bluuebunny/crossref_metadata_2025 huggingface dataset:
The Changing Psychology of Culture From 1800 Through 2000
Authors: Greenfield Patricia M.
Published: August 2013

The Google Books Ngram Viewer allows researchers to quantify culture across centuries by searching millions of books. This tool was used to test theory-based predictions about implications of an urbanizing population for the psychology of culture. Adaptation to rural environments prioritizes social obligation and duty, giving to other people, social belonging, religion in everyday life, authority relations, and physical activity. Adaptation to urban environments requires more individualistic and materialistic values; such adaptation prioritizes choice, personal possessions, and child-centered socialization in order to foster the development of psychological mindedness and the unique self. The Google Ngram Viewer generated relative frequencies of words indexing these values from the years 1800 to 2000 in American English books. As urban populations increased and rural populations declined, word frequencies moved in the predicted directions. Books published in the United Kingdom replicated this pattern. The analysis established long-term relationships between ecological change and cultural change, as predicted by the theory of social change and human development (Greenfield, 2009).
Nicotine induces alteration of H3K27 demethylase UTX in kidney cancer cell
Authors: Guo X , Li X , Wang Y , Tian Z , Duan X , Cai Z
Published: August 2013

Cigarette smoking is one of the most important risk factors for kidney cancer, but the molecular mechanism is poorly understood. To examine the expression change of histone H3 on lysine 27 trimethylase (H3K27me3) demethylases ubiquitously transcribed TPR gene on the X chromosome (UTX) in kidney cancer cell line 786-O after nicotine treatment, quantitative real-time-polymerase chain reaction and western blotting analysis were carried out. These results showed that nicotine can increase UTX messenger RNA and protein levels and also decrease the content of H3K27me3. The decreased content of H3K27me3 may activate specific gene expression and lead to kidney cancer. Future investigation on nicotine induced UTX expression and its epigenetic effect would deepen our understanding on nicotine toxicity and carcinogenicity.
Carvacrol ameliorates thioacetamide-induced hepatotoxicity by abrogation of oxidative stress, inflammation, and apoptosis in liver of Wistar rats
Authors: Nafees S , Ahmad ST , Arjumand W , Rashid S , Ali N , Sultana S
Published: August 2013

The present study was designed to investigate the protective effects of carvacrol against thioacetamide (TAA)-induced oxidative stress, inflammation and apoptosis in liver of Wistar rats. In this study, rats were subjected to concomitant prophylactic oral pretreatment of carvacrol (25 and 50 mg kg−1 body weight (b.w.)) against the hepatotoxicity induced by intraperitoneal administration of TAA (300 mg kg−1 b.w.). Efficacy of carvacrol against the hepatotoxicity was evaluated in terms of biochemical estimation of antioxidant enzyme activities, histopathological changes, and expressions of inflammation and apoptosis. Carvacrol pretreatment prevented deteriorative effects induced by TAA through a protective mechanism in a dose-dependent manner that involved reduction of oxidative stress, inflammation and apoptosis. We found that the protective effect of carvacrol pretreatment is mediated by its inhibitory effect on nuclear factor kappa B activation, Bax and Bcl-2 expression, as well as by restoration of histopathological changes against TAA administration. We may suggest that carvacrol efficiently ameliorates liver injury caused by TAA.
Youth voice(s) in EU countries and social movements in southern Europe
Authors: Lima Maria da Paz Campos , Artiles Antonio Martín
Published: August 2013

This article discusses social mobilization of young people in European countries over the last four years in the context of economic crisis, austerity policies and worsening conditions for young people. Two main issues are explored. First, the article examines, on the basis of the European Social Survey 2010, youth participation in protests in European countries and the factors influencing their participation: labour market conditions, education, institutional participation, and satisfaction with the functioning of democracy and the economy. Secondly, it takes a closer look at recent youth protest developments in 2011 and 2012 in southern European countries, focusing on their extent, nature and agendas.
Structural Factors That Increase HIV/STI Vulnerability Among Indigenous People in the Peruvian Amazon
Authors: Orellana E. Roberto , Alva Isaac E. , Cárcamo Cesar P. , García Patricia J.
Published: August 2013

We examined structural factors—social, political, economic, and environmental—that increase vulnerability to HIV among indigenous people in the Peruvian Amazon. Indigenous adults belonging to 12 different ethnic groups were purposively recruited in four Amazonian river ports and 16 indigenous villages. Qualitative data revealed a complex set of structural factors that give rise to environments of risk where health is constantly challenged. Ferryboats that cross Amazonian rivers are settings where unprotected sex—including transactional sex between passengers and boat crew and commercial sex work—often take place. Population mobility and mixing also occurs in settings like the river docks, mining sites, and other resource extraction camps, where heavy drinking and unprotected sex work are common. Multilevel, combination prevention strategies that integrate empirically based interventions with indigenous knowledge are urgently needed, not only to reduce vulnerability to HIV transmission, but also to eliminate the structural determinants of indigenous people’s health.
Pharmacokinetics of MMB4 DMS in Rats, Rabbits, and Dogs Following a Single IV Administration
Authors: Hong S. Peter , Gibbs Seth T. , Kobs Dean J. , Osheroff Merrill R. , Johnson Jerry D. , Burback Brian L.
Published: August 2013

