bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forfeited hepatogenesis program and increased embryonic stem cell traits in young hepatocellular carcinoma (HCC) comparing to elderly HCC
Authors: Wang Hsei-Wei , Hsieh Tsung-Han , Huang SSu-Yi , Chau Gar-Yang , Tung Chien-Yi , Su Chien-Wei , Wu Jaw-Ching 
Published: October 2013

Abstract

Background
Hepatocellular carcinoma (HCC) in young subjects is rare but more devastating. We hypothesize that genes and etiological pathways are unique to young HCC (yHCC; ≤40 years old at diagnosis) patients. We therefore compared the gene expression profiles between yHCCs and HCCs from elderly patients.

Results
All 44 young HCCs (≤40 years old at the diagnosis; 23 cases in the training set while another 21 in the validation cohort) were positive for serum hepatitis B surface antigen (HBsAg), but negative for antibodies to hepatitis C virus (anti-HCV). All 48 elderly (>40 years old; 38 in the training set while another 10 in the validation cohort) HCC patients enrolled were also serum HBsAg positive and anti-HCV negative. Comparative genomics analysis was further performed for elucidating enriched or suppressed biological activities in different HCC subtypes.
The yHCC group showed more macroscopic venous invasions (60.9% vs. 10.5%, p < 0.001), fewer associated cirrhosis (17.4% vs. 63.2%, p < 0.001), and distinct profiles of expressed genes, especially those related to DNA replication and repair. yHCCs possessed increased embryonic stem cell (ESC) traits and were more dedifferentiated. A 309-gene signature was obtained from two training cohorts and validated in another independent data set. The ILF3 ESC gene, which was previously reported in poorly differentiated breast cancers and bladder carcinomas, was also present in yHCCs. Genes associated with HCC suppression, including AR and ADRA1A, were less abundant in yHCCs. ESC genes were also more enriched in advanced HCCs from elderly patients.

Conclusion
This study revealed the molecular makeup of yHCC and the link between ESC traits and HCC subtypes. Findings in elderly tumors, therefore, cannot be simply extrapolated to young patients, and yHCC should be treated differently.
Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies
Authors: Kulkarni Bina B , Powe Desmond G , Hopkinson Andrew , Dua Harminder S 
Published: October 2013

Abstract

Background
The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays.

Methods
Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at −80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection.

Results
The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 μm2 in LEC to 392,887 μm2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/μl. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 μl. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 μm2 to 130,0000 μm2. RNA concentration of these samples ranged from 10.88 ng/12 μl to 25.8 ng/12 μl, with the RNA integrity numbers (RIN) for these samples from 3.3 to 7.9. RNA samples with RIN values below 2, that had failed to amplify satisfactorily were discarded.

Conclusions
The optimised protocol for sample collection and laser microdissection improved the RNA yield of the insitu ocular surface epithelial regions for effective microarray studies on spotted oligonucleotide and affymetrix platforms.
Influence of smoking and diet on glycated haemoglobin and 'pre-diabetes’ categorisation: a cross-sectional analysis
Authors: Vlassopoulos Antonis , Lean Michael EJ , Combet Emilie 
Published: October 2013

Abstract

Background
The new HbA1c criteria for diagnosis of pre-diabetes have been criticised for misdiagnosis. It is possible that some elevation of HbA1c is not driven by hyperglycaemia. This study assesses associations of HbA1c, commonly assumed to relate solely to glucose concentration, with (i) smoking, a major source of reactive oxygen species (ROS) and (ii) fruit & vegetables consumption associated with improved redox status.

Methods
One-way ANOVA, Chi-squared and multivariate linear regressions, adjusted for all known confounders were used to explore associations of HbA1c with self-reported smoking status and fruit & vegetables consumptions in the Scottish Health Surveys 2003–2010, among individuals without known diabetes and HbA1c < 6.5%.

