bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing synthesis of PET oligomers end capped with phthalic/maleic anhydride via recycling of off grade PET using design of experiments
Authors: Zahedi Ali Reza , Rafizadeh Mehdi , Taromi Faramarz Afshar 
Published: February 2013

Poly(ethylene terephthalate) (PET) from off grades of industrial manufacturer was partially and thoroughly depolymerized using excess glycol to synthesize PET oligomers and bis(hydroxyethyl) terephthalate (BHET), respectively. Design of experiments and analysis of variance were applied for optimization of samples. Effects of reaction time, volume of glycol, catalyst concentrations and particle size of off grade PET on the yield of products were investigated based on the design of experiments. Thermal analysis of glycolyzed products is performed by differential scanning calorimetry. The optimum samples were also well characterized by Fourier-transform infrared spectroscopy and nuclear magnetic resonance spectroscopy (proton nuclear magnetic resonance spectroscopy and carbon nuclear magnetic resonance spectroscopy). The optimal conditions to synthesize PET oligomers were glycol/PET molar ratio of 2 with no catalyst using granule-shape PET for a 120-min glycolysis reaction time. Desired oligomer repeating units were 3–8. On the other hand, a reaction time of 180 min, weight ratio (catalyst to PET) of 0.25 wt% and glycol/PET molar ratio of 5 were obtained as the suitable conditions of BHET production. Then, end capped PET oligomers, as a compatiblizer for preparing PET nanocomposites, were produced via reaction between maleic anhydride and phthalic anhydride (MA/PhA) composition. The combination of reaction time of 106 min and PhA/MA molar ratio of 0.85 produced the best results based on d-spacing and peak intensity of nanocomposite samples. Moreover, the reaction of MA and BHET from glycolyzation of PET was successfully performed at 160°C and 190°C for 8 h.
The impact properties of poly-p-phenyle nebenzobisoxazole fibers reinforced with polytetrafluoroethylene composite
Authors: Chunhua Cao , Di Yang , Gang Xie , Rongxing Li , Xiaohua Yu 
Published: February 2013

Poly- p-phenylenebenzobisoxazole (PBO)-filled polytetrafluoroethylene (PTFE) has been successfully prepared at different compositions in a corotating twin-screw extruder, where PTFE acts as the polymer matrix and PBO as the dispersed phase. The morphology and impact properties of these blends were investigated using scanning electron microscopy. The presence of PBO particles dispersed in the PTFE continuous phase exhibited a coarse morphology. Increasing PBO contents in the blend improved the impact properties at weak deformation. It was found that the interfacial adhesion played an important role in the creation of an interphase that was formed by the interaction between the PTFE and the PBO. This induced an improvement in impact properties. In addition, the optimum impact properties were obtained when the content of PBO is 30 vol%.
Assessment of Protective Effects of Pheniramine Maleate on Reperfusion Injury in Lung After Distant Organ Ischemia
Authors: Gokalp Orhan , Yurekli Ismail , Kiray Muge , Bagriyanik Alper , Yetkin Ufuk , Yurekli Banu Sarer , Gur Serkan , Aksun Murat , Satoglu Ismail Safa , Gokalp Gamze , Gurbuz Ali 
Published: February 2013

Objective: The aim of this study is to investigate the protective effects of methylprednisolone (MP) and pheniramine maleate (PM) on reperfusion injury of lungs developing after ischemia of the left lower extremity of rats. Materials and methods: A total of 28 randomly selected male rats were divided into 4 groups, each consisting of 7 rats. Group 1 was the control group. Group 2 was the sham group (ischemia/reperfusion [I/R]). Rats in group 3 were subjected to I/R and given PM (Ph group) and rats in group 4 were subjected to I/R and given MP (Pn group). Results: Malondialdehyde levels were significantly lower in Ph group than in I/R group ( P < .05). Superoxide dismutase and glutathione peroxidase enzyme activities were found to be significantly higher in Ph group than in the I/R group ( P < .05). Histological examination demonstrated that PM had protective effects against I/R injury. Conclusions: The PM has a protective effect against I/R injury in rat lung.
Monitoring futility in a two-by-two factorial design: The SPS3 experience
Authors: McClure Leslie A , Coffey Christopher S , Howard George 
Published: February 2013

