigonal region; the diagnosis was grade II urothelial carcinoma. The patient underwent an open anterior rectal resection with loco-regional lymphadenectomy. An enlarged appendix and a voluminous whitish soft-tissue lesion requiring an appendicectomy were detected perioperatively. Transurethral resection of the bladder lesion was also performed. The histological examination revealed that the nodular lesions in the appendix were due to a cystadenoma. For mutation analysis, genomic deoxyribonucleic acid was isolated from tumor tissue samples; for PIK3CA mutations, screening revealed that all three samples analyzed carried mutations in exon 9.

Conclusions

Appendiceal mucoceles are rare but require adequate surgical treatment, given their malignant potential and the possibility of causing peritoneal pseudomyxoma. It is essential to make a correct preoperative evaluation based on a colonoscopy rather than ultrasound and computed tomography to exclude synchronous neoplasias often associated with mucoceles and to plan the optimum surgical strategy. The association between appendiceal mucoceles and other neoplasias is relatively frequent, especially with colorectal cancer. Oncogenic activation in the PIK3CA-depending pathway may contribute substantially to the pathogenesis of the different solid tumors in the same patient.
Alteration of human blood cell transcriptome in uremia
Authors: Scherer Andreas , Günther Oliver P , Balshaw Robert F , Hollander Zsuzsanna , Wilson-McManus Janet , Ng Raymond , McMaster W Robert , McManus Bruce M , Keown Paul A
Published: June 2013

Background

End-stage renal failure is associated with profound changes in physiology and health, but the molecular causation of these pleomorphic effects termed “uremia” is poorly understood. The genomic changes of uremia were explored in a whole genome microarray case-control comparison of 95 subjects with end-stage renal failure (n = 75) or healthy controls (n = 20).

Methods

RNA was separated from blood drawn in PAXgene tubes and gene expression analyzed using Affymetrix Human Genome U133 Plus 2.0 arrays. Quality control and normalization was performed, and statistical significance determined with multiple test corrections (qFDR). Biological interpretation was aided by knowledge mining using NIH DAVID, MetaCore and PubGene

Results

Over 9,000 genes were differentially expressed in uremic subjects compared to normal controls (fold change: -5.3 to +6.8), and more than 65% were lower in uremia. Changes appeared to be regulated through key gene networks involving cMYC, SP1, P53, AP1, NFkB, HNF4 alpha, HIF1A, c-Jun, STAT1, STAT3 and CREB1. Gene set enrichment analysis showed that mRNA processing and transport, protein transport, chaperone functions, the unfolded protein response and genes involved in tumor genesis were prominently lower in uremia, while insulin-like growth factor activity, neuroactive receptor interaction, the complement system, lipoprotein metabolism and lipid transport were higher in uremia. Pathways involving cytoskeletal remodeling, the clathrin-coated endosomal pathway, T-cell receptor signaling and CD28 pathways, and many immune and biological mechanisms were significantly down-regulated, while the ubiquitin pathway and certain others were up-regulated.

Conclusions

End-stage renal failure is associated with profound changes in human gene expression which appears to be mediated through key transcription factors. Dialysis and primary kidney disease had minor effects on gene regulation, but uremia was the dominant influence in the changes observed. This data provides important insight into the changes in cellular biology and function, opportunities for biomarkers of disease progression and therapy, and potential targets for intervention in uremia.
Treatment reality in elderly patients with advanced ovarian cancer: a prospective analysis of the OVCAD consortium
Authors: Trillsch Fabian , Woelber Linn , Eulenburg Christine , Braicu Ioana , Lambrechts Sandrina , Chekerov Radoslav , van Nieuwenhuysen Els , Speiser Paul , Zeimet Alain , Castillo-Tong Dan Cacsire , Concin Nicole , Zeillinger Robert , Vergote Ignace , Mahner Sven , Sehouli Jalid
Published: June 2013

Background

Approximately one third of women diagnosed with ovarian cancer is 70 years or older. Information on the treatment reality of these elderly patients is limited.

Methods

275 patients with primary epithelial ovarian cancer FIGO stage II-IV undergoing cytoreductive surgery and platinum-based chemotherapy were prospectively included in this European multicenter study. Patients <70 and ≥70 years were compared regarding clinicopathological variables and prognosis.

Results

Median age was 58 years (18–85); 47 patients (17.1%) were 70 years or older. The postoperative 60-day-mortality rate was 2.1% for elderly and 0.4% for younger patients (p < 0.001). Elderly patients were less likely to receive optimal therapy (no residual disease after surgery and platinum combination chemotherapy) compared to patients <70 years (40.4% vs. 70.1%, p < 0.001) and their outcome was less favorable regarding median PFS (12 vs. 20 months, p = 0.022) and OS (30 vs. 64 months, p < 0.001). However, in multivariate analysis age itself was not a prognostic factor for PFS while the ECOG performance status had prognostic significance in elderly patients.