Results
Compared to non-smokers (n = 2831), smokers (n = 1457) were younger, consumed less fruit & vegetables, had lower physical activity levels, lower BMI, higher HbA1c and CRP (p < 0.05). HbA1c was higher in smokers by 0.25 SDs (0.08%), and 0.38 SDs higher (0.14%) in heavy smokers (>20 cigarettes/day) than non-smokers (p < 0.001 both). Smokers were twice as likely to have HbA1c in the 'pre-diabetic’ range (5.7-6.4%) (p < 0.001, adj.model). Pre-diabetes and low grade inflammation did not affect the associations. For every extra 80 g vegetable portion consumed, HbA1c was 0.03 SDs (0.01%) lower (p = 0.02), but fruit consumption did not impact on HbA1c, within the low range of consumptions in this population.

Conclusion
This study adds evidence to relate smoking (an oxidative stress proxy) with protein glycation in normoglycaemic subjects, with implications for individuals exposed to ROS and for epidemiological interpretation of HbA1c.
New colorimetric screening assays for the directed evolution of fungal laccases to improve the conversion of plant biomass
Authors: Pardo Isabel , Chanagá Xiomara , Vicente Ana Isabel , Alcalde Miguel , Camarero Susana 
Published: October 2013

Abstract

Background
Fungal laccases are multicopper oxidases with huge applicability in different sectors. Here, we describe the development of a set of high-throughput colorimetric assays for screening laccase libraries in directed evolution studies.

Results
Firstly, we designed three colorimetric assays based on the oxidation of sinapic acid, acetosyringone and syringaldehyde with λmax of 512, 520 and 370 nm, respectively. These syringyl-type phenolic compounds are released during the degradation of lignocellulose and can act as laccase redox mediators. The oxidation of the three compounds by low and high-redox potential laccases evolved in Saccharomyces cerevisiae produced quantifiable and linear responses, with detection limits around 1 mU/mL and CV values below 16%. The phenolic substrates were also suitable for pre-screening mutant libraries on solid phase format. Intense colored-halos were developed around the yeast colonies secreting laccase. Furthermore, the oxidation of violuric acid to its iminoxyl radical (λmax of 515 nm and CV below 15%) was devised as reporter assay for laccase redox potential during the screening of mutant libraries from high-redox potential laccases. Finally, we developed three dye-decolorizing assays based on the enzymatic oxidation of Methyl Orange (470 nm), Evans Blue (605 nm) and Remazol Brilliant Blue (640 nm) giving up to 40% decolorization yields and CV values below 18%. The assays were reliable for direct measurement of laccase activity or to indirectly explore the oxidation of mediators that do not render colored products (but promote dye decolorization). Every single assay reported in this work was tested by exploring mutant libraries created by error prone PCR of fungal laccases secreted by yeast.

Conclusions
The high-throughput screening methods reported in this work could be useful for engineering laccases for different purposes. The assays based on the oxidation of syringyl-compounds might be valuable tools for tailoring laccases precisely enhanced to aid biomass conversion processes. The violuric assay might be useful to preserve the redox potential of laccase whilst evolving towards new functions. The dye-decolorizing assays are useful for engineering ad hoc laccases for detoxification of textile wastewaters, or as indirect assays to explore laccase activity on other natural mediators.
Antagonistic effect of alkaloids and saponins on bioactivity in the quinine tree (Rauvolfia caffra sond.): further evidence to support biotechnology in traditional medicinal plants
Authors: Milugo Trizah K , Omosa Leonida K , Ochanda James O , Owuor Bethwell O , Wamunyokoli Fred A , Oyugi Julius O , Ochieng Joel W 
Published: October 2013

Abstract

Background
The Quinine tree (Rauvolfia caffra) is used as a medicinal plant among traditional communities in many countries to manage tumors and other diseases associated with oxidative stress. To validate indigenous knowledge and possibly position this herb for technology uptake and utilization, we established the level of antioxidant activity in R. caffra, and probed for the presence of associated phytochemicals.

Methods
Antioxidant activity was determined on 1,1-diphenyl-2-picrylhydrazyl (DPPH) while major phytochemicals were identified by multiple tests on methanol fractions.