Organophosphorus (OP) nerve agents pose tremendous threats to both military and civilian populations. The substance 1,1′-methylenebis[4-[(hydroxyimino)methyl]-pyridinium] (MMB4) is being developed as a replacement for the currently fielded 2-pyridine aldoxime, or pralidoxime (2-PAM) as a treatment for OP nerve agent–induced toxicity. The present study characterized pharmacokinetic (PK) profiles of MMB4 in male and female Sprague-Dawley rats, New Zealand White rabbits, and beagle dogs given a single intravenous (IV) administration of MMB4 dimethanesulfonate (DMS) at 55, 25, and 15 mg/kg dose, respectively. The plasma MMB4 concentration versus time profiles were biphasic for all species tested and fit a 2-compartment model with first-order elimination. There were no overt sex-related differences in the calculated PK parameters. For the rat, rabbit, and dog, the average systemic exposure parameters predicted Cmax (µg/mL) and AUC∞ (µg·h/mL) were 273 and 71.0, 115 and 48.1, and 87.4 and 39.6; the average volume of distribution (mL/kg) values to the central and peripheral compartments were 207 and 143, 242 and 172, and 198 and 213; and the average elimination half-life (hour) and clearance (mL/h/kg) values were 0.18 and 778, 0.29 and 577, and 0.32 and 430, respectively, when the PK parameters for males and females were combined. The current study revealed a similarity in the volume of distribution to the central compartment for MMB4 among the 3 species tested while demonstrating species-related differences in the elimination half-life and clearance of MMB4.
In Vivo Acetylcholinesterase Reactivation in Male Guinea Pigs and Rhesus Macaques Following Cyclosarin Exposure and Treatment With 1,1′-Methylenebis{4-[(hydroxyimino)methyl] pyridinium} Dimethanesulfonate
Authors: Harvilchuck Jill A. , Hong S. Peter , Richey Jamie S. , Osheroff Merrill R. , Johnson Jerry D.
Published: August 2013

Acetylcholinesterase (AChE) reactivation studies were conducted in guinea pigs (GPs) and nonhuman primates (NHPs) to determine the 1,1′-methylenebis{4-[(hydroxyimino)methyl] pyridinium} dimethanesulfonate (MMB4 DMS) dose that reactivated at least 20% of blood AChE within 15 minutes following cyclosarin (GF) dosing (used as the criterion for efficacy). Male GPs and male rhesus macaques (NHPs) were pretreated with atropine 15 minutes prior to GF administration (1 × median lethal dose [LD50]) and MMB4 DMS 15 minutes following GF administration. The GP survival was 5 of 8, 8 of 8, 8 of 8, and 6 of 8 for the 0.75, 3.0, 6.0, or 12.0 mg/kg MMB4 DMS treatment groups, respectively. In NHPs, survival was 6 of 6 at 0.5, 1.2, 3.0, or 9.3 mg/kg MMB4 DMS, respectively, 24 hours post-challenge, with the majority of animals noted as clinically normal by 24 hours. Pharmacokinetic/pharmacodynamic modeling revealed that 1.8 mg/kg in GPs or 0.013 mg/kg in NHPs would result in an average 20% reactivation; human equivalent doses were calculated as 0.39 mg/kg (based on GP data) and 0.004 mg/kg (based on NHP data). The model suggested that MMB4 plasma concentrations of 1000 ng/mL and AChE reactivation of 80% would be most effective. Although a 0.5 mg/kg MMB4 DMS dose in NHPs resulted in 100% survival and an average of 78% AChE reactivation, adverse effects associated with GF administration were still observed 24 hours post-challenge (tremors, mydriasis, and weakness were observed in 3 of 6 animals). In comparison, 6 of 6 animals treated with 1.2 mg/kg MMB4 DMS were observed as clinically normal 24 hours post-challenge.
Approaching/departure: effacement, erasure and ‘undoing’ the fear of crime
Authors: Fanghanel Alexandra
Published: August 2013

This paper contributes to contemporary debates about the geographies of gendered fear of crime by examining the way in which a group of young women negotiate fear of crime in public space by creating affective distance between themselves and the approaching menace of fear. These distances are presented here as lacunae that young women construct in order to promote feelings of safety in public spaces. Bringing Sara Ahmed’s work on the circulation of affect and Jacques Derrida’s notion of erasure (or sous-rature) into a dialogue with each other, and building on a Heideggerian phenomenological understanding of fear as dynamic, this paper argues that constructing lacunae enables young women to undo the approach of signifiers of fear in public space, which in turn enables them to contest dominant discourses of the gendered nature of fear of crime. Such erasure also has implications for the politics of safe-keeping. This paper complicates conventional understandings of safe-keeping by highlighting how, in the pursuit of safety, erasures based on classed, raced, or gendered ‘othering’ manifest themselves and it highlights the importance, not only of attending to silences and absences used to promote feelings of safety, but also to the politics of these in the pursuit of safe-keeping.
A Method for Building Evaluation Competency Among Community-Based Organizations
Authors: Kelly Cheryl M. , LaRose Jessi , Scharff Darcell P.
Published: August 2013