Conclusions

Elderly patients with ovarian cancer are often treated less radically. Their outcome is impaired despite no consistent prognostic effect of age itself. Biological age and functional status should be considered before individualized treatment plans are defined.
Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection
Authors: Vincent Caroline , Stephens David A , Loo Vivian G , Edens Thaddeus J , Behr Marcel A , Dewar Ken , Manges Amee R
Published: June 2013

Background

Antimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowingClostridium difficileto infect the gut. Additional risk factors such as proton-pump inhibitors may also alter the intestinal microbiota and predispose patients toClostridium difficileinfection (CDI). This comparative metagenomic study investigates the relationship between epidemiologic exposures, intestinal bacterial populations and subsequent development of CDI in hospitalized patients. We performed a nested case–control study including 25 CDI cases and 25 matched controls. Fecal specimens collected prior to disease onset were evaluated by 16S rRNA gene amplification and pyrosequencing to determine the composition of the intestinal microbiota during the at-risk period.

Results

The diversity of the intestinal microbiota was significantly reduced prior to an episode of CDI. Sequences corresponding to the phylum Bacteroidetes and to the families Bacteroidaceae and Clostridiales Incertae Sedis XI were depleted in CDI patients compared to controls, whereas sequences corresponding to the family Enterococcaceae were enriched. In multivariable analyses, cephalosporin and fluoroquinolone use, as well as a decrease in the abundance of Clostridiales Incertae Sedis XI were significantly and independently associated with CDI development.

Conclusions

This study shows that a reduction in the abundance of a specific bacterial family - Clostridiales Incertae Sedis XI - is associated with risk of nosocomial CDI and may represent a target for novel strategies to prevent this life-threatening infection.
Evaluation of Fenton oxidation process coupled with biological treatment for the removal of reactive black 5 from aqueous solution
Authors: Bahmani Pegah , Rezaei Kalantary Roshanak , Esrafili Ali , Gholami Mitra , Jonidi Jafari Ahmad
Published: June 2013

Biodegradation of azo dyes is difficult due to their complex structures and low BOD to COD ratios. In the present study, the efficiency of using Fenton’s reagent (H2O2 + Fe2+) as a pretreatment process to enhance microbial transformation of reactive black 5 (RB5) in an aqueous system was evaluated. The RB5 with an initial concentration of 250 mg/L was decolorized up to 90% in 60 h by using a bacterial consortium. Fenton’s reagent at a Fe2+ concentration of 0.5 mM and H2O2 concentration of 2.9 mM (molar ratio, 1:5.8) was most effective for decolorization at pH = 3.0. The extent of RB5 removal by the combined Fenton–biotreatment was about 2 times higher than that of biotreatment alone. The production of some aromatic amines intermediates implied partial mineralization of the RB5 in Fenton treatment alone; in addition, decreasing of GC-MS peaks suggested that dearomatization occurred in Fenton-biological process. Fenton pretreatment seems to be a cost–effective option for the biotreatment of azo dyes, due mainly to the lower doses of chemicals, lower sludge generation, and saving of time. Our results demonstrated positive effects of inoculating bacterial consortium which was capable of dye biodegradation with a Fenton’s pretreatment step as well as the benefits of low time required for the biological process. In addition, the potential of field performance of Fenton-biological process because of using bacterial consortium is an other positive effect of it.
Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease
Authors: Mesko Bertalan , Poliska Szilard , Váncsa Andrea , Szekanecz Zoltan , Palatka Karoly , Hollo Zsolt , Horvath Attila , Steiner Laszlo , Zahuczky Gabor , Podani Janos , Nagy and Laszlo
Published: June 2013

Background

Biological therapies have been introduced for the treatment of chronic inflammatory diseases including rheumatoid arthritis (RA) and Crohn's disease (CD). The efficacy of biologics differs from patient to patient. Moreover these therapies are rather expensive, therefore treatment of primary non-responders should be avoided.

Method

We addressed this issue by combining gene expression profiling and biostatistical approaches. We performed peripheral blood global gene expression profiling in order to filter the genome for target genes in cohorts of 20 CD and 19 RA patients. Then RT-quantitative PCR validation was performed, followed by multivariate analyses of genes in independent cohorts of 20 CD and 15 RA patients, in order to identify sets ofinterrelated genes that can separate responders from non-responders to the humanized chimeric anti-TNFalpha antibody infliximab at baseline.

Results

Gene panels separating responders from non-responders were identified using leave-one-out cross-validation test, and a pool of genes that should be tested on larger cohorts was created in both conditions.

