bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNAP II Index
Authors: Nievas I. Federico Fernandez , Spentzas Thomas , Bogue Clifford W. 
Published: February 2013

Sedation monitoring is essential in pediatric patients on ventilatory support to achieve comfort and safety. The COMFORT scale was designed and validated to assess the level of sedation in intubated pediatric patients. However, it remains unreliable in pharmacologically paralyzed patients. The SNAP II index is calculated using an algorithm that incorporates high-frequency (80-420 Hz) electroencephalogram (EEG) components, known to be useful in discriminating between awake and unconscious states, unlike other measurements that only include low-frequency EEG segments such as the bispectral index score. Previous studies suggested that the SNAP II index is a reliable and sensitive indicator of the level of consciousness in adult patients. Despite its potential, no data are currently available in the pediatric critically ill population on ventilatory support. This is the first pilot study assessing the potential application of the SNAP II index in critically ill pediatric patients by comparing it to the commonly used COMFORT scale.
Effect of accelerated weathering and termite attack on the tensile properties and aesthetics of recycled HDPE-pinewood composites
Authors: López-Naranjo Edgar J , Alzate-Gaviria Liliana M , Hernández-Zárate Galdy , Reyes-Trujeque Javier , Cruz-Estrada Ricardo H 
Published: February 2013

Although wood–plastic composites (WPCs) are materials widely used in the construction industry, their durability constitutes a serious issue especially when used for outdoor applications. Therefore, this work gives account on the effect of biotic and abiotic degradation agents on two different WPCs prepared from recycled high-density polyethylene (HDPE) and pinewood residues. Two aspects were evaluated, namely mechanical properties and aesthetics. Compression-molded samples obtained from two different formulations based on 40% of wood and 60% of HDPE, containing 0 and 5% of coupling agent with respect to wood content, were subjected to 0, 1000 and 2000 h of accelerated weathering (AW), using an ultraviolet-type accelerated tester equipped with UVA-340 fluorescent lamps. Afterward, the aged specimens were exposed to attack by termites (TA) of the species Nasutitermes nigriceps for 15 and 30 days. Tensile properties after AW and TA were assessed using an Instron 5500R (1125) universal tester. Similarly, the aesthetic aspect was studied to evaluate the color changes on the specimens’ surfaces using a Minolta CR-200 Chroma Meter. The results of this work show drops in the mechanical properties of both composites that were not significant, even after being exposed to 2000 h of AW in combination with 30 days of TA. However, their aesthetics was seriously affected by both degradation agents, as reflected by the variations registered on the total color change and relative lightness of the tested samples.
Analyzing the Factors for VMI Implementation: A Framework
Authors: Singh Rajesh K. 
Published: February 2013

Vendor-managed inventory (VMI) is a collaborative strategy between a buyer and supplier to optimize the availability of products at minimal cost. Overall, inventory management cost plays a significant role in reducing supply chain cost. Specifically in the fast-moving consumer goods (FMCG) sector, inventory–turnover ratio needs to be very high to compete in the global market. Throughout the supply chain, VMI is used to cut inventory-related costs and keep inventory levels low. VMI helps organizations to reduce the inventory-associated costs by shifting the responsibility of managing and replenishing inventory to vendors. In this article, various critical factors of VMI are identified from the literature review and experts’ opinions. The interpretive structural modelling (ISM) approach has been employed to develop the structural relationship among different factors of VMI to improve the performance of the supply chain.  The article also defines the levels of different factors for VMI on the basis of their driving or dependence power and their mutual relationships. These factors have been further categorized according to their driving and dependence power. The insight from this model will help supply chain managers in implementing VMI to improve the overall performance of the supply chain.
Safety Area for Proximal Metatarsal Procedures
Authors: Chuckpaiwong Bavornrit , Korwutthikulrangsri Ekkapoj 
Published: February 2013

