bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of Effluents from Baitfish Holding Sheds in Central Arkansas
Authors: Adhikari Puspa L , Stone Nathan , Kelly Anita M , Thomforde Hugh K 
Published: June 2012

Abstract
This study characterized effluents from commercial baitfish holding sheds in central Arkansas, the source of about half of U.S. farm-raised baitfish. Nutrient and solid concentrations in effluents were relatively dilute compared with other aquaculture effluents because fish are not fed while in vats. Total phosphorus concentrations, however, were relatively high (median of 0.52 mg/L in spring, 0.32 mg/L in fall), but source water contributed from 83% to 96% of the total phosphorus concentration in baitfish holding shed effluents. Concentrations of total phosphorus similar to those found in study source waters have been documented for other waters from the Mississippi River Valley alluvial aquifer. Daily variations in effluent quality generally overshadowed other temporal variation, with the exception of higher total ammonia concentrations in the spring. Higher loading rates are common in vats in the spring owing to increased baitfish sales. Daily flushing resulted in brief spikes in concentrations of total suspended solids, 5-d biochemical oxygen demand, and total phosphorus; the average contribution of flushing events to total daily loading was estimated to be 5–13%. Results suggest that holding shed effluents could be reused, at least for pond culture, as long as potential disease transmission issues are resolved.
Targeted retrieval of gene expression measurements using regulatory models
Authors: Georgii Elisabeth , Salojärvi Jarkko , Brosché Mikael , Kangasjärvi Jaakko , Kaski Samuel 
Published: June 2012

AbstractMotivation: Large public repositories of gene expression measurements offer the opportunity to position a new experiment into the context of earlier studies. While previous methods rely on experimental annotation or global similarity of expression profiles across genes or gene sets, we compare experiments by measuring similarity based on an unsupervised, data-driven regulatory model around pre-specified genes of interest. Our experiment retrieval approach is novel in two conceptual respects: (i) targetable focus and interpretability: the analysis is targeted at regulatory relationships of genes that are relevant to the analyst or come from prior knowledge; (ii) regulatory model-based similarity measure: related experiments are retrieved based on the strength of inferred regulatory links between genes.Results: We learn a model for the regulation of specific genes from a data repository and exploit it to construct a similarity metric for an information retrieval task. We use the Fisher kernel, a rigorous similarity measure that typically has been applied to use generative models in discriminative classifiers. Results on human and plant microarray collections indicate that our method is able to substantially improve the retrieval of related experiments against standard methods. Furthermore, it allows the user to interpret biological conditions in terms of changes in link activity patterns. Our study of the osmotic stress network for Arabidopsis thaliana shows that the method successfully identifies relevant relationships around given key genes.Availability: The code (R) is available at http://research.ics.tkk.fi/mi/software.shtml.Contact: elisabeth.georgii@aalto.fi; jarkko.salojarvi@helsinki.fi; samuel.kaski@hiit.fiSupplementary Information: Supplementary data are available at Bioinformatics online.
PurityEst: estimating purity of human tumor samples using next-generation sequencing data
Authors: Su Xiaoping , Zhang Li , Zhang Jianping , Meric-Bernstam Funda , Weinstein John N. 
Published: June 2012

Abstract
Summary: We developed a novel algorithm, PurityEst, to infer the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data. We applied our tool to a whole cancer genome sequencing datasets and demonstrated the accuracy of PurityEst compared with DNA copy number-based estimation.
Availability: PurityEst has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/PurityEst.html
Contact: xsu1@mdanderson.org
Integration of Bioinformatics and Synthetic Promoters Leads to the Discovery of Novel Elicitor-Responsive cis-Regulatory Sequences in Arabidopsis
Authors: Koschmann Jeannette , Machens Fabian , Becker Marlies , Niemeyer Julia , Schulze Jutta , Bülow Lorenz , Stahl Dietmar J. , Hehl Reinhard 
Published: June 2012

AbstractA combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction.
LYK4, a Lysin Motif Receptor-Like Kinase, Is Important for Chitin Signaling and Plant Innate Immunity in Arabidopsis
Authors: Wan Jinrong , Tanaka Kiwamu , Zhang Xue-Cheng , Son Geon Hui , Brechenmacher Laurent , Nguyen Tran Hong Nha , Stacey Gary 
Published: June 2012

