bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Humanized Antibody That Regulates the Alternative Pathway Convertase: Potential for Therapy of Renal Disease Associated with Nephritic Factors
Authors: Paixão-Cavalcante Danielle , Torreira Eva , Lindorfer Margaret A. , Rodriguez de Cordoba Santiago , Morgan B. Paul , Taylor Ronald P. , Llorca Oscar , Harris Claire L. 
Published: April 2014

Abstract
Dysregulation of the complement alternative pathway can cause disease in various organs that may be life-threatening. Severe alternative pathway dysregulation can be triggered by autoantibodies to the C3 convertase, termed nephritic factors, which cause pathological stabilization of the convertase enzyme and confer resistance to innate control mechanisms; unregulated complement consumption followed by deposition of C3 fragments in tissues ensues. The mAb, 3E7, and its humanized derivative, H17, have been shown previously to specifically bind activated C3 and prevent binding of both the activating protein, factor B, and the inhibitor, factor H, which are opposite effects that complicate its potential for therapy. Using ligand binding assays, functional assays, and electron microscopy, we show that these Abs bind C3b via a site that overlaps the binding site on C3 for the Ba domain within factor B, thereby blocking an interaction essential for convertase formation. Both Abs also bind the preformed convertase, C3bBb, and provide powerful inhibition of complement activation by preventing cleavage of C3. Critically, the Abs also bound and inhibited C3 cleavage by the nephritic factor–stabilized convertase. We suggest that by preventing enzyme formation and/or cleavage of C3 to its active downstream fragments, H17 may be an effective therapy for conditions caused by severe dysregulation of the C3 convertase and, in particular, those that involve nephritic factors, such as dense deposit disease.
Autoantibodies Induced by Chimeric Cytokine-HIV Envelope Glycoprotein Immunogens
Authors: Isik Gözde , van Montfort Thijs , Chung Nancy P. Y. , Moore John P. , Sanders Rogier W. 
Published: April 2014

Abstract
Cytokines are often used as adjuvants to increase the immunogenicity of vaccines because they can improve the immune response and/or direct it into a desired direction. As an alternative to codelivering Ags and cytokines separately, they can be fused into a composite protein, with the advantage that both moieties act on the same immune cells. The HIV-1 envelope glycoprotein (Env) spike, located on the outside of virus particles and the only relevant protein for the induction of neutralizing Abs, is poorly immunogenic. The induction of anti-Env Abs can be improved by coupling Env proteins to costimulatory molecules such as a proliferation inducing ligand (APRIL). In this study, we evaluated the immunogenicity of chimeric molecules containing uncleaved Env gp140 fused to the species-matched cytokines IL-21 or GM-CSF in rabbits and mice. Each cytokine was either fused to the C terminus of Env or embedded within Env at the position of the variable loops 1 and 2. The cytokine components of the chimeric Env-GM-CSF and Env-IL-21 molecules were functional in vitro, but none of the Env-cytokine fusion proteins resulted in improved Ab responses in vivo. Both the Env-GM-CSF and the Env-IL-21 molecules induced strong anticytokine Ab responses in both test species. These autoimmune responses were independent of the location of the cytokine in the chimeric Env molecules in that they were induced by cytokines inserted within the variable loops 1 and 2 of Env or fused to its C terminus. The induction of undesired autoimmune responses should be considered when using cytokines as costimulatory molecules in fusion proteins.
The 2007 eruptions and caldera collapse of the Piton de la Fournaise volcano (La Réunion Island) from tilt analysis at a single very broadband seismic station
Authors: Fontaine Fabrice R. , Roult Geneviève , Michon Laurent , Barruol Guilhem , Muro Andrea Di 
Published: April 2014

AbstractSeismic records from La Réunion Island very broadband Geoscope station are investigated to constrain the link between the 2007 eruptive sequence and the related caldera collapse of the Piton de la Fournaise volcano. Tilt estimated from seismic records reveals that the three 2007 eruptions belong to a single inflation‐deflation cycle. Tilt trend indicates that the small‐volume summit eruption of 18 February occurred during a phase of continuous inflation that started in January 2007. Inflation decelerated 24 days before a second short‐lived, small‐volume eruption on 30 March, almost simultaneous with a sudden, large‐scale deflation of the volcano. Deflation rate, which had stabilized at relatively low level, increased anew on 1 April while no magma was erupted, followed on 2 April by a major distal eruption and on 5 April by a summit caldera collapse. Long‐term tilt variation suggests that the 2007 eruptive succession was triggered by a deep magma input.
Effect of granular activated carbon concentration on the content of organic matter and salt, influencing E. coli activity and survival in fluidized bed disinfection reactor
Authors: Racyte Justina , Langenhoff Alette A.M. , Ribeiro Ana F.M.M.R. , Paulitsch‐Fuchs Astrid H. , Bruning Harry , Rijnaarts Huub H.M. 
Published: April 2014