Background: Forefoot and tarsometatarsal surgery may be performed on the first and second metatarsal through the intermetatarsal space. However, no study has identified the safety area of the proximal metatarsal bone to avoid vascular injury. Methods: One hundred and twenty-two uninjured embalmed feet of 31 female and 33 male cadavers aged 15 to 91 years (mean, 69.9 years) were studied. The dorsalis pedis artery was identified and dissected from its origin to the deep plantar artery. The distances from the artery to the dorsomedial aspect of first metatarsal bone, from the artery to the first tarsometatarsal joint, and from dorsalis pedis artery to the most plantar surface of second metatarsal bone were measured. Results: The distance from the artery to the first tarsometatarsal joint averaged 23.1 mm (range, 12-31 mm) and the distance from the artery to the most plantar surface of the second metatarsal bone averaged 6.3 mm (range, 3-13 mm). Conclusions: The safety area for proximal metatarsal procedure is about a 69-mm2 triangular area (23 mm from first tarsometatarsal joint and 6 mm from the most plantar surface of the second metatarsal bone). Clinical Relevance: The study provides information of normal location and variation of deep plantar artery is which related to medial midfoot complex. This information may be used during proximal metatarsal procedures.
Thromboembolic Complications After Endovascular Repair of Abdominal Aortic Aneurysm With Neck Thrombus
Authors: Shintani Tsunehiro , Mitsuoka Hiroshi , Atsuta Kouji , Saitou Takaaki , Higashi Shigeki 
Published: February 2013

Objective: To evaluate outcomes after endovascular aneurysm repair (EVAR) for abdominal aortic aneurysm (AAA) with neck thrombus. Methods: We retrospectively reviewed patients who underwent EVAR for AAA at our institution from 2007 to 2011. Patients with ruptured AAA, chronic renal failure, or hostile neck characteristics other than thrombus were excluded. Patients were divided into 2 groups: group T (with neck thrombus) and group N (without neck thrombus). We compared complications and mid-term outcomes. Results: There were no differences in success rates between the groups, but there were higher rates of thromboembolic complications such as distal embolization (20% vs 0%, P = .02) and renal dysfunction (36.8% vs 11.1%, P = .03) in group T than in group N. Suprarenal thrombus and suprarenal fixation in the presence of suprarenal thrombus were associated with postoperative renal dysfunction ( P = .01). Conclusion: The EVAR for AAA with neck thrombus is associated with thromboembolic complications.
Low-level HLA antibodies do not predict platelet transfusion failure in TRAP study participants
Authors: Jackman Rachael P. , Deng Xutao , Bolgiano Douglas , Lebedeva Mila , Heitman John W. , Busch Michael P. , Slichter Sherrill J. , Norris Philip J. 
Published: February 2013

Key Points
High, but not low to moderate, HLA antibody levels are associated with platelet refractoriness.
The interpretation of disease phenotypes to identify TSE strains in mice: characterisation of BSE using PrPSc distribution patterns in the brain
Authors: Corda Erica , Beck Katy E , Sallis Rosemary E , Vickery Christopher M , Denyer Margaret , Webb Paul R , Bellworthy Susan J , Spencer Yvonne I , Simmons Marion M , Spiropoulos John 
Published: February 2013

Abstract
In individual animals affected by transmissible spongiform encephalopathies, different disease phenotypes can be identified which are attributed to different strains of the agent. In the absence of reliable technology to fully characterise the agent, classification of disease phenotype has been used as a strain typing tool which can be applied in any host. This approach uses standardised data on biological parameters, established for a single host, to allow comparison of different prion sources. Traditionally prion strain characterisation in wild type mice is based on incubation periods and lesion profiles after the stabilisation of the agent into the new host which requires serial passages. Such analysis can take many years, due to prolonged incubation periods. The current study demonstrates that the PrPSc patterns produced by one serial passage in wild type mice of bovine or ovine BSE were consistent, stable and showed minimal and predictable differences from mouse-stabilised reference strains. This biological property makes PrPSc deposition pattern mapping a powerful tool in the identification and definition of TSE strains on primary isolation, making the process of characterisation faster and cheaper than a serial passage protocol. It can be applied to individual mice and therefore it is better suited to identify strain diversity within single inocula in case of co-infections or identify strains in cases where insufficient mice succumb to disease for robust lesion profiles to be constructed. The detailed description presented in this study provides a reference document for identifying BSE in wild type mice.
A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
Authors: Dwivedi Bhakti , Xue Bingjie , Lundin Daniel , Edwards Robert A , Breitbart Mya 
Published: February 2013

Abstract

Background
Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively.

Results
RNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host’s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage.