Results

R. caffra showed promise as a cure, with antioxidant activity comparable to the commercially used drug quercetin (R. caffra = 79.7% ±1.9; quercetin = 82.6% ± 2.0). However, we found two phytochemicals with possible antagonistic effect: co-occurrence of alkaloids and saponins significantly reduced antioxidant activity (alkaloids only = 63%; alkaloids plus saponins = 15%; steroids, terpenoids and cardiac glycosides = 82%), thus alkaloids and saponins should be exclusive to each other in drug formulations.

Conclusions
Antagonistic relationship among phytochemicals would affect the efficacy of crude extracts as used in traditional medicine. Unlike in herbal medicine, use of modern biotechnology in extraction, purification and design of optimal combinations will ensure efficient drug formulations with optimum bioactivity and minimum toxicity. Metabolic pathway engineering under a controlled environment may optimize availability of desired compounds.
Disrupting rhythms in Plasmodium chabaudi: costs accrue quickly and independently of how infections are initiated
Authors: O’Donnell Aidan J , Mideo Nicole , Reece Sarah E 
Published: October 2013

Abstract

Background
In the blood, the synchronous malaria parasite, Plasmodium chabaudi, exhibits a cell-cycle rhythm of approximately 24 hours in which transitions between developmental stages occur at particular times of day in the rodent host. Previous experiments reveal that when the timing of the parasite’s cell-cycle rhythm is perturbed relative to the circadian rhythm of the host, parasites suffer a (~50%) reduction in asexual stages and gametocytes. Why it matters for parasites to have developmental schedules in synchronization with the host’s rhythm is unknown. The experiment presented here investigates this issue by: (a) validating that the performance of P. chabaudi is negatively affected by mismatch to the host circadian rhythm; (b) testing whether the effect of mismatch depends on the route of infection or the developmental stage of inoculated parasites; and, (c) examining whether the costs of mismatch are due to challenges encountered upon initial infection and/or due to ongoing circadian host processes operating during infection.

Methods
The experiment simultaneously perturbed the time of day infections were initiated, the stage of parasite inoculated, and the route of infection. The performance of parasites during the growth phase of infections was compared across the cross-factored treatment groups (i e, all combinations of treatments were represented).

Results
The data show that mismatch to host rhythms is costly for parasites, reveal that this phenomenon does not depend on the developmental stage of parasites nor the route of infection, and suggest that processes operating at the initial stages of infection are responsible for the costs of mismatch. Furthermore, mismatched parasites are less virulent, in that they cause less anaemia to their hosts.

Conclusion
It is beneficial for parasites to be in synchronization with their host’s rhythm, regardless of the route of infection or the parasite stage inoculated. Given that arrested cell-cycle development (quiescence) is implicated in tolerance to drugs, understanding how parasite schedules are established and maintained in the blood is important.
An integrated strategy for efficient vector construction and multi-gene expression in Plasmodium falciparum
Authors: Wagner Jeffrey C , Goldfless Stephen J , Ganesan Suresh M , Lee Marcus CS , Fidock David A , Niles Jacquin C 
Published: October 2013

Abstract

Background
The construction of plasmid vectors for transgene expression in the malaria parasite, Plasmodium falciparum, presents major technical hurdles. Traditional molecular cloning by restriction and ligation often yields deletions and re-arrangements when assembling low-complexity (A + T)-rich parasite DNA. Furthermore, the use of large 5′- and 3′- untranslated regions of DNA sequence (UTRs) to drive transgene transcription limits the number of expression cassettes that can be incorporated into plasmid vectors.

Methods
To address these challenges, two high fidelity cloning strategies, namely yeast homologous recombination and the Gibson assembly method, were evaluated for constructing P. falciparum vectors. Additionally, some general rules for reliably using the viral 2A-like peptide to express multiple proteins from a single expression cassette while preserving their proper trafficking to various subcellular compartments were assessed.

