bluuebunny/crossref_metadata_2025_split huggingface dataset:
DARNED: a DAtabase of RNa EDiting in humans
Authors: Kiran Anmol , Baranov Pavel V. 
Published: June 2010

Abstract
Motivation: RNA editing is a phenomenon, which is responsible for the alteration of particular nucleotides in RNA sequences relative to their genomic templates. Recently, a large number of RNA editing instances in humans have been identified using bioinformatic screens and high-throughput experimental investigations utilizing next-generation sequencing technologies. However, the available data on RNA editing are not uniform and difficult to access.
Results: Here, we describe a new database DARNED (DAtabase of RNa EDiting) that provides centralized access to available published data related to RNA editing. RNA editing locations are mapped on the reference human genome. The current release of the database contains information on approximately 42 000 human genome coordinates corresponding to RNA locations that undergo RNA editing, mostly involving adenosine-to-inosine (A-to-I) substitutions. The data can be queried using a range of genomic coordinates, their corresponding functional localization in RNA molecules [Exons, Introns, CoDing Sequence (CDS) and UnTranslated Regions (UTRs)] and information regarding tissue/organ/cell sources where RNA editing has been observed. It is also possible to obtain RNA editing information for a specific gene or an RNA molecule using corresponding accession numbers. Search results provide information on the number of expressed sequence tags (ESTs) supporting edited and genomic bases, functional localization of RNA editing and existence of known single nucleotide polymorphisms (SNPs). Editing data can be explored in UCSC and Ensembl genome browsers, in conjunction with additional data provided by these popular genome browsers. DARNED has been designed for researchers seeking information on RNA editing and for the developers of novel algorithms for its prediction.
Availability: DARNED is accessible at http://darned.ucc.ie
Contact: p.baranov@ucc.ie; brave.oval.pan@gmail.com
Evidence for a common genetic aetiology in high‐risk families with multiple haematological malignancy subtypes
Authors: Tegg Elizabeth M. , Thomson Russell J. , Stankovich Jim , Banks Annette , Flowers Ceri , McWhirter Rebekah , Panton Jean , Piaszczyk Anne , Bahlo Melanie , Marsden Katherine A. , Lowenthal Ray M. , Foote Simon J. , Dickinson Joanne L. 
Published: June 2010

SummaryA family history of a haematological malignancy (HM) is known to be a risk factor for HMs. However, collections of large families with multiple cases of varied disease types are relatively rare. We describe a collection of 12 families with dense aggregations of multiple HM subtypes. Cases were ascertained from a population based study conducted between 1972 and 1980 in Tasmania, Australia. Diagnoses were confirmed through review and re‐examination of stored tissue, pathology reports, Tasmanian Cancer Registry and flow cytometry records. Family trees were generated and kinship coefficients were calculated for all pairs of affected individuals. 120 cases were found in these families. Cases diagnosed with chronic lymphocytic leukaemia (CLL) demonstrated the most significantly increased aggregation (P < 0·0001). There was also significant evidence that those individuals diagnosed at an older age (>53 years), did not aggregate together in families with disease that presented at an earlier age (<20 years) (P = 0·009).
Degradation of coeliac disease-inducing rye secalin by germinating cereal enzymes: diminishing toxic effects in intestinal epithelial cells
Authors: Stenman S M , Lindfors K , Venäläinen J I , Hautala A , Männistö P T , Garcia-Horsman J A , Kaukovirta-Norja A , Auriola S , Mauriala T , Mäki M , Kaukinen K 
Published: June 2010

Summary
Currently the only treatment for coeliac disease is a lifelong gluten-free diet excluding food products containing wheat, rye and barley. There is, however, only scarce evidence as to harmful effects of rye in coeliac disease. To confirm the assumption that rye should be excluded from the coeliac patient's diet, we now sought to establish whether rye secalin activates toxic reactions in vitro in intestinal epithelial cell models as extensively as wheat gliadin. Further, we investigated the efficacy of germinating cereal enzymes from oat, wheat and barley to hydrolyse secalin into short fragments and whether secalin-induced harmful effects can be reduced by such pretreatment. In the current study, secalin elicited toxic reactions in intestinal Caco-2 epithelial cells similarly to gliadin: it induced epithelial cell layer permeability, tight junctional protein occludin and ZO-1 distortion and actin reorganization. In high-performance liquid chromatography and mass spectroscopy (HPLC-MS), germinating barley enzymes provided the most efficient degradation of secalin and gliadin peptides and was thus selected for further in vitro analysis. After germinating barley enzyme pretreatment, all toxic reactions induced by secalin were ameliorated. We conclude that germinating enzymes from barley are particularly efficient in the degradation of rye secalin. In future, these enzymes might be utilized as a novel medical treatment for coeliac disease or in food processing in order to develop high-quality coeliac-safe food products.
The effect of Longan seed polyphenols on colorectal carcinoma cells
Authors: Chung Yuan‐Chiang , Lin Chih‐Cheng , Chou Chih‐Chung , Hsu Chih‐Ping 
Published: June 2010