Abstract
Chitin is commonly found in fungal cell walls and is one of the well-studied microbe/pathogen-associated molecular patterns. Previous studies showed that lysin motif (LysM)-containing proteins are essential for plant recognition of chitin, leading to the activation of plant innate immunity. In Arabidopsis (Arabidopsis thaliana), the LYK1/CERK1 (for LysM-containing receptor-like kinase1/chitin elicitor receptor kinase1) was shown to be essential for chitin recognition, whereas in rice (Oryza sativa), the LysM-containing protein, CEBiP (for chitin elicitor-binding protein), was shown to be involved in chitin recognition. Unlike LYK1/CERK1, CEBiP lacks an intracellular kinase domain. Arabidopsis possesses three CEBiP-like genes. Our data show that mutations in these genes, either singly or in combination, did not compromise the response to chitin treatment. Arabidopsis also contains five LYK genes. Analysis of mutations in LYK2, -3, -4, or -5 showed that LYK4 is also involved in chitin signaling. The lyk4 mutants showed reduced induction of chitin-responsive genes and diminished chitin-induced cytosolic calcium elevation as well as enhanced susceptibility to both the bacterial pathogen Pseudomonas syringae pv tomato DC3000 and the fungal pathogen Alternaria brassicicola, although these phenotypes were not as dramatic as that seen in the lyk1/cerk1 mutants. Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. Therefore, LYK4 may play a role in the chitin recognition receptor complex to assist chitin signal transduction and plant innate immunity.
Meta‐analysis: the impact of IL28B polymorphisms on rapid and sustained virological response in HCV‐2 and ‐3 patients
Authors: Schreiber J. , Moreno C. , Garcia B. Garcia , Louvet A. , Trepo E. , Henrion J. , Thabut D. , Mathurin P. , Deltenre P. 
Published: June 2012

SummaryBackgroundRecent studies suggested that IL28B polymorphisms may affect rapid and sustained virological response rates in HCV patients infected with genotype 2 or 3.AimTo assess the role of IL28B polymorphisms on the virological response in HCV‐2 and ‐3 patients.MethodsWe performed meta‐analysis of studies evaluating the impact of rs12979860 and rs8099917 polymorphisms on rapid and sustained virological response in HCV‐2 or ‐3 patients.ResultsTwenty‐three studies involving 3042 patients were included. The first meta‐analysis evaluated the impact of rs12979860 polymorphism and included 1963 patients. When compared with rs12979860 CT/TT patients, CC patients had a higher rapid virological response rate (mean difference: 12.9%, 95% CI: 6.5–19.4%, P < 0.001) and a higher sustained virological response rate (mean difference: 4.9%, 95% CI: 0.1–9.8%, P = 0.046). The second meta‐analysis evaluated the impact of rs8099917 polymorphism and included 2246 patients. When compared with rs8099917 TG/GG patients, TT patients had a higher rapid virological response rate (mean difference: 14.8%, 95% CI: 7.2–22.4%, P < 0.001) and a higher sustained virological response rate (mean difference: 5.5%, 95% CI: 0.4–10.6%, P = 0.033). When considering only patients treated for 24 weeks, results were unchanged. No potential sources of between‐study heterogeneity were identified.ConclusionsFavourable IL28B polymorphisms are associated with higher rapid and sustained virological response rates in HCV‐2 and ‐3 patients. However, as the impact on a sustained response is very limited, it is unlikely that IL28B polymorphisms provide additional predictive value when considering other predictors of a sustained response.
Baseline corticosterone is positively related to juvenile survival in a migrant passerine bird
Authors: Rivers James W. , Liebl Andrea L. , Owen Jennifer C. , Martin Lynn B. , Betts Matthew G. 
Published: June 2012