Results
Yeast homologous recombination and Gibson assembly were found to be effective strategies for successfully constructing P. falciparum plasmid vectors. Using these cloning methods, a validated family of expression vectors that provide a flexible starting point for user-specific applications was created. These vectors are also compatible with traditional cloning by restriction and ligation, and contain useful combinations of commonly used features for enhancing plasmid segregation and site-specific integration in P. falciparum. Additionally, application of a 2A-like peptide for the synthesis of multiple proteins from a single expression cassette, and some rules for combinatorially directing proteins to discrete subcellular compartments were established.

Conclusions
A set of freely available, sequence-verified and functionally validated parts that offer greater flexibility for constructing P. falciparum vectors having expanded expression capacity is provided.
The effect of clustering on lot quality assurance sampling: a probabilistic model to calculate sample sizes for quality assessments
Authors: Hedt-Gauthier Bethany L , Mitsunaga Tisha , Hund Lauren , Olives Casey , Pagano Marcello 
Published: October 2013

Abstract
Background
Traditional Lot Quality Assurance Sampling (LQAS) designs assume observations are collected using simple random sampling. Alternatively, randomly sampling clusters of observations and then individuals within clusters reduces costs but decreases the precision of the classifications. In this paper, we develop a general framework for designing the cluster(C)-LQAS system and illustrate the method with the design of data quality assessments for the community health worker program in Rwanda.

Results
To determine sample size and decision rules for C-LQAS, we use the beta-binomial distribution to account for inflated risk of errors introduced by sampling clusters at the first stage. We present general theory and code for sample size calculations.
The C-LQAS sample sizes provided in this paper constrain misclassification risks below user-specified limits. Multiple C-LQAS systems meet the specified risk requirements, but numerous considerations, including per-cluster versus per-individual sampling costs, help identify optimal systems for distinct applications.

Conclusions
We show the utility of C-LQAS for data quality assessments, but the method generalizes to numerous applications. This paper provides the necessary technical detail and supplemental code to support the design of C-LQAS for specific programs.
Comprehensive profiling of Epstein-Barr virus-encoded miRNA species associated with specific latency types in tumor cells
Authors: Yang Hong-Jie , Huang Tie-Jun , Yang Chang-Fu , Peng Li-Xia , Liu Ran-Yi , Yang Guang-Da , Chu Qiao-Qiao , Huang Jia-Ling , Liu Na , Huang Hong-Bing , Zhu Zhen-Yu , Qian Chao-Nan , Huang Bi-Jun 
Published: October 2013

Abstract

Background
Epstein-Barr virus (EBV) is an etiological cause of many human lymphocytic and epithelial malignancies. EBV expresses different genes that are associated with three latency types. To date, as many as 44 EBV-encoded miRNA species have been found, but their comprehensive profiles in the three types of latent infection that are associated with various types of tumors are not well documented.

Methods
In the present study, we utilized poly (A)-tailed quantitative real-time RT-PCR in combination with microarray analysis to measure the relative abundances of viral miRNA species in a subset of representative lymphoid and epithelial tumor cells with various EBV latency types.

Results
Our findings showed that the miR-BHRF1 and miR-BART families were expressed differentially in a tissue- and latency type-dependent manner. Specifically, in nasopharyngeal carcinoma (NPC) tissues and the EBV-positive cell line C666-1, the miR-BART family accounted for more than 10% of all detected miRNAs, suggesting that these miRNAs have important roles in maintaining latent EBV infections and in driving NPC tumorigenesis. In addition, EBV miRNA-based clustering analysis clearly distinguished between the three distinct EBV latency types, and our results suggested that a switch from type I to type III latency might occur in the Daudi BL cell line.

