bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond the M‐CSF receptor – novel therapeutic targets in tumor‐associated macrophages
Authors: Bonelli Stefano , Geeraerts Xenia , Bolli Evangelia , Keirsse Jiri , Kiss Mate , Pombo Antunes Ana Rita , Van Damme Helena , De Vlaminck Karen , Movahedi Kiavash , Laoui Damya , Raes Geert , Van Ginderachter Jo A.
Published: August 2017

Tumor‐associated macrophages (TAM) are by now established as important regulators of tumor progression by impacting on tumor immunity, angiogenesis, and metastasis. Hence, a multitude of approaches are currently pursued to intervene with TAM's protumor activities, the most advanced of which being a blockade of macrophage‐colony stimulating factor (M‐CSF)/M‐CSF receptor (M‐CSFR) signaling. M‐CSFR signaling largely impacts on the differentiation of macrophages, including TAM, and hence strongly influences the numbers of these cells in tumors. However, a repolarization of TAM toward a more antitumor phenotype may be more elegant and may yield stronger effects on tumor growth. In this respect, several aspects of TAM behavior could be altered, such as their intratumoral localization, metabolism and regulatory pathways. Intervention strategies could include the use of small molecules but also new generations of biologicals which may complement the current success of immune checkpoint blockers. This review highlights current work on the search for new therapeutic targets in TAM.
Archaeal MutS5 tightly binds to Holliday junction similarly to eukaryotic MutSγ
Authors: Ohshita Koki , Fukui Kenji , Sato Mizuki , Morisawa Takashi , Hakumai Yuichi , Morono Yuki , Inagaki Fumio , Yano Takato , Ashiuchi Makoto , Wakamatsu Taisuke
Published: August 2017

Archaeal DNA recombination mechanism and the related proteins are similar to those in eukaryotes. However, no functional homolog of eukaryotic MutSγ, which recognizes Holliday junction to promote homologous recombination, has been identified in archaea. Hence, the whole molecular mechanism of archaeal homologous recombination has not yet been revealed. In this study, to identify the archaeal functional homolog of MutSγ, we focused on a functionally uncharacterized MutS homolog, MutS5, from a hyperthermophilic archaeon Pyrococcus horikoshii (phMutS5). Archaeal MutS5 has a Walker ATPase motif‐containing amino acid sequence that shows similarity to the ATPase domain of MutSγ. It is known that the ATPase domain of MutS homologs is also a dimerization domain. Chemical cross‐linking revealed that purified phMutS5 has an ability to dimerize in solution. phMutS5 bound to Holliday junction with a higher affinity than to other branched and linear DNAs, which resembles the DNA‐binding specificities of MutSγ and bacterial MutS2, a Holliday junction‐resolving MutS homolog. However, phMutS5 has no nuclease activity against branched DNA unlike MutS2. The ATPase activity of phMutS5 was significantly stimulated by the presence of Holliday junction similarly to MutSγ. Furthermore, site‐directed mutagenesis revealed that the ATPase activity is dependent on the Walker ATPase motif of the protein. These results suggest that archaeal MutS5 should stabilize the Holliday junction and play a role in homologous recombination, which is analogous to the function of eukaryotic MutSγ.
RFTS‐dependent negative regulation of Dnmt1 by nucleosome structure and histone tails
Authors: Mishima Yuichi , Brueckner Laura , Takahashi Saori , Kawakami Toru , Arita Kyohei , Oka Shota , Otani Junji , Hojo Hironobu , Shirakawa Masahiro , Shinohara Akira , Watanabe Mikio , Suetake Isao
Published: August 2017

DNA methylation in promoter regions represses gene expression and is copied over mitotic divisions by Dnmt1. Dnmt1 activity is regulated by its replication foci targeting sequence (RFTS) domain which masks the catalytic pocket. It has been shown that Dnmt1 activity on unmethylated DNA is inhibited in nucleosome cores. In the present study, we aimed to assess the effect of nuclesome formation on maintenance methylation at single CpG resolution. We show that Dnmt1 fully methylates naked linker DNA in dinucleosomes, whereas maintenance methylation was repressed at all CpG sites in nucleosome core particles. Deletion of RFTS partly released obstruction of Dnmt1 activity in core particles. Histone H3 tail peptides inhibited Dnmt1 in an RFTS‐dependent manner and repression was modulated by acetylation or methylation. We propose a novel function of RFTS to regulate Dnmt1 activity in nucleosomes.
Changes in serum lipid profiles caused by three regimens of interferon‐free direct‐acting antivirals for patients infected with hepatitis C virus
Authors: Inoue Takako , Goto Takaaki , Iio Etsuko , Matsunami Kayoko , Fujiwara Kei , Shinkai Noboru , Matsuura Kentaro , Matsui Takeshi , Nojiri Shunsuke , Tanaka Yasuhito
Published: August 2017

Aim

Serum low‐density lipoprotein cholesterol (LDL‐C) increases during treatment of chronic hepatitis C (CHC) with interferon‐free direct‐acting antivirals (DAAs). We sought to compare the changes of serum lipid profiles caused by three regimens.