Community-based organizations often lack the capacity (e.g., time, staff, skills) to effectively evaluate programs, policies, and environmental changes. Providing evaluation technical assistance and training can be an effective and feasible way to build individual evaluation competency. The purpose of this article is to present a practical approach and related tools that can be used by evaluators and others (e.g., academic partners, funders) providing assistance to build evaluation skills in community organizations. The approach described was developed in collaboration with local universities and a regional health foundation to provide intensive technical support to 19 community-based organizations awarded funding to implement obesity prevention projects. Technical assistance processes and tools were designed to be tailored to organizations’ capacity and needs and can be used as templates by others who provide technical assistance. Evaluators, funders, and academic partners can use lessons learned from this experience to help shape and implement evaluation technical assistance approaches with community-based organizations.
MiR-223 modulates multidrug resistance via downregulation of ABCB1 in hepatocellular carcinoma cells
Authors: Yang Tao , Zheng Zhi-min , Li Xiao-na , Li Zhen-fu , Wang Yan , Geng Yun-feng , Bai Li , Zhang Xian-bo
Published: August 2013

Multidrug resistance (MDR) has become a major impediment to a successful treatment for liver cancer patients, and one of the common reasons for MDR is the activation of ABCB1 gene, leading to the over-expression of P-glycoprotein (P-gp), which conferred cancer cells be resistant to a broad range of anticancer drugs. MicroRNAs (miRNAs) are a class of short, non-coding RNA moleculars that can regulate gene expression at the post-transcriptional level. In the current study, the aim is to explore whether miRNA participates in the regulation of MDR mediated by ABCB1. We found that the expression of ABCB1 was correlated with the doxorubicin IC50 dose in eight hepatocellular carcinoma (HCC) cell lines: Hep3B, HCC3, LM-6, SMMC7721, Huh-7, SK-Hep-1, HepG2 and BEL-7402. Using the bioinformatics, we discovered that there were several miRNAs that can bind to the 3’UTR of ABCB1 gene. Among these candidate miRNAs, miR-223 was chosen for further study. Then, EGFP reporter assay, real-time PCR and Western blot were performed to verify that miR-223 targeted ABCB1 3’UTR directly, and miR-223 downregulated ABCB1 at both mRNA and protein levels. Finally, we found that the over-expression of miR-223 increased the HCC cell sensitivity to anticancer drugs, and the inhibition of miR-223 had the opposite effect. Importantly, the over-expression or silencing of ABCB1 can rescue the cell response to the anticancer drugs mediated by miR-223 over-expression or inhibition, respectively. In conclusion, our findings indicated that miR-223 played an important role in the regulation of MDR mediated by ABCB1, and it suggests that miR-223 may be considered as a therapeutic biomarker for HCC patients who had MDR problems induced by high expression of ABCB1.
Mammary gland morphology and gene expression signature of weanling male and female rats following exposure to exogenous estradiol
Authors: Miousse Isabelle R , Gomez-Acevedo Horacio , Sharma Neha , Vantrease Jamie , Hennings Leah , Shankar Kartik , Cleves Mario A , Badger Thomas M , Ronis Martin JJ
Published: August 2013

In order to characterize the actions of xenoestrogens, it is essential to possess a solid portrait of the physiological effects of exogenous estradiol. We assessed effects of three doses of exogenous estradiol (E2) (0.1, 1.0 and 10 µg/kg/day) given between postnatal days 21 and 33 on the mammary gland morphology and gene expression profiles of male and female rats compared to vehicle-treated controls. The male mammary gland was more responsive to E2 treatment than in females, with 509 genes regulated >2-fold in a dose-dependent manner in males and only 174 in females. In males, E2 treatment significantly ( P < 0.01) increased the number of terminal end buds (TEBs) and the expression of proliferating cell nuclear antigen (PCNA) protein ( P < 0.05), both of which are indicators of proliferation. This change was linked to a significant increase ( P < 0.05) in the expression of the gene encoding amphiregulin, which is known to induce TEB formation. There was also a dose-dependent increase ( P < 0.001) in the estrogen-regulated gene encoding the progesterone receptor. In intact females, despite lack of changes in mammary morphology, we observed a dose-dependent increase ( P < 0.05) in the expression of genes encoding three milk proteins: whey acidic protein, casein beta and casein kappa. There was a significant ( P < 0.05) downregulation of both estrogen receptors in response to E2 treatment. These results suggest that mammary glands of male rats are very sensitive to exogenous E2 during development post-weaning. The dose-dependent increase observed in amphiregulin and progesterone receptor gene expression was linked to morphological changes and represents a reliable and sensitive tool to evaluate estrogenicity. In contrast, intact weanling female rats were less responsive.
The influence of the speed of food intake on multichannel impedance in patients with gastro‐oesophageal reflux disease
Authors: Bor Serhat , Bayrakci Berna , Erdogan Askin , Yildirim Esra , Vardar Rukiye
Published: August 2013

Background

There is a general belief that gastro‐oesophageal reflux increases after meals and especially following a rapid intake.

Objective

To evaluate the impact of rapid vs. slow food intake on gastro‐oesophageal reflux disease (GORD) patients.

