bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling detention basins measured from high‐resolution light detection and ranging data
Authors: Wang Lei , Yu Jaehyung 
Published: September 2011

AbstractThe construction of stormwater detention basins is a best management practice to effectively control floods, to provide additional surface storage for excess floodwater and to compensate for the adverse effects of urban development. Traditional field‐based levelling survey methods are very time consuming and subject to human‐induced arbitrariness and error. This article presents an approach to modelling detention basins measured from light detection and ranging remote sensing data. A case study is illustrated by using the White Oak Bayou watershed of Harris County, Texas. The storage–stage curve obtained from the volumetric analysis is used in a modified detention basins routing model, which was developed by adding the weir structure control to the traditional hydrologic reservoir routing equations. The model simulation showed that the peak flow of the synthetic 100‐year reoccurrence event was effectively reduced and delayed by the detention basins. The comparison with the simulation results from the traditional reservoir routing model suggested that previous studies using the reservoir routing model were likely to underestimate the flood reduction effect of detention basins. The sensitivity analysis of the parameters showed that the detention basin design and evaluation should pay more attention on the weir height and river channel's roughness. Copyright © 2011 John Wiley & Sons, Ltd.
Oncogenic PIK3CA mutations in colorectal cancers and polyps
Authors: Whitehall Vicki L.J. , Rickman Celestine , Bond Catherine E. , Ramsnes Ingunn , Greco Sonia A. , Umapathy Aarti , McKeone Diane , Faleiro Rebecca J. , Buttenshaw Ron L. , Worthley Daniel L. , Nayler Sam , Zhao Zhen Zhen , Montgomery Grant W. , Mallitt Kylie‐Ann , Jass Jeremy R. , Matsubara Nagahide , Notohara Kenji , Ishii Tatsuhiro , Leggett Barbara A. 
Published: September 2011

AbstractOncogenic PIK3CA mutations contribute to colorectal tumorigenesis by activating AKT signaling to decrease apoptosis and increase tumor invasion. A synergistic association of PIK3CA mutation with KRAS mutation has been suggested to increase AKT signaling and resistance to antiepidermal growth factor receptor inhibitor therapy for advanced colorectal cancer, although studies have been conflicting. We sought to clarify this by examining PIK3CA mutation frequency in relation to other key molecular features of defined pathways of tumorigenesis. PIK3CA mutation was assessed by high resolution melt analysis in 829 colorectal cancer samples and 426 colorectal polyps. Mutations were independently correlated with clinicopathological features including patient age, sex and tumor location as well as molecular features including microsatellite instability, KRAS and BRAF mutation, MGMT methylation and the CpG Island Methylator Phenotype (CIMP). Mutation of the helical (Exon 9) and catalytic (Exon 20) domain mutation hotspots were also examined independently. Overall, PIK3CA mutation was positively correlated with KRAS mutation (p < 0.001), MGMT methylation (p = 0.007) and CIMP (p < 0.001). Novel, exon‐specific associations linked Exon 9 mutations to a subgroup of cancers characterized by KRAS mutation, MGMT methylation and CIMP‐Low, whilst Exon 20 mutations were more closely linked to features of serrated pathway tumors including BRAF mutation, microsatellite instability and CIMP‐High or Low. PIK3CA mutations were uncommonly, but exclusively, seen in tubulovillous adenomas (4/124, 3.2%) and 1/4 (25.0%) tubulovillous adenomas with a focus of cancer. These data provide insight into the molecular events driving traditional versus serrated pathway tumorigenesis.
Regulation of cell volume by glycosaminoglycans
Authors: Joerges Jelena , Schulz Tobias , Wegner Jeannine , Schumacher Udo , Prehm Peter 
Published: September 2011

AbstractCell volume is regulated by a delicate balance between ion distribution across the plasma membrane and the osmotic properties of intra‐ and extracellular components. Using a fluorescent calcein indicator, we analysed the effects of glycosaminoglycans on the cell volume of hyaluronan producing fibroblasts and hyaluronan deficient HEK cells over a time period of 30 h. Exogenous glycosaminoglycans induced cell blebbing after 2 min and swelling of fibroblasts to about 110% of untreated cell volume at low concentrations which decreased at higher concentrations. HEK cells did not show cell blebbing and responded by shrinking to 65% of untreated cell volume. Heparin induced swelling of both fibroblasts and HEK cells. Hyaluronidase treatment or inhibition of hyaluronan export led to cell shrinkage indicating that the hyaluronan coat maintained fibroblasts in a swollen state. These observations were explained by the combined action of the Donnan effect and molecular crowding. J. Cell. Biochem. 113: 340–348, 2012. © 2011 Wiley Periodicals, Inc.
Using hyperpolarized 3He MRI to evaluate treatment efficacy in cystic fibrosis patients
Authors: Sun Yanping , O'Sullivan Brian P. , Roche John P. , Walvick Ronn , Reno Austin , Baker Dawn , Mansour Joey K. , Albert Mitchell S. 
Published: September 2011