Methods

A total of 216 CHC patients were enrolled. Among 170 patients infected with hepatitis C virus (HCV) genotype 1b, 85 received daclatasvir plus asunaprevir (DCV/ASV) and 85 received sofosbuvir plus ledipasvir (SOF/LDV). Forty‐six infected with HCV genotype 2 received sofosbuvir plus ribavirin (SOF/RBV). Serum total cholesterol (TC), LDL‐C, high‐density lipoprotein cholesterol, and triglyceride were measured at baseline and 4, 8, 12 (for all regimens), and 24 weeks (for DCV/ASV) during treatment (4w, 8w, 12w, and 24w, respectively) and 12 and 24 weeks after treatment (p12w and p24w, respectively).

Results

In 69 (81.2%) patients who received DCV/ASV and achieved a sustained virologic response at 24 weeks after the end of treatment (SVR24), TC and LDL‐C increased significantly from baseline to p24w. In 84 (98.8%) treated with SOF/LDV who achieved SVR24, TC and LDL‐C increased significantly from baseline to 8w, and TC decreased significantly from 8w to p12w. The 45 (97.8%) who received SOF/RBV and achieved SVR24 showed no significant changes. At 12w, TC and LDL‐C increased to a greater degree in patients receiving SOF/LDV than in those receiving DCV/ASV or SOF/RBV.

Conclusion

During treatment with DAAs, the serum lipid profile may reflect not only recovery from the disruption of lipid metabolism induced by HCV, but also the pharmacological effects of DAAs. Further investigations are needed to elucidate the effect of DAAs on serum lipid profiles.
Testing environmental correlates of clines in clades: an example from cassidine beetles
Authors: Simões Marianna V. P. , Lieberman Bruce S. , Soberón Jorge , Peterson A. Townsend
Published: August 2017

Phenotypic change across environmental gradients has been an important topic in evolutionary biology. Members of the tortoise beetle tribe Dorynotini are characterised by an elytral suture adorned with either a tubercle or a large, vertical spine. Overall spine height across species had previously been posited to exhibit a latitudinal gradient of increasing height and decreasing width towards the southern extreme of the tribe's range, and this pattern had been linked to environmental variation.

We explore the evidence behind such a cline by testing associations between climate and morphology across the clade's geographic distribution using an approach based on ecological niche modelling (ENM) and morphological and environmental hypervolumes. The degree of overlap between the respective hypervolumes was assessed, and the correlation of matrix overlap values was quantified using Mantel tests. Degrees of niche similarity and conservatism at the genus level were also assessed using both Schoener's index and Hellinger distances.

Overall, we observed that characters defining our morphological hypervolumes were informative, and capable of grouping taxa into discrete units in morphospace. In contrast, environmental hypervolumes were largely homogeneous across the tribe, with high overlap among taxa. No significant correlations were found between environmental and morphological hypervolumes.

Our results indicate that morphological divergence occurs along with high levels of environmental overlap; perhaps historical biogeographic factors along with sexual selection may have promoted its diversification. Our approach based on ENM and statistical comparisons between environmental and morphological hypervolumes can provide a useful approach to testing the existence of gradients and clines.
Sensitivity of an oral health‐related quality‐of‐life questionnaire in detecting oral health impairment in preschool children
Authors: Guedes Renata S. , Ardenghi Thiago M. , Emmanuelli Bruno , Piovesan Chaiana , Mendes Fausto M.
Published: August 2017

Aim

This two‐year cohort study evaluated whether the Early Childhood Oral Health Impact Scale (ECOHIS) is responsive to detect changes related to dental caries.

Design

Preschool children were examined in 2010 regarding dental caries, and their parents responded to the ECOHIS. After 2 years, 352 children (response rate = 73.6%) were re‐examined and a new ECOHIS was responded. Children were categorized according to caries increment (no new caries, 1–3 surfaces with new lesions, and four or more decayed surfaces). The outcome variables were related to the decline of quality of life as determined via ECOHIS: decline, severe decline, and differences between baseline and follow‐up scores. Effect sizes (ES) were calculated, and the associations were evaluated through Poisson regression.

Results

ES was small for children with 1–3 new lesions (ES = 0.19) and moderate for children with four or more new carious lesions (ES = 0.61). Children who developed 1–3 new lesions were significantly associated with all outcome variables compared to children with no new lesions, but the associations were stronger for children with four or more new carious lesions.

Conclusions

The ECOHIS is sensitive to the deterioration of quality of life due to caries increments in preschool children.
Effects of microstructure on electrochemical reactivity and conductivity in nanostructured ceria thin films
Authors: Ding Jilai , Strelcov Evgheni , Bassiri‐Gharb Nazanin
Published: August 2017

The proton conductivity in functional oxides is crucial in determining electrochemistry and transport phenomena in a number of applications such as catalytic devices and fuel cells. However, single characterization techniques are usually limited in detecting the ionic dynamics at the full range of environmental conditions. In this report, we probe and uncover the links between the microstructure of nanostructured ceria (NC) and parameters that govern its electrochemical reaction and proton transport, by coupling experimental data obtained with time‐resolved Kelvin probe force microscopy (tr‐KPFM), electrochemical impedance spectroscopy (EIS), and finite element analysis. It is found that surface morphology determines the water splitting rate and proton conductivity at 25°C and wet conditions, when protons are mainly generated and transported within surface physisorbed water layers. However, at higher temperature (i.e., ≥125°C) and dry conditions, when physisorbed water evaporates, grain size, and crystallographic orientation become significant factors. Specifically, the proton generation rate is negatively correlated with the grain size, whereas proton diffusivity is facilitated by surface {111} planes and additional conduction pathways offered by cracks and open pores connected to the surface.
Molecular Phylogenetic Positions of Two New Marine Gregarines (Apicomplexa)—Paralecudina anankea n. sp. and Lecudina caspera n. sp.—from the Intestine of Lumbrineris inflata (Polychaeta) Show Patterns of Co‐evolution
Authors: Iritani Davis , Wakeman Kevin C. , Leander Brian S.
Published: August 2017