Conclusions
This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.
Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination
Authors: Mugal Carina F , Nabholz Benoit , Ellegren Hans 
Published: February 2013

Abstract

Background
Polymorphism is key to the evolutionary potential of populations. Understanding which factors shape levels of genetic diversity within genomes forms a central question in evolutionary genomics and is of importance for the possibility to infer episodes of adaptive evolution from signs of reduced diversity. There is an on-going debate on the relative role of mutation and selection in governing diversity levels. This question is also related to the role of recombination because recombination is expected to indirectly affect polymorphism via the efficacy of selection. Moreover, recombination might itself be mutagenic and thereby assert a direct effect on diversity levels.

Results
We used whole-genome re-sequencing data from domestic chicken (broiler and layer breeds) and its wild ancestor (the red jungle fowl) to study the relationship between genetic diversity and several genomic parameters. We found that recombination rate had the largest effect on local levels of nucleotide diversity. The fact that divergence (a proxy for mutation rate) and recombination rate were negatively correlated argues against a mutagenic role of recombination. Furthermore, divergence had limited influence on polymorphism.

Conclusions
Overall, our results are consistent with a selection model, in which regions within a short distance from loci under selection show reduced polymorphism levels. This conclusion lends further support from the observations of strong correlations between intergenic levels of diversity and diversity at synonymous as well as non-synonymous sites. Our results also demonstrate differences between the two domestic breeds and red jungle fowl, where the domestic breeds show a stronger relationship between intergenic diversity levels and diversity at synonymous and non-synonymous sites. This finding, together with overall lower diversity levels in domesticates compared to red jungle fowl, seem attributable to artificial selection during domestication.
A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts
Authors: Wang Minghui , Wang Lin , Jiang Ning , Jia Tianye , Luo Zewei 
Published: February 2013

Abstract

Background
The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemented for such analyses are vulnerable to several key demographic factors and deliver a poor statistical power for detecting genuine associations and also a high false positive rate. Here, we present a likelihood-based statistical approach that accounts properly for non-random nature of case–control samples in regard of genotypic distribution at the loci in populations under study and confers flexibility to test for genetic association in presence of different confounding factors such as population structure, non-randomness of samples etc.

Results
We implemented this novel method together with several popular methods in the literature of GWAS, to re-analyze recently published Parkinson’s disease (PD) case–control samples. The real data analysis and computer simulation show that the new method confers not only significantly improved statistical power for detecting the associations but also robustness to the difficulties stemmed from non-randomly sampling and genetic structures when compared to its rivals. In particular, the new method detected 44 significant SNPs within 25 chromosomal regions of size < 1 Mb but only 6 SNPs in two of these regions were previously detected by the trend test based methods. It discovered two SNPs located 1.18 Mb and 0.18 Mb from the PD candidates, FGF20 and PARK8, without invoking false positive risk.

Conclusions
We developed a novel likelihood-based method which provides adequate estimation of LD and other population model parameters by using case and control samples, the ease in integration of these samples from multiple genetically divergent populations and thus confers statistically robust and powerful analyses of GWAS. On basis of simulation studies and analysis of real datasets, we demonstrated significant improvement of the new method over the non-parametric trend test, which is the most popularly implemented in the literature of GWAS.
Changes in the gut microbiota of cloned and non-cloned control pigs during development of obesity: gut microbiota during development of obesity in cloned pigs
Authors: Pedersen Rebecca , Andersen Anders Daniel , Mølbak Lars , Stagsted Jan , Boye Mette 
Published: February 2013

Abstract

Background
Obesity induced by a high-caloric diet has previously been associated with changes in the gut microbiota in mice and in humans. In this study, pigs were cloned to minimize genetic and biological variation among the animals with the aim of developing a controlled metabolomic model suitable for a diet-intervention study. Cloning of pigs may be an attractive way to reduce genetic influences when investigating the effect of diet and obesity on different physiological sites. The aim of this study was to assess and compare the changes in the composition of the gut microbiota of cloned vs. non-cloned pigs during development of obesity by a high-fat/high-caloric diet. Furthermore, we investigated the association between diet-induced obesity and the relative abundance of the phyla Firmicutes and Bacteroidetes in the fecal-microbiota. The fecal microbiota from obese cloned (n = 5) and non-cloned control pigs (n= 6) was investigated biweekly over a period of 136 days, by terminal restriction fragment length polymorphism (T-RFLP) and quantitative real time PCR (qPCR).