ABSTRACTGranular activated carbon (GAC) is used in water treatment systems, typically to remove pollutants such as natural organic matter, volatile organic compounds, chlorine, taste, and odor. GAC is also used as a key component of a new technology that combines a fluidized bed reactor with radio frequency electric fields for disinfection. So far, the effects of GAC on bacteria in these fluidized bed reactors are unclear. This paper describes a systematic study of the physico‐chemical changes in five microbial media compositions caused by different concentrations (23–350 g/L) of GAC, and the effects of these physico‐chemical changes on the metabolic activity and survival of a model microorganism (Escherichia coli YMc10) in a fluidized bed reactor. The chemical adsorption taking place in suspensions with specific GAC changed nutritional, osmotic, and pH conditions in the investigated microbial media (LB, diluted LB, PBS, diluted PBS, and tap water), leading to a decay of the metabolic activity and survival of E. coli. Especially media that are poor in organic and mineral compounds (e.g., PBS) with suspended GAC showed a concentration decay of 3.5 Log CFU/mL E. coli after 6 h. Organic compounds depletion and severe pH variation were enhanced in the presence of higher GAC concentrations. Biotechnol. Bioeng. 2014;111: 2009–2018. © 2014 Wiley Periodicals, Inc.
Segmented flow is controlling growth of catalytic biofilms in continuous multiphase microreactors
Authors: Karande Rohan , Halan Babu , Schmid Andreas , Buehler Katja 
Published: April 2014

ABSTRACTBiofilm reactors are often mass transfer limited due to excessive biofilm growth, impeding reactor performance. Fluidic conditions play a key role for biofilm structural development and subsequently for overall reactor performance. Continuous interfacial forces generated by aqueous‐air segmented flow are controlling biofilm structure and diminish mass transfer limitations in biofilm microreactors. A simple three step method allows the formation of robust biofilms under aqueous‐air segmented flow conditions: a first‐generation biofilm is developing during single phase flow, followed by the introduction of air segments discarding most of the established biofilm. Finally, a second‐generation, mature biofilm is formed in the presence of aqueous‐air segments. Confocal laser scanning microscopy experiments revealed that the segmented flow supports the development of a robust biofilm. This mature biofilm is characterized by a three to fourfold increase in growth rate, calculated from an increase in thickness, a faster spatial distribution (95% surface coverage in 24 h), and a significantly more compact structure (roughness coefficient <1), as compared to biofilms grown under single phase flow conditions. The applicability of the concept in a segmented flow biofilm microreactor was demonstrated using the epoxidation of styrene to (S)‐styrene oxide (ee > 99.8%) catalyzed by Pseudomonas sp. strain VLB120ΔC cells in the mono‐species biofilm. The limiting factor affecting reactor performance was oxygen transfer as the volumetric productivity rose from 11 to 46 g Ltube−1 day−1 after increasing the air flow rate. In summary, different interfacial forces can be applied for separating cell attachment and adaptation resulting in the development of a robust catalytic biofilm in continuous microreactors. Biotechnol. Bioeng. 2014;111: 1831–1840. © 2014 Wiley Periodicals, Inc.
A pilot study linking reduced fronto–Striatal recruitment during reward processing to persistent bingeing following treatment for binge‐eating disorder
Authors: Balodis Iris M. , Grilo Carlos M. , Kober Hedy , Worhunsky Patrick D. , White Marney A. , Stevens Michael C. , Pearlson Godfrey D. , Potenza Marc N. 
Published: April 2014