AbstractPurpose:To use hyperpolarized (HP) 3He MR imaging to assess functional lung ventilation in subjects with cystic fibrosis (CF) before and after treatment.Materials and Methods:We performed HP 3He static ventilation MRI scans on three subjects, using a Philips 3.0 Tesla (T) Achieva MRI scanner, before and after 11 days of in‐patient treatment with combined intravenous and inhaled therapies for pulmonary exacerbations of CF. We also collected spirometry data. We quantified pulmonary ventilation volume measured with HP 3He MRI using an advanced semi‐automated analysis technique.Results:Following 11 days of treatment with intravenous antibiotics, hypertonic saline, and rhDNase, HP 3He MR images in one subject displayed a 25% increase in total ventilation volume. Total ventilation volume in the other two subjects slightly decreased. All three subjects showed increases in FEV1 and FVC following treatment.Conclusion:In all subjects, the HP 3He MR images provided detailed information on precisely where in the lungs gas was reaching. These data provide additional support for the conclusion that HP noble gas MRI can be a powerful tool for evaluating lung ventilation in patients with cystic fibrosis, but also raise important questions about the correlation between spirometry and HP gas MRI measurements. J. Magn. Reson. Imaging 2011. © 2011 Wiley Periodicals, Inc.
Chronic administration of the neurotrophic agent cerebrolysin ameliorates the behavioral and morphological changes induced by neonatal ventral hippocampus lesion in a rat model of schizophrenia
Authors: Vázquez‐Roque Rubén Antonio , Ramos Brenda , Tecuatl Carolina , Juárez Ismael , Adame Anthony , de la Cruz Fidel , Zamudio Sergio , Mena Raúl , Rockenstein Edward , Masliah Eliezer , Flores Gonzalo 
Published: September 2011

AbstractNeonatal ventral hippocampal lesion (nVHL) in rats has been widely used as a neurodevelopmental model to mimic schizophrenia‐like behaviors. Recently, we reported that nVHLs result in dendritic retraction and spine loss in prefrontal cortex (PFC) pyramidal neurons and medium spiny neurons of the nucleus accumbens (NAcc). Cerebrolysin (Cbl), a neurotrophic peptide mixture, has been reported to ameliorate the synaptic and dendritic pathology in models of aging and neurodevelopmental disorder such as Rett syndrome. This study sought to determine whether Cbl was capable of reducing behavioral and neuronal alterations in nVHL rats. The behavioral analysis included locomotor activity induced by novel environment and amphetamine, social interaction, and sensoriomotor gating. The morphological evaluation included dendritic analysis by using the Golgi‐Cox procedure and stereology to quantify the total cell number in PFC and NAcc. Behavioral data show a reduction in the hyperresponsiveness to novel environment‐ and amphetamine‐induced locomotion, with an increase in the total time spent in social interactions and in prepulse inhibition in Cbl‐treated nVHL rats. In addition, neuropathological analysis of the limbic regions also showed amelioration of dendritic retraction and spine loss in Cbl‐treated nVHL rats. Cbl treatment also ameliorated dendritic pathology and neuronal loss in the PFC and NAcc in nVHL rats. This study demonstrates that Cbl promotes behavioral improvements and recovery of dendritic neuronal damage in postpubertal nVHL rats and suggests that Cbl may have neurotrophic effects in this neurodevelopmental model of schizophrenia. These findings support the possibility that Cbl has beneficial effects in the management of schizophrenia symptoms. © 2011 Wiley Periodicals, Inc.
A retrospective study of surgical treatment of chronic radiation enteritis
Authors: Zhu Weiming , Gong Jianfeng , Li Yi , Li Ning , Li Jieshou 
Published: September 2011

