bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface expression and genotypes of Toll-like receptors 2 and 4 in patients with juvenile idiopathic arthritis and systemic lupus erythematosus
Authors: Kirchner Martina , Sonnenschein Anja , Schoofs Simon , Schmidtke Peter , Umlauf Volker N , Mannhardt-Laakmann Wilma 
Published: March 2013

AbstractBackgroundChronic arthritis is a common feature of juvenile idiopathic arthritis (JIA) and systemic lupus erythematosus (SLE). It was subsequently discovered that Toll-likereceptors (TLRs) are able to upregulate cytokine production in response to endogenous ligands released after tissue damage, suggesting that TLRs can maintain an inflammatory response even in absence of pathogen. Thus, TLRs may contribute to increased inflammation in JIA and SLE patients. The aim of this study was to investigate the role of TLRs in JIA and SLE. We examined the in vivo expression and polymorphisms of TLR2 and TLR4 in peripheral monocytes of patients with JIA and SLE during active and inactive disease phases.MethodsThis single center cohort study consisted of JIA and SLE affected children and control subjects. TLR2 and TLR4 protein expression on CD14+monocytes was examined by flow cytometry. TLR2 and TLR4 genotypes were determined using the polymerase chain reaction-restriction fragment length polymorphism method (RFLP-PCR).ResultsA significant reduction in the level of TLR4 expression (p ≤ 0.001) was observed on monocytes of patients with JIA and SLE compared with that of healthy control subjects. There was no correlation between the TLR2 or TLR4 genotypes and the observed differential TLR protein expression on monocytes.ConclusionsTo conclude, our observations suggest involvement of investigated TLRs in the pathogenesis of JIA and SLE. It still remains to be elucidated whether reduced TLR4 expression is cause of chronic arthritis or a result of some feedback loop.
DNA nanotechnology: a future perspective
Authors: Zahid Muniza , Kim Byeonghoon , Hussain Rafaqat , Amin Rashid , Park Sung Ha 
Published: March 2013

AbstractIn addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.
Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
Authors: Xu Tao , Holzapfel Christina , Dong Xiao , Bader Erik , Yu Zhonghao , Prehn Cornelia , Perstorfer Katrin , Jaremek Marta , Roemisch-Margl Werner , Rathmann Wolfgang , Li Yixue , Wichmann H -Erich , Wallaschofski Henri , Ladwig Karl H , Theis Fabian , Suhre Karsten , Adamski Jerzy , Illig Thomas , Peters Annette , Wang-Sattler Rui 
Published: March 2013

AbstractBackgroundMetabolomics helps to identify links between environmental exposures and intermediate biomarkers of disturbed pathways. We previously reported variations in phosphatidylcholines in male smokers compared with non-smokers in a cross-sectional pilot study with a small sample size, but knowledge of the reversibility of smoking effects on metabolite profiles is limited. Here, we extend our metabolomics study with a large prospective study including female smokers and quitters.MethodsUsing targeted metabolomics approach, we quantified 140 metabolite concentrations for 1,241 fasting serum samples in the population-based Cooperative Health Research in the Region of Augsburg (KORA) human cohort at two time points: baseline survey conducted between 1999 and 2001 and follow-up after seven years. Metabolite profiles were compared among groups of current smokers, former smokers and never smokers, and were further assessed for their reversibility after smoking cessation. Changes in metabolite concentrations from baseline to the follow-up were investigated in a longitudinal analysis comparing current smokers, never smokers and smoking quitters, who were current smokers at baseline but former smokers by the time of follow-up. In addition, we constructed protein-metabolite networks with smoking-related genes and metabolites.ResultsWe identified 21 smoking-related metabolites in the baseline investigation (18 in men and six in women, with three overlaps) enriched in amino acid and lipid pathways, which were significantly different between current smokers and never smokers. Moreover, 19 out of the 21 metabolites were found to be reversible in former smokers. In the follow-up study, 13 reversible metabolites in men were measured, of which 10 were confirmed to be reversible in male quitters. Protein-metabolite networks are proposed to explain the consistent reversibility of smoking effects on metabolites.ConclusionsWe showed that smoking-related changes in human serum metabolites are reversible after smoking cessation, consistent with the known cardiovascular risk reduction. The metabolites identified may serve as potential biomarkers to evaluate the status of smoking cessation and characterize smoking-related diseases.
What is the appropriate size criterion for proton radiotherapy for hepatocellular carcinoma? A dosimetric comparison of spot-scanning proton therapy versus intensity-modulated radiation therapy
Authors: Toramatsu Chie , Katoh Norio , Shimizu Shinichi , Nihongi Hideaki , Matsuura Taeko , Takao Seishin , Miyamoto Naoki , Suzuki Ryusuke , Sutherland Kenneth , Kinoshita Rumiko , Onimaru Rikiya , Ishikawa Masayori , Umegaki Kikuo , Shirato Hiroki 
Published: March 2013