Materials and methods

Forty‐six GORD patients with heartburn and / or acid regurgitation once a week or more often common were included in this study. Participants were asked to eat the same standard meal within either 5 or 30 minutes under observation in a random order on 2 consecutive days. A total of 28 hours of recording were obtained by intraoesophageal impedance pH and number of liquid and mixed reflux episodes within 3 hours of the slow‐ and fast‐eating postprandial periods were calculated.

Results

While all patients defined GORD symptoms, 10 (21.7%) had pathological 24‐h intraoesophageal impedance measurement, 15 (32.6%) had pathological DeMeester and 21.7% had erosive oesophagitis. No difference has been shown according to the eating speed when all reflux episodes were taken together (754 vs. 733). Speed of food intake also did not have an impact on patients with normal vs. pathological 24‐h intraoesophageal impedance or erosive vs. non‐erosive. During the first postprandial hour, approximately half of the reflux events were non‐acid, compared to 34.2% during the second hour and 26.8% during the third hour (p  < 0.001). The number of acid reflux episodes was significantly higher than non‐acid reflux especially during the second and third hours and in total for 3 hours.

Conclusions

This first study addressing the effect of eating speed on reflux episodes in GORD patients did not support the general belief that reflux increases following fast eating. Acid and non‐acid reflux were similar at the first postprandial hour, then acid reflux episodes were predominantly higher, which implicate the importance of acid pockets.
Urban Code or Urban Legend
Authors: Keith Shelley , Griffiths Elizabeth
Published: August 2013

Elijah Anderson’s subcultural explanation for the adoption of the “code of the street” has directed scholarly attention toward specific cultural norms and scripts that encourage or sanction violence in disadvantaged urban neighborhoods. We provide an explicit test of the general assumption that the code of the street is predominantly endorsed by youth residing in urban communities. Using data on 2,183 juvenile offenders committed to the State of Georgia’s Department of Juvenile Justice between July 2002 and December 2003, we examine youths’ strength of endorsement of code-specific attitudes. Importantly, these delinquent youth formerly resided in Georgia zip codes of varying degrees of urbanism, from highly urbanized to isolated rural areas. The findings suggest a considerable generalizability in strength of endorsement of the street code among delinquent youth residing in very distinctive types of territorial units. These analyses illustrate that the contemporary preoccupation among criminologists with an urban-based theory of the code may be misguided; the street code has broader reach than the inner city and is, in general, neither race-specific nor more strongly endorsed among delinquent youth in highly urbanized areas.
Autism, Personality, and Human Diversity
Authors: Ekblad Leif
Published: August 2013

The aim of this study was to define neurodiversity in a scientific manner so it can be researched in further studies without involving disorders defined by psychiatry or popular beliefs about neurodiversity in the autistic community. Neurodiversity was defined as the primary factor output by factor analysis of a data set of human behaviors which contains evenly distributed traits of all sorts that cover all of human diversity. Neurotypical function was defined as the second factor. The study used many different traits and a large sample to find the full extent of neurodiversity, and to provide evenly distributed traits. The result was a test with 145 scoring items and 5 control items that could give participants a neurodiverse and a neurotypical score, and an indication that the participant was neurodiverse, neurotypical, or mixed. It was found that the neurodiversity score was independent of gender and age, and that the prevalence appears to have remained unchanged. There were possible differences in racial prevalence that need further research. The results correlated to many disorders defined by psychiatry, and also with several factors in personality tests. People who had been diagnosed with these disorders had considerably higher neurodiversity scores. The idea that neurodiversity was at the extreme end of a normal distribution was not supported, rather it was found that neurodiversity had its own normal distribution overlapping typical traits.
Multilevel Research in the Field of Organizational Behavior
Authors: Costa Patrícia Lopes , Graça Ana Margarida , Marques-Quinteiro Pedro , Santos Catarina Marques , Caetano António , Passos Ana Margarida
Published: August 2013

During the last 30 years, significant debate has taken place regarding multilevel research. However, the extent to which multilevel research is overtly practiced remains to be examined. This article analyzes 10 years of organizational research within a multilevel framework (from 2001 to 2011). The goals of this article are (a) to understand what has been done, during this decade, in the field of organizational multilevel research and (b) to suggest new arenas of research for the next decade. A total of 132 articles were selected for analysis through ISI Web of Knowledge. Through a broad-based literature review, results suggest that there is equilibrium between the amount of empirical and conceptual papers regarding multilevel research, with most studies addressing the cross-level dynamics between teams and individuals. In addition, this study also found that the time still has little presence in organizational multilevel research. Implications, limitations, and future directions are addressed in the end.
Calibrating Questionnaires by Psychometric Analysis to Evaluate Knowledge
Authors: Gómez-Soberón J. Manuel , Gómez-Soberón M. Consolación , Corral-Higuera Ramón , Arredondo-Rea S. Paola , Almaral-Sánchez J. Luis , Cabrera-Covarrubias F. Guadalupe
Published: August 2013