Gregarine apicomplexans are unicellular parasites commonly found in the intestines and coeloms of invertebrate hosts. Traits associated with the conspicuous feeding stage of gregarines, known as the trophozoite, have been used in combination with molecular phylogenetic data for species delimitation and the reconstruction of evolutionary history. Trophozoite morphology alone is often inadequate for inferring phylogenetic relationships and delimiting species due to frequent cases of high intraspecific variation combined with relatively low interspecific variation. The current study combined morphological data with small subunit (SSU) rDNA sequences to describe and establish two novel marine gregarine species isolated from the intestine of a polychaete host Lumbrineris inflata collected in British Columbia (Canada): Paralecudina anankea n. sp. and Lecudina caspera n. sp. The sister species to the host is Lumbrineris japonica, which can be found on the opposite side of the Pacific Ocean (Japan) and contains two different species of gregarine parasites: Paralecudina polymorpha and Lecudina longissima. Molecular phylogenetic analyses placed P. anankea n. sp. as the sister species to P. polymorpha and L. caspera n. sp. as the sister species to L. longissima. This phylogenetic pattern demonstrates a co‐evolutionary history whereby speciation of the host (Lumbrineris) corresponds with simultaneous speciation of the two different lineages of intestinal gregarines (Paralecudina and Lecudina).
Fitness consequences of a clock pollinator filter in Nicotiana attenuata flowers in nature
Authors: Yon Felipe , Kessler Danny , Joo Youngsung , Kim Sang‐Gyu , Baldwin Ian T.
Published: August 2017

Nicotiana attenuata flowers, diurnally open, emit scents and move vertically to interact with nocturnal hawkmoth and day‐active hummingbird pollinators. To examine the fitness consequences of these floral rhythms, we conducted pollination trials in the plant's native habitat with phase‐shifted flowers of plants silenced in circadian clock genes. The results revealed that some pollination benefits observed under glasshouse conditions were not reproduced under natural field conditions. Floral arrhythmicity increased pollination success by hummingbirds, while reducing those by hawkmoths in the field. Thus, floral circadian rhythms may influence a plant's fitness by filtering pollinators leading to altered seed set from outcrossed pollen.
Enhanced motivation to alcohol in transgenic mice expressing human α‐synuclein
Authors: Rotermund Carola , Reolon Gustavo K. , Leixner Sarah , Boden Cindy , Bilbao Ainhoa , Kahle Philipp J.
Published: August 2017

α‐Synuclein (αSYN) is the neuropathological hallmark protein of Parkinson's disease (PD) and related neurodegenerative disorders. Moreover, the gene encoding αSYN (SNCA) is a major genetic contributor to PD. Interestingly, independent genome‐wide association studies also identified SNCA as the most important candidate gene for alcoholism. Furthermore, single‐nucleotide‐polymorphisms have been associated with alcohol‐craving behavior and alcohol‐craving patients showed augmented αSYN expression in blood. To investigate the effect of αSYN on the addictive properties of chronic alcohol use, we examined consumption, motivation, and seeking responses induced by environmental stimuli and relapse behavior in transgenic mice expressing the human mutant [A30P]αSYN throughout the brain. The primary reinforcing effects of alcohol under operant self‐administration conditions were increased, while consumption and the alcohol deprivation effect were not altered in the transgenic mice. The same mice were subjected to immunohistochemical measurements of immediate‐early gene inductions in brain regions involved in addiction‐related behaviors. Acute ethanol injection enhanced immunostaining for the phosphorylated form of cAMP response element binding protein in both amygdala and nucleus accumbens of αSYN transgenic mice, while in wild‐type mice no effect was visible. However, at the same time, levels of cFos remain unchanged in both genotypes. These results provide experimental confirmation of SNCA as a candidate gene for alcoholism in addition to its known link to PD.

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Potentially malignant disorders—The case for intervention
Authors: Thomson P. J.
Published: August 2017

Potentially malignant disorders (PMD) are recognisable mucosal conditions preceding invasive squamous carcinoma development. Established oral cancer remains a lethal and deforming disease, with a rising incidence. Management techniques for identifiable oral precursor lesions have traditionally been polarised between observational and interventional surgical techniques. By defining salient management goals for treating potentially malignant disease, and examining the evidence supporting the efficacy of treatment intervention, this paper presents the case for interventional laser surgery as a definitive diagnostic and treatment modality.
Towards resolving the evolutionary history of Caucasian pears (Pyrus, Rosaceae)—Phylogenetic relationships, divergence times and leaf trait evolution
Authors: Korotkova Nadja , Parolly Gerald , Khachatryan Anahit , Ghulikyan Lusine , Sargsyan Harutyun , Akopian Janna , Borsch Thomas , Gruenstaeudl Michael
Published: August 2017

