bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution, structure and function of mitochondrial carriers: a review with new insights
Authors: Palmieri Ferdinando , Pierri Ciro L. , De Grassi Anna , Nunes‐Nesi Adriano , Fernie Alisdair R. 
Published: March 2011

SummaryThe mitochondrial carriers (MC) constitute a large family (MCF) of inner membrane transporters displaying different substrate specificities, patterns of gene expression and even non‐mitochondrial organelle localization. In Arabidopsis thaliana 58 genes encode these six trans‐membrane domain proteins. The number in other sequenced plant genomes varies from 37 to 125, thus being larger than that of Saccharomyces cerevisiae and comparable with that of Homo sapiens. In addition to displaying highly similar secondary structures, the proteins of the MCF can be subdivided into subfamilies on the basis of substrate specificity and the presence of specific symmetry‐related amino acid triplets. We assessed the predictive power of these triplets by comparing predictions with experimentally determined data for Arabidopsis MCs, and applied these predictions to the not yet functionally characterized mitochondrial carriers of the grass, Brachypodium distachyon, and the alga, Ostreococcus lucimarinus. We additionally studied evolutionary aspects of the plant MCF by comparing sequence data of the Arabidopsis MCF with those of Saccharomyces cerevisiae and Homo sapiens, then with those of Brachypodium distachyon and Ostreococcus lucimarinus, employing intra‐ and inter‐genome comparisons. Finally, we discussed the importance of the approaches of global gene expression analysis and in vivo characterizations in order to address the relevance of these vital carrier proteins.
The family of terpene synthases in plants: a mid‐size family of genes for specialized metabolism that is highly diversified throughout the kingdom
Authors: Chen Feng , Tholl Dorothea , Bohlmann Jörg , Pichersky Eran 
Published: March 2011

SummarySome plant terpenes such as sterols and carotenes are part of primary metabolism and found essentially in all plants. However, the majority of the terpenes found in plants are classified as ‘secondary’ compounds, those chemicals whose synthesis has evolved in plants as a result of selection for increased fitness via better adaptation to the local ecological niche of each species. Thousands of such terpenes have been found in the plant kingdom, but each species is capable of synthesizing only a small fraction of this total. In plants, a family of terpene synthases (TPSs) is responsible for the synthesis of the various terpene molecules from two isomeric 5‐carbon precursor ‘building blocks’, leading to 5‐carbon isoprene, 10‐carbon monoterpenes, 15‐carbon sesquiterpenes and 20‐carbon diterpenes. The bryophyte Physcomitrella patens has a single TPS gene, copalyl synthase/kaurene synthase (CPS/KS), encoding a bifunctional enzyme producing ent‐kaurene, which is a precursor of gibberellins. The genome of the lycophyte Selaginella moellendorffii contains 18 TPS genes, and the genomes of some model angiosperms and gymnosperms contain 40–152 TPS genes, not all of them functional and most of the functional ones having lost activity in either the CPS‐ or KS‐type domains. TPS genes are generally divided into seven clades, with some plant lineages having a majority of their TPS genes in one or two clades, indicating lineage‐specific expansion of specific types of genes. Evolutionary plasticity is evident in the TPS family, with closely related enzymes differing in their product profiles, subcellular localization, or the in planta substrates they use.
Decoding algal genomes: tracing back the history of photosynthetic life on Earth
Authors: Tirichine Leïla , Bowler Chris 
Published: March 2011

SummaryThe last decade has witnessed outstanding progress in sequencing the genomes of photosynthetic eukaryotes, from major cereal crops to single celled marine phytoplankton. For the algae, we now have whole genome sequences from green, red, and brown representatives, and multiple efforts based on comparative and functional genomics approaches have provided information about the unicellular origins of higher plants, and about the evolution of photosynthetic life in general. Here we present some of the highlights from such studies, including the endosymbiotic origins of photosynthetic protists and their positioning with respect to plants and animals, the evolution of multicellularity in photosynthetic lineages, the role of sex in unicellular algae, and the potential relevance of epigenetic processes in contributing to the adaptation of algae to their environment.
Chloroplast genomes of photosynthetic eukaryotes
Authors: Green Beverley R. 
Published: March 2011

