bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of parasite sharing among Neotropical freshwater fishes
Authors: Braga Mariana P. , Razzolini Emanuel , Boeger Walter A. 
Published: October 2014

Summary

Because host–parasite interactions are so ubiquitous, it is of primary interest for ecologists to understand the factors that generate, maintain and constrain these associations. Phylogenetic comparative studies have found abundant evidence for host‐switching to relatively unrelated hosts, sometimes related to diversification events, in a variety of host–parasite systems. For Monogenoidea (Platyhelminthes) parasites, it has been suggested that the co‐speciation model alone cannot explain host occurrences, hence host‐switching and/or non‐vicariant modes of speciation should be associated with the origins and diversification of several monogenoid taxa.

The factors that shape broad patterns of parasite sharing were investigated using path analysis as a way to generate hypotheses about the origins of host–parasite interactions between monogenoid gill parasites and Neotropical freshwater fishes.

Parasite sharing was assessed from an interaction matrix, and explanatory variables included phylogenetic relationships, environmental preferences, biological traits and geographic distribution for each host species.

Although geographic distribution of hosts and host ecology are important factors to understand host–parasite interactions, especially within host lineages that share a relatively recent evolutionary history, phylogeny had the strongest overall direct effect on parasite sharing.

Phylogenetic contiguity of host communities may allow a ‘stepping‐stone’ mode of host‐switching, which increases parasite sharing. Our results reinforce the importance of including evolutionary history in the study of ecological associations, including emerging infectious diseases risk assessment.
A review of the effects of formaldehyde release from endodontic materials
Authors: Athanassiadis B. , George G. A. , Abbott P. V. , Wash L. J. 
Published: October 2014

AbstractFormaldehyde is present in most living cells and the environment. In dentistry, patients may be exposed to formaldehyde through the use of several endodontic materials (e.g. AH 26) and during formocresol pulpotomies. This review outlines how the human body reacts to formaldehyde exposure, how recent data has relooked at the issue of carcinogenicity and leukaemia associated with formaldehyde, and whether it is possible to quantify the amount of formaldehyde produced by endodontic cements. The review analyses the way formaldehyde is produced from epoxy resins and addresses the question of whether the amount of formaldehyde from endodontic cements is large enough to override the body's ability to deal with its own endogenous levels of formaldehyde and should the amount of formaldehyde produced be a concern.
CD8+ T‐cell recognition of a synthetic epitope formed by t‐butyl modification
Authors: Reid Reiss A. , Redman James E. , Rizkallah Pierre , Fegan Chris , Pepper Chris , Man Stephen 
Published: October 2014

SummaryWe set out to clone Bax‐specific CD8+ T cells from peripheral blood samples of patients with primary chronic lymphocytic leukaemia. A number of clones were generated using a Bax peptide pool and their T‐cell epitope was mapped to two peptides sharing a common 9‐amino‐acid sequence (LLSYFGTPT), restricted by HLA‐A*0201. However, when these T‐cell clones were tested against highly purified syntheses (> 95%) of the same peptide sequence, there was no functional response. Subsequent mass spectrometric analysis and HPLC fractionation suggested that the active component in the original crude peptide preparations (77% pure) was a peptide with a tert‐butyl (tBu) modification of the tyrosine residue. This was confirmed by modification of the inactive wild‐type sequence to generate functionally active peptides. Computer modelling of peptide:HLA‐A*0201 structures predicted that the tBu modification would not affect interactions between peptide residues and the HLA binding site. However, these models did predict that the tBu modification of tyrosine would result in an extension of the side chain out of the peptide‐binding groove up towards the T‐cell receptor. This modified product formed < 1% of the original P603 crude peptide preparation and < 0·05% of the original 23‐peptide mixture used for T‐cell stimulation. The data presented here, illustrate the potential for chemical modifications to change the immunogenicity of synthetic peptides, and highlight the exquisite capacity of T‐cell receptors to discriminate between structurally similar peptide sequences. Furthermore, this study highlights potential pitfalls associated with the use of synthetic peptides for the monitoring and modulating of human immune responses.
Recent Clinical Trials for the Etiological Treatment of Chronic Chagas Disease: Advances, Challenges and Perspectives
Authors: Urbina Julio A. 
Published: October 2014