Summary1. Glucocorticoid hormones are an integral part of the vertebrate stress response, and theoretical models argue for a link between glucocorticoid levels and individual fitness. The cort‐fitness hypothesis posits that elevated levels of baseline glucocorticoids are reflective of an individual in poor condition and with a reduced likelihood of survival. Surprisingly, this hypothesis remains virtually untested for the juvenile life‐history stage, a period that is often characterized by high mortality rates.2. To address this issue, we explored whether glucocorticoid levels just prior to fledging were related to survival during the juvenile period in the Swainson's thrush (Catharus ustulatus), a short‐lived, temperate‐breeding passerine bird. Over 2 years, we blood‐sampled nestling thrushes to quantify glucocorticoid levels and then used radio telemetry to assess whether individuals died or survived to emigrate from the study area. Finally, we measured vegetation characteristics at the nest and at locations used by individuals during the juvenile period to quantify the relative importance of habitat features and glucocorticoid levels on survival.3. Predation was the leading cause of death, and overall juvenile survival rate was 34·6%. We found that survival was positively associated with baseline corticosterone and, to a lesser extent, size‐corrected body mass and date of fledging. Contrary to expectations, we found no evidence that the amount of vegetative cover at the nest site or at locations used during the juvenile period was associated with survival.5. Although we cannot completely rule out the cort‐fitness hypothesis, our data appear to support the cort‐activity hypothesis and suggest that elevated baseline corticosterone levels in juvenile thrushes may be linked to enhanced post‐fledging survival via increased locomotor activity that promotes foraging, more effective escape from predators or both.
Diversity of non‐structural carbohydrates in grasses (Poaceae) from Brazil
Authors: Moraes M. G. , Chatterton N. J. , Harrison P. A. , Filgueiras T. S. , Figueiredo‐Ribeiro R. C. L. 
Published: June 2012

AbstractNon‐structural carbohydrates (NSC) are the primary energy available for growth and dry‐mass production in forage grasses. They are also associated with tolerance to environmental stresses, including drought. Soluble carbohydrates, especially fructans of temperate forage grasses, have been extensively studied; however, little is known about NSC of tropical grasses. These plants are abundant in the Cerrado, a savanna‐like vegetation with a definite seasonality in rainfall distribution. Such an environment presents an ideal condition for the occurrence of fructans. However, the present analysis of carbohydrates in aerial parts of twenty‐four tropical grass species, mainly from the Panicoideae subfamily in the Cerrado, shows a distinctively different NSC profile when compared with temperate grasses. Free glucose and starch are common NSC found in most plant organs. However, free fructose and sucrose‐based oligosaccharides were only found in very low amounts. Sucrose was detected in higher amounts only in stems. A linear series of malto‐oligosaccharides was found in leaf blades, sheaths and stems of most of the Cerrado grasses, except for those from the Andropogoneae tribe. These results indicate a diversity of regulatory pathways of NSC metabolism in tropical forage grasses from the Cerrado.
Mutation spectrum and inhibitor risk in 100 Korean patients with severe haemophilia A
Authors: Kim H.‐J. , Chung H.‐S. , Kim S. K. , Yoo K.Y. , Jung S.‐Y. , Park I.‐A. , Lee K.‐O. , Kim S.‐H. , Kim H.‐J. 
Published: June 2012

SummaryHaemophilia A (HA) is an X‐linked recessive bleeding disorder caused by defects in the F8 gene encoding the coagulation factor VIII. Mutation analysis in HA is important to confirm the diagnosis, genotype‐phenotype correlations and for genetic counselling and family study. The aim of this study was to detect causative mutations of F8 in severe HA patients in Korea and to correlate the mutation type with the risk of inhibitor development. A total of 100 unrelated Korean patients with severe HA were enrolled for this study. The Nijeman modification of the Bethesda assay was used to determine the presence of inhibitor. Molecular analysis of F8 was performed using a combination of molecular techniques, including long‐distance polymerase chain reaction, direct sequencing and multiplex ligation‐dependent probe amplification (MLPA). We identified causative mutations in 98% of severe HA patients (98/100). Inv22 and Inv1 mutations were detected in 30 patients and one patient, respectively. A total of 59 unique mutations were identified in 69 non‐inversion patients, including 24 novel mutations. The overall prevalence of inhibitor was 26%. Inhibitor risk was highest in patients with large deletion mutations identified using MLPA (100%). Among those with point mutations, the prevalence of inhibitor was highest when the mutation occurred in the A3 and C2 domains (60% and 50%, respectively). The molecular diagnostic strategy involving multiplex PCR, sequencing and dosage analyses identified causative mutations in most cases of severe HA. The high inhibitor risk was associated with large deletion mutations and point mutations in A3 and C2 domains.
Immunohistological study of a pediatric patient with plasma cell‐rich acute rejection
Authors: Chikamoto Hiroko , Sugawara Noriko , Akioka Yuko , Shimizu Tomokazu , Horita Shigeru , Honda Kazuho , Moriyama Takahito , Koike Junki , Yamaguchi Yutaka , Hattori Motoshi 
Published: June 2012