ABSTRACTObjectiveThe primary purpose of this study was to examine neurobiological underpinnings of reward processing that may relate to treatment outcome for binge‐eating disorder (BED).MethodPrior to starting treatment, 19 obese persons seeking treatment for BED performed a monetary incentive delay task during functional magnetic resonance imaging (fMRI). Analyses examined how the neural correlates of reward processing related to binge‐eating status after 4‐months of treatment.ResultsTen individuals continued to report binge‐eating (BEpost‐tx) following treatment and 9 individuals did not (NBEpost‐tx). The groups did not differ in body mass index. The BEpost‐tx group relative to the NBEpost‐tx group showed diminished recruitment of the ventral striatum and the inferior frontal gyrus during the anticipatory phase of reward processing and reduced activity in the medial prefrontal cortex during the outcome phase of reward processing.DiscussionThese results link brain reward circuitry to treatment outcome in BED and suggest that specific brain regions underlying reward processing may represent important therapeutic targets in BED. © 2013 Wiley Periodicals, Inc. (Int J Eat Disord 2014; 47:376–384)
Visible‐light photocatalytic degradation of methyl orange over spherical activated carbon‐supported and Er3+:YAlO3‐doped TiO2 in a fluidized bed
Authors: Dong Shanshan , Zhang Xueying , He Furong , Dong Shuangshi , Zhou Dandan , Wang Bo 
Published: April 2014

AbstractBACKGROUNDPowdered photocatalyst by doping TiO2 with upconversion luminescence agents achieved visible light induced photocatalysis. However, slurry photocatalysts are difficult to recover from the treated liquor. In the present study, spherical activated carbon (SAC)‐supported and Er3+:YAlO3‐doped visible‐light responsive photocatalyst (Er3+:YAlO3/TiO2‐SAC) was synthesized and characterized. The photocatalytic performance of photocatalyst was examined for degradation of methyl orange (MO) in a liquid–solid fluidized bed photoreactor under visible‐light irradiation.RESULTSTwo notable UV emission peaks at 320 and 360 nm were observed for Er3+:YAlO3 by visible light excitation, which were assigned to the transition of 2P3/2→4I15/2 and 4D5/2→4I11/2, respectively. An optimum 8 h photodecolorization efficiency of 65.3% was obtained from the fluidized bed with reaction rate constant 22.17 mg L−1 h−1. The degradation rate first increased and then decreased with the increasing expansion ratio, and the optimum expansion ratio was found to be 130%.CONCLUSIONOptical characterization revealed that Er3+:YAlO3 could convert incident visible‐light to UV, which can then be utilized by TiO2 for photocatalysis. The visible light generated by Er3+:YAlO3 emissions were not used by TiO2 because of its high band gap. The photocatalytic degradation of MO in the fluidized bed photoreactor followed the Langmuir–Hinshelwood kinetics model. © 2014 Society of Chemical Industry
The quality of carp (Cyprinus carpio L.) cultured in various Polish regions
Authors: Tkaczewska Joanna , Migdał Władysław , Kulawik Piotr 
Published: April 2014

AbstractBACKGROUNDAlthough environmental factors greatly affect the quality of carp meat, no regulations impose labelling the place of cultivation of freshwater fish. That is why the purpose of this study was to determine the quality of carp meat cultivated in several regions of Poland as well as to assess the necessity of implementing such regulations.RESULTSThe influence of the cultivation region on colour, nutrition value, health safety and sensory quality of carp meat was assessed. The analysis included colour measurement, determination of fatty acid profile and sensory evaluation of carp muscle. Moreover, microbiological analysis of the fish surface was performed. The results show that the place of cultivation does not influence the lightness (L*) of fillet, but has an impact on other colour parameters (a*, b*). The microbiological quality of fish from all studied farms was satisfactory, since no pathogenic microorganisms were observed on the fish surface. The fatty acid profile was fairly varied (P < 0.01), depending on the place of cultivation.CONCLUSIONSince final results seem ambiguous, further analyses of quality features of carp from various regions and cultures should be performed, before any recommendation for the necessity of labelling the place and method of cultivation should be suggested. © 2014 Society of Chemical Industry
Human placental extract reduces allergic inflammation in a murine allergic rhinitis model
Authors: Kim Boo‐Young , Park Hyang Rim , Shin Ji‐Hyeon , Kim Sung Won , Kim Soo Whan 
Published: April 2014