AbstractChagas disease, a chronic systemic parasitosis caused by the Kinetoplastid protozoon Trypanosoma cruzi, is the first cause of cardiac morbidity and mortality in poor rural and suburban areas of Latin America and the largest parasitic disease burden in the continent, now spreading worldwide due to international migrations. A recent change in the scientific paradigm on the pathogenesis of chronic Chagas disease has led to a consensus that all T. cruzi‐seropositive patients should receive etiological treatment. This important scientific advance has spurred the rigorous evaluation of the safety and efficacy of currently available drugs (benznidazole and nifurtimox) as well as novel anti‐T. cruzi drug candidates in chronic patients, who were previously excluded from such treatment. The first results indicate that benznidazole is effective in inducing a marked and sustained reduction in the circulating parasites’ level in the majority of these patients, but adverse effects can lead to treatment discontinuation in 10–20% of cases. Ergosterol biosynthesis inhibitors, such as posaconazole and ravuconazole, are better tolerated but their efficacy at the doses and treatment duration used in the initial studies was significantly lower; such results are probably related to suboptimal exposure and/or treatment duration. Combination therapies are a promising perspective but the lack of validated biomarkers of response to etiological treatment and eventual parasitological cures in chronic patients remains a serious challenge.
Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon
Authors: Larson Wesley A. , Seeb James E. , Dann Tyler H. , Schindler Daniel E. , Seeb Lisa W. 
Published: October 2014

AbstractThe genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen‐mediated selection in wild populations. Here, we examined variation at the MHC class II peptide‐binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in south‐western Alaska. We also obtained genotypes from 90 putatively neutral single nucleotide polymorphisms for each population to compare the relative roles of demography and selection in shaping the observed MHC variation. We found that MHC divergence was generally partitioned by spawning ecotype (lake beaches, rivers and streams) and was 30 times greater than variation at neutral markers. Additionally, we observed substantial differences in modes of selection and diversity among ecotypes, with beach populations displaying higher levels of directional selection and lower MHC diversity than the other two ecotypes. Finally, the level of MHC differentiation in our study system was comparable to that observed over much larger geographic ranges, suggesting that MHC variation does not necessarily increase with increasing spatial scale and may instead be driven by fine‐scale differences in pathogen communities or pathogen virulence. The low levels of neutral structure and spatial proximity of populations in our study system indicate that MHC differentiation can be maintained through strong selective pressure even when ample opportunities for gene flow exist.
Measurement of tear secretion in healthy pigeons by using the phenol red thread test
Authors: Hayat A. , Biricik H. S. 
Published: October 2014

The objectives of this study were to determine the applicability of the phenol red thread (PRT) test as a new method for the evaluation of tear secretion in healthy male and female pigeons, to establish normal physiologic reference values in these animals, and to compare seasonal variations in these values. Seventy‐five pigeons of both sexes, with no ocular abnormalities, were included in the study. The phenol red impregnated thread was inserted into the recessus conjunctiva inferior for measuring tear secretion. After 15 seconds, the thread was removed and the wet portion of the thread was measured (in mm). The mean±sd PRT values were 23.02±2.98 mm/15 seconds and 24.04±2.60 mm/15 seconds for the April and June measurements, respectively. There were significant differences in the PRT between the two months, with a significant increase in June. Mean PRT values for males and females were, respectively, 23.30±3.35 and 22.79±2.65 mm/15 seconds in April, and 24.57±2.41 and 23.61±2.68 mm/15 seconds in June. There was no significant correlation (r=0.075, P>0.05) between bodyweight and tear production in both eyes of the male and female birds in April and June. The results indicated that seasonal variations have an effect on tear production. The PRT was a viable method for the measurement of tear production in pigeons and these measurements could be accepted as reference values for healthy pigeons.
Transforming Trauma Teams Through Transactive Memory
Authors: Gardner Aimee K. , Ahmed Rami A. 
Published: October 2014