With approximately 25 endemic species, the genus Pyrus (pears) is highly diverse in the Caucasus ecoregion. The majority of Caucasian pears inhabit xerophytic open woodlands or similar habitats, to which they display morphological adaptations, such as narrow leaves. The other species, both Caucasian and non‐Caucasian taxa, mainly inhabit mesophytic forests and display broad leaves. Using a representative taxon sampling of Pyrus from the Caucasus, Europe and Asia, we reconstruct phylogenetic relationships in the genus based on multiple plastid regions. We also estimate the divergence times of major clades in Pyrus, reconstruct the evolution of leaf shapes, and discuss the emergence of xeromorphic leaf traits. Our results confirm the monophyly of Pyrus and the existence of two major clades: (a) an E Asian clade with a crown group age of 15.7 (24.02–8.37 95% HPD) My, and (b) a W Eurasian clade that comprises species from Europe, SW Asia and the Caucasus and that displays a slightly younger crown group of 12.38 (19.02–6.41 95% HPD) My. The existing infrageneric classification of Pyrus was found partially incongruent with the inferred phylogenetic trees. Several currently accepted species were not recovered as monophyletic, indicating that current species limits require re‐evaluation. Ancestral character state reconstructions revealed several independent transitions from broad‐ to narrow‐shaped leaves in Pyrus, probably via intermediate‐shaped leaves.
The Relationship between Brachycephalic Head Features in Modern Persian Cats and Dysmorphologies of the Skull and Internal Hydrocephalus
Authors: Schmidt M.J. , Kampschulte M. , Enderlein S. , Gorgas D. , Lang J. , Ludewig E. , Fischer A. , Meyer‐Lindenberg A. , Schaubmar A.R. , Failing K. , Ondreka N.
Published: August 2017

Background

Cat breeders observed a frequent occurrence of internal hydrocephalus in Persian cats with extreme brachycephalic head morphology.

Objective

To investigate a possible relationship among the grade of brachycephaly, ventricular dilatation, and skull dysmorphologies in Persian cats.

Animals

92 Persian‐, 10 Domestic shorthair cats.

Methods

The grade of brachycephaly was determined on skull models based on CT datasets. Cranial measurements were examined with regard to a possible correlation with relative ventricular volume, and cranial capacity. Persians with high (peke‐face Persians) and lower grades of brachycephaly (doll‐face Persians) were investigated for the presence of skull dysmorphologies.

Results

The mean cranial index of the peke‐face Persians (0.97 ± 0.14) was significantly higher than the mean cranial index of doll‐face Persians (0.66 ± 0.04; P < 0.001). Peke‐face Persians had a lower relative nasal bone length (0.15 ± 0.04) compared to doll‐face (0.29 ± 0.08; P < 0.001). The endocranial volume was significantly lower in doll‐face than peke‐face Persians (89.6 ± 1.27% versus 91.76 ± 2.07%; P < 0.001). The cranial index was significantly correlated with this variable (Spearman's r: 0.7; P < 0.0001). Mean ventricle: Brain ratio of the peke‐face group (0.159 ± 0.14) was significantly higher compared to doll‐face Persians (0.015 ± 0.01; P < 0.001).

Conclusion and Clinical Relevance

High grades of brachycephaly are also associated with malformations of the calvarial and facial bones as well as dental malformations. As these dysmorphologies can affect animal welfare, the selection for extreme forms of brachycephaly in Persian cats should be reconsidered.
Evaluation of Gastric pH and Serum Gastrin Concentrations in Cats with Chronic Kidney Disease
Authors: Tolbert M.K. , Olin S. , MacLane S. , Gould E. , Steiner J.M. , Vaden S. , Price J.
Published: August 2017

Background

Chronic kidney disease (CKD) is a highly prevalent condition in cats. Advanced CKD is associated with hyporexia and vomiting, which typically are attributed to uremic toxins and gastric hyperacidity. However, gastric pH studies have not been performed in cats with CKD.

Hypothesis/Objectives

To determine if cats with CKD have decreased gastric pH compared to age‐matched, healthy cats. Based on previous work demonstrating an association of hypergastrinemia and CKD, we hypothesized that cats with CKD would have decreased gastric pH compared to healthy, age‐matched control cats.

Animals

10 CKD cats; 9 healthy control cats.

Methods

All cats with concurrent disease were excluded on the basis of history, physical examination, CBC, plasma biochemistry profile, urinalysis, urine culture, serum total thyroxine concentration, and serum symmetric dimethylarginine concentration (controls only) obtained within 24 hours of pH monitoring and assessment of serum gastrin concentrations. Serum for gastrin determination was collected, and 12‐hour continuous gastric pH monitoring was performed in all cats. Serum gastrin concentration, mean pH, and percentage time that gastric pH was strongly acidic (pH <1 and <2) were compared between groups.

Results

No significant differences in serum gastrin concentrations were observed between groups (medians [range]: CKD, 18.7 ng/dL [<10–659.0]; healthy, 54.6 ng/dL [<10–98.0]; P‐value = 0.713) or of any pH parameters including mean ± SD gastric pH (CKD, 1.8 ± 0.5; healthy, 1.6 ± 0.3; P‐value = 0.23).