The experience achieved using the tool “Questionnaires,” available inside the Virtual Campus of an architectural engineering school in northeast Spain, is presented. “Questionnaires” is a mechanism/tool adequate and simple to evaluate the knowledge level achieved by students. This work shows and identifies the control indices of adaptation for questionnaires, such as the Facility Index, the standard deviation, the Discrimination Index, and the Discrimination Coefficient. From these parameters, educational performance is inferred, identified, and predicted. The conclusions of this work will allow the modification of deficient knowledge-evaluation practices and the identification of needs for specific groups or for students with particular requirements, thus making it feasible to apply these parameters with a guarantee of success in similar evaluation processes.
Factor VIII gene (F8) mutation and risk of inhibitor development in nonsevere hemophilia A
Authors: Eckhardt Corien L. , van Velzen Alice S. , Peters Marjolein , Astermark Jan , Brons Paul P. , Castaman Giancarlo , Cnossen Marjon H. , Dors Natasja , Escuriola-Ettingshausen Carmen , Hamulyak Karly , Hart Daniel P. , Hay Charles R. M. , Haya Saturnino , van Heerde Waander L. , Hermans Cedric , Holmström Margareta , Jimenez-Yuste Victor , Keenan Russell D. , Klamroth Robert , Laros-van Gorkom Britta A. P. , Leebeek Frank W. G. , Liesner Ri , Mäkipernaa Anne , Male Christoph , Mauser-Bunschoten Evelien , Mazzucconi Maria G. , McRae Simon , Meijer Karina , Mitchell Michael , Morfini Massimo , Nijziel Marten , Oldenburg Johannes , Peerlinck Kathelijne , Petrini Pia , Platokouki Helena , Reitter-Pfoertner Sylvia E. , Santagostino Elena , Schinco Piercarla , Smiers Frans J. , Siegmund Berthold , Tagliaferri Annarita , Yee Thynn T. , Kamphuisen Pieter Willem , van der Bom Johanna G. , Fijnvandraat Karin
Published: August 2013

Key Points

The inhibitor incidence in nonsevere hemophilia A patients with certain F8 mutations approaches the inhibitor incidence in severe patients. These findings are highly relevant for clinical practice, as they facilitate identification of high-risk patients based on F8 genotype.
JAK of all trades: JAK2-STAT5 as novel therapeutic targets in BCR-ABL1+ chronic myeloid leukemia
Authors: Warsch Wolfgang , Walz Christoph , Sexl Veronika
Published: August 2013

The transcription factor signal transducers and activators of transcription 5 (STAT5) has an important and unique role in Breakpoint Cluster Region - Abelson 1 (BCR-ABL1)–driven neoplasias. STAT5 is an essential component in the signaling network that maintains the survival and growth of chronic myeloid leukemia (CML) cells. In contrast, the function of the prototypical upstream kinase of STAT5, the Janus kinase JAK2, in CML is still under debate. Although there is widespread agreement that JAK2 is part of the signaling network downstream of BCR-ABL1, it is unclear whether and under what circumstances JAK2 inhibitors may be beneficial for CML patients. Recent studies in murine models have cast doubt on the importance of JAK2 in CML maintenance. Nevertheless, JAK2 has been proposed to have a central role in the cytokine signaling machinery that allows the survival of CML stem cells in the presence of BCR-ABL1 tyrosine kinase inhibitors. In this review, we summarize the current debate and provide an overview of the arguments on both sides of the fence. We present recent evidence showing that CML stem cells do not depend on BCR-ABL1 kinase activity but require the continuous support of the hematopoietic niche and its distinct cytokine environment and suggest that it has the potential to resolve the dispute.
A role for IRF4 in the development of CLL
Authors: Shukla Vipul , Ma Shibin , Hardy Richard R. , Joshi Shantaram S. , Lu Runqing
Published: August 2013

Key Points

IRF4−/−Vh11 mice develop spontaneous CLL at 100% penetrance, indicating that a low level of IRF4 is critical for CLL development. IRF4−/−Vh11 mice are a novel mouse model of CLL.
Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis
Authors: Pallavicini Alberto , Canapa Adriana , Barucca Marco , Alfőldi Jessica , Biscotti Maria Assunta , Buonocore Francesco , De Moro Gianluca , Di Palma Federica , Fausto Anna Maria , Forconi Mariko , Gerdol Marco , Makapedua Daisy Monica , Turner-Meier Jason , Olmo Ettore , Scapigliati Giuseppe
Published: August 2013

Background

Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.

Results

The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.

The RNA-seq analysis revealed remarkable differences in the expression profiles between the two tissues, allowing the identification of liver- and testis-specific transcripts which may play a fundamental role in important biological processes carried out by these two organs.

Conclusion

Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.
Variability of antibiotic susceptibility and toxin production of Staphylococcus aureus strains isolated from skin, soft tissue, and bone related infections
Authors: Sina Haziz , Ahoyo Théodora A , Moussaoui Wardi , Keller Daniel , Bankolé Honoré S , Barogui Yves , Stienstra Ymkje , Kotchoni Simeon O , Prévost Gilles , Baba-Moussa Lamine
Published: August 2013

Background

Staphylococcus aureus is an opportunistic commensal bacterium that mostly colonizes the skin and soft tissues. The pathogenicity of S. aureus is due to both its ability to resist antibiotics, and the production of toxins. Here, we characterize a group of genes responsible for toxin production and antibiotic resistance of S. aureus strains isolated from skin, soft tissue, and bone related infections.