Background In situ simulation holds promise to enhance the effectiveness of performance. However, a dearth of theory remains to explain the efficacy of simulation-based education within health care teams. Aim The aim of this study was to examine team cognitive processes across two trauma simulations and to identify whether these processes impact observer-rated performance. Method Twenty-four health care professionals within an emergency department participated in one of two 30-minute trauma scenarios. Before and after participating, they reported their team transactive memory perceptions. Performance in the scenarios was video recorded for evaluation. Results Participants reported significant increases in transactive memory ( p < .05) after participating in the trauma simulations. Furthermore, transactive memory was positively related to observer-rated performance ( r = .58, p < .01). Conclusion Our results suggest that simulation has potential to be an effective method to increase transactive memory perceptions among team members. In addition, the increase in transactive memory systems is associated with higher performance ratings. Further consideration concerning the design and evaluation of simulation-based training programs to facilitate the development of such cognitive processes among teams is recommended.
One‐Pot Synthesis of Triazoles from Organic Halides and Alkynes in Nonionic Nanomicelles at Room Temperature
Authors: Xie Aming , Xu Xiao , Li Junjian , Wang Boliang , Dong Wei 
Published: October 2014

AbstractA mild method for the one‐pot synthesis of triazoles from benzyl halides in a nonionic nanomicelle system has been developed. In this protocol, water was used as the solvent and the preparation of hazardous organic azides were avoided. A plausible micelle catalytic process has been suggested.
Increasing the Size of an Aromatic Helical Foldamer Cavity by Strand Intercalation
Authors: Singleton Michael L. , Pirotte Geert , Kauffmann Brice , Ferrand Yann , Huc Ivan 
Published: October 2014

AbstractThe postsynthetic modulation of capsules based on helical aromatic oligoamide foldamers would be a powerful approach for controlling their receptor properties without altering the initial monomer sequences. With the goal of developing a method to increase the size of a cavity within a helix, a single‐helical foldamer capsule was synthesized with a wide‐diameter central segment that was designed to intercalate with a second shorter helical strand. Despite the formation of stable double‐helical homodimers (Kdim>107 M−1) by the shorter strand, when it was mixed with the single‐helical capsule sequence, a cross‐hybridized double helix was formed with Ka>105 M−1. This strategy makes it possible to direct the formation of double‐helical heterodimers. On the basis of solution‐ and solid‐state structural data, this intercalation resulted in an increase in the central‐cavity size to give a new interior volume of approximately 150 Å3.
High‐Performance Liquid‐Catalyst Fuel Cell for Direct Biomass‐into‐Electricity Conversion
Authors: Liu Wei , Mu Wei , Deng Yulin 
Published: October 2014

AbstractHerein, we report high‐performance fuel cells that are catalyzed solely by polyoxometalate (POM) solution without any solid metal or metal oxide. The novel design of the liquid‐catalyst fuel cells (LCFC) changes the traditional gas–solid‐surface heterogeneous reactions to liquid‐catalysis reactions. With this design, raw biomasses, such as cellulose, starch, and even grass or wood powders can be directly converted into electricity. The power densities of the fuel cell with switchgrass (dry powder) and bush allamanda (freshly collected) are 44 mW cm−2 and 51 mW cm−2 respectively. For the cellulose‐based biomass fuel cell, the power density is almost 3000 times higher than that of cellulose‐based microbial fuel cells. Unlike noble‐metal catalysts, POMs are tolerant to most organic and inorganic contaminants. Therefore, almost any raw biomass can be used directly to produce electricity without prior purification.
Forming Buried Junctions to Enhance the Photovoltage Generated by Cuprous Oxide in Aqueous Solutions
Authors: Dai Pengcheng , Li Wei , Xie Jin , He Yumin , Thorne James , McMahon Gregory , Zhan Jinhua , Wang Dunwei 
Published: October 2014