Conclusions and Clinical Importance

These findings suggest that cats with CKD may not have gastric hyperacidity compared to healthy cats and, therefore, may not need acid suppression. Thus, further studies to determine if there is a benefit to acid suppression in cats with CKD are warranted.
An exceptional family: Ophiocordyceps‐allied fungus dominates the microbiome of soft scale insects (Hemiptera: Sternorrhyncha: Coccidae)
Authors: Gomez‐Polo Priscila , Ballinger Matthew J. , Lalzar Maya , Malik Assaf , Ben‐Dov Yair , Mozes‐Daube Neta , Perlman Steve J. , Iasur‐Kruh Lilach , Chiel Elad
Published: August 2017

Hemipteran insects of the suborder Sternorrhyncha are plant sap feeders, where each family is obligately associated with a specific bacterial endosymbiont that produces essential nutrients lacking in the sap. Coccidae (soft scale insects) is the only major sternorrhynchan family in which obligate symbiont(s) have not been identified. We studied the microbiota in seven species from this family from Israel, Spain and Cyprus, by high‐throughput sequencing of ribosomal genes, and found that no specific bacterium was prevalent and abundant in all the tested species. In contrast, an Ophiocordyceps‐allied fungus sp.—a lineage widely known as entomopathogenic—was highly prevalent. All individuals of all the tested species carried this fungus. Phylogenetic analyses showed that the Ophiocordyceps‐allied fungus from the coccids is closely related to fungi described from other hemipterans, and they appear to be monophyletic, although the phylogenies of the Ophiocordyceps‐allied fungi and their hosts do not appear to be congruent. Microscopic observations show that the fungal cells are lemon‐shaped, are distributed throughout the host's body and are present in the eggs, suggesting vertical transmission. Taken together, the results suggest that the Ophiocordyceps‐allied fungus may be a primary symbiont of Coccidae—a major evolutionary shift from bacteria to fungi in the Sternorrhyncha, and an important example of fungal evolutionary lifestyle switch.
The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles
Authors: Pallarés Susana , Arribas Paula , Bilton David T. , Millán Andrés , Velasco Josefa , Ribera Ignacio
Published: August 2017

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso‐ and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation‐resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso‐ and hypersaline habitats.
Shared evolutionary origin of major histocompatibility complex polymorphism in sympatric lemurs
Authors: Kaesler Eva , Kappeler Peter M. , Brameier Markus , Demeler Janina , Kraus Cornelia , Rakotoniaina Josué H. , Hämäläinen Anni. M. , Huchard Elise
Published: August 2017

Genes of the major histocompatibility complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite‐mediated selective pressures, either favouring the long maintenance of ancestralMHCallelic lineages across successive speciation events by balancing selection (“trans‐species polymorphism”), or alternatively favouring the independent emergence of functionally similar alleles post‐speciation via convergent evolution. Here, we investigate the origins ofMHCsimilarity across several species of dwarf and mouse lemurs (Cheirogaleidae). We examinedMHCclassIIvariation in two highly polymorphic loci (DRB,DQB) and evaluated the overlap of gut–parasite communities in four sympatric lemurs. We tested for parasite‐MHCassociations across species to determine whether similar parasite pressures may select for similarMHCalleles in different species. Next, we integrated ourMHCdata with those previously obtained from otherCheirogaleidaeto investigate the relative contribution of convergent evolution and co‐ancestry to sharedMHCpolymorphism by contrasting patterns of codon usage at functional vs. neutral sites. Our results indicate that parasites shared across species may select for functionally similarMHCalleles, implying that the dynamics ofMHC‐parasite co‐evolution should be envisaged at the community level. We further show that balancing selection maintaining trans‐species polymorphism, rather than convergent evolution, is the primary mechanism explaining sharedMHCsequence motifs between species that diverged up to 30 million years ago.
Integrated Train Timetabling and Rolling Stock Scheduling Model Based on Time‐Dependent Demand for Urban Rail Transit
Authors: Yue Yixiang , Han Juntao , Wang Shifeng , Liu Xiang
Published: August 2017

The congestion of urban transportation is becoming an increasingly critical problem for many metropolises. The Urban Rail Transit (URT) system has attracted substantial attention due to its safety, high speed, high capacity, and sustainability. With a focus on a holistic modeling framework for train scheduling problems, this article proposes a novel optimization methodology that integrates both train timetabling and rolling stock scheduling based on time‐dependent passenger flow demands. We particularly consider the tradeoff between waiting times for passengers and the train frequency of the URT system. By using train paths and rolling stock indicators as decision variables, this problem is formulated as a bi‐level programming model. A simulated‐annealing (SA)‐based heuristic algorithm is employed to solve the proposed model and generate approximate optimal solutions. In the case study of Line 10 of Beijing Subway, GAMS (The General Algebraic Modeling System) with the IBM ILOG CPLEX Optimization Studio (CPLEX) solver can barely obtain a solution in more than 2 hours, whereas the SA‐based heuristic can obtain the solution within 16 minutes and 44 seconds with the objective value improved by more than 14%. The calculation results and comparisons indicate that the SA‐based heuristic can efficiently produce approximate optimal scheduling strategies; these findings demonstrate the practical value of our proposed approaches.
Response of the plant hormone network to boron deficiency
Authors: Eggert Kai , von Wirén Nicolaus
Published: August 2017

Plant hormones (PH) adjust plant growth to environmental conditions such as nutrient availability. Although responses of individualPHs to growth‐determining nutrient supplies have been reported, little is known about simultaneous dynamics in the metabolism of differentPHspecies.