Eur J Clin Invest 2010; 40 (8): 713–721AbstractBackground  Polyphenol‐rich longan seed extract (LSP) is a free radical scavenger and antioxidant. However, the effect of LSP on the growth of human colorectal carcinoma cells (CRC) has not yet been evaluated.Materials and methods  Polyphenols of longan seeds were extracted and measured by colorimetry. Four CRC cell lines (Colo 320DM, SW480, HT‐29 and LoVo) were treated with LSP and assessed for viability by trypan blue exclusion, for cell cycle distribution by flow cytometry, for apoptosis by annexin V labelling and for changes in the levels of proteins involved in cell cycle control or apoptosis by immunoblotting.Results  Total phenol content of LSP was 695 mg g−1 and total flavonoids were 150 mg g−1. LSP inhibited the proliferation (25 μg mL−1–200 μg mL−1) of Colo 320DM, SW480 and HT‐29, but not LoVo. LSP inhibited the proliferation by blocking cell cycle progression during the DNA synthesis phase and inducing apoptotic death. Western blotting indicated that LSP blocks the S phase, reducing the expression of cyclin A and cyclin D1. Colo 320DM and SW480 treated with LSP also showed the activation of caspase 3 and increased Bax : Bcl‐2 ratio.Conclusion  LSP induces S phase arrest of the cell cycle and apoptotic death in three CRC cell lines. The results indicate that LSP is a potential novel chemoprevention and treatment agent for colorectal cancer.
Potential functional redundancy and resource facilitation between tadpoles and insect grazers in tropical headwater streams
Authors: COLÓN‐GAUD CHECO , WHILES M. R. , BRENES R. , KILHAM S. S. , LIPS K. R. , PRINGLE C. M. , CONNELLY S. , PETERSON S. D. 
Published: June 2010

Summary1. We quantified production and consumption of stream‐dwelling tadpoles and insect grazers in a headwater stream in the Panamanian uplands for 2 years to assess their effects on basal resources and energy fluxes. At the onset of our study, this region had healthy, diverse amphibian populations, but a catastrophic disease‐driven decline began in September 2004, which greatly reduced amphibian populations.2. Insect grazer production was 348 mg ash‐free dry mass (AFDM) m−2 year−1 during the first year of the study and increased slightly to 402 mg AFDM m−2 year−1 during the second year.3. Prior to amphibian declines, resource consumption by grazers (tadpoles and insects) was estimated at 2.9 g AFDM m−2 year−1 of algal primary production, which was nearly twice the estimated amount available. Insect grazers alone accounted for c. 81% of total primary consumption. During the initial stages of the declines, consumption remained at c. 2.9 g AFDM m−2 year−1, but only 35% of the available resource was being consumed and insect grazers accounted for c. 94% of total consumption.4. Production and resource consumption of some insect grazers increased during the second year, as tadpoles declined, indicating a potential for functional redundancy in this system. However, other insect grazer taxa declined or did not respond to tadpole losses, suggesting a potential for facilitation between tadpoles and some insects; differential responses among taxa resulted in the lack of a response by insect grazers as a whole.5. Our results suggest that before massive population declines, tadpoles exerted strong top‐down control on algal production and interacted in a variety of ways with other primary consumers.6. As amphibian populations continue to decline around the globe, changes in the structure and function of freshwater habitats should be expected. Although our study was focused on tropical headwater streams, our results suggest that these losses of consumer diversity could influence other aquatic systems as well and may even reach to adjacent terrestrial environments.
Are more productive varieties of Paspalum dilatatum less tolerant to drought?
Authors: Couso L. L. , Gatti M. L. , Cornaglia P. S. , Schrauf G. E. , Fernández R. J. 
Published: June 2010