Abstract

Background
We performed a dosimetric comparison of spot-scanning proton therapy (SSPT) and intensity-modulated radiation therapy (IMRT) for hepatocellular carcinoma (HCC) to investigate the impact of tumor size on the risk of radiation induced liver disease (RILD).

Methods
A number of alternative plans were generated for 10 patients with HCC. The gross tumor volumes (GTV) varied from 20.1 to 2194.5 cm3. Assuming all GTVs were spherical, the nominal diameter was calculated and ranged from 3.4 to 16.1 cm. The prescription dose was 60 Gy for IMRT or 60 cobalt Gy-equivalents for SSPT with 95% planning target volume (PTV) coverage. Using IMRT and SSPT techniques, extensive comparative planning was conducted. All plans were evaluated by the risk of RILD estimated using the Lyman-normal-tissue complication probability model.

Results
For IMRT the risk of RILD increased drastically between 6.3–7.8 cm nominal diameter of GTV. When the nominal diameter of GTV was more than 6.3 cm, the average risk of RILD was 94.5% for IMRT and 6.2% for SSPT.

Conclusions
Regarding the risk of RILD, HCC can be more safely treated with SSPT, especially if its nominal diameter is more than 6.3 cm.
Ultrametric networks: a new tool for phylogenetic analysis
Authors: Apostolico Alberto , Comin Matteo , Dress Andres , Parida Laxmi 
Published: March 2013

Abstract

Background
The large majority of optimization problems related to the inference of distance‐based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by the postulate of a molecular clock, now dismissed, whereby phylogeny could be represented by a weighted tree in which the sum of the weights of the edges separating any given leaf from the root is the same for all leaves. Both, molecular clocks and rooted ultrametric trees, fell out of fashion as credible representations of evolutionary change. At the same time, ultrametric dendrograms have shown good potential for purposes of classification in so far as they have proven to provide good approximations for additive trees. Most of these approximations are still intractable, but the problem of finding the nearest ultrametric distance matrix to a given distance matrix with respect to the L

∞
distance has been long known to be solvable in polynomial time, the solution being incarnated in any minimum spanning tree for the weighted graph subtending to the matrix.

Results
This paper expands this subdominant ultrametric perspective by studying ultrametric networks, consisting of the collection of all edges involved in some minimum spanning tree. It is shown that, for a graph with n vertices, the construction of such a network can be carried out by a simple algorithm in optimal time O(n
2) which is faster by a factor of n than the direct adaptation of the classical O(n
3) paradigm by Warshall for computing the transitive closure of a graph. This algorithm, called UltraNet, will be shown to be easily adapted to compute relaxed networks and to support the introduction of artificial points to reduce the maximum distance between vertices in a pair. Finally, a few experiments will be discussed to demonstrate the applicability of subdominant ultrametric networks.