SummaryChloroplast genomes have retained a core set of genes from their cyanobacterial ancestor, most of them required for the light reactions of photosynthesis or functions connected with transcription and translation. Other genes have been transferred to the nucleus or were lost in a lineage‐specific manner. The genomes are distinguished by the selection of genes retained, whether or not transcripts are edited, presence/absence of introns and small repeats and their physical organization. Plants and green algae have kept fewer plastid genes than either the red algae or the chromistan algae, which obtained their plastids from red algae by secondary endosymbiosis. Photosynthetic dinoflagellates have the fewest (fewer than 20), but still grow photoautotrophically. All chloroplast genomes map as a circle, but there have been extensive rearrangements of gene order even between related species. Genome sizes vary much more than gene content, depending on the extent of gene duplication and small repeats and the size of intergenic spacers.
Adrenal insufficiency during physiological stress in children after kidney or liver transplantation
Authors: Bilavsky Efraim , Dagan Adi , Yarden‐Bilavsky Havatzelet , Davidovits Miriam , Shapiro Rivka , Mor Eytan , Weintrob Naomi , Amir Jacob , Avitzur Yaron 
Published: March 2011

Bilavsky E, Dagan A, Yarden‐Bilavsky H, Davidovits M, Shapiro R, Mor E, Weintrob N, Amir J, Avitzur Y. Adrenal insufficiency during physiological stress in children after kidney or liver transplantation. Pediatr Transplantation 2011: 15: 314–320. © 2011 John Wiley & Sons A/S.Abstract:  The aim of this study was to assess the prevalence and risk factors of AI in pediatric recipients of kidney or liver transplantation admitted because of a physiological stress episode and to identify patients that might be at risk of adrenal crises by clinical and laboratory parameters at admission. Adrenal function was prospectively evaluated by a standard (250 μg) adrenocorticotropin test in 48 recipients. Data on clinical and laboratory parameters were collected. AI was diagnosed in 11 patients: 10/32 (31.3%) children on long‐term steroid treatment and 1/16 (6.25%) untreated. The only risk factor for AI was corticosteroids cumulative dose of >0.15 mg/kg/day during the last six months (p = 0.02, OR 6.67; 95% CI: 0.97–45.79). No correlation was found between clinical or laboratory signs of adrenal crisis on admission and the presence of AI. None of the patients with AI who did not receive stress dose (n = 8) developed adrenal crisis. AI is relatively common in children receiving prolonged corticosteroid treatment after kidney or liver transplantation. Clinical parameters on admission could not reliably identify patients with AI. Universal administration of a stress dose during physiological stress might not be required. However, at this point, the only method to identify patients that will benefit from a stress dose is through the ACTH test.
Diagnosis and treatment of functional gastrointestinal disorders in the Asia‐Pacific region: A survey of current practices
Authors: Miura Soichiro , Sugano Kentaro , Kinoshita Yoshikazu , Fock Kwong Ming , Goh Khean Lee , Gibson Peter ,   Members of the first Asian‐Pacific Topic Conference organized by the Japanese Society of Gastroenterology and Asian Pacific Association of Gastroenterology
Published: March 2011

AbstractBackground and Aims:  Functional gastrointestinal disorders (FGIDs), namely functional dyspepsia (FD) and irritable bowel syndrome (IBS) are common disorders important to public health in the Asia‐Pacific region. Our objectives were to determine the current practices in diagnosis and management of these disorders in the Asia‐Pacific region.Methods:  Forty‐three physicians and researchers in FGID who attended the first Asian Pacific Topic Conference at Tokyo in November 2010 were invited to answer a questionnaire. Twenty‐three Japanese doctors and twenty doctors from other Asia‐Pacific Societies answered the questionnaire, which consisted of 60 multiple‐choice questions concerning physician's preferences in diagnosis and management of FGIDs.Results:  Overall, there were similarities in diagnostic approach, such as differential diagnosis, exclusion of organic diseases, psychophysiological assessment, medical advice or medication with psychological drugs, not only among different Asia‐Pacific region but also between FD and IBS. Several notable differences were seen. For example, general practitioners did not commonly use the term FD or diagnose FD by themselves, while the term IBS was widely used and frequently diagnosed. Sub‐categorization was more common in IBS than FD. There was also a difference between Japan and other Asia‐Pacific region; upper GI endoscopy and blood examination were more common in Japan, while eradication of Helicobacter pylori was more frequently done in other countries. Anti‐secretory drugs for FD and mild laxatives or anti‐diarrheal drug for IBS were frequently used, and prokinetics were used for all patients with FD or IBS. Interestingly, drugs developed in Japan and Chinese herbal medicines were more frequently prescribed in Japan.Conclusion:  Information obtained in this survey is useful for understanding the most common clinical approaches for FGIDs in the Asia‐Pacific region.
Molecular mechanisms of hepatocarcinogenesis in chronic hepatitis C virus infection
Authors: Yamashita Taro , Honda Masao , Kaneko Shuichi 
Published: March 2011

