bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local parasite lineage sharing in temperate grassland birds provides clues about potential origins of Galapagos avian Plasmodium
Authors: Levin Iris I. , Colborn Rachel E. , Kim Daniel , Perlut Noah G. , Renfrew Rosalind B. , Parker Patricia G. 
Published: January 2016

AbstractOceanic archipelagos are vulnerable to natural introduction of parasites via migratory birds. Our aim was to characterize the geographic origins of two Plasmodium parasite lineages detected in the Galapagos Islands and in North American breeding bobolinks (Dolichonyx oryzivorus) that regularly stop in Galapagos during migration to their South American overwintering sites. We used samples from a grassland breeding bird assemblage in Nebraska, United States, and parasite DNA sequences from the Galapagos Islands, Ecuador, to compare to global data in a DNA sequence registry. Homologous DNA sequences from parasites detected in bobolinks and more sedentary birds (e.g., brown‐headed cowbirds Molothrus ater, and other co‐occurring bird species resident on the North American breeding grounds) were compared to those recovered in previous studies from global sites. One parasite lineage that matched between Galapagos birds and the migratory bobolink, Plasmodium lineage B, was the most common lineage detected in the global MalAvi database, matching 49 sequences from unique host/site combinations, 41 of which were of South American origin. We did not detect lineage B in brown‐headed cowbirds. The other Galapagos‐bobolink match, Plasmodium lineage C, was identical to two other sequences from birds sampled in California. We detected a close variant of lineage C in brown‐headed cowbirds. Taken together, this pattern suggests that bobolinks became infected with lineage B on the South American end of their migratory range, and with lineage C on the North American breeding grounds. Overall, we detected more parasite lineages in bobolinks than in cowbirds. Galapagos Plasmodium had similar host breadth compared to the non‐Galapagos haemosporidian lineages detected in bobolinks, brown‐headed cowbirds, and other grassland species. This study highlights the utility of global haemosporidian data in the context of migratory bird–parasite connectivity. It is possible that migratory bobolinks bring parasites to the Galapagos and that these parasites originate from different biogeographic regions representing both their breeding and overwintering sites.
Bioconcentration of two basic pharmaceuticals, verapamil and clozapine, in fish
Authors: Nallani Gopinath C. , Edziyie Regina E. , Paulos Peter M. , Venables Barney J. , Constantine Lisa A. , Huggett Duane B. 
Published: January 2016

Abstract

The present study examined the bioconcentration of 2 basic pharmaceuticals: verapamil (a calcium channel blocker) and clozapine (an antipsychotic compound) in 2 fresh water fishes, fathead minnow and channel catfish. In 4 separate bioconcentration factor (BCF) experiments (2 chemicals × 1 exposure concentration × 2 fishes), fathead minnow and channel catfish were exposed to 190 μg/L and 419 μg/L of verapamil (500 μg/L nominal) or 28.5 μg/L and 40 μg/L of clozapine (50 μg/L nominal), respectively. Bioconcentration factor experiments with fathead consisted of 28 d uptake and 14 d depuration, whereas tests conducted on catfish involved a minimized test design, with 7 d each of uptake and depuration. Fish (n = 4–5) were sampled during exposure and depuration to collect different tissues: muscle, liver, gills, kidneys, heart (verapamil tests only), brain (clozapine tests only), and blood plasma (catfish tests only). Verapamil and clozapine concentrations in various tissues of fathead and catfish were analyzed using liquid chromatography–mass spectrometry. In general, higher accumulation rates of the test compounds were observed in tissues with higher perfusion rates. Accumulation was also high in tissues relevant to pharmacological targets in mammals (i.e. heart in verapamil test and brain in the clozapine test). Tissue-specific BCFs (wet wt basis) for verapamil and clozapine ranged from 0.7 to 75 and from 31 to 1226, respectively. Tissue-specific concentration data were used to examine tissue–blood partition coefficients. Environ Toxicol Chem 2016;35:593–603. © 2016 SETAC
Bare fiber Bragg grating immunosensor for real‐time detection of Escherichia coli bacteria
Authors: Srinivasan Rajesh , Umesh Sharath , Murali Swetha , Asokan Sundarrajan , Siva Gorthi Sai 
Published: January 2016