Background For studies with two-by-two factorial designs, the complexity of determining an appropriate futility analysis plan is increased as compared to studies where patients are randomized to one treatment. Issues that must be addressed include the possibility of a significant interaction and the need to determine how to proceed given evidence of futility in one arm. Suggested approaches include a two-stage plan, which first assesses futility of the interaction term and proceeds to examine the main effects, given sufficient evidence that no interaction is present, and variations on one-stage plans, which assume the trial will not be stopped for futility in the interaction. Purpose To discuss different approaches to monitoring futility in two-by-two factorial clinical trials and compare their properties. Methods We utilized a simulation study, designed to mimic the Secondary Prevention of Small Subcortical Strokes (SPS3) Study, to determine which approach to monitoring futility in two-by-two factorial studies had the most desirable statistical properties. Results We found that in most scenarios typical of clinical trials, monitoring futility in each arm simultaneously was superior to or as good as monitoring the interaction and then assessing futility in each arm only when the interaction was deemed futile. Monitoring each arm simultaneously lead to early stopping more often when no treatment effect was present, and lower average sample numbers (ASNs). The exception to this was the unlikely case when a qualitative interaction was present. Limitations We assumed that one-sided tests were to be performed, and only assessed some of the possible methods for monitoring futility under the study design. Conclusions Futility monitoring in two-by-two factorial studies should proceed by assessing each arm simultaneously, rather than monitoring the interaction first. If sizeable interactions are anticipated, study design, rather than study monitoring, should account for this.
Uptake of novel statistical methods for early-phase clinical studies in the UK public sector
Authors: Jaki Thomas 
Published: February 2013

Background In recent years, the success rate of confirmatory studies has been poor resulting in more emphasis on the conduct of exploratory studies. As one possibility to improve decision-making during the early stages of development, adaptive and Bayesian methods have been recommended. Purpose To investigate the current practice in designing early-phase studies in UK public sector research institutions and the use of adaptive and Bayesian methods in particular and to determine factors that hinder the penetration of methodological advances into practice. Methods A questionnaire was sent to all UK clinical trials units (CTUs) to gauge their involvement in early-phase studies and to learn about the designs used in these studies. Follow-up visits to units conducting early-phase studies with round-table discussions around the methods used and the obstacles faced when using adaptive methods were undertaken. Results More than half of the CTUs are involved in early-phase studies, but conservatism in the methods used in these studies is present. Reasons for novel methodology not being used include a lack of expertise, incompatible funding and unit structure, and a lack of software. Limitations Information is collected from UK CTUs, which undertake a large portion (but not all) publicly funded trials. Conclusions The use of adaptive and Bayesian methods for early-phase clinical studies in the UK public sector is at present limited. Various different initiatives aim to support and facilitate the use of these methods, however, so that an increased use of these methods can be anticipated in the future.
Perforin forms transient pores on the target cell plasma membrane to facilitate rapid access of granzymes during killer cell attack
Authors: Lopez Jamie A. , Susanto Olivia , Jenkins Misty R. , Lukoyanova Natalya , Sutton Vivien R. , Law Ruby H. P. , Johnston Angus , Bird Catherina H. , Bird Phillip I. , Whisstock James C. , Trapani Joseph A. , Saibil Helen R. , Voskoboinik Ilia 
Published: February 2013

Key PointsGranzymes diffuse through perforin pores on the target cell plasma membrane.
FANTOM: Functional and taxonomic analysis of metagenomes
Authors: Sanli Kemal , Karlsson Fredrik H , Nookaew Intawat , Nielsen Jens 
Published: February 2013

Abstract

Background
Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.

Results
Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases.

Conclusions
The software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom
QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits
Authors: Xu Pei , Wu Xiaohua , Wang Baogen , Hu Tingting , Lu Zhongfu , Liu Yonghua , Qin Dehui , Wang Sha , Li Guojing 
Published: February 2013

Abstract

Background
Asparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean.

Results
A similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops.

Conclusion
Major, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection.
Draft genome sequence of the rubber tree Hevea brasiliensis
Authors: Rahman Ahmad Yamin Abdul , Usharraj Abhilash O , Misra Biswapriya B , Thottathil Gincy P , Jayasekaran Kandakumar , Feng Yun , Hou Shaobin , Ong Su Yean , Ng Fui Ling , Lee Ling Sze , Tan Hock Siew , Sakaff Muhd Khairul Luqman Muhd , Teh Beng Soon , Khoo Bee Feong , Badai Siti Suriawati , Aziz Nurohaida Ab , Yuryev Anton , Knudsen Bjarne , Dionne-Laporte Alexandre , Mchunu Nokuthula P , Yu Qingyi , Langston Brennick J , Freitas Tracey Allen K , Young Aaron G , Chen Rui , Wang Lei , Najimudin Nazalan , Saito Jennifer A , Alam Maqsudul 
Published: February 2013

Abstract

Background

Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876.

Results
Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified.