AbstractHepatitis C virus (HCV) infection is a major cause of hepatocellular carcinoma (HCC) and chronic liver disease worldwide. Recent developments and advances in HCV replication systems in vitro and in vivo, transgenic animal models, and gene expression profiling approaches have provided novel insights into the mechanisms of HCV replication. They have also helped elucidate host cellular responses, including activated/inactivated signaling pathways, and the relationship between innate immune responses by HCV infection and host genetic traits. However, the mechanisms of hepatocyte malignant transformation induced by HCV infection are still largely unclear, most likely due to the heterogeneity of molecular paths leading to HCC development in each individual. In this review, we summarize recent advances in knowledge about the mechanisms of hepatocarcinogenesis induced by HCV infection.
Metabolomic phenotype of gastric cancer and precancerous stages based on gas chromatography time‐of‐flight mass spectrometry
Authors: Yu Lianzhen , Aa Jiye , Xu Jin , Sun Min , Qian Sixuan , Cheng Liping , Yang Shuping , Shi Ruihua 
Published: March 2011

AbstractBackground and Aim:  To study the low‐molecular‐weight metabolites in blood plasma of patients with the progressive disease, gastric cancer, and to characterize different stages from chronic superficial gastritis (CSG) to chronic atrophic gastritis (CAG), intestinal metaplasia (IM), gastric dysplasia (DYS) and finally gastric cancer (GC).Methods:  We applied gas chromatography time‐of‐flight mass spectrometry (GC/TOF‐MS) to determine metabolites levels in plasma obtained from 80 patients including 19 with CSG, 13 with CAG, 10 with IM, 15 with DYS and 22 with GC (nine preoperation and 13 postoperation). Principal component analysis (PCA) and statistics were used to differentiate the stages and to identify the markers of gastric cancer.Results:  Totally, 223 peaks were detected in GC/TOF‐MS and 72 compounds were authentically identified. CSG showed distinct difference from the other groups of CAG, IM, DYS and GC, whose plots clustered closely. IM clustered closely to GC, suggesting similar metabolic patterns of them. Fifteen identified metabolites contributed most to the differentiating between CSG and GC, and characterized different stages of GC. Statistics revealed elevated levels of 2‐Hydroxybutyrate, pyroglutamate, glutamate, asparagine, azelaic acid, ornithine, urate, 11‐eicosenoic acid, 1‐monohexadecanoylglycerol and γ‐tocopherol, while downregulation of creatinine, threonate in GC group, indicating that GC patients were obviously involved in oxidative stress, and perturbed metabolism of amino acids and fatty acids.Conclusion:  The metabolic phenotype of CSG is significantly different from GC, while that of IM is similar to it. The discriminatory metabolites characterizing progressive stages from CSG to GC might be the potential markers to indicate a risk of GC.
Target biopsy using magnifying endoscopy in clinical management of gastric mucosa‐associated lymphoid tissue lymphoma
Authors: Ono Shouko , Kato Mototsugu , Ono Yuji , Nishida Urara , Yamamoto Keiko , Shimizu Yuichi , Asaka Masahiro 
Published: March 2011

AbstractBackground and Aim:  We have reported the characteristics of magnified endoscopic images of gastric mucosa‐associated lymphoid tissue (MALT) lymphoma before and after treatment. In this study, we investigated the diagnostic efficacy of magnified endoscopic images for target biopsy and evaluation of clinical remission.Methods:  Twenty‐one patients diagnosed with localized gastric MALT lymphoma were enrolled. Magnified endoscopy was performed prior to treatment and at a mean period of 1.8 months (1–6 months) after therapy (Helicobacter pylori eradication in 19 patients and radiation therapy in two patients). Microstructural pattern and abnormal vessels in the lesions were assessed, and corpus mucosa without lymphoma was divided into H. pylori‐negative mucosa and H. pylori‐positive mucosa. Biopsy was the gold standard in this study.Results:  Nonstructural areas with abnormal vessels were observed in all patients before treatment. Fifteen patients achieved pathological complete remission. Disappearance of nonstructural areas and abnormal vessels after therapy was associated with pathological remission. Sensitivities of these findings for diagnosis were 76.9% and 85.7%, respectively, and the specificities were 87.5% and 85.7%, respectively. H. pylori eradication therapy was invalid in three patients with H. pylori‐negative mucosa in magnified images.Conclusions:  Magnifying endoscopy may be useful for target biopsy of superficial gastric MALT lymphoma in clinical management.
Liver cirrhosis in Malaysia: Peculiar epidemiology in a multiracial Asian country
Authors: Qua Choon‐Seng , Goh Khean‐Lee 
Published: March 2011