Escherichia coli (E. coli) bacteria have been identified to be the cause of variety of health outbreaks resulting from contamination of food and water. Timely and rapid detection of the bacteria is thus crucial to maintain desired quality of food products and water resources. A novel methodology proposed in this paper demonstrates for the first time, the feasibility of employing a bare fiber Bragg grating (bFBG) sensor for detection of E. coli bacteria. The sensor was fabricated in a photo‐sensitive optical fiber (4.2 µm/80 µm). Anti‐E. coli antibody was immobilized on the sensor surface to enable the capture of target cells/bacteria present in the sample solution. Strain induced on the sensor surface as a result of antibody immobilization and subsequent binding of E. coli bacteria resulted in unique wavelength shifts in the respective recording of the reflected Bragg wavelength, which can be exploited for the application of biosensing. Functionalization and antibody binding on to the fiber surface was cross validated by the color development resulting from the reaction of an appropriate substrate solution with the enzyme label conjugated to the anti‐E. coli antibody. Scanning electron microscope image of the fiber, further verified the E. coli cells bound to the antibody immobilized sensor surface.
magnified image
Determining in vivo elasticity and viscosity with dynamic Scheimpflug imaging analysis in keratoconic and healthy eyes
Authors: Wang Li‐Ke , Tian Lei , Zheng Yong‐Ping 
Published: January 2016

The paper presents a novel analysis method of corneal elasticity and viscosity based on corneal visualization Scheimpflug technology (CorVis ST) for keratoconus diagnosis. Methods for air puff force measurement and corneal imaging boundary extraction were proposed. Corneal biomechanical properties, described as tangent stiffness coefficient (STSC) and energy absorbed area (Aabsorbed), were assessed using the curves of the applied air puff force with corneal displacement to form a loading‐unloading cycle. Twenty‐five patients with keratoconus and 34 healthy control subjects, matched for intraocular pressure (IOP), were enrolled in this prospective study. The results showed that the intraclass correlation coefficients (ICC) of the STSC and Aabsorbed were 0.941 and 0.878 in Healthy group; and were 0.891 and 0.809 in Keratoconus group, respectively. Both STSC and Aabsorbed of keratoconus patients were significantly different from that of controls (both probability value P < 0.001). ROC curve analysis showed that the area under curve for STSC was 0.918 and for Aabsorbed was 0.894, which reached a good level of predictive accuracy for detecting keratoconus. Our results demonstrated that this new analysis method could be used to characterize the biomechanical properties of corneas.
(a) The air puff force of CorVis ST was measured by a custom‐designed force detection system. (b) Corneal displacement was extracted from CorVis ST using a proposed imaging analysis. (c) With the utilization of the air puff force and corneal dynamic displacement, an analysis method was developed to introduce new corneal biomechanical parameters – STSC and Aabsorbed.magnified image(a) The air puff force of CorVis ST was measured by a custom‐designed force detection system. (b) Corneal displacement was extracted from CorVis ST using a proposed imaging analysis. (c) With the utilization of the air puff force and corneal dynamic displacement, an analysis method was developed to introduce new corneal biomechanical parameters – STSC and Aabsorbed.
A Novel Domain-Specific Mutation in a Sclerosteosis Patient Suggests a Role of LRP4 as an Anchor for Sclerostin in Human Bone
Authors: Fijalkowski Igor , Geets Ellen , Steenackers Ellen , Van Hoof Viviane , Ramos Feliciano J , Mortier Geert , Fortuna Ana Maria , Van Hul Wim , Boudin Eveline 
Published: January 2016

ABSTRACT

Mutations in the LRP4 gene, coding for a Wnt signaling coreceptor, have been found to cause several allelic conditions. Among these, two are characterized by a strong skeletal involvement, namely sclerosteosis and Cenani-Lenz syndrome. In this work, we evaluated the role of LRP4 in the pathophysiology of these diseases. First, we report a novel LRP4 mutation, leading to the substitution of arginine at position 1170 in glutamine, identified in a patient with sclerosteosis. This mutation is located in the central cavity of the third β-propeller domain, which is in line with two other sclerosteosis mutations we previously described. Reporter assays demonstrate that this mutation leads to impaired sclerostin inhibition of Wnt signaling. Moreover, we compared the effect of this novel variant to mutations causing Cenani-Lenz syndrome and show that impaired membrane trafficking of the LRP4 protein is the likely mechanism underlying Cenani-Lenz syndrome. This is in contrast to sclerosteosis mutations, previously shown to impair the binding between LRP4 and sclerostin. In addition, to better understand the biology of LRP4, we investigated the circulating sclerostin levels in the serum of a patient suffering from sclerosteosis owing to a LRP4 mutation. We demonstrate that impaired sclerostin binding to the mutated LRP4 protein leads to dramatic increase in circulating sclerostin in this patient. With this study, we provide the first evidence suggesting that LRP4 is responsible for the retention of sclerostin in the bone environment in humans. These findings raise potential concerns about the utility of determining circulating sclerostin levels as a marker for other bone-related parameters. Although more studies are needed to fully understand the mechanism whereby LRP4 facilitates sclerostin action, it is clear that this protein represents a potent target for future osteoporosis therapies and an interesting alternative for the antisclerostin treatment currently under study. © 2016 American Society for Bone and Mineral Research.
Molecular Characterization of a Copper Metallothionein Gene From a Ciliate Tetrahymena farahensis
Authors: Zahid Muhammad Tariq , Shakoori Farah Rauf , Zulifqar Soumble , Ahmed Ishtiaq , Al‐Ghanim Khalid , Mehboob Shahid , Shakoori Abdul Rauf 
Published: January 2016