Abstract Paspalum dilatatum Poir., is a perennial C4 grass widely distributed in the Argentinean Pampas. The response to water availability for materials developed with forage‐production purposes is unknown. We hypothesized that genetic differences between commercial varieties are reflected in their regrowth capacity under water stress. The effect of five levels of constant water supply on three plant varieties (two derived from apomictic materials: ‘Relincho’ and ‘Alonso’ and one from sexually‐derived material: ‘Primo’) were examined in the greenhouse. Leaf‐ and plant‐response traits were followed during 38 d after a single defoliation event. Seven response variables were measured: three of them were morphogenetic (leaf elongation rate, leaf appearance rate and leaf elongation duration) and four were structural (number of live leaves, lamina length, tiller biomass and tiller production). The sexual material showed higher values for growth variables than the apomictic varieties (leaf elongation rate, leaf length and tiller biomass) across the environmental range. Apomictic varieties showed a proportionally similar drought response to the sexual material for the seven variables. No intra‐specific trade‐off (statistical interaction) was found between growth under high water availability conditions and drought tolerance.
Nutritive value of two meadows and relationships with some vegetation traits
Authors: Andueza D. , Cruz P. , Farruggia A. , Baumont R. , Picard F. , Michalet‐Doreau B. 
Published: June 2010

AbstractThis study was designed to compare the evolution in nutritive value between two permanent grasslands that had different botanical composition, during 2 years (2003 and 2004), and to study the relationships between a set of vegetation and digestibility characteristics. Botanical composition, lamina proportions (LP), and in vivo organic matter digestibility (OMD) of grasslands were measured at three different times during the first growth cycle over 2 years: last week in May, third week in June and second week of July. Foliar traits [specific leaf area (SLA) and leaf dry matter content (LDMC)] were measured on grasses in the first period of both years. The LDMC and botanical composition values were used to calculate plant functional types (PFT) of the grasslands at each period. Relationships between OMD and SLA, LDMC, LP and forbs proportions (FP) were tested. Grassland rich in forbs, which was classified in PFT B, showed higher OMD in the first stage of maturity and lower OMD at the end of the cycle in 2004 than grassland rich in grasses, which was classified as PFT C. There were significant relationships between LDMC and OMD across the two first periods. There were also significant relationships between LP and OMD in the first period and between FP and OMD in the third period. The botanical composition of the grassland and consequently its PFT is an important factor explaining the evolution of the nutritive value of permanent grasslands during the first growth cycle.
Decreased production of interleukin‐10 and transforming growth factor‐β in Toll‐like receptor‐activated intestinal B cells in SAMP1/Yit mice
Authors: Mishima Yoshiyuki , Ishihara Shunji , Aziz Md. Monowar , Oka Akihiko , Kusunoki Ryusaku , Otani Aya , Tada Yasumasa , Li Yong‐Yu , Moriyama Ichiro , Oshima Naoki , Yuki Takafumi , Amano Yuji , Matsumoto Satoshi , Kinoshita Yoshikazu 
Published: June 2010

SummaryA unique subset of B cells expressing interleukin‐10 (IL‐10) and transforming growth factor‐β (TGF‐β) plays an essential role in preventing inflammation and autoimmunity. We investigated the presence of this cell subset in intestines and its role in the pathogenesis of ileitis using SAMP1/Yit and age‐matched control AKR/J mice. Mononuclear cells were isolated from mesenteric lymph nodes (MLNs) and the expressions of B220, CD1d, CD5, Toll‐like receptor 4 (TLR4) and TLR9 in isolated cells were analysed. Purified B cells were stimulated with lipopolysaccharide (LPS) or CpG‐DNA, then IL‐10 and TGF‐β1 expressions were examined by enzyme immunoassay and flow cytometry. Production of IL‐1β by TLR‐mediated macrophages co‐cultured with or without purified MLN B cells from SAMP1/Yit and AKR/J mice was evaluated. In addition, interferon‐γ (IFN‐γ) production in intestinal T cells co‐cultured with MLN B cells were also assessed in SAMP1/Yit and AKR/J strains. The production levels of IL‐10 and TGF‐β1 stimulated by LPS and CpG‐DNA were significantly lower in B cells separated from MLNs from the SAMP1/Yit strain. B cells expressing IL‐10 and TGF‐β1 were mainly located in a population characterized by the cell surface marker CD1d+. Interleukin‐1β production by TLR‐activated macrophages co‐cultured with MLN B cells from SAMP1/Yit mice was significantly higher than that of those from AKR/J mice. Interestingly, IFN‐γ production by T cells was noted only when they were co‐cultured with SAMP1/Yit but not the AKR/J B cells. These results are the first to show that disorders of regulatory B‐cell function under innate immune activation may cause disease pathogenesis in a murine model of Crohn’s disease.
Kinetic analysis of oxytetracycline residues in Chinese mitten crab,Eriocheir sinensis,muscle following intramuscular administration
Authors: Feng Q , Gao T , Ji H , Jiang X , Liang T , Gu W , Wu G , Gao G , Wang W 
Published: June 2010