Objectives/HypothesisIn this study, we addressed the immunotherapeutic potential of human placental extract (HPE) in a murine allergic rhinitis (AR) model and explored its immunological mechanisms.Study DesignIn vivo study using an animal model.MethodsHPE was administered to BALB/c mice before sensitization with allergen (Dermatophagoides farinae [Derf]) (pre‐S group) or after allergen challenge (post‐C group). The groups were compared with Derf‐treated mice that received no HPE (Derf group) and phosphate buffered saline (PBS)‐treated mice (control). Allergic symptom scores, eosinophil counts, and serum Derf‐specific IgE levels were measured. mRNA expression levels of interferon (IFN)‐γ, T‐bet, interleukin (IL)‐4, GATA‐3, and Foxp3 in nasal mucosa were determined by real‐time polymerase chain reaction. IFN‐γ, T‐bet, IL‐4, and GATA‐3 were confirmed by Western blotting analysis. Spleen CD4+CD25+Foxp3+ T cells were detected using flow cytometry.ResultsRubbing motions, serum Derf‐specific IgE, GATA‐3 mRNA levels, IL‐4 mRNA levels, and tissue eosinophil counts were decreased in both pre‐S and post‐C groups (all P < 0.05). Western blots showed decreased expression of GATA‐3 and IL‐4 in both pre‐S and post‐C groups as compared to the Derf group. An increased percentage of CD4+CD25+Foxp3+ T cells and an increased level of Foxp3 mRNA were found in pre‐S and post‐C groups as compared to those in the Derf group (all P < 0.05).ConclusionBoth prophylactic and therapeutic treatments with HPE significantly reduced allergic inflammation in nasal mucosa and had the potential to induce regulatory T cells in a murine model of AR.Level of EvidenceN/A. Laryngoscope 124:E399–E404, 2014
The homozygous VHLD126N missense mutation is associated with dramatically elevated erythropoietin levels, consequent polycythemia, and early onset severe pulmonary hypertension
Authors: Sarangi Susmita , Lanikova Lucie , Kapralova Katarina , Acharya Suchitra , Swierczek Sabina , Lipton Jeffrey M. , Wolfe Lawrence , Prchal Josef T. 
Published: April 2014

Abstractvon Hippel‐Lindau (VHL) protein is the principal negative regulator of hypoxia sensing mediated by transcription factors. Mutations in exon 3 of the VHL gene lead to Chuvash (VHLR200W) and Croatian (VHLH191D) polycythemias. Here, we describe an infant of Bangladesh ethnicity with a novel homozygous VHLD126N mutation with congenital polycythemia and dramatically elevated erythropoietin (EPO) levels, who developed severe fatal pulmonary hypertension. In contrast to Chuvash polycythemia, erythroid progenitors (BFU‐Es) did not reveal a marked EPO hypersensitivity. Further, NF‐E2 and RUNX1 transcripts that correlate with BFU‐Es EPO hypersensitivity in polycythemic mutations were not elevated. Pediatr Blood Cancer 2014;61:2104–2106. © 2014 Wiley Periodicals, Inc.
Gene silencing of two acetylcholinesterases reveals their cholinergic and non‐cholinergic functions in Rhopalosiphum padi and Sitobion avenae
Authors: Xiao Da , Lu Yan‐Hui , Shang Qing‐Li , Song Dun‐Lun , Gao Xi‐Wu 
Published: April 2014

AbstractBACKGROUDThe function of acetylcholinesterase (AChE) is to terminate synaptic transmission by hydrolysing the neurotransmitter acetylcholine (ACh) in the synaptic cleft, and thus it is an effective target for organophosphate (OP) and carbamate (CB) insecticides.RESULTSThe transcript levels of the four Ace genes were dramatically suppressed by injection of their respective dsRNA in Rhopalosiphum padi and Sitobion avenae. However, the AChE activity changes in the Ace1 knockdown aphids were consistent with the significant transcript level changes of Ace1 genes in these aphids, but not for Ace2. Bioassay results indicated that the suppression of RpAce1 increased its susceptibilities to pirimicarb and malathion, and SaAce1 silencing also increased susceptibility to pirimicarb in S. avenae, whereas the knockdowns of RpAce2 and SaAce2 had a slight effect on their susceptibilities. The knockdown of Ace1 genes also caused significant reductions in fecundity in the aphids of their parental generation.CONCLUSIONSThese results suggest that AChE1 is a predominant cholinergic enzyme and is the target of anticholinesterase insecticides in both R. padi and S. avenae. It also plays a non‐cholinergic role in fecundity of these aphids. AChE2 may also be important for the toxicological function, although its importance appeared to be lower than that of AChE1. © 2014 Society of Chemical Industry
Use of an OSSE to evaluate background‐error covariances estimated by the NMC method
Authors: Errico Ronald M. , Privé Nikki C. , Gu Wei 
Published: April 2014