AbstractWe report here the case of a girl who developed plasma cell‐rich acute rejection (PCAR), a condition characterized by the presence of mature plasma cells infiltrating a renal allograft. The patient's creatinine level increased sharply to 4.3 mg/dL from 0.9 mg/dL at 19 months post‐renal transplantation. She showed no response to methylprednisolone pulse therapy at a dose of 500 mg for three d but did show an immediate clinical and histopathological response to muromonab‐CD3 (OKT3) administration. She had two episodes of PCAR recurrence and subsequently lost her graft. She had no evidences of antibody‐mediated rejection including C4d deposition in peritubular capillaries and donor‐specific antibodies during the entire follow‐up period. To elucidate the pathogenesis of PCAR, immunohistological examination of infiltrating cells was performed. CD3‐positive cells infiltration seemed to be associated with the CD138‐positive cells infiltration, and the number of CD3‐positive cells was increased preceding PCAR recurrence. Additionally, a rapid decrease in the number of CD138‐positive cells and CD3‐positive cells following the OKT3 administration was observed. This case suggests that T‐cell mediated immune mechanisms might play a role in the development of PCAR.
Pentraxin‐3 expression in acute renal allograft rejection
Authors: Imai Naofumi , Nishi Shinichi , Yoshita Kazuhiro , Ito Yumi , Osawa Yutaka , Takahashi Kaori , Nakagawa Yuki , Saito Kazuhide , Takahashi Kota , Narita Ichiei 
Published: June 2012

AbstractPentraxin‐3 (PTX3) is an acute phase reactant produced by a variety of cell types at sites of local inflammation. We examined by immunohistochemistry renal biopsies from patients with acute rejection (n = 10), protocol biopsies without rejection (n = 37), and peri‐operative donor biopsies of the same transplant patients (n = 94) for intra‐renal expression of PTX3, and its correlation with clinical, laboratory, and histopathologic parameters. PTX3 was mainly expressed in the interstitium of renal allograft. In the non‐rejection biopsies (pre‐ and post‐reperfusion and protocol biopsies), PTX3 expression area (PTX3%) was equally maintained at a low level, whereas in the rejection biopsies, PTX3% was significantly higher (p < 0.0001). Treatment of acute rejection resulted in a significant reduction of PTX3% (p < 0.0001). PTX3% positively correlated with the degree of allograft dysfunction and acute rejection scores of Banff classification (2009). This study suggests that PTX3% may be an available histological marker of acute renal allograft rejection.
A case of recurrent light chain deposition disease after living‐related renal transplantation – detailed process of the recurrence
Authors: Horike Keiji , Takeda Asami , Otsuka Yasuhiro , Inaguma Daijyo , Goto Norihiko , Watarai Yoshihiko , Uchida Kazuharu , Morozumi Kunio 
Published: June 2012