AbstractBackground and Aim:  To determine the etiology of liver cirrhosis and risk factors for hepatocellular carcinoma (HCC) in a multiracial Asian population.Methods:  Consecutive patients with liver cirrhosis presenting to outpatient clinics and inpatient service at the University of Malaya Medical Centre from 1 April 2006 to 31 May 2009 were included.Results:  A total of 460 patients were included in the study: 317 male patients (68.9%) and 143 female patients (31.1%), with a mean age of 58.8 years (range: 15–87 years). The major causes of cirrhosis were: chronic hepatitis B, n = 212, 46.1%; chronic hepatitis C, n = 85, 18.5%; cryptogenic, n = 71, 15.4%; alcohol, n = 58, 12.6% and autoimmune, n = 9, 2.0%. Alcohol was the main etiology in Indians (51.1%) compared to Malay (0%) and Chinese (4.4%) (both P < 0.001). Hepatitis B was the predominant etiology in Malay (47.9%) and Chinese (58.8%) compared to Indians (5.6%) (both P < 0.001). Hepatitis C cirrhosis was highest in Malays (25.0%). 136 patients (29.6%) had concurrent HCC. Male sex (P < 0.001), age > 60 years (P = 0.014), hepatitis B (P < 0.001), hepatitis C (P = 0.006) and cryptogenic cause (P = 0.002) were found to be independent risk factors for HCC.Conclusions:  The etiology of cirrhosis has a peculiar pattern based on racial differences in alcohol intake and in the prevalence of hepatitis B.
Transient elastographic evaluation in adult subjects without overt liver disease: Influence of alanine aminotransferase levels
Authors: Kumar Manoj , Sharma Praveen , Garg Hitendra , Kumar Ramesh , Bhatia Vikram , Sarin Shiv K 
Published: March 2011

AbstractBackground and Aim:  Studies on normal values of liver stiffness (LS) in subjects at “low risk” for liver disease are scant. The aim of the present study was to assess liver stiffness values in the subjects without overt liver disease with normal alanine aminotransferases (ALT) and to determine potential factors, which may influence these values with special reference to newly suggested updated upper limits of normal for ALT.Methods:  Liver stiffness measurements were performed in 445 subjects without overt liver disease (mean age, 41.1 ± 13.6; male, 73.5%) and normal liver enzymes.Results:  Mean LS value was 5.10 ± 1.19 kPa. LS values were higher in men than in women (5.18 ± 1.67 vs 4.86 ± 1.24 kPa, respectively, P = 0.008); in subjects with higher body mass index (BMI) category (Normal, overweight and obese subjects; 4.10 ± 0.75, 5.08 ± 0.66, and 6.05 ± 1.28 kPa, respectively; P < 0.001); in subjects with metabolic syndrome than in those without (5.63 ± 1.37 vs 5.01 ± 1.14 kPa, P = 0.001); and in subjects with ALT levels more than updated limits of normal compared to subjects with ALT levels less than updated limits of normal (5.68 ± 1.21 vs 4.77 ± 1.05 kPa, P < 0.001). On multiple linear regression, BMI and ALT was found to be significant predictor of LS.Conclusions:  Liver stiffness values in subjects without overt liver disease with normal ALT are influenced by BMI and ALT levels. Subjects with ALT levels less than updated limits of normal have lower LS values as compared to those with higher levels.
Stable nuclear transformation of the diatom Chaetoceros sp.
Authors: Miyagawa‐Yamaguchi Arisa , Okami Takuma , Kira Nozomu , Yamaguchi Haruo , Ohnishi Kouhei , Adachi Masao 
Published: March 2011

SUMMARYA nuclear transformation system for the centric diatom Chaetoceros sp. has been established using two plasmids pTpfcp/nat and pTpNR/green fluorescent protein (GFP) that had been used for Thalassiosira pseudonana transformation. These contain the nourseothricin resistance gene (nat) with the fucoxanthin chlorophyll a/c binding protein (fcp) promoter/terminator from T. pseudonana and the enhanced green fluorescent protein gene (egfp), with the nitrate reductase (NR) promoter/terminator from T. pseudonana, respectively. Transformants were recovered in the presence of the antibiotic nourseothricin. One to four copies of both nat and egfp genes were integrated into genomic DNA of the transformants. Transformation efficiency was 1.5–6.0 transformants per 108 cells. This work is the first report of stable genetic transformation of Chaetoceros, which is important as not only a constituent member of marine ecosystem but also feed for aquaculture.
Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp
Authors: Ishida Ken‐ichiro , Endo Hiroko , Koike Sayaka 
Published: March 2011