AbstractThe NMC method has proven utility for prescribing approximate background‐error covariances required by variational data assimilation systems. Here, untuned NMC method estimates are compared with explicitly determined error covariances produced within an OSSE context by exploiting availability of the true simulated states. Such a comparison provides insights into what kind of rescaling is required to render the NMC method estimates usable. It is shown that rescaling of variances and directional correlation lengths depends greatly on both pressure and latitude. In particular, some scaling coefficients appropriate in the Tropics are the reciprocal of those in the Extratropics. Also, the degree of dynamic balance is grossly overestimated by the NMC method. These results agree with previous examinations of the NMC method which used ensembles as an alternative for estimating background‐error statistics.
Regular and Novel Metonymy: Can You Curl up with a Good Agatha Christie in Your Second Language?
Authors: Slabakova Roumyana , Cabrelli Amaro Jennifer , Kyun Kang Sang 
Published: April 2014

AbstractThis article presents results of two off-line comprehension tasks investigating the acceptability of unconventional and conventional metonymy by native speakers of Korean and Spanish who speak English as a second language. We are interested in discovering whether learners differentiate between conventional and unconventional metonymy, and whether the acceptability of metonymic expressions in the native language has an effect on learners’ judgments in the second language. The findings of this study constitute further experimental support for the psychological reality of the distinction between conventional and unconventional metonymy, but only in English. Learners of English at intermediate levels of proficiency exhibit transfer from the native language in comprehending metonymic shifts of meanings. Restructuring of the grammar is evident in later stages of development. Finally, complete success in acquiring L2 metonymic patterns is attested in our experimental study. Implications for L2A theories and teaching practices are discussed.
A comprehensive comparison of association estimators for gene network inference algorithms
Authors: Kurt Zeyneb , Aydin Nizamettin , Altay Gökmen 
Published: April 2014

Abstract
Motivation: Gene network inference (GNI) algorithms enable the researchers to explore the interactions among the genes and gene products by revealing these interactions. The principal process of the GNI algorithms is to obtain the association scores among genes. Although there are several association estimators used in different applications, there is no commonly accepted estimator as the best one for the GNI applications. In this study, 27 different interaction estimators were reviewed and 14 most promising ones among them were evaluated by using three popular GNI algorithms with two synthetic and two real biological datasets belonging to Escherichia coli bacteria and Saccharomyces cerevisiae yeast. Influences of the Copula Transform (CT) pre-processing operation on the performance of the interaction estimators are also observed. This study is expected to assist many researchers while studying with GNI applications.
Results: B-spline, Pearson-based Gaussian and Spearman-based Gaussian association score estimators outperform the others for all datasets in terms of the performance and runtime. In addition to this, it is observed that, when the CT operation is used, inference performances of the estimators mostly increase, especially for two synthetic datasets. Detailed evaluations and discussions are given in the experimental results.
Contact: gokmen.altay@bahcesehir.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Lossy compression of quality scores in genomic data
Authors: Cánovas Rodrigo , Moffat Alistair , Turpin Andrew 
Published: April 2014

Abstract
Motivation: Next-generation sequencing technologies are revolutionizing medicine. Data from sequencing technologies are typically represented as a string of bases, an associated sequence of per-base quality scores and other metadata, and in aggregate can require a large amount of space. The quality scores show how accurate the bases are with respect to the sequencing process, that is, how confident the sequencer is of having called them correctly, and are the largest component in datasets in which they are retained. Previous research has examined how to store sequences of bases effectively; here we add to that knowledge by examining methods for compressing quality scores. The quality values originate in a continuous domain, and so if a fidelity criterion is introduced, it is possible to introduce flexibility in the way these values are represented, allowing lossy compression over the quality score data.
Results: We present existing compression options for quality score data, and then introduce two new lossy techniques. Experiments measuring the trade-off between compression ratio and information loss are reported, including quantifying the effect of lossy representations on a downstream application that carries out single nucleotide polymorphism and insert/deletion detection. The new methods are demonstrably superior to other techniques when assessed against the spectrum of possible trade-offs between storage required and fidelity of representation.
Availability and implementation: An implementation of the methods described here is available at https://github.com/rcanovas/libCSAM .
Contact: rcanovas@student.unimelb.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.