Results

A total of 136 S. aureus strains were collected from five different types of infection: furuncles, pyomyositis, abscesses, Buruli ulcers, and osteomyelitis, from hospital admissions and out-patients in Benin. All strains were resistant to benzyl penicillin, while 25% were resistant to methicillin, and all showed sensitivity to vancomycin. Panton-Valentine leukocidin (PVL) was the most commonly produced virulence factor (70%), followed by staphylococcal enterotoxin B (44%). Exfoliative toxin B was produced by 1.3% of the strains, and was only found in isolates from Buruli ulcers. The tsst-1, sec, and seh genes were rarely detected (≤1%).

Conclusions

This study provides new insight into the prevalence of toxin and antibiotic resistance genes in S. aureus strains responsible for skin, soft tissue, and bone infections. Our results showed that PVL was strongly associated with pyomyositis and osteomyelitis, and that there is a high prevalence of PVL-MRSA skin infections in Benin.
Assessment of the feasibility and coverage of a modified universal hearing screening protocol for use with newborn babies of migrant workers in Beijing
Authors: Qi Beier , Cheng Xiaohua , En Hui , Liu Bo , Peng Shichun , Zhen Yong , Cai Zhenghua , Huang Lihui , Zhang Luo , Han Demin
Published: August 2013

Background

Although migrant workers account for the majority of newborns in Beijing, their children are less likely to undergo appropriate universal newborn hearing screening/rescreening (UNHS) than newborns of local non-migrant residents. We hypothesised that this was at least in part due to the inadequacy of the UNHS protocol currently employed for newborn babies, and therefore aimed to modify the protocol to specifically reflect the needs of the migrant population.

Methods

A total of 10,983 healthy babies born to migrant mothers between January 2007 and December 2009 at a Beijing public hospital were investigated for hearing abnormalities according to a modified UNHS protocol. This incorporated two additional/optional otoacoustic emissions (OAE) tests at 24–48 hours and 2 months after birth. Infants not passing a screening test were referred to the next test, until any hearing loss was confirmed by the auditory brainstem response (ABR) test.

Results

A total of 98.91% (10983/11104) of all newborn children underwent the initial OAE test, of which 27.22% (2990/10983) failed the test. 1712 of the failed babies underwent the second inpatient OAE test, with739 failing again; thus significantly decreasing the overall positive rate for abnormal hearing from 27.22% to 18.36% ([2990–973 /10983)]; p = 0). Overall, 1147(56.87%) babies underwent the outpatient OAE test again after1-month, of whom 228 failed and were referred for the second outpatient OAE test (i.e. 2.08% (228/10983) referral rate at 1month of age). 141 of these infants underwent the referral test, of whom 103 (73.05%) tested positive again and were referred for a final ABR test for hearing loss (i.e. final referral rate of 1.73% ([228-38/10983] at 2 months of age). Only 54 infants attended the ABR test and 35 (0.32% of the original cohort tested) were diagnosed with abnormal hearing.

Conclusions

Our study shows that it is feasible and practical to achieve high coverage rates for screening hearing loss and decrease the referral rates in newborn babies of migrant workers, using a modification of the currently employed UNHS protocol.
A rare case of primary malignant small cell carcinoma combined with urothelial cell carcinoma in the ureter
Authors: Jang Hoon , Yuk Seung Mo , Kim Jong Ok , Han Dong Seok
Published: August 2013

Background

Extrapulmonary small cell carcinomas have been reported in a variety of organs, and their incidence in the genitourinary tract is second only to that in the gastrointestinal tract. To date, however, only a few cases of small cell carcinoma of the ureter have been reported. Because the extreme rarity of this type of carcinoma, its clinical behaviour, diagnostic methods, and effective treatment modalities have not yet been determined.

Case presentation

A 59-year-old man presented with a 1-month history of painless gross haematuria. Urine cytopathology revealed a urothelial carcinoma and computed tomography revealed left hydronephroureterosis with a distal ureteral stone and a mildly enhanced fungating mass just below the stone-impacted site. The preoperative TNM stage was T2N0M0. The patient underwent simultaneous diagnostic ureterorenoscopy and left laparoscopic nephroureterectomy with bladder cuff resection. Gross examination showed a 3.5 × 3.0 × 0.8 cm white, partly yellow mass in the left distal ureter. Light microscopy showed a small cell carcinoma, overlaid on a urothelial carcinoma in situ, invading the ureter and external lateral resection margins. The small cell carcinoma was diffusely positive for neuron-specific enolase, and exhibited focal positivity for CD 56, synaptophysin, chromogranin and cytokeratin 20. The patient was treated with adjuvant chemotherapy, consisting of cisplatin and etoposide, and radiation therapy, and has been well, without evidence of tumour recurrence or metastasis in the 10 months after surgery.

Conclusion

Small cell carcinoma of the ureter is rare. Although its clinical behaviour and diagnostic modalities have not been determined and it has yet to be diagnosed immunohistopathologically, multimodality treatment including surgery, chemotherapy and radiotherapy may improve patient survival.
Systematic review and meta-analysis of laparoscopic and open gastrectomy for advanced gastric cancer
Authors: Chen Ke , Xu Xiao-Wu , Mou Yi-Ping , Pan Yu , Zhou Yu-Cheng , Zhang Ren-Chao , Wu Di
Published: August 2013

Background

The use of laparoscopic gastrectomy (LG) in advanced gastric cancer (AGC) remains a controversial topic, mainly because of doubts about its oncologic validity. This study is a systematic review and meta-analysis of the available evidence.