AbstractWhereas wide‐bandgap metal oxides have been extensively studied for the photooxidation of water, their utilization for photoreduction is relatively limited. An important reason is the inability to achieve meaningful photovoltages with these materials. Using Cu2O as a prototypical photocathode material, it is now shown that the photovoltage barrier can be readily broken by replacing the semiconductor/water interface with a semiconductor/semiconductor one. A thin ZnS layer (ca. 5 nm) was found to form high‐quality interfaces with Cu2O to increase the achievable photovoltage from 0.60 V to 0.72 V. Measurements under no net exchange current conditions confirmed that the change was induced by a thermodynamic shift of the flatband potentials rather than by kinetic factors. The strategy is compatible with efforts aimed at stabilizing the cathode that otherwise easily decomposes and with surface catalyst decorations for faster hydrogen evolution reactions. A combination of NiMo and CoMo dual‐layer alloy catalysts was found to be effective in promoting hydrogen production under simulated solar radiation.
Carboxyl Group (CO2H) Functionalized Coordination Polymer Nanoparticles as Efficient Platforms for Drug Delivery
Authors: Novio Fernando , Lorenzo Julia , Nador Fabiana , Wnuk Karolina , Ruiz‐Molina Daniel 
Published: October 2014

AbstractFunctionalization of nanoparticles can significantly influence their properties and potential applications. Although researchers can now functionalize metal, metal oxide, and organic polymer nanoparticles with a high degree of precision, controlled surface functionalization of nanoscale coordination polymer particles (CPPs) has remained a significant challenge. The lack of methodology is perhaps one of the greatest roadblocks to the advancement of CPPs into high added‐value drug delivery applications. Here, we report having achieved this goal through a stepwise formation and functionalization protocol. We fabricated robust nanoparticles with enhanced thermal and colloidal stabilities by incorporation of carboxyl groups and these surface carboxyl groups could be subsequently functionalized through well‐known peptide coupling reactions. The set of chemistries that we employed as proof‐of‐concept enabled a plethora of new functional improvements for the application of CPPs as drug delivery carriers, including enhanced colloidal stabilities and the incorporation of additional functional groups such as polyethylene glycol (PEG) or fluorescent dyes that enabled tracking of their cellular uptake. Finally, we ascertained the cytotoxicity of the new CPP nanoparticles loaded with camptothecin to human breast adenocarcinoma (MCF‐7). Efflux measurements show that the encapsulation of camptothecin enhances the potency of the drug 6.5‐fold and increases the drug retention within the cell.
Efficient End‐Capping Synthesis of Neutral Donor–Acceptor [2]Rotaxanes Under Additive‐Free and Mild Conditions
Authors: Domoto Yuya , Sase Shohei , Goto Kei 
Published: October 2014

AbstractEfficient end‐capping synthesis of neutral donor–acceptor (D–A) [2]rotaxanes without loading any catalysts or activating agents was achieved by utilizing high reactivity of a pentacoordinated hydrosilane toward salicylic acid derivatives. As components of [2]rotaxanes, an electron‐deficient naphthalenediimide‐containing axle with a salicylic acid terminus and several electron‐rich bis(naphthocrown) ether macrocycles were employed. End‐capping reactions with the pentacoordinated hydrosilane underwent smoothly even at low temperature to afford the corresponding [2]rotaxanes in good yields. A [2]rotaxane containing bis‐1,5‐(dinaphtho)‐38‐crown‐10 ether as a wheel molecule was synthesized and isolated in 84 % yield by the end‐capping at −10 °C, presenting the highest yield ever reported for the end‐capping synthesis of a neutral D–A [2]rotaxane. It was found that the yields of the [2]rotaxanes in the end‐capping reactions were almost parallel to the formation ratios of the corresponding pseudo[2]rotaxanes estimated by utilizing model systems. These results indicate that the end‐capping reaction using the pentacoordinated hydrosilane proceeded without perturbing the threading process, and most of the pseudo[2]rotaxanes underwent efficient end‐capping reaction even at low temperature.
Lutetium‐Methanediide‐Alkyl Complexes: Synthesis and Chemistry
Authors: Li Shihui , Wang Meiyan , Liu Bo , Li Lei , Cheng Jianhua , Wu Chunji , Liu Dongtao , Liu Jingyao , Cui Dongmei 
Published: October 2014