Conclusions
The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.
Repeat-encoded poly-Q tracts show statistical commonalities across species
Authors: Willadsen Kai , Cao Minh Duc , Wiles Janet , Balasubramanian Sureshkumar , Bodén Mikael 
Published: February 2013

Abstract

Background
Among repetitive genomic sequence, the class of tri-nucleotide repeats has received much attention due to their association with human diseases. Tri-nucleotide repeat diseases are caused by excessive sequence length variability; diseases such as Huntington’s disease and Fragile X syndrome are tied to an increase in the number of repeat units in a tract. Motivated by the recent discovery of a tri-nucleotide repeat associated genetic defect in Arabidopsis thaliana, this study takes a cross-species approach to investigating these repeat tracts, with the goal of using commonalities between species to identify potential disease-related properties.

Results
We find that statistical enrichment in regulatory function associations for coding region repeats – previously observed in human – is consistent across multiple organisms. By distinguishing between homo-amino acid tracts that are encoded by tri-nucleotide repeats, and those encoded by varying codons, we show that amino acid repeats – not tri-nucleotide repeats – fully explain these regulatory associations. Using this same separation between repeat- and non-repeat-encoded homo-amino acid tracts, we show that poly-glutamine tracts are disproportionately encoded by tri-nucleotide repeats, and those tracts that are encoded by tri-nucleotide repeats are also significantly longer; these results are consistent across multiple species.

Conclusion
These findings establish similarities in tri-nucleotide repeats across species at the level of protein functionality and protein sequence. The tendency of tri-nucleotide repeats to encode longer poly-glutamine tracts indicates a link with the poly-glutamine repeat diseases. The cross-species nature of this tendency suggests that unknown repeat diseases are yet to be uncovered in other species. Future discoveries of new non-human repeat associated defects may provide the breadth of information needed to unravel the mechanisms that underpin this class of human disease.
Differential neuronal expression of receptor interacting protein 3 in rat retina: involvement in ischemic stress response
Authors: Huang Ju-Fang , Shang Lei , Zhang Meng-Qi , Wang Hui , Chen Dan , Tong Jian-Bin , Huang He , Yan Xiao-Xin , Zeng Le-Ping , Xiong Kun 
Published: February 2013

AbstractBackgroundReceptor-interacting protein 3 (RIP3), a member of RIP family proteins, has been shown to participate in programmed necrosis or necroptosis in cell biology studies. Evidence suggests that necroptosis may be a mode of neuronal death in the retina.ResultsIn the present study we determined the expression of RIP3 in normal rat retina and its changes following acute high intraocular pressure (aHIOP). RIP3 immunoreactivity (IR) was largely present in the inner retinal layers, localized to subsets of cells expressing neuron-specific nuclear antigen (NeuN), parvalbumin and calbindin in the ganglion cell layer (GCL) and inner nuclear layer (INL). No double labeling was detected for RIP3 with PKC-α or rhodopsin. RIP3 immunoreactivity was increased in the GCL at 6 hr and 12 hr, but reduced at 24 hr in the retina, without apparent alteration in laminar or cellular distribution pattern. Western blot analysis confirmed the above time-dependent alteration in RIP3 protein expression. RIP3 expressing cells frequently co-localized with propidium iodide (PI). A few co-localized cells were observed between RIP3 and Bax or cleaved caspase-3 in the GCL in 12 hr following aHIOP.ConclusionsThe results indicate that RIP3 is expressed differentially in retinal neurons in adult rats, including subsets of ganglion cells, amacrine and horizontal cells. RIP3 protein levels are elevated rapidly following aHIOP. RIP3 labeling co-localized with PI, Bax or cleaved caspase-3 among cells in the ganglion cell layer following aHIOP, which suggest its involvement of RIP3 in neuronal responses to acute ischemic insults.
Outcome after hepatectomy-delirium as an independent predictor for mortality
Authors: Veiga Dalila , Luís Clara , Parente Daniela , Abelha Fernando 
Published: February 2013

Abstract

Background
Most studies that follow up hepatectomy cases are limited in scope to an investigation of mortality and morbidity rates or the costs and length of hospital stay. In this study the authors aimed to characterize the quality of life and to evaluate mortality and its determinants after hepatectomy.

Methods
This prospective study was carried in a Post-Anaesthesia Care Unit (PACU) over 15 months, and 70 patients submitted to hepatectomy were enrolled. Demographic and peri-operative characteristics were evaluated for associations with mortality. At admission and 6 months after discharge, patients completed a Short Form-36 questionnaire (SF-36) and have their independence in Activities of Daily Living (ADL) was evaluated. Binary and multiple logistic regression analyses were used to evaluate of associations with mortality, and the Wilcoxon signed rank test was used to compare SF-36 scores before and after 6 months after hepatectomy.