AbstractCrab culture is a very important economic industry in China. An epidemic of tremor disease of Chinese mitten crabs,Eriocheir sinensis,has become a serious problem in recent years. A spiroplasm has been proved to be the causative agent of this disease. Oxytetracycline (OTC) is used widely in aquaculture and was confirmed to be very effective against this pathogen. In this study, the distribution and depletion patterns of OTC in crab muscle were evaluated following single intramuscular doses of 2, 8 and 40 mg kg−1body weight. OTC was detected with a validated HPLC method. Concentration–time profiles were well described by a three‐compartment model with first‐order absorption after a single dose of 8 and 40 mg kg−1. For comparison, a non‐compartment model was employed. A withdrawal time of 48.29 and 55.92 days was suggested prior to consumption after receiving 8 and 40 mg kg−1. A recommended therapeutic dose of OTC in theory was calculated to be 36.37 mg kg−1. OTC was distributed well throughout the body. The elimination of OTC in muscle was slower compared with fish and other crustaceans. A dose of 40 mg kg−1is suggested for practical use.
The ABC‐transporter hutCD genes of Photobacterium damselae subsp. piscicida are essential for haem utilization as iron source and are expressed during infection in fish
Authors: Osorio C R , Juiz‐Río S , Lemos M L 
Published: June 2010

AbstractThe marine fish pathogen Photobacterium damselae subsp. piscicida utilizes haem compounds as the sole iron source. In a previous work, we characterized a gene cluster with ten potential haem uptake and utilization genes. Two of these genes, hutC and hutD, which are iron‐regulated, conform a putative inner membrane haem ABC transporter. In this study, we constructed an insertional mutant, leading to the inactivation of hutCD genes. Reverse transcriptase‐PCR analyses demonstrated that an insertion between the hutB and hutC genes abolished transcription of the downstream hutC and hutD genes. The hutCD mutant was unable to utilize haem as the sole iron source, demonstrating that the putative ABC‐transporter proteins HutC and HutD are essential for haem utilization as an iron source in P. damselae subsp. piscicida. In addition, reverse transcriptase‐PCR assays conducted with RNA samples isolated from experimentally infected fish revealed the presence of hutCD transcripts. The results demonstrate for the first time that haem uptake genes of a fish pathogen are expressed during the infective process in fish.
Antiparasitic activity of the antimicrobial peptide HbβP‐1, a member of the β‐haemoglobin peptide family
Authors: Ullal A J , Noga E J 
Published: June 2010

AbstractA family of antimicrobial peptides (AMPs) derived from the β‐subunit of haemoglobin was recently isolated from channel catfish, Ictalurus punctatus, infected with Ichthyophthirius multifiliis (ich), an important freshwater fish parasite that causes ichthyophthiriosis. We previously discovered that one of these AMPs, HbβP‐1, had strong cidal activity against ich as well as another ectoparasite, Tetrahymena pyriformis. HbβP‐1 toxicity was specific, primarily affecting the trophozoite (trophont) stage of ich. Here, we show that HbβP‐1 acts more rapidly to kill smaller (presumably less mature) trophonts of ich, taking almost twice as long to kill larger trophonts (P < 0.0001). It acts more rapidly than an unrelated AMP, piscidin 1, which is haemolytic and also lethal to ich trophonts. HbβP‐1 is potently and selectively lethal to the trophont stage of the dinoflagellate ectoparasite, Amyloodinium ocellatum, one of the most important pathogens of warmwater marine fish. HbβP‐1 has no effect on the fish gill cell line feeder layer (G1B cells) used to propagate Amyloodinium, further suggesting a highly selective action. These findings suggest that HbβP‐1 or related AMPs might function in protecting marine as well as freshwater fish and that HbβP‐1 has highly selective activity against specific life stages of important fish ectoparasites.
A new distensibility technique to measure sphincter of Oddi function
Authors: Kunwald P. , Drewes A. M. , Kjær D. , Gravesen F. H. , Mcmahon B. P. , Madácsy L. , Funch‐jensen P. , Gregersen H. 
Published: June 2010