Availability

http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html
Simultaneous determination of seven hydrophilic bioactive compounds in water extract of Polygonum multiflorumusing pressurized liquid extraction and short-end injection micellar electrokinetic chromatography
Authors: Lao Ka-meng , Han Dong-qi , Chen Xiao-jia , Zhao Jing , Wang Tie-jie , Li Shao-ping 
Published: March 2013

Abstract

Background
Polygoni Multiflori Radix, He-Shou-Wu in Chinese, is a widely used traditional Chinese medicine. Clinically, water decoction is the major application form of He-Shou-Wu. Therefore, simultaneous determination of bioactive compounds in water extract is very important for its quality control.

Results
A pressurized liquid extraction and short-end injection micellar electrokinetic chromatography (MEKC) were first developed for simultaneous determination of seven hydrophilic bioactive compounds in water extract of He-Shou-Wu. The influence of parameters, such as pH, concentration of phosphate, SDS and HP-β-CD, capillary temperature and applied voltage, on the analysis were carefully investigated. Optimum separation was obtained within 14 min by using 50 mM phosphate buffer containing 90 mM SDS and 2% (m/v) HP-β-CD (pH 2.5) at 15 kV and 20°C. All calibration curves showed good linearity (R

2
>0.9978) within test ranges. The overall LOD and LOQ were lower than 2.0 μg/mL and 5.5 μg/mL, respectively. The RSDs for intra- and inter-day of seven analytes were less than 3.2% and 4.6%, and the recoveries were 97.0%-104.2%.

Conclusion
The validated method was successfully applied to the analysis of He-Shou-Wu samples, which is helpful for its quality control.
Post-weaning selenium and folate supplementation affects gene and protein expression and global DNA methylation in mice fed high-fat diets
Authors: Bermingham Emma N , Bassett Shalome A , Young Wayne , Roy Nicole C , McNabb Warren C , Cooney Janine M , Brewster Di T , Laing William A , Barnett Matthew PG 
Published: March 2013

Abstract

Background
Consumption of high-fat diets has negative impacts on health and well-being, some of which may be epigenetically regulated. Selenium and folate are two compounds which influence epigenetic mechanisms. We investigated the hypothesis that post-weaning supplementation with adequate levels of selenium and folate in offspring of female mice fed a high-fat, low selenium and folate diet during gestation and lactation will lead to epigenetic changes of potential importance for long-term health.

Methods
Female offspring of mothers fed the experimental diet were either maintained on this diet (HF-low-low), or weaned onto a high-fat diet with sufficient levels of selenium and folate (HF-low-suf), for 8 weeks. Gene and protein expression, DNA methylation, and histone modifications were measured in colon and liver of female offspring.

Results
Adequate levels of selenium and folate post-weaning affected gene expression in colon and liver of offspring, including decreasing Slc2a4 gene expression. Protein expression was only altered in the liver. There was no effect of adequate levels of selenium and folate on global histone modifications in the liver. Global liver DNA methylation was decreased in mice switched to adequate levels of selenium and folate, but there was no effect on methylation of specific CpG sites within the Slc2a4 gene in liver.

Conclusions
Post-weaning supplementation with adequate levels of selenium and folate in female offspring of mice fed high-fat diets inadequate in selenium and folate during gestation and lactation can alter global DNA methylation in liver. This may be one factor through which the negative effects of a poor diet during early life can be ameliorated. Further research is required to establish what role epigenetic changes play in mediating observed changes in gene and protein expression, and the relevance of these changes to health.
Pichia fabianii blood infection in a premature infant in China: case report
Authors: Wu Yuan , Wang Jing , Li Wenge , Jia Hongbin , Che Jie , Lu Jinxing , Liu Lanzheng , Cheng Ying 
Published: March 2013

Abstract

Background
Invasive fungal infections caused by uncommon fungi have increased in recent years. Hospitalized low-birth-weight infants are at high risk for neonatal fungal infections. Pichia fabianii is a rare pathogen causing blood infection, which has reportedly caused only 4 cases of fungemia and 1 case of endocarditis worldwide. Here, we describe the first case of a P. fabianii blood infection in a premature infant in China.