SUMMARYThe nucleomorph genome size of the recently described chlorarachniophyte Partenskyella glossopodia, which forms an independent lineage in the phylogeny of chlorarachniophytes, was analyzed by pulse‐field gel electrophoresis and Southern hybridization. These analyses showed that the nucleomorph genome of P. glossopodia is composed of three linear chromosomes that are about 445 kbp, 313 kbp, and 275 kbp in size. Thus, the total genome size is approximately 1033 kbp, which is significantly larger than the known size of chlorarachniophyte nucleomorph genomes, i.e. 330–610 kbp. This is the first study to report a nucleomorph genome that reaches approximately 1 Mbp in size.
Sterols of Glaucocystophytes
Authors: Leblond Jeffrey D. , Timofte Hermina Ilea , Roche Shannon A. , Porter Nicole M. 
Published: March 2011

SUMMARYGlaucocystophytes are a group of evolutionarily important freshwater algae that have an almost intact cyanobacterium, referred to as a cyanelle, as the photosynthetic organelle. Because of this, they have been the subject of a large number of studies over the past few decades on how a cyanobacterium transitioned into a chloroplast. However, studies on their lipid composition have lagged behind those on other areas of glaucocystophyte cell biology. To this end, we have examined the sterol composition of Cyanophora paradoxa Korshikov and Glaucocystis nostochinearum Itzigsohn in order to identify sterols left unidentified in previous studies. We have found that two isolates of G. nostochinearum and one of C. paradoxa uniformly produced three sterols: 24‐methylcholest‐5‐en‐3β‐ol, 24‐ethylcholesta‐5,22E‐dien‐3β‐ol, and 24‐ethylcholest‐5‐en‐3β‐ol.
The short‐term use of erythropoetin‐stimulating agents: impact on the biochemical recurrence of prostate cancer
Authors: Djavan Bob , Laze Juliana , Eckersberger Elisabeth , Finkelstein Julia , Agalliu Ilir , Lepor Herbert 
Published: March 2011

Study Type – Harm (case series)Level of Evidence 4What’s known on the subject? and What does the study add?Erythropoletin‐stimulating agents (ESAs) have been widely prescribed for treating anaemia secondary to advanced maligancies with the objective of reducing the need for red blood cell transfusions and improving the quality of life. However, the risk/benefit of ESAs has recently been questioned and metaanalyses showing that these agents are associated with an increased risk of mortality when chronically administered to patients with advanced/metastatic cancers.In this study we examined the impact of short‐term preoperative utilization of ESAs on biochemical recurrence – free survival rates after open radical retropubic prostatectomy (ORRP).OBJECTIVE
To examine the impact of short‐term preoperative utilization of erythropoietin‐stimulating agents (ESAs) on biochemical recurrence (BCR)‐free survival rates after open radical retropubic prostatectomy (ORRP) in light of the fact that the risk/benefit of ESAs has recently been questioned by the Food and Drug Administration (FDA) after reports showing a decreased survival.
PATIENTS AND METHODS
From 2000 to 2008, 1567 patients underwent ORRP and 97.5% of these signed informed consent to participate in the New York University Prospective and Longitudinal Outcomes Study.
Of the remaining 1528 patients, 1317 (86%) received preoperative ESA (group 1) and 211 (14%) did not (group 2).
Patients were also classified as having low‐, intermediate‐ or high‐risk disease based on D’Amico risk categories.
Kaplan–Meier survival curves and Cox’s proportional hazard models were used to estimate BCR‐free survival by ESA treatment.
RESULTS
A significant difference was observed for BCR‐free survival between the low‐ and intermediate/high‐risk groups.
There were no statistically significant differences between groups 1 and 2 for BCR‐free survival in the entire study populations and within risk groups.
In addition, Cox regression models showed no statistically significant differences in BCR‐free survival according to preoperative ESA administration in the entire cohort as well as among the low‐ and intermediate/high‐risk groups.
CONCLUSIONS
The short‐term use of ESAs as a preoperative blood management strategy for patients undergoing ORRP has no clinically relevant adverse effects on the biology of prostate cancer.
The present study supports the use of these agents before the procedure in patients undergoing surgery for localized disease.