Brassica napusseedlings were grown under increasing supply of B, andLC‐MS/MSwas used to characterize bioactive forms of differentPHspecies together with several of their precursors, storage and inactivated forms.

Increasing shoot B concentrations in response to B supply were accompanied by decreasing concentrations of abscisic acid (ABA) and indole‐3‐acetic acid (IAA), which appeared to be synthesized under B deficiency mainly via indole‐3‐acetonitrile (IAN). By contrast, shoot B concentrations correlated closely with cytokinins, and the B‐dependent growth response appeared to be triggered primarily byde‐novosynthesis of cytokinins and by re‐routing less active towards highly active forms of cytokinin. Also gibberellin biosynthesis strongly increased with B supply, in particular gibberellin species from the non‐13‐hydroxylation pathway. The brassinosteroid castasterone appeared to support shoot growth primarily at suboptimal B nutrition.

These results indicate that a variable B nutritional status causes coordinated changes inPHmetabolism as prerequisite for an adjusted growth response.
Effector‐mediated discovery of a novel resistance gene against Bremia lactucae in a nonhost lettuce species
Authors: Giesbers Anne K. J. , Pelgrom Alexandra J. E. , Visser Richard G. F. , Niks Rients E. , Van den Ackerveken Guido , Jeuken Marieke J. W.
Published: August 2017

Candidate effectors from lettuce downy mildew (Bremia lactucae) enable high‐throughput germplasm screening for the presence of resistance (R) genes. The nonhost species Lactuca saligna comprises a source of B. lactucae R genes that has hardly been exploited in lettuce breeding. Its cross‐compatibility with the host species L. sativa enables the study of inheritance of nonhost resistance (NHR).

We performed transient expression of candidate RXLR effector genes from B. lactucae in a diverse Lactuca germplasm set. Responses to two candidate effectors (BLR31 and BLN08) were genetically mapped and tested for co‐segregation with disease resistance.

BLN08 induced a hypersensitive response (HR) in 55% of the L. saligna accessions, but responsiveness did not co‐segregate with resistance to Bl:24. BLR31 triggered an HR in 5% of the L. saligna accessions, and revealed a novel R gene providing complete B. lactucae race Bl:24 resistance. Resistant hybrid plants that were BLR31 nonresponsive indicated other unlinked R genes and/or nonhost QTLs.

We have identified a candidate avirulence effector of B. lactucae (BLR31) and its cognate R gene in L. saligna. Concurrently, our results suggest that R genes are not required for NHR of L. saligna.
Association of sickle cell haemoglobinopathies with dental and jaw bone abnormalities
Authors: Souza SFC , de Carvalho HLCC , Costa CPS , Thomaz EBAF
Published: August 2017

Objective

To estimate the association between sickle cell anaemia and trait with dental and jaw bone abnormalities.

Subjects and Methods

Subjects (n = 369) were allocated to three groups: sickle cell anaemia, trait and control. Dental shape, number, size and position and changes in pulp chamber, root and periapex were analysed by intra‐oral periapical radiographs. Integrity of lamina dura, quality of cancellous bone and bone trabeculation were also evaluated. Prevalence ratios (PR) were calculated (α = 0.05).

Results

Sickle cell anaemia had higher prevalence (PR:8.31) and number of teeth (PR:13.40) with external resorption; higher number of teeth with pulp calcification; partial and total loss of lamina dura; and higher prevalence of changes in trabecular structure of maxilla (PR:6.45) and mandible (PR:5.34). Sickle cell trait showed higher prevalence (PR:1.26) and higher number of teeth (PR:1.98) with partial loss of lamina dura; higher number of teeth with hypercementosis, changes in shape, size, periapex, total loss of lamina dura; and higher prevalence of changes in mandibular trabecular bone (PR:1.43).

Conclusion

Pulp calcification and external resorption of the root were the most frequent dental alterations in sickle cell anaemia group, while in trait was higher frequency of changes in shape, size, periapex and root. Jaw bone changes were most prevalent in both homozygous and heterozygous subjects.
Anatomy and affinities of a new 535‐million‐year‐old medusozoan from the Kuanchuanpu Formation, South China
Authors: Wang Xing , Han Jian , Vannier Jean , Ou Qiang , Yang Xiaoguang , Uesugi Kentaro , Sasaki Osamu , Komiya Tsuyoshi
Published: August 2017

We describe here Sinaster petalon gen. et sp. nov., a new embryonic form from the c. 535 million‐year‐old Kuanchuanpu Formation of South China (Ningqiang, Shaanxi Province). The excellent three‐dimensional, phosphatic preservation of these microfossils allowed us to use x‐ray microtomographic techniques to make accurate reconstructions of their internal structures and to compare their anatomy point‐by‐point with that of extant cnidarians and other animal groups. Sinaster petalon has anatomical features typical of extant Medusozoa (Cnidaria), such as coronal muscles, perradial and adradial frenula, interradial septa, accessory septa, gonad‐lamellae, tentacle buds and perradial pockets. Although Sinaster cannot be straightforwardly assigned to any crown‐group within Medusozoa, the presence of marginal lappets and endodermal lamellae suggests that it is closer to Cubozoa and Scyphozoa than to any other group of modern cnidarians. The tentative placement of Sinaster within the stem‐group Cubozoa is justified by the presence of a velarium supported by a frenulum. The cubozoan affinities of Sinaster are also supported by cladistic analysis.
Urological complications following unstented pediatric renal transplantation
Authors: Maison Patrick Opoku Manu , Smit Shaun , McCulloch Mignon , Gajjar Priya , Nourse Peter , Thomson Dave , Muller Elmi , Millar Alastair , Numanoglu Alp , Kahn Delawir , Lazarus John
Published: August 2017