Case presentation
On July 28th, a low-birth-weight (LBW, 1760 g) female infant born at 33+4 weeks of gestation was admitted to the pediatric intensive care unit with mild neonatal asphyxia. Until August 2nd, a mechanical respirator was used to assist respiration under the Continuous Positive Airway Pressure (CPAP) model. The baby had an increased body temperature and a fever. To prevent infection, Ceftriaxone Sodium (CS) was administered intravenously for three days, after which Cefepime was administered until August 13th. Chest X-rays showed suspected plaque-like shadows in the right lung. Blood cultures twice tested positive for fungal infection caused by Candida pelliculosa (recognized as Pichia fabianii later), which is first mis-identified by commercial kit. Hence, intravenous fluconazole was administered. However, cultures of other body fluids (e.g., urine, feces and sputum) tested negative for fungal infection. Routine tests and biochemistry of cerebrospinal fluid (CSF) were normal. Latex agglutination of Cryptococcus neoformans and fungi cultures in the CSF were also negative. After 14 days of intravenous fluconazole, blood was re-cultured, the result of which was negative. On August 30th, intravenous fluconazole was suspended. On Sep 3rd, the infant left the hospital in good health.

Conclusions
This is the first case of a blood infection caused by P. fabianii in a LBW premature female infant in China. Risk factors for fungal infection include premature birth, as well as mechanical invasive operation and antibacterial drug usage. Whether such risk factors necessitate prophylactic use of antifungal drugs is an important question that has yet to be fully addressed. Additionally, the pathogen P. fabianii collected in this study was resistant to amphotericin B (AMB) and itraconazole (ITR). With the exception of the azole-resistant endocarditis case, all other cases have not demonstrated such a resistance. Finally, commercial biochemical methods used in routine practice are limited in their ability to identify P. fabianii. Molecular genetic based methods are imperative for identification of uncommon fungal species from disseminated infections.
Effect of thong style flip‐flops on children's barefoot walking and jogging kinematics
Authors: Chard Angus , Greene Andrew , Hunt Adrienne , Vanwanseele Benedicte , Smith Richard 
Published: March 2013

AbstractBackgroundThong style flip‐flops are a popular form of footwear for children. Health professionals relate the wearing of thongs to foot pathology and deformity despite the lack of quantitative evidence to support or refute the benefits or disadvantages of children wearing thongs. The purpose of this study was to compare the effect of thong footwear on children's barefoot three dimensional foot kinematics during walking and jogging.MethodsThirteen healthy children (age 10.3 ± 1.6 SD years) were recruited from the metropolitan area of Sydney Australia following a national press release. Kinematic data were recorded at 200 Hz using a 14 camera motion analysis system (Cortex, Motion Analysis Corporation, Santa Rosa, USA) and simultaneous ground reaction force were measured using a force platform (Model 9281B, Kistler, Winterthur, Switzerland). A three‐segment foot model was used to describe three dimensional ankle, midfoot and one dimensional hallux kinematics during the stance sub‐phases of contact, midstance and propulsion.ResultsThongs resulted in increased ankle dorsiflexion during contact (by 10.9°, p; = 0.005 walk and by 8.1°, p; = 0.005 jog); increased midfoot plantarflexion during midstance (by 5.0°, p; = 0.037 jog) and propulsion (by 6.7°, p; = 0.044 walk and by 5.4°, p;= 0.020 jog); increased midfoot inversion during contact (by 3.8°, p;= 0.042 jog) and reduced hallux dorsiflexion during walking 10% prior to heel strike (by 6.5°, p; = 0.005) at heel strike (by 4.9°, p; = 0.031) and 10% post toe‐off (by 10.7°, p; = 0.001).ConclusionsAnkle dorsiflexion during the contact phase of walking and jogging, combined with reduced hallux dorsiflexion during walking, suggests a mechanism to retain the thong during weight acceptance. Greater midfoot plantarflexion throughout midstance while walking and throughout midstance and propulsion while jogging may indicate a gripping action to sustain the thong during stance. While these compensations exist, the overall findings suggest that foot motion whilst wearing thongs may be more replicable of barefoot motion than originally thought.
Improvement in self-reported confidence in nurses’ professional skills in the emergency department
Authors: Rautava Veli-Pekka , Palomäki Erika , Innamaa Tapio , Perttu Mika , Lehto Päivi , Palomäki Ari 
Published: March 2013

Abstract

Background
The aim of this study was to assess nurses’ self-reported confidence in their professional skills before and after an extensive Emergency Department (ED) reform in Kanta-Häme Central Hospital.