Results
The mortality rate was 19% at 6 months. Multivariate analysis identified postoperative delirium as an independent determinant for mortality. Six months after discharge, 46% patients stated that their health in general was better or much better than that 1 year previously. Six months after hepatectomy, patients had worse scores in the physical function domain of SF-36; however, scores for all the other domains did not differ. At this time point, patients were more dependent in instrumental ADL than before surgery (32% versus 7%, p = 0.027).

Conclusion
This study identified postoperative delirium as an independent risk factor for mortality 6 months after hepatectomy. After 6 months, survivors were more dependent in instrumental ADL tasks and had worse scores in the physical function domain of SF-36.
Analysis of HCV quasispecies dynamic under selective pressure of combined therapy
Authors: Jardim Ana CG , Bittar Cíntia , Matos Renata PA , Yamasaki Lílian HT , Silva Rafael A , Pinho João RR , Fachini Roberta M , Carareto Claudia MA , de Carvalho-Mello Isabel MVG , Rahal Paula 
Published: February 2013

Abstract

Background
The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy.

Methods
Viral RNA was isolated from serum samples collected before, during and after treatment from virological sustained responder (SVR), non-responder (NR) and the end-of-treatment responder patients (ETR). NS5A region was amplified, cloned and sequenced. Six hundred and ninety full-length NS5A sequences were analyzed.

Results
This study provides evidence that lower nucleotide diversity of the NS5A region pre-therapy is associated with viral clearance. Analysis of samples of NRs and the ETRs time points showed that genetic diversity of populations tend to decrease over time. Post-therapy population of ETRs presented higher genetic distance from baseline probably due to the bottleneck phenomenon observed for those patients in the end of treatment. The viral effective population of those patients also showed a strong decrease after therapy. Otherwise, NRs demonstrated a continuous variation or stability of effective populations and genetic diversity over time that did not seem to be related to therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. Codons 157 (P03), 182 and 440 (P42), 62 and 404 (P44) were found to be under positive selective pressure but it failed to be related to the therapy.

Conclusion
These results confirm the hypothesis that a relationship exists between NS5A heterogeneity and response to therapy in patients infected with chronic hepatitis C.
Low prevalence of Leishmania donovani infection among the blood donors in kala-azar endemic areas of Bangladesh
Authors: Huda M Mamun , Rudra Shikha , Ghosh Debashis , Bhaskar Khondaker Rifat Hasan , Chowdhury Rajib , Dash Aditya Prasad , Bhattacharya Sujit Kumar , Haque Rashidul , Mondal Dinesh 
Published: February 2013

AbstractBackgroundVisceral leishmaniasis (VL) is a major public health problem in Bangladesh with the highest disease burden in the Mymensingh District. The disease is transmitted by sand fly bites, but it may also be transmitted through blood transfusions. No information is available about the prevalence of Leishmania infection among blood donors in Bangladesh; therefore we aimed to investigate this question.MethodsThe study was carried out in the Blood Transfusion Department of Mymensingh Medical College Hospital. One thousand one hundred and ninety five adult healthy blood donors attending in this department were enrolled in the study from August 2010 to April 2011. After obtaining written consent, socio-demographic data and a detailed health history were collected. The medical officer in the unit performed a complete physical examination to exclude any acute or chronic diseases, which was followed by sero-diagnosis for exposure to Leishmania by rK39 strip test using finger prick blood. Blood donors with a positive rK39 strip test underwent a PCR test for detection of leishmania DNA in their peripheral blood buffy coat.ResultsEighty two percent of enrolled blood donors were male (n=985) and 18% (n=210) were female. The mean age of blood donors was 27 years (SD, 7.95 years). The majority of donors were literate and had mid-to-higher socioeconomic condition reflected by household conditions reported by the subject. Only 2.6% had a family member with VL in the past. Three blood donors were positive for leishmania infection by rK39 strip test (0.3%, 95%CI, 0.05%-0.73%). None of these 3 had active leishmania infection as demonstrated by PCR analysis. During six months of follow up, neither rK39 positive (n=3) nor rK39 negative (n=1192) donors developed VL.ConclusionThe prevalence ofLeishmania donovaniinfection among blood donors attending the Blood Transfusion Department of Mymensingh Medical College Hospital was very low. Therefore the chance for transmission of VL through blood transfusion is negligible. We believe that the National VL Elimination Program does not need set up routine screening forLeishmania donovaniinfection in blood transfusion departments located in VL endemic areas of Bangladesh.