ABSTRACTA new copper metallothionein (TfCuMT) gene has been identified from a locally isolated ciliate Tetrahymena farahensis. It contains 327 nucleotides encoding a peptide chain of 108 amino acids and belongs to class MTT2 and subfamily 7b. Amplification from both gDNA and mRNA confirmed the intronless nature of this gene. Like most of the metallohtioneins, cysteine residues contribute nearly 30% content with the specific CKC motifs. Structural repeats present in peptide sequence of TfCuMT indicate internal duplication of gene at some stage of gene evolution. The predicted model of copper metallothionein protein showed that copper ions are mainly chelated by thiol sulfur of cysteine residues and are embedded in the folds of polypeptide chain. For in vivo expression of TfCuMT in Escherichia coli host cells the classical stop codons, which coded for glutamine in the ciliate were mutated to CAA and CAG through site directed mutagenesis. The mutated gene showed higher expression in pET28a expression vector compared with pET21a. Optimum expression was obtained after 6–8 h of 0.1 mM IPTG induction. Stability of His tagged TfCuMT in 5% SDS was low, with half‐life of about 104 min. Presence of 1.0 μM copper increased the expression level by 1.65‐fold. Presence of 100 μM Cysteine in culture medium caused 2.4‐fold increase in expression level. His tagged TfCuMT was purified through affinity chromatography using NTN‐His binding resin in the presence of 0.1 M imidazole and NaCl. The modeled structure of the TfCuMT showed a cleft for Cu binding with correct orientation of Cys residues in the motif CKC. J. Cell. Biochem. 117: 1843–1854, 2016. © 2016 Wiley Periodicals, Inc.
The Effects of Severe Hypoxia on Glycolytic Flux and Enzyme Activity in a Model of Solid Tumors
Authors: Smith Hannah , Board Mary , Pellagatti Andrea , Turley Helen , Boultwood Jacqueline , Callaghan Richard 
Published: January 2016

ABSTRACTSolid tumors contend with, and adapt to, a hostile micro‐environment that includes limited availability of nutrient fuels and oxygen. The presence of hypoxia (O2 <5%) stabilizes the transcription factor Hif1 and results in numerous cellular adaptations including increased flux of glucose through glycolysis. Increasingly, more sophisticated analysis of tumor oxygenation has revealed large gradients of oxygen tension and significant regions under severe hypoxia (O2 ∼0.1%). The present investigation has demonstrated a significant increase in the glycolytic flux rate when tumor spheroids were exposed to 0.1% O2. The severe hypoxia was associated with uniform pimonidazole adduct formation and elevated levels of Hif1α and c‐Myc. This resulted in elevated expression of GLUT and MCT transporters, in addition to increased activity of PFK1 in comparison to that observed in normoxia. However, the protein expression and enzymatic capacity of HK2, G6PDH, PK, and LDH were all reduced by severe hypoxia. Clearly, the effects of exposure to severe hypoxia lead to a significantly abridged Hif1 response, yet one still able to elevate glycolytic flux and prevent loss of intermediates to anabolism. J. Cell. Biochem. 117: 1890–1901, 2016. © 2016 Wiley Periodicals, Inc.
HIV‐1 Infection Dysregulates Cell Cycle Regulatory Protein p21 in CD4+ T Cells Through miR‐20a and miR‐106b Regulation
Authors: Guha Debjani , Mancini Allison , Sparks Jessica , Ayyavoo Velpandi 
Published: January 2016