AbstractBackground and aimsWe assessed the role of surgery in the management of patients with intestinal obstruction or enterocutaneous fistula after chronic radiation enteritis (CRE) referred to our department, a specialist gastrointestinal surgical center, and analysis was made for the success of surgery.MethodsA retrospective analysis was made of 156 patients receiving radiation therapy for malignancy from Jan 2000 to Nov 2010, among which 134 received surgery for intestinal or urinary complications. The demographic data, nutritional status, previous surgery, disease location and clinical manifestations, concomitant urinary complications, and surgical procedures were analyzed.ResultsAlthough malnutrition was prevalent (84/156, 53.9%) in this group of patients, the majority of them (101/134, 75.4%) recovered uneventfully after surgery following nutrition therapy, and resection and anastomosis (102/134) was the predominant surgical procedure for radiation injury to the ileocecal region. Sixteen patients received surgery for radiation‐induced urinary complications. There were 36 postoperative morbidities (26.87%), mainly wound complications (21/134), intestinal obstruction (5/134), and anastomotic dehiscence (3/134).ConclusionsSurgery is justified for patients with bowel obstruction or fistula after CRE. A comprehensive perioperative management, especially perioperative nutrition therapy was important for the success of the surgery. J. Surg. Oncol. 2012; 105:632–636. © 2011 Wiley Periodicals, Inc.
Innovative manufacturing of 3D‐lightweight components
Authors: Brecher Christian , Dubratz Markus , Stimpfl Joffrey , Emonts Michael 
Published: September 2011

AbstractFibre‐reinforced plastics (or: fibre‐reinforced polymers, FRPs) – a group of materials with excellent and largely adjustable properties – have found their way into many industries over the past yearsn and have established themselves in various sectors. Continuous FRPs have a wide potential for lightweight designs due to their ability to withstand high mechanical loads despite their tare weight. Today's air and space technologies or the wind power industry are unimaginable without this material. Fibre‐reinforced components will form one of the most importantkey factors for the European industry with its energy‐efficient production to fulfil the increasing global demands e.g. energy efficiency, waste avoidance and reduction of CO2‐emissions.
Hepatocyte-derived MicroRNAs as Serum Biomarkers of Hepatic Injury and Rejection after Liver Transplantation
Authors: Farid Waqar R. R. , Pan Qiuwei , van der Meer Adriaan J. P. , de Ruiter Petra E. , Ramakrishnaiah Vedashree , de Jonge Jeroen , Kwekkeboom Jaap , Janssen Harry L. A. , Metselaar Herold J. , Tilanus Hugo W. , Kazemier Geert , van der Laan Luc J.W. 
Published: September 2011

Abstract
Recent animal and human studies have highlighted the potential of hepatocyte-derived microRNAs (HDmiRs) in serum as early, stable, sensitive, and specific biomarkers of liver injury. Their usefulness in human liver transplantation, however, has not been addressed. The aim of this study was to investigate serum HDmiRs as markers of hepatic injury and rejection in liver transplantation. Serum samples from healthy controls and liver transplant recipients (n = 107) and peritransplant liver allograft biopsy samples (n = 45) were analyzed via the real-time polymerase chain reaction quantification of HDmiRs (miR-122, miR-148a, and miR-194). The expression of miR-122 and miR-148a in liver tissue was significantly reduced with prolonged graft warm ischemia times. Conversely, the serum levels of these HDmiRs were elevated in patients with liver injury and positively correlated with aminotransferase levels. HDmiRs appear to be very sensitive because patients with normal aminotransferase values (<50 IU/L) had 6- to 17-fold higher HDmiR levels in comparison with healthy controls (P < 0.005). During an episode of acute rejection, serum HDmiRs were elevated up to 20-fold, and their levels appeared to rise earlier than aminotransferase levels. HDmiRs in serum were stable during repeated freezing and thawing. In conclusion, this study shows that liver injury is associated with the release of HDmiRs into the circulation. HDmiRs are promising candidates as early, stable, and sensitive biomarkers of rejection and hepatic injury after liver transplantation.
Liver Transpl 18:290–297, 2012.
© 2012 AASLD.
Long-Term Outcome of Hepatitis C Virus Infections Acquired After Pediatric Liver Transplantation
Authors: Venturi Carla , Bueno Javier , Castells Lluís , Quintero Jesus , Casas Isabel , Allende Helena , Martinez-Ibañez Vicente , Charco Ramón 
Published: September 2011