Urological complications which develop post‐renal transplantation can be associated with significant morbidity especially in children. We evaluated the occurrence and management of all urological complications in a series of unstented pediatric renal transplants in a tertiary pediatric hospital. We reviewed the medical records of children who underwent unstented renal transplant between January 1996 and December 2014. Postoperative urological complications and the outcomes of their management were analyzed. A total of 160 unstented renal transplants were performed, and 32 urological complications were noted in 29 transplants (18%). There were 20 boys and nine girls with an age range of 2.5 years to 18.4 years. Nine (31%) of these patients had LUTD. The most common complication was VUR occurring in 17 patients (10.6%). Urine leaks occurred in six patients (3.8%) and ureteric obstruction in six patients (3.8%), and three patients (1.9%) had unexplained hydronephrosis. Loss of graft occurred in three patients (1.9%), and one patient died from sepsis post‐uretero‐ureterostomy. Patients with LUTD had more urological complications (P = .037). Unstenting is feasible in most pediatric renal transplants. LUTD is associated with a higher incidence of urological complications, especially VUR.
You'd better walk alone: Changes in forest composition affect pollination efficiency and pre‐dispersal cone damage in Iberian Juniperus thurifera forests
Authors: Rodríguez‐García E. , Mezquida E. T. , Olano J. M.
Published: August 2017

Changes in land‐use patterns are a major driver of global environmental change. Cessation of traditional land‐use practices has led to forest expansion and shifts in forest composition. Consequently, former monospecific forests maintained by traditional management are progressing towards mixed forests. However, knowledge is scarce on how the presence of other tree species will affect reproduction of formerly dominant species. We explored this question in the wind‐pollinated tree Juniperus thurifera. We hypothesised that the presence of heterospecific trees would have a negative effect on cone production and on the proportion of cones attacked by specialised predators.

We assessed the relative importance of forest composition on cone production, seed development and pre‐dispersal cone damage on nine paired pure and mixed J. thurifera forests in three regions across the Iberian Peninsula. The effects of forest composition on crop size, cone and seed characteristics, as well as damage by pre‐dispersal arthropods were tested using mixed models.

Cone production was lower and seed abortion higher in mixed forests, suggesting higher pollination failure. In contrast, cone damage by arthropods was higher in pure forests, supporting the hypothesis that presence of non‐host plants reduces damage rates. However, the response of each arthropod to forest composition was species‐specific and the relative rates of cone damage varied depending on individual tree crops.

Larger crop sizes in pure forests compensated for the higher cone damage rates, leading to a higher net production of sound seeds compared to mixed forests. This study indicates that ongoing changes in forest composition after land abandonment may impact tree reproduction.
Beneficial roles of feed additives as immunostimulants in aquaculture: a review
Authors: Dawood Mahmoud A.O. , Koshio Shunsuke , Esteban Maria Ángeles
Published: August 2017

The use of antibiotics in the aquafeeds to mitigate infectious diseases or to boost growth performance is commonly practiced. Recently, the prophylactic use of antibiotics and chemotherapies have been criticized which eventually led to their ban in aquaculture by law on many countries. In view of the current restrictions on antibiotic use, there is a critical need to evaluate other possible alternatives. One potential substitute for antibiotics in aquafeeds is the use of functional feed additives. The present review is a comprehensive and an updated compilation of the available works on different feed additives, their examples, modes of action and useful applications for improving aquafeeds. It highlights several functional feed additives including probiotics, prebiotics, synbiotics, immunostimulants, organic acids, nucleotides and medicinal herbs. Apart from boosting aquafeeds and safeguarding general health of aquatic animals, some of these substances have been found to possess beneficial immunostimulant and anti‐stress relieving properties. Furthermore, the use of these natural substances increases the consumer confidence of farmed fish. Due care has been taken to cover the on‐going trends and recent advances with a perspective vision and their holistic usages and beneficial applications in aquatic animals’ systems. The current study also shed light regarding the management and production aspects of aquatic animals which will enlighten farmers and producers for better economic growth.
Long‐term monitoring of shrub species translocation in degraded Neotropical mountain grassland
Authors: Gomes Vanessa M. , Negreiros Daniel , Fernandes G. Wilson , Pires Ana C. V. , Silva Ana C. D. R. , Le Stradic Soizig
Published: August 2017