Conclusions

Our data show that peripheral blood gene expression profiles are suitable for determining gene panels with high discriminatory power to differentiate responders from non-responders in infliximab therapy at baseline in CD and RA, which could be cross-validated successfully. Biostatistical analysis of peripheral blood gene expression data leads to the identification of gene panels that can help predict responsiveness of therapy and support the clinical decision-making process.
Mode misidentification in Rayleigh waves: Ellipticity as a cause and a cure
Authors: Boaga Jacopo , Cassiani Giorgio , Strobbia Claudio L. , Vignoli Giulio
Published: June 2013

The surface wave method is a popular tool for geotechnical characterization because it supplies a cost-effective testing procedure capable of retrieving the shear wave velocity structure of the near-surface. Several acquisition and processing approaches have been developed to infer the Rayleigh wave dispersion curve which is then inverted. Typically, in active testing, single-component vertical receivers are used. In most cases, the inversion is carried out assuming that the experimental dispersion curve corresponds to a single mode, mostly the fundamental Rayleigh mode, unless clear evidence dictates the existence of a more complex response, e.g., in presence of low-velocity layers and inversely dispersive sites. A correct identification of the modes is essential to avoid serious errors. Here we consider the typical case of higher-mode misidentification known as “osculation” (“kissing”), where the energy peak shifts at low frequencies from the fundamental to the first higher mode. This jump occurs, with a continuous smooth transition, around a well-defined frequency where the two modes get very close to each other. Osculation happens generally in presence of strong velocity contrasts, typically with a fast bedrock underlying loose sediments. The practical limitations of the acquired active data affect the spectral and modal resolution, making it often impossible to identify the presence of two modes. In some cases, modes have a very close root and cannot be separated at the osculation point. In such cases, mode misidentification can create a large overestimation of the bedrock velocity and a large error on its depth. We examine the subsoil conditions that can generate this unwanted condition, and the common field acquisition procedures that can contribute to producing data having such deceptive Rayleigh dispersion characteristics. This mode misidentification depends strongly on the usual approach of measuring only the vertical component of ground motion, as the mode osculation is linked to the Rayleigh wave ellipticity polarization, and therefore we conclude that multicomponent data, using also horizontal receivers, can help discern the multimodal nature of surface waves. Finally, we introduce a priori detectors of subsoil conditions, based on passive microtremor measurements, that can act as warnings against the presence of mode osculation, and relate these detectors to the frequencies at which dispersion curves can be misidentified. Theoretical results are confirmed by real data acquisition tests.
Improved estimation of mineral and fluid volumetric concentrations in thinly bedded carbonate formations
Authors: Heidari Zoya , Torres-Verdín Carlos , Preeg William E.
Published: June 2013

We recently introduced new petrophysical and compositional methods for joint interpretation of multiple conventional well logs. These inversion-based methods are suited for petrophysical interpretation of rock formations that exhibit complex solid composition, include thin beds, and are subject to mud-filtrate invasion. They combine nuclear and resistivity logs to assess porosity and volumetric/weight concentrations of mineral and fluid constituents, and are ideal for the quantitative interpretation of carbonate formations. We document the successful application of the newly introduced inversion-based interpretation methods to three carbonate formations. Interpretation results are compared to those obtained with commercial software and core/X-ray diffraction (XRD) data whenever available. For two of the carbonate field examples where XRD data are available, nonlinear joint inversion of well logs improves the assessment of porosity by more than 30% and up to 100% in the presence of thin beds when compared to conventional interpretation methods.
An introduction to this special section: Hydrogeophysics
Authors: Miller Rick , Singha Kamini
Published: June 2013

Complexities of today's water challenges rival any faced in the world of applied geophysics. Unfortunately, after a quick glance into the crystal ball, these problems look to do nothing but escalate as time marches on. It seems, with ever-increasing frequency, questions and needs more probing and demanding keep floating to the surface, each with seemingly unfathomable goals. For example, it has become common on contaminant investigations to request/require not only identification of potential source locations but delineation of actual volumes within an aquifer. Or let's not forget the frequent requests to tackle the daunting task of monitoring and predicting flow and transport characteristics in highly variable and complex aquifers. As the demands for water increase, hydrogeophysicists will continue to be asked to examine stifling problems given the most recent advances and capabilities technology has to offer.
The need to adapt the exploration model from the oil patch to contaminated-site characterization: A case from Hill AFB, Utah, USA
Authors: Bradford John H. , Babcock Esther
Published: June 2013

For decades, the oil industry has employed a working model for hydrocarbon exploration in which large-scale geophysical surveys are undertaken prior to a second phase of intensive, targeted drilling. This latter phase may be conducted in conjunction with further focused geophysical studies. The geophysical surveys provide lateral coverage and continuity that are used to drive placement of drilling locations. The reason for this approach is simple: wells are expensive relative to geophysical surveys. Also, practical limits on lateral coverage preclude optimization of exploration targets based on well information alone.