Methods

A comprehensive search was performed until June 2013 to identify comparative studies evaluating survival rates, recurrence rates, surgical outcomes and complications. Pooled risk ratios (RR) and weighted mean differences (WMD) with 95% confidence intervals (CI) were calculated using the random effects model. Data synthesis and statistical analysis were carried out using RevMan 5.1 software.

Results

Fifteen trials were involved in this analysis. Compared to open gastrectomy (OG), LG involved a longer operating time (WMD = 48.67 min, 95% CI 34.09 to 63.26, P < 0.001); less blood loss (WMD = −139.01 ml, 95% CI −174.57 to −103.44, P < 0.001); earlier time to flatus (WMD = −0.79 days, 95% CI −1.14 to −0.44, P < 0.001); shorter hospital stay (WMD = −3.11 days, 95% CI −4.13 to −2.09, P < 0.001); and a decrease in complications (RR = 0.74, 95% CI 0.61 to 0.90, P = 0.003). There was no significant difference in the number of harvested lymph nodes, margin distance, mortality, cancer recurrence rate and long-term survival rate between the AGC patients treated with LG or OG (P > 0.05).

Conclusions

Despite a longer operation, LG is a safe technical alternative to OG for AGC with a lower complication rate and enhanced postoperative recovery. Moreover, there were similar outcomes between both approaches in terms of cancer recurrence and the long-term survival rate. Because of the limitation of this study, methodologically high-quality studies are needed for further evaluation.
Uniform SiGe/Si quantum well nanorod and nanodot arrays fabricated using nanosphere lithography
Authors: Chang Hung-Tai , Wu Bo-Lun , Cheng Shao-Liang , Lee Tu , Lee Sheng-Wei
Published: August 2013

This study fabricates the optically active uniform SiGe/Si multiple quantum well (MQW) nanorod and nanodot arrays from the Si0.4Ge0.6/Si MQWs using nanosphere lithography (NSL) combined with the reactive ion etching (RIE) process. Compared to the as-grown sample, we observe an obvious blueshift in photoluminescence (PL) spectra for the SiGe/Si MQW nanorod and nanodot arrays, which can be attributed to the transition of PL emission from the upper multiple quantum dot-like SiGe layers to the lower MQWs. A possible mechanism associated with carrier localization is also proposed for the PL enhancement. In addition, the SiGe/Si MQW nanorod arrays are shown to exhibit excellent antireflective characteristics over a wide wavelength range. These results indicate that SiGe/Si MQW nanorod arrays fabricated using NSL combined with RIE would be potentially useful as an optoelectronic material operating in the telecommunication range.
Screening for duplications, deletions and a common intronic mutation detects 35% of second mutations in patients with USH2A monoallelic mutations on Sanger sequencing
Authors: Steele-Stallard Heather B , Le Quesne Stabej Polona , Lenassi Eva , Luxon Linda M , Claustres Mireille , Roux Anne-Francoise , Webster Andrew R , Bitner-Glindzicz Maria
Published: August 2013

Background

Usher Syndrome is the leading cause of inherited deaf-blindness. It is divided into three subtypes, of which the most common is Usher type 2, and the USH2A gene accounts for 75-80% of cases. Despite recent sequencing strategies, in our cohort a significant proportion of individuals with Usher type 2 have just one heterozygous disease-causing mutation in USH2A, or no convincing disease-causing mutations across nine Usher genes. The purpose of this study was to improve the molecular diagnosis in these families by screening USH2A for duplications, heterozygous deletions and a common pathogenic deep intronic variant USH2A: c.7595-2144A>G.

Methods

Forty-nine Usher type 2 or atypical Usher families who had missing mutations (mono-allelic USH2A or no mutations following Sanger sequencing of nine Usher genes) were screened for duplications/deletions using the USH2A SALSA MLPA reagent kit (MRC-Holland). Identification of USH2A: c.7595-2144A>G was achieved by Sanger sequencing. Mutations were confirmed by a combination of reverse transcription PCR using RNA extracted from nasal epithelial cells or fibroblasts, and by array comparative genomic hybridisation with sequencing across the genomic breakpoints.

Results

Eight mutations were identified in 23 Usher type 2 families (35%) with one previously identified heterozygous disease-causing mutation in USH2A. These consisted of five heterozygous deletions, one duplication, and two heterozygous instances of the pathogenic variant USH2A: c.7595-2144A>G. No variants were found in the 15 Usher type 2 families with no previously identified disease-causing mutations. In 11 atypical families, none of whom had any previously identified convincing disease-causing mutations, the mutation USH2A: c.7595-2144A>G was identified in a heterozygous state in one family. All five deletions and the heterozygous duplication we report here are novel. This is the first time that a duplication in USH2A has been reported as a cause of Usher syndrome.