ABSTRACTBoth CD4+ T lymphocytes and macrophages are the major targets of human immunodeficiency virus type 1 (HIV‐1); however, they respond differently to HIV‐1 infection. We hypothesized that HIV‐1 infection alters gene expression in CD4+ T cells and monocyte‐derived macrophages (MDMs) in a cell specific manner and microRNAs (miRNAs) in part play a role in cell‐specific gene expression. Results indicate that 183 and 31 genes were differentially regulated in HIV‐1 infected CD4+ T cells and MDMs, respectively, compared to their mock‐infected counterparts. Among the differentially expressed genes, cell cycle regulatory gene, p21 (CDKN1A) was upregulated in virus infected CD4+ T cells both at the mRNA and protein level in CD4+ T cells, whereas no consistent change was observed in MDMs. Productively infected CD4+ T cells express higher amount of p21 compared to bystander cells. In determining the mechanism(s) of cell type specific regulation of p21, we found that the miRNAs miR‐106b and miR‐20a that target p21 were specifically downregulated in HIV‐1 infected CD4+ T cells. Overexpression of these two miRNAs reduced p21 expression significantly in HIV‐1 infected CD4+ T cells. These findings provide a potential mechanism, by which, HIV‐1 could exploit host cellular machineries to regulate selective gene expression in target cells. J. Cell. Biochem. 117: 1902–1912, 2016. © 2016 Wiley Periodicals, Inc.
Platelet count is more useful for predicting posthepatectomy liver failure at surgery for hepatocellular carcinoma than indocyanine green clearance test
Authors: Tomimaru Yoshito , Eguchi Hidetoshi , Gotoh Kunihito , Kawamoto Koichi , Wada Hiroshi , Asaoka Tadafumi , Noda Takehiro , Yamada Daisaku , Ogawa Hisataka , Umeshita Koji , Nagano Hiroaki , Doki Yuichiro , Mori Masaki 
Published: January 2016

Background and ObjectivesPreoperatively evaluating reserved liver function is critical in preventing posthepatectomy liver failure (PHLF) in patients undergoing liver resection. The commonly used indocyanine green (ICG) clearance test has several drawbacks. Patients would benefit from a more reliable and straightforward means of assessing the risk of PHLF.MethodsThis study included 277 patients with hepatocellular carcinoma (HCC) undergoing liver resection. The predictive value of known risk factors for PHLF was compared to that of ICG.ResultsPHLF was identified in 25 out of 277 patients (9.0%). Multivariate logistic regression analysis for identifying predictors for the PHLF development revealed platelet count and resected liver volume as significant independent predictors. In a subgroup analysis based on resected liver volume, platelet count was significantly correlated with PHLF in both larger volume (≥100 g) and smaller volume resection groups (<100 g), although ICG R15 level was associated with PHLF only in larger volume group.ConclusionsPlatelet count is superior to ICG R15 level in predicting PHLF development in HCC patients. J. Surg. Oncol. 2016;113:565–569. © 2016 Wiley Periodicals, Inc.
Prognostic factors in patients with malignant pleural effusion: Is it possible to predict mortality in patients with good performance status?
Authors: Abrao Fernando Conrado , Peixoto Renata D'Alpino , de Abreu Igor Renato Louro Bruno , Janini Maria Cláudia , Viana Geisa Garcia , de Oliveira Mariana Campello , Younes Riad Naim 
Published: January 2016

Background and ObjectivesThe aim of this study was to identify predictors of mortality only in patients with malignant pleural effusion (MPE) showing good performance status which required pleural palliative procedures.MethodsAll patients with MPE submitted to pleural palliative procedure were enrolled in a prospective study between 2013 and 2014. Patients with Eastern cooperative oncology group (ECOG) score zero, one, and two were considered with good performance status. The possible prognostic factors were tested for significance using the log‐rank test (Kaplan–Meier method) and those with significance on univariate analysis were entered into a multivariable Cox model.ResultsA total of 64 patients were included in the analysis. Median follow‐up time for surviving patients was 263 days. Median survival for the entire cohort was not reached yet. In the multivariate analysis, gastrointestinal primary site (P = 0.006), low albumin concentration in the pleural fluid (P = 0.017), and high serum NLR (P = 0.007) were associated with mortality.ConclusionIn our cohort of ECOG 0–2 patients with MPE submitted to pleural palliative procedures, gastrointestinal malignancy compared to other sites, low pleural fluid albumin and high NLR were significantly associated with mortality. The identification of these prognostic factors may assist the choice of the optimal palliative technique. J. Surg. Oncol. 2016;113:570–574. © 2016 Wiley Periodicals, Inc.
Raindrop size distribution properties associated with vertical air motion in the stratiform region of a springtime rain event from 1290 MHz wind profiler, micro rain radar and Parsivel disdrometer measurements
Authors: Kim Dong‐Kyun , Lee Dong‐In 
Published: January 2016