AbstractBackground  Evaluation of the biliary tract is important in physiological, pathophysiological, and clinical studies. Although the sphincter of Oddi (SO) can be evaluated with manometry, this technique has several limitations. This may explain the difficulties in identifying pathophysiological mechanisms for dysfunction of the SO and in identifying patients who may benefit from certain therapies. To encompass problems with manometry, methods such as the functional lumen imaging probe (FLIP) technique have been developed to study GI sphincters. This study set about miniaturising the FLIP probe and validating it for measurements in the SO. In order to get a better physiological understanding of the SO the aims were to show the sphincter profile in vivo and motility patterns of SO in pilot studies using volunteers that were experiencing biliary type pain but had normal SO manometry.Methods  The SO probe was constructed to measure eight cross‐sectional areas (CSA) along a length of 25 mm inside a saline‐filled bag. To validate the technique for profiling the SO, six perspex cylinders with different CSAs were measured nine times to assess reproducibility and accuracy.Key Results  Reproducibility and accuracy for these measurements were good. The probe performed well in bench tests and was therefore tested in four humans. The data indicated that it was possible to make distensions in the human SO and that a geometric sphincter profile could be obtained.Conclusions & Inferences  The probe will in future studies be tested for diagnostic purposes related to sphincter of Oddi diseases.
Long‐term outcome of patients with lamivudine after early cessation of hepatitis B immunoglobulin for prevention of recurrent hepatitis B following liver transplantation
Authors: Yuefeng M. , Weili F. , Wenxiang T. , Ligang X. , Guiling L. , Hongwei G. , Wencai L. , Xiaoguang W. , Wei M. , Zhongyi F. 
Published: June 2010

Yuefeng M, Weili F, Wengxiang T, Ligang X, Guiling L, Hongwei G, Wencai L, Xiaoguang W, Wei M, Zhongyi F. Long‐term outcome of patients with lamivudine after early cessation of hepatitis B immunoglobulin for prevention of recurrent hepatitis B following liver transplantation. Clin Transplant 2011: 25: 517–522. © 2010 John Wiley & Sons A/S.Abstract: Background: The aim of this study is to examine the efficacy of long‐term prophylaxis with lamivudine (LAM) after a course of post‐operative hepatitis B immunoglobulin (HBIG) in patients who underwent liver transplantation (LT) for hepatitis B virus (HBV)‐related disease.Result: The medical records of HBV‐infected patients who underwent a LT in our institution between July 2001 and May 2005 were reviewed. There were 15 liver transplant recipients who were administered HBIG for <18 months and used LAM as a maintenance prophylaxis regime enrolled in this study. At enrollment, all patients were hepatitis B surface antigen (HBsAg) positive and three patients were HBeAg positive. There were 13 patients who were HBV DNA positive with a mean viral load of 5.4 log copies/mL, and among them, 12 recipients were on antiviral therapy with LAM (100 mg/d orally) for 12–168 d, resulting in HBV DNA negative levels in nine patients prior to their transplant. HBV recurrence post‐LT was noted in two patients who had very high‐HBV DNA levels pre‐LT. Both of these patients showed LAM‐resistant mutation at the time of recurrence. The 11 patients who were HBV DNA negative before LT (low‐risk patients) had no HBV recurrence during a follow‐up at a median of 58 months post‐LT. This included five patients who had intermittent low‐level HBV DNA post‐LT (HBsAg negative), of whom two had YMDD mutation and these two were given adefovir in addition to LAM.Conclusion: Our retrospective study demonstrated excellent long‐term outcomes in the low‐risk patients treated with LAM after a short course of HBIG.