Conclusions

We found that 8 of 23 (35%) of ‘missing’ mutations in Usher type 2 probands with only a single heterozygous USH2A mutation detected with Sanger sequencing could be attributed to deletions, duplications or a pathogenic deep intronic variant. Future mutation detection strategies and genetic counselling will need to take into account the prevalence of these types of mutations in order to provide a more comprehensive diagnostic service.
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Authors: Ebrahim Ali , Lerman Joshua A , Palsson Bernhard O , Hyduke Daniel R
Published: August 2013

Background

COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software.

Results

Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes.

Conclusion

COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets.

Availability

http://opencobra.sourceforge.net/
Relationship between foot function and medial knee joint loading in people with medial compartment knee osteoarthritis
Authors: Levinger Pazit , Menz Hylton B , Morrow Adam D , Bartlett John R , Feller Julian A , Bergman Neil R
Published: August 2013

Background

Dynamic joint loading, particularly the external knee adduction moment (KAM), is an important surrogate measure for the medio‐lateral distribution of force across the knee joint in people with knee osteoarthritis (OA). Foot motion may alter the load on the medial tibiofemoral joint and hence affect the KAM. Therefore, this study aimed to investigate the relationship between tibia, rearfoot and forefoot motion in the frontal and transverse planes and the KAM in people with medial compartment knee OA.

Method

Motion of the knee, tibia, rearfoot and forefoot and knee moments were evaluated in 32 patients with clinically and radiographically‐confirmed OA, predominantly in the medial compartment. Pearson's correlation coefficient was used to investigate the association between peak values of tibia, rearfoot and forefoot motion in the frontal and transverse planes and 1st peak KAM, 2nd peak KAM, and the knee adduction angular impulse (KAAI).

Results

Lateral tilt of the tibia was significantly associated with increased 1st peak KAM (r = 0.60, p < 0.001), 2nd peak KAM (r = 0.67, p = 0.001) and KAAI (r = 0.82, p = 0.001). Increased peak rearfoot eversion was significantly correlated with decreased 2nd peak KAM (r = 0.59, p < 0.001) and KAAI (r = 0.50, p = 0.004). Decreased rearfoot internal rotation was significantly associated with increased 2nd peak KAM (r = −0.44, p = 0.01) and KAAI (r = −0.38, p = 0.02), while decreased rearfoot internal rotation relative to the tibia was significantly associated with increased 2nd peak KAM (r = 0.43, p = 0.01). Significant negative correlations were found between peak forefoot eversion relative to the rearfoot and 2nd peak KAM (r = −0.53, p = 0.002) and KAAI (r = −0.51, p = 0.003) and between peak forefoot inversion and 2nd peak KAM (r = −0.54, p = 0.001) and KAAI (r = −0.48, p = 0.005).

Conclusion

Increased rearfoot eversion, rearfoot internal rotation and forefoot inversion are associated with reduced knee adduction moments during the stance phase of gait, suggesting that medial knee joint loading is reduced in people with OA who walk with greater foot pronation. These findings have implications for the design of load‐modifying interventions in people with knee OA.
The Sex Chromosome Trisomy mouse model of XXY and XYY: metabolism and motor performance
Authors: Chen Xuqi , Williams-Burris Shayna M , McClusky Rebecca , Ngun Tuck C , Ghahramani Negar , Barseghyan Hayk , Reue Karen , Vilain Eric , Arnold Arthur P
Published: August 2013

Background

Klinefelter syndrome (KS), caused by XXY karyotype, is characterized by low testosterone, infertility, cognitive deficits, and increased prevalence of health problems including obesity and diabetes. It has been difficult to separate direct genetic effects from hormonal effects in human studies or in mouse models of KS because low testosterone levels are confounded with sex chromosome complement.

Methods

In this study, we present the Sex Chromosome Trisomy (SCT) mouse model that produces XXY, XYY, XY, and XX mice in the same litters, each genotype with either testes or ovaries. The independence of sex chromosome complement and gonadal type allows for improved recognition of sex chromosome effects that are not dependent on levels of gonadal hormones. All mice were gonadectomized and treated with testosterone for 3 weeks. Body weight, body composition, and motor function were measured.

Results

Before hormonal manipulation, XXY mice of both sexes had significantly greater body weight and relative fat mass compared to XY mice. After gonadectomy and testosterone replacement, XXY mice (both sexes) still had significantly greater body weight and relative fat mass, but less relative lean mass compared to XY mice. Liver, gonadal fat pad, and inguinal fat pad weights were also higher in XXY mice, independent of gonadal sex. In several of these measures, XX mice also differed from XY mice, and gonadal males and females differed significantly on almost every metabolic measure. The sex chromosome effects (except for testis size) were also seen in gonadally female mice before and after ovariectomy and testosterone treatment, indicating that they do not reflect group differences in levels of testicular secretions. XYY mice were similar to XY mice on body weight and metabolic variables but performed worse on motor tasks compared to other groups.

Conclusions

We find that the new SCT mouse model for XXY and XYY recapitulates features found in humans with these aneuploidies. We illustrate that this model has significant promise for unveiling the role of genetic effects compared to hormonal effects in these syndromes, because many phenotypes are different in XXY vs. XY gonadal female mice which have never been exposed to testicular secretions.