Conclusions
Our data provide a comprehensive profiling of the EBV miRNA transcriptome that is associated with specific tumor cells in the three types of latent EBV infection states. EBV miRNA species represent a cluster of non-encoding latency biomarkers that are differentially expressed in tumor cells and may help to distinguish between the different latency types.
A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus
Authors: Lee Raphael Tze Chuen , Gunalan Vithiagaran , Van Thanh Dac , Le Ly Thi , Eisenhaber Frank , Maurer-Stroh Sebastian 
Published: October 2013

Abstract

Reviewers

This article was reviewed by Prof Xiufan Liu (nominated by Dr Purificacion Lopez-Garcia) and Prof Sandor Pongor.
Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China. We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.
Ovarian Sertoli–Leydig cell tumors: MRI findings and pathological correlation
Authors: Cai Song-Qi , Zhao Shu-Hui , Qiang Jin-Wei , Zhang Guo-Fu , Wang Xue-Zhen , Wang Li 
Published: October 2013

Abstract

Background
To investigate the magnetic resonance imaging (MRI) characteristics of ovarian Sertoli-Leydig cell tumors (SLCT).

Methods
The clinical, MRI and pathological findings of five cases of SLCT were reviewed retrospectively. MRI appearances of tumors including laterality, shape and size, architecture, wall, septa and vegetation, signal intensity and contrast-enhancement pattern were evaluated and correlated with pathological findings.

Results
Two tumors were solid which appeared as low signal intensity on T1-weighted imaging (T1WI) and moderate on T2-weighted imaging (T2WI) with multiple small cysts in one of them. The remaining three SLCT were multilocular cystic with the irregularly thickened wall and septa, and with solid area and mural nodules in one of them. The cystic components had the same signal intensity as urine. All the solid components were intensely enhanced after administration of contrast medium. All five tumors were pathologically intermediate differentiation and at FIGO stage I.

Conclusions
SLCT demonstrate variable MRI morphological appearances. However, the irregularly thickened wall and septa, the moderate T2WI signal intensity and obvious enhancement in the solid components are three MRI features.
Analysis of bortezomib inhibitor docked within the catalytic subunits of the Plasmodium falciparum 20S proteasome
Authors: Sridhar Settu , Bhat Gayathri , Guruprasad Kunchur 
Published: October 2013

Abstract
The three-dimensional fold of Plasmodium falciparum (Pf) 20S proteasome is similar to yeast Saccharomyces cerevisiae 20S proteasome. The twenty eight subunits complex corresponding to two copies of seven distinct α and seven distinct β subunits shares >35% sequence identity with equivalent subunits of the yeast 20S proteasome. Bortezomib (Velcade®) – a known inhibitor of the three catalytic subunits; β1, β2, β5 of the yeast 20S proteasome can bind in the equivalent subunits of the Pf 20S proteasome and is in agreement with experimental results. The model defines the binding mode of the bortezomib inhibitor within the catalytic subunits of the Pf 20S proteasome and provides the structural basis for the design of Pf 20S proteasome-specific inhibitors. The substitutions associated within the catalytic subunits of Pf 20S proteasome relative to yeast 20S proteasome; Thr21-Ser, Thr22-Ser, Thr31-Ser, Thr35-Asn, Ala49-Ser (in β1 subunit), Ser20-Ala, Gln22-Glu (β2) and Thr21-Ser, Ala22-Met, Gln53-Leu (β5) may influence the relative caspase-like, tryptic-like and chymotryptic-like activities of the Pf 20S proteasome. The plasmodia-specific 'large’ insert comprising fifty four amino acid residues (in β1 subunit) of the Pf 20S proteasome is distant from the catalytic sites.
Bronchopleural fistula following M. abscessus infection 11 years after lobectomy for lung cancer
Authors: Inayama Mami , Shinohara Tsutomu , Yoshida Mitsuteru , Hino Hiroyuki , Hatakeyama Nobuo , Ogushi Fumitaka 
Published: October 2013

Abstract
Bronchopleural fistula (BPF) is a potentially fatal complication of lung cancer resection surgery that occurs during the healing process of the bronchial stump. However, the vulnerability of the healed surgical wound to overlapping acquired airway destruction has not yet been determined in detail. We herein present a case of fatal BPF following Mycobacterium abscessus (M. abscessus) infection, which occurred 11 years after right upper lobectomy for lung cancer. The findings of the present study suggest that patients with M. abscessus pulmonary disease in which airway destruction is progressing towards the bronchial stump of previous lobectomy should be considered for early completion pneumonectomy to prevent fatal BPF.