Abstract
The outcomes and characterization of hepatitis C virus (HCV) infections after pediatric liver transplantation (LT) have rarely been reported. We describe our experience with HCV infections after pediatric LT. Ten of 207 children (4.8%) who underwent LT at our institution (1985-2010) developed previously undiagnosed HCV disease. Eight received a liver graft before blood product and donor screening for HCV became available. The mean age at transplantation was 8.9 ± 4.3 years, and the median time from transplantation to the diagnosis of HCV was 15.1 years (range = 0.2-19.7 years). The genotypes were 1 (n = 8), 3 (n = 1), and undetermined (n = 1). At the time of this writing, all the patients were still alive with a mean follow-up of 7.3 ± 5.5 years after the diagnosis of HCV. Five patients did not receive treatment; 2 of these patients achieved spontaneous viral clearance (SVC). Four of the 5 treated patients achieved a sustained virological response, and 3 had an early virological response (EVR). Two of these 4 patients developed chronic rejection while they were on treatment, but this was resolved with a conversion from cyclosporine A to tacrolimus. The remaining patient was continuing treatment and had achieved EVR. In conclusion, despite the limitations of our series, de novo HCV infections after pediatric LT seem to have a slow histological progression. Even with genotype 1, the patients have a good long-term prognosis and respond well to treatment. Nevertheless, chronic rejection during antiviral therapy may develop. In addition, SVC may occur in this population. Liver Transpl, 2011. © 2011 AASLD.
Mining the malignant ascites proteome for pancreatic cancer biomarkers
Authors: Kosanam Hari , Makawita Shalini , Judd Bramford , Newman Alice , Diamandis Eleftherios P. 
Published: September 2011

AbstractPancreatic cancer (PC) is one of the most lethal malignancies and disease‐specific biomarkers are desperately needed for better diagnosis, prognosis, monitoring treatment efficacy and for accelerating the development of novel targeted therapeutics. Being an advanced stage manifestation and a proximal fluid in contact with cancer tissues, the ascitic fluid presents itself as a promising rich source of biomarkers. Herein, we present a comprehensive proteomic analysis of pancreatic ascitic fluid. To fractionate the complex ascites proteome, we adopted a multi‐dimensional chromatographic approach that included size‐exclusion, ion‐exchange and lectin‐affinity chromatographic techniques. Our detailed proteomic analysis with high‐resolution Orbitrap® mass spectrometer resulted in the identification of 816 proteins. We followed rigorous filtering criteria that consisted of PC‐specific information obtained from three publicly available databases (Oncomine, Protein Atlas and Unigene) to segregate 20 putative biomarker candidates for future validation. Since these proteins are of membranous and extra‐cellular origin, most are glycosylated, and many of them are over‐expressed in cancer tissues, the probability of these proteins entering the peripheral blood circulation is high. Their validation as serological PC biomarkers in the future is highly warranted.
ErbB2/Her‐2 regulates the expression of Akt2 in prostate cancer cells
Authors: Le Page Cécile , Koumakpayi Ismaël Hervé , Péant Benjamin , Delvoye Nathalie , Saad Fred , Mes‐Masson Anne‐Marie 
Published: September 2011

AbstractBACKGROUNDWe have previously reported that ErbB family members regulate the signaling pathway leading to Akt and NF‐kappaB activation in prostate cancer cells. In this study, the regulation of Akt2 expression in LNCaP, DU145, and PC‐3 prostate cancer cell lines was investigated.METHODSAkt‐2 expression was analyzed by western‐blotting and Q‐PCR in cell lines. We also analyzed the Akt‐2 protein expression in a tissue microarray from 64 prostate cancer patients. Akt‐2 promoter activity was assessed and analyzed by luciferase assay.RESULTSA concomitant over‐expression of Her‐2 and Akt2 expression was observed by western‐blotting and quantitative‐PCR in prostate cancer cell lines. A significant correlation between Her‐2 and Akt2 protein expression was also observed by immunohistochemistry assay on prostate cancer tissues. In LNCaP cells, over‐expression of Akt2 protein and mRNA was decreased by Her‐2 pharmacologic inhibitors as well as small interfering RNA (siRNA) specific to Her‐2. Cloning of the AKT2 promoter in a luciferase reporter plasmid further showed that Akt2 over‐expression in cell lines is associated with increased AKT2 promoter activity suggesting that Her‐2 modulates a signaling pathway involving AKT2 gene regulation.CONCLUSIONThis study reveals a novel mechanism of Akt2 regulation in prostate cancer cells. Prostate 72:777–788, 2012. © 2011 Wiley Periodicals, Inc.
Phase II study of personalized peptide vaccination for castration‐resistant prostate cancer patients who failed in docetaxel‐based chemotherapy
Authors: Noguchi Masanori , Moriya Fukuko , Suekane Shigetaka , Matsuoka Kei , Arai Gaku , Matsueda Satoko , Sasada Tetsuro , Yamada Akira , Itoh Kyogo 
Published: September 2011