Methods
Emergency nurses participated in transitional training commencing two years before the establishment of the new organization in 2007. Training was followed by weekly practical educational sessions in the new ED. During this process nurses improved their transition skills, defined house rules for the new clinic and improved their knowledge of new technology and instruments. The main processes involving critically ill ED patients were described and modelled with an electronic flow chart software.
During the transitional training nurses compiled lists of practical skills and measures needed in the ED. These were updated after feedback from physicians in primary and secondary care and head physicians in Kanta-Häme Central Hospital. The final 189-item list comprised 15 different categories, each containing from 4 to 35 items. Based on the work described above, a questionnaire was developed to reflect ED nurses’ skills in clinical measures but also to estimate the need for professional education and practical training. Nurses working in the ED were asked to fill the questionnaire in January 2007 (response rate 97%) and in January 2011 (response rate 98%).

Results
Nurses’ self-reported confidence in their professional skills improved significally in eight classes out of fifteen. These classes were cannulations, urinary catheterizations, patient monitoring, cardiac patients, equipment, triage and nurse practising, psychiatric patients as well as infection risk. Best results were noted in urinary catheterizations, patient monitoring and infection risk. When studying the group of nurses participating in both surveys in 2007 and 2011, improvements were observed in all fifteen categories. All but two of these changes were significant (p<0.05).

Conclusions
During an extensive reform of emergency services, we noted a significant improvement in the professional skills of nurses. This improvement was especially consistent among nurses working in the ED during the whole transition process. Nurses’ education and training program in the ED may be successfully put into practice when based on co-operation between nurses and physicians dedicated to emergency services.
A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity
Authors: Vital Marius , Penton Christopher R , Wang Qiong , Young Vincent B , Antonopoulos Dion A , Sogin Mitchell L , Morrison Hilary G , Raffals Laura , Chang Eugene B , Huffnagle Gary B , Schmidt Thomas M , Cole James R , Tiedje James M 
Published: March 2013

Abstract

Background
Butyrate, which is produced by the human microbiome, is essential for awell-functioning colon. Bacteria that produce butyrate are phylogeneticallydiverse, which hinders their accurate detection based on conventional phylogeneticmarkers. As a result, reliable information on this important bacterial group isoften lacking in microbiome research.

Results
In this study we describe a gene-targeted approach for 454 pyrotag sequencing andquantitative polymerase chain reaction for the final genes in the two primarybacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase(but) and butyrate kinase (buk). We monitored theestablishment and early succession of butyrate-producing communities in fourpatients with ulcerative colitis who underwent a colectomy with ileal pouch analanastomosis and compared it with three control samples from healthy colons. Allpatients established an abundant butyrate-producing community (approximately 5% to26% of the total community) in the pouch within the 2-month study, but patternswere distinctive among individuals. Only one patient harbored a community profilesimilar to the healthy controls, in which there was a predominance of butgenes that are similar to reference genes from Acidaminococcus sp.,Eubacterium sp., Faecalibacterium prausnitzii andRoseburia sp., and an almost complete absence of buk genes.Two patients were greatly enriched in buk genes similar to those ofClostridium butyricum and C. perfringens, whereas a fourthpatient displayed abundant communities containing both genes. Most butyrateproducers identified in previous studies were detected and the general patterns oftaxa found were supported by 16S rRNA gene pyrotag analysis, but thegene-targeted approach provided more detail about the potential butyrate-producingmembers of the community.

Conclusions
The presented approach provides quantitative and genotypic insights intobutyrate-producing communities and facilitates a more specific functionalcharacterization of the intestinal microbiome. Furthermore, our analysis refinesbut and buk reference annotations found in centraldatabases.