AbstractThe first four‐coordinate methanediide/alkyl lutetium complex (BODDI)Lu2(CH2SiMe3)2(μ2‐CHSiMe3)(THF)2 (BODDI=ArNC(Me)CHCOCHC(Me)NAr, Ar=2,6‐iPr2C6H3) (1) was synthesized by a thermolysis methodology through α‐H abstraction from a Lu–CH2SiMe3 group. Complex 1 reacted with equimolar 2,6‐iPrC6H3NH2 and Ph2CO to give the corresponding lutetium bridging imido and oxo complexes (BODDI)Lu2(CH2SiMe3)2(μ2‐N‐2,6‐iPr2C6H3)(THF)2 (2) and (BODDI)Lu2(CH2SiMe3)2(μ2‐O)(THF)2 (3). Treatment of 3 with Ph2CO (4 equiv) caused a rare insertion of Lu–μ2‐O bond into the CO group to afford a diphenylmethyl diolate complex 4. Reaction of 1 with PhN=CO (2 equiv) led to the migration of SiMe3 to the amido nitrogen atom to give complex (BODDI)Lu2(CH2SiMe3)2‐μ‐{PhNC(O)CHC(O)NPh(SiMe3)‐κ3N,O,O}(THF) (5). Reaction of 1 with tBuNC formed an unprecedented product (BODDI)Lu2(CH2SiMe3){μ2‐[η2:η2‐tBuNC(=CH2)SiMe2CHCNtBu‐κ1N]}(tBuNC)2 (6) through a cascade reaction of NC bond insertion, sequential cyclometalative γ‐(sp3)‐H activation, CC bond formation, and rearrangement of the newly formed carbene intermediate. The possible mechanistic pathways between 1, PhNCO, and tBuNC were elucidated by DFT calculations.
Lösungsbeispiele – Eine besondere Form von Lernaufgaben zur Unterstützung individuellen Lernens in den Naturwissenschaften
Authors: Kölbach Eva , Maier‐Richter Andrea , Sumfleth Elke 
Published: October 2014

AbstractLösungsbeispiele enthalten im Gegensatz zu konventionellen Lernaufgaben neben der Problemstellung auch die mehr oder weniger detailliert ausgearbeitete Lösung. Bei optimaler Gestaltung eignen sich Lösungsbeispiele daher vor allem für Lernende mit wenig Vorwissen in einer Dömane. Damit könnten Lösungsbeispiele als individuelle Lernmaterialien z. B. im Förderunterricht, in Vertretungsstunden, als wiederholende Hausaufgaben, etc. eingesetzt werden. Im folgenden Artikel werden nach einer kurzen, theoretischen Einführung in das Themenfeld zunächst einige Ergebnisse aus Studien zum Lernen mit Lösungsbeispielen zusammengestellt, um danach die Entwicklung und Gestaltung von Lösungsbeispielen sowie deren Evaluation zu thematisieren.
VCF2Networks: applying genotype networks to single-nucleotide variants data
Authors: Dall'Olio Giovanni Marco , Vahdati Ali R. , Bertranpetit Jaume , Wagner Andreas , Laayouni Hafid 
Published: October 2014

Abstract
Summary: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, here we present VCF2Networks, a tool to determine and study genotype network structure from single-nucleotide variant data.
Availability and implementation: VCF2Networks is available at https://bitbucket.org/dalloliogm/vcf2networks .
Contact: giovanni.dallolio@kcl.ac.uk
Supplementary information : Supplementary data are available at Bioinformatics online.
CompMap: a reference-based compression program to speed up read mapping to related reference sequences
Authors: Zhu Zexuan , Li Linsen , Zhang Yongpeng , Yang Yanli , Yang Xiao 
Published: October 2014

Abstract
Summary : Exhaustive mapping of next-generation sequencing data to a set of relevant reference sequences becomes an important task in pathogen discovery and metagenomic classification. However, the runtime and memory usage increase as the number of reference sequences and the repeat content among these sequences increase. In many applications, read mapping time dominates the entire application. We developed CompMap, a reference-based compression program, to speed up this process. CompMap enables the generation of a non-redundant representative sequence for the input sequences. We have demonstrated that reads can be mapped to this representative sequence with a much reduced time and memory usage, and the mapping to the original reference sequences can be recovered with high accuracy.
Availability and implementation : CompMap is implemented in C and freely available at http://csse.szu.edu.cn/staff/zhuzx/CompMap/ .
Contact : xiaoyang@broadinstitute.org
Supplementary information : Supplementary data are available at Bioinformatics online.