AbstractBACKGROUNDDocetaxel‐based chemotherapy (DBC) showed limited clinical efficacy for castration‐resistant prostate cancer (CRPC) patients. To explore cancer vaccine as a new treatment modality, we conducted a phase II study of personalized peptide vaccine (PPV) for DBC‐resistant CRPC patients.METHODSTwenty DBC‐resistant CRPC patients and 22 patients with no prior DBC, as a control, were treated with PPV using peptides chosen from 31 peptides in patients, respectively. Cytokines, inflammatory markers, and immune responses were measured as candidate biomarkers. DBC‐resistant CRPC patients without PPV was set as a historical control for evaluation of clinical benefit of PPV.RESULTSMedian overall survival (OS) time from the first vaccination was 14.8 months or not reached in DBC‐resistant CRPC patients and patients with no prior DBC (log‐rank; P = 0.07), respectively. Median OS time from the first day of progression disease was 17.8 and 10.5 months in DBC‐resistant CRPC patients receiving PPV and those with no PPV (P = 0.1656), respectively. Elevated IL‐6 levels before vaccination was an unfavorable factor for OS of DBC‐resistant CRPC patients (P = 0.0161, hazard ratio (HR): 0.024, 95% CI:0.001–0.499) as well as all 42 patients with PPV(P = 0.0011, HR: 0.212, 95% CI:0.068–0.661) by multivariable analysis.CONCLUSIONSFurther clinical study of PPV is recommended for DBC‐resistant CRPC patients, because of the safety and possible prolongation of MST. Control of elevated IL‐6 by combined therapy may provide much better clinical outcome. Prostate 72:834–845, 2012. © 2011 Wiley Periodicals, Inc.
Predicting flexible loop regions that interact with ligands: The challenge of accurate scoring
Authors: Danielson Matthew L. , Lill Markus A. 
Published: September 2011

AbstractFlexible loop regions play a critical role in the biological function of many proteins and have been shown to be involved in ligand binding. In the context of structure‐based drug design, using or predicting an incorrect loop configuration can be detrimental to the study if the loop is capable of interacting with the ligand. Three protein systems, each with at least one flexible loop region in close proximity to the known binding site, were selected for loop prediction using the CorLps program; a six residue loop region from phosphoribosylglycinamide formyltransferase (GART), two nine residue loop regions from cytochrome P450 (CYP) 119, and an 11 residue loop region from enolase were selected for loop prediction. The results of this study indicate that the statistically based DFIRE scoring function implemented in the CorLps program did not accurately rank native‐like predicted loop configurations in any protein system. In an attempt to improve the ranking of the native‐like predicted loop configurations, the MM/GBSA and the optimized MM/GBSA‐dsr scoring functions were used to re‐rank the predicted loops with and without bound ligand. In general, single snapshot MM/GBSA scoring provided the best ranking of native‐like loop configurations. Based on the scoring function analyses presented, the optimal ranking of native‐like loop configurations is still a difficult challenge and the choice of the “best” scoring function appears to be system dependent. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Critical assessment of methods of protein structure prediction (CASP)—round IX
Authors: Moult John , Fidelis Krzysztof , Kryshtafovych Andriy , Tramontano Anna 
Published: September 2011

AbstractThis article is an introduction to the special issue of the journal PROTEINS, dedicated to the ninth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Methods for modeling protein structure continue to advance, although at a more modest pace than in the early CASP experiments. CASP developments of note are indications of improvement in model accuracy for some classes of target, an improved ability to choose the most accurate of a set of generated models, and evidence of improvement in accuracy for short “new fold” models. In addition, a new analysis of regions of models not derivable from the most obvious template structure has revealed better performance than expected. Proteins 2011; © 2011 Wiley‐Liss, Inc.