ABSTRACTOn 12 March 2012, a frontal rain system elongated east–west occurred over the southern coast of Korea, a frequently observation during springtime. Characteristics of raindrop size distributions (RSDs) in the stratiform region of the rain system observed by a 1290 MHz wind profiler collocated with a Parsivel disdrometer and K‐band micro rain radar (MRR) are investigated. Temporal RSD variations are in close agreement between the instruments in spite of different sampling volume and height. It is found that number concentrations at small drop range around 1 mm measured from the profiler at 800 m AGL are noticeably fewer particularly at times of high rainfall rates, compared to those at the same drop range from the MRR and disdrometer. This is likely attributed to downdrafts that were enhanced below a strong bright band. Profiler Doppler spectra and RSD retrievals are susceptible to vertical air motion effects (especially at small drop range) at higher levels, compared to surface disdrometer retrievals. Thus, vertical air motion retrievals from profiler Doppler spectra were performed and showed good agreement in comparison with vertical air motions derived from a conventional method (i.e. radar reflectivity–fallspeed relation). Following this, vertical air motion effects on rain rate and mass‐weighted mean diameter parameters were examined quantitatively using a profiler spectral model for conditions of updrafts and downdrafts.
Optimal layer division for low latency in DHT‐based hierarchical P2P network
Authors: Li Jun , Li Cuilian , Fang Zhaoxi , Wang Haoyun , Wu Yaohui 
Published: January 2016

SummaryHierarchical architecture can significantly reduce the workload overheads and facilitate effective search in peer‐to‐peer (P2P) network by dividing the peers into two layers: a supernode layer and an ordinary node layer. System scalability is therefore improved, which is critical to the deployment of P2P applications, particularly for the P2P‐based Voice over Internet Protocol systems. However, the lack of appropriate size ratio of the supernode layer to the ordinary node layer makes the system search performance far from being optimal. To address the problem, the goal of this paper is to find the optimal layer ratio, such that lookup latency is minimized, subject to the capacity constraint of supernodes. With this particular objective, this paper first formulates a search delay model for the distributed hash table (DHT)‐based layered P2P architecture, taking account of two main sources of latency: DHT routing and queuing delay at the supernode. Then the optimal ratio between supernodes and ordinary nodes is found with the analytical model. Simulation and numerical results show that the obtained solution can improve the performance of a two‐layer P2P system in terms of lookup latency. Copyright © 2016 John Wiley & Sons, Ltd.
Neonicotinoid concentrations in UK honey from 2013
Authors: Jones Ainsley , Turnbull Gordon 
Published: January 2016

AbstractBACKGROUNDConcentrations of the neonicotinoid insecticides clothianidin, thiamethoxam and imidacloprid were determined in honey collected in Spring 2013 from a variety of locations in England. The honey was produced before the moratorium in the EU on the use of neonicotinoids in pollinator‐attractive crops became effective.RESULTSNeither imidacloprid nor its metabolites were detected in any honey samples. Concentrations of clothianidin ranged from <0.02 to 0.82 µg kg−1, and thiamethoxam concentrations were between <0.01 and 0.79 µg kg−1.CONCLUSIONNeonicotinoid concentrations were below those likely to cause any chronic mortality. The concentrations detected should provide a useful baseline against which the effectiveness of the moratorium in reducing exposure of honeybees can be measured. © 2016 Society of Chemical Industry
Preventing aspartimide formation in Fmoc SPPS of Asp‐Gly containing peptides — practical aspects of new trialkylcarbinol based protecting groups
Authors: Behrendt Raymond , Huber Simon , White Peter 
Published: January 2016

AbstractIn our efforts to develop a universal solution to the problem of aspartimide formation in Fmoc SPPS, we investigated the application of our new β‐trialkylmethyl protected aspartic acid building blocks to the synthesis of peptides containing the Asp‐Gly motif. The Nα‐Fmoc aspartic acid β‐tri‐(ethyl/propyl/butyl)methyl esters were used in the synthesis of the classic model peptide scorpion toxin II (VKDGYI), and their effectiveness in minimising aspartimide formation during extended piperidine treatments was evaluated. Furthermore, we compared their efficacy against that of the commonly used approach of adding acids to the Fmoc deprotection solution. Finally, we applied our aspartic acid building blocks to the stepwise Fmoc SPPS of teduglutide, a human GLP‐2 analogue, whose synthesis is made challenging by extensive aspartimide formation. In all experiments, our approach led to almost complete reduction of aspartimide formation with accompanied suppression of aspartic acid epimerisation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.