AbstractA 53‐yr‐old woman with end‐stage renal disease was admitted for renal transplantation (RTX). About a decade ago, she had presented with urinary abnormalities. Monoclonal IgA lambda was detected. Renal biopsy showed nodular glomerulosclerosis, and an immunohistochemical study for lambda was negative. Fibrillary glomerulonephritis was suggested as the most likely diagnosis. RTX was successfully performed, and graft function was stable for the first half year. Graft biopsy was performed at one yr post‐transplant. Glomeruli showed nodular lesion similar to native kidney biopsy findings. Immunofluorescence microscopy (IF) indicated strong lambda staining along the glomerular basement membrane, the tubular basement membrane (TBM), and the peritubular capillary. The diagnosis of recurrent light chain deposition disease (LCDD) was confirmed. A series of biopsies are available to conduct studies on the recurrent process of LCDD. Light microscopy showed no remarkable changes up to six months post‐RTX. However, the IF study revealed evident granular depositions of lambda along the TBM only at the one‐h biopsy. Typical IF staining pattern of lambda and EDD compatible with LCDD were noted after six months post‐transplant. This is the first case report that elucidated the details of the recurrent process of LCDD at one yr after the operation.
No evidence of association between functional polymorphisms located within IL6R and IL6ST genes and systemic sclerosis
Authors: Cénit M. C. , Simeón C. P. , Fonollosa V. , Espinosa G. , Beltrán E. , Sáez‐Comet L. , Vicente‐Rabaneda E. , García‐Hernández F. J. , Martínez‐Estupiñán L. , Rodríguez‐Carballeira M. , Hernández V. , de la Peña P. G. , Fernández‐Castro M. , Narváez F. J. , Pros A. , Gallego M. , Ríos‐Fernández R. , Camps M. T. , Fernández‐Nebro A. , Egurbide M. V. , Carreira P. , González‐Gay M. A. , Martín J. ,   Spanish Scleroderma Group
Published: June 2012

AbstractSystemic sclerosis (SSc) is a complex autoimmune disease which genetic component has not been yet completely understood. IL6 encodes a cytokine with a crucial role in the development of autoimmunity and fibrosis and its actions mainly are controlled by IL‐6 receptor (IL‐6R). We aimed to investigate whether the functional genetic variants rs8192284 and rs2228044 previously associated with several autoimmune diseases, located within the IL‐6 receptor (IL‐6R) subunits IL6R and IL6ST genes, respectively, are involved in the susceptibility to SSc and/or its major clinical subphenotypes. A Spanish cohort including 1013 SSc patients and 1375 controls was genotyped using the TaqMan® allelic discrimination technology. SSc patients were subdivided according to the major clinical forms, autoantibody status and presence of fibrotic lung affection. Our data showed no influence of the selected variants in global SSc susceptibility (rs8192284: P = 0.67, odds ratios (OR) = 0.98; rs2228044: P = 0.99, OR = 1.00). Similarly, the clinical/autoantibody subphenotype analyses did not yielded significant results. Our data suggest that the analyzed polymorphisms may not play a significant role in the SSc susceptibility.
Rosellinia necatrix attack according to soil features in the Mediterranean environment
Authors: Carlucci A. , Manici L. M. , Colatruglio L. , Caputo A. , Frisullo S. 
Published: June 2012

SummaryA study was carried out on Rosellinia necatrix attack on young woody plants, as possibly affected by selected soil features under three water regimes. Six different soil systems representing five agro‐environments and one forest in the Puglia Region (southern Italy – Mediterranean climate) were compared. R. necatrix attack on sweet cherry trees was simulated using artificial inoculum and saplings of Prunus mahaleb, the most widely used rootstock of sweet and sour cherries, monitored during the spring period. Soil features significantly influenced disease score, which did not differ from one water regime to another, even though disease level in the different soils was affected by water content. Rosellinia mahaleb saplings grown in forest soil showed the highest disease score, which differed significantly from that observed in all the agricultural soils tested in this study. Amongst these, disease score was lower in sandy soils than in soils that were richer in loamy fraction.
Ontogeny and tissue differentiation of the pelvic girdle and hind limbs of anurans
Authors: Manzano Adriana , Abdala Virginia , Ponssa María L. , Soliz Mónica 
Published: June 2012

AbstractWe present the ontogeny of the integrated musculoskeletal complex that comprises the pelvic girdle and hind limbs of anurans. Our histological data show that the pelvic girdle originates from a single mesenchymatic condensation. The tissue differentiation sequence is cartilage, muscle and tendon. The intrusion of the ischiadic nerve into the limb bud is produced very early in ontogeny. The pre‐cartilage appears in the pre‐motile stage. Therefore, the nerve produces a movement analogous to the ‘embryonic motility’ that would induce the emergence of the pre‐cartilage. The acetabulum is the first of all cavitation processes to form, the second one being the knee. The acetabulum appears before the muscles are mature, although it has been stressed that the muscle contraction maintains joint progenitors committed to their fate. Our data indicate an explosive differentiation of all 11 muscular masses together. We provide three new characters that support the monophyly of Hyloides, Acosmanura and Neobatrachia.