Results
A positive correlation was observed between body-weight at endpoint and percent body-fat in cloned (r=0.9, P<0.0001) and in non-cloned control pigs (r=0.9, P<0.0001). Shannon Weaver and principal component analysis (PCA) of the terminal restriction fragments (T-RFs) revealed no differences in the bacterial composition or variability of the fecal microbiota between the cloned pigs or between cloned and non-cloned control pigs. Body-weight correlated positively with the relative abundance of Firmicutes in both cloned (r=0.37; P<0.02) and non cloned-control pigs (r=0.45; P<0.006), and negatively with the abundance of Bacteroidetes in cloned pigs (r=−0.33, P<0.04), but not in the non-cloned control pigs.

Conclusion
The cloned pigs did not have reduced inter-individual variation as compared to non-cloned pigs in regard to their gut microbiota in neither the obese nor the lean state. Diet-induced obesity was associated with an increase in the relative abundance of Firmicutes over time. Our results suggest that cloned pigs are not a more suitable animal model for gut microbiota-obesity related studies than non-cloned pigs. This study is the first to evaluate if cloned pigs provide a better animal model than conventional pigs in diet-intervention, obesity and gut microbiota research.
Synergistic effect of paclitaxel and epigenetic agent phenethyl isothiocyanate on growth inhibition, cell cycle arrest and apoptosis in breast cancer cells
Authors: Liu Katherine , Cang Shundong , Ma Yuehua , Chiao Jen Wei 
Published: February 2013

Abstract
This study examined whether combining paclitaxel (taxol) with a novel epigenetic agent phenethyl isothiocyanate (PEITC) will yield a synergistic effect on inhibiting breast cancer cells. Two drug-resistant breast cancer cell lines, MCF7 and MDA-MB-231, were treated with PEITC and taxol. Cell growth, cell cycle, and apoptosis were examined. The combination of PEITC and taxol significantly decreased the IC50 of PEITC and taxol over each agent alone. The combination also increased apoptosis by more than two fold over each single agent in both cell lines. A significant increase of cells in the G2/M phases was detected. In conclusion, the combination of PEITC and taxol exhibits a synergistic effect on growth inhibition in breast cancer cells. This combination deserves further study in vivo.
Applying a gender lens on human papillomavirus infection: cervical cancer screening, HPV DNA testing, and HPV vaccination
Authors: Branković Ivan , Verdonk Petra , Klinge Ineke 
Published: February 2013

Abstract

Background
Our aim is to provide a state-of-the-art overview of knowledge on sex (biological) and gender (sociocultural) aspects of Human papillomavirus (HPV) and cervical cancer for educational purposes. Considerable disparities exist in cervical cancer incidences between different subgroups of women. We provide an outline on the crucial issues and debates based on the recent literature published in leading gender medicine journals. Intersectionality was applied in order to help categorise the knowledge.

Methods
Key terms (HPV, cervical cancer) were screened in Gender Medicine, Journal of Women’s Health and Women & Health from January 2005-June 2012. Additional searches were conducted for topics insufficiently mentioned, such as HPV vaccination of boys. In total, 71 publications were included (56 original papers, four reviews, six reports, three commentaries, one editorial and one policy statement).

Results
Research reveals complexity in the way various subgroups of women adhere to cervical screening. Less educated women, older women, uninsured women, homeless women, migrant women facing language barriers, women who have sex with women and obese women participate in Pap smears less frequently. A series of barriers can act to impede decisions to vaccinate against HPV.

Conclusions
Both male and female controlled preventive methods and treatment measures should be developed in order to tackle HPV infection and different strategies are needed for different subgroups. A substantial discussion and research on alternative methods of prevention was and is lacking. In future research, sex and gender aspects of HPV-related diseases of boys and men as well as subgroup differences in HPV risk need to be addressed.
Important steps to improve translation from medical research to health policy
Authors: Jiang Fan , Zhang Jun , Wang Xiangdong , Shen Xiaoming 
Published: February 2013

Abstract
Translational medicine entails not only “from-bench-to-bedside” but also preventive medicine. The present article proposes a conceptual framework of translational research from scientific research to health care policy and public health policy. We highlight the importance of translational medicine to bridge between research and policy and share our experience of translating medical research to public health policy in China as well as obstacles and challenges we are facing in the translation process.