The introduction of plant species is a central topic in restoration ecology research. It is an effective technique to restore degraded ecosystems that present low resilience, such as the rupestrian grasslands. Once implemented, the transplantation of native species is monitored only in the short term, whereas long‐term monitoring should be preferred to identify potential changes in the restoration results. Our study is the first assessment of the transplantation success of 10 native shrub species in a degraded area of rupestrian grasslands, 8.5 years after transplantation. Survival, growth, and recruitment were assessed in 2004, 2008, and 2012. For all species, survival, growth, and recruitment varied over time. Although some species exhibited great mortality during the last 4 years, they also showed a great resprouting ability. Our results highlighted a trade‐off between survival and recruitment capacity. Most of the studied species showed remarkable ability to adapt to the extreme environment of the degraded area, persisting either through surviving or recruiting new individuals. We list nine native species, which are well appropriated for rupestrian grasslands restoration. In constrained environments, survival and resistance should represent criteria to select species for restoration project rather than fast growth and ground cover.
Morpho‐sedimentary characteristics of proximal gravel braided river deposits in a Froude‐scaled physical model
Authors: Gardner Tobi , Ashmore Peter , Leduc Pauline
Published: August 2017

A Froude‐scaled physical model of a proximal gravel‐bed braided river was used to connect the river morphological characteristics, and sedimentary processes and forms, to deposit geometry. High resolution continuous three‐dimensional topographic data were acquired from sequential photogrammetric digital elevation models paired with grain‐size surface maps derived from image analysis of textural properties of the surface. From these data, the full three‐dimensional development of the braided river deposit and grain‐size sorting patterns was compiled over an experimental time period of 41 h during which the model river reworked a large portion of the braided channel. The minimum surface of the deposit is developed progressively over time by erosion, migration and avulsion of channels, and by local scour at channel confluences. The maximum surface of the deposit is formed by amalgamation of braid bar surfaces and has less overall relief than the minimum surface. Confluence scour constitutes about 5% of the area of the minimum surface. Migration of individual confluences is limited to distances of the order of the width and length of the confluence, so that confluences do not form laterally extensive deposits and basal surfaces. Maximum and minimum surfaces have very similar grain‐size distributions, and there is no extensive basal coarse layer. Deposit maximum thickness is strongly associated with large channel confluences which occur as deeper areas along the main channel belt and make up a large proportion of the thickest portions of the deposit.
BK polyomavirus infection after renal transplantation: Surveillance in a resource‐challenged setting
Authors: Bagchi Soumita , Gopalakrishnan Vikraman , Srivastava Sandeep Kumar , Upadhayay Ashish , Singh Geetika , Bhowmik Dipankar , Mahajan Sandeep , Dinda Amit , Agarwal Sanjay Kumar
Published: August 2017

Background

There is a paucity of data available about BK polyomavirus (BKPyV) infection after renal transplantation (RTX) in resource‐limited countries with a predominantly living‐donor, ABO‐compatible RTX program. We aimed to assess BKPyV infection in such patients in a public hospital in India.

Methods

We prospectively evaluated plasma BKPyV replication in 62 patients at 1, 3, 6, 9, and 12 months after RTX. Sustained significant BK viremia (SSBKV) was defined as significant viremia (≥10 000 copies/mL) detected ≥2 times, and BKPyV‐associated nephropathy (BKVAN) as histologic changes of BKVAN with BK viremia with/without graft dysfunction.

Results

All patients underwent RTX without requiring desensitization. Incidence of BK viremia was: 17.7%, 41.9%, 16.1%, 25.8%, and 17.7% at 1, 3, 6, 9, and 12 months, respectively. Of 62 patients, 64.5% had BKPyV viremia during the study, 32.2% had significant viremia, all except one detected in the first 6 months. Nine (14.5%) patients had SSBKV. There was no biopsy‐proven BKVAN. At the end of 1 year, mean serum creatinine was higher and graft dysfunction was significantly more common in patients with SSBKV compared to those without SSBKV.

Conclusion

Transient BK viremia is common in low/intermediate immunologic risk RTX recipients in India, with a peak occurring at 3‐6 months. Most clear their viremia by 12 months. Graft dysfunction seems to be more frequent in patients with SSBKV, although BKVAN is uncommon on biopsy in these patients.
Fluid geographies: Marine territorialisation and the scaling up of local aquatic epistemologies on the Pacific coast of Colombia
Authors: Satizábal Paula , Batterbury Simon P. J.
Published: August 2017

The Pacific region of Colombia, like many sparsely populated places in developing countries, has been imagined as empty in social terms, and yet full in terms of natural resources and biodiversity. These imaginaries have enabled the creation of frontiers of land and sea control, where the state as well as private and illegal actors have historically dispossessed Afro‐descendant and indigenous peoples. This paper contributes to the understanding of territorialisation in the oceans, where political and legal framings of the sea as an open‐access public good have neglected the existence of marine social processes. It shows how Afro‐descendant communities and non‐state actors are required to use the language of resources, rather than socio‐cultural attachment, to negotiate state marine territorialisation processes. Drawing on a case study on the Pacific coast of Colombia, we demonstrate that Afro‐descendant communities hold local aquatic epistemologies, in which knowledge and the production of space are entangled in fluid and volumetric spatio‐temporal dynamics. However, despite the social importance of aquatic environments, they were excluded from Afro‐descendants' collective territorial rights in the 1990s. Driven by their local aquatic epistemologies, coastal communities are reclaiming authority over the seascape through the creation of a marine protected area. We argue that they have transformed relations of authority at sea to ensure local access and control, using state institutional instruments to subvert and challenge the legal framing of the sea as an open access public good. As such, this marine protected area represents a place of resistance that ironically subjects coastal communities to disciplinary technologies of conservation.