bluuebunny/crossref_metadata_2025 huggingface dataset:
Imperfect pathogen detection from non‐invasive skin swabs biases disease inference
Authors: DiRenzo Graziella V. , Campbell Grant Evan H. , Longo Ana V. , Che‐Castaldo Christian , Zamudio Kelly R. , Lips Karen R.
Published: August 2017

Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low‐level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals.

Our objectives were two‐fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis (Bd) on non‐invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model, using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity.

We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections <10 zoospores have <95% probability of being detected. If imperfect Bd detection was not considered, then Bd prevalence was underestimated by as much as 71%. In the Bd‐amphibian system, this indicates a need to correct for imperfect pathogen detection in enzootic host populations persisting with low‐level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions.

Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modelling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.
Environmental factors affecting the distribution of African elephants in the Kasigau wildlife corridor, SE Kenya
Authors: Williams Harry F. , Bartholomew David C. , Amakobe Bernard , Githiru Mwangi
Published: August 2017

The African elephant, Loxodonta africana, is under threat from habitat loss, poaching and human–elephant conflict. To mitigate for impact of habitat loss and reduce conflict, connectivity between elephant habitats can be improved through the protection of corridor areas. This study looks at elephant distribution and movement patterns within the Kasigau Wildlife Corridor (KWC) within the Tsavo Conservation Area in South‐east Kenya. Elephant presence data were obtained from observations by rangers during routine patrols across KWC, and were analysed in MaxEnt. The environmental factors predicting elephant distribution and density were tested, as well as the relationship between elephant maximum entropy and the presence and abundance of other wildlife. Seasonal variations in temperature and precipitation, plus presence of waterholes were found to play significant roles in elephant distribution across KWC. Higher elephant densities were not found to correlate with lower densities of other wildlife species; indeed, during the dry seasons, elephant presence was associated with greater wild herbivore densities. Besides illustrating the importance of the KWC for elephant conservation in the Tsavo ecosystem, both as a key corridor and habitat, this study also hopes to highlight the untapped utility of routine ranger patrol data, and encourage the use of such presence‐only data for deducing important knowledge for conservation of biodiversity.
Mindfulness of voices, self‐compassion, and secure attachment in relation to the experience of hearing voices
Authors: Dudley James , Eames Catrin , Mulligan John , Fisher Naomi
Published: August 2017

Objectives

Developing compassion towards oneself has been linked to improvement in many areas of psychological well‐being, including psychosis. Furthermore, developing a non‐judgemental, accepting way of relating to voices is associated with lower levels of distress for people who hear voices. These factors have also been associated with secure attachment. This study explores associations between the constructs of mindfulness of voices, self‐compassion, and distress from hearing voices and how secure attachment style related to each of these variables.

Design

Cross‐sectional online.

Method

One hundred and twenty‐eight people (73% female; Mage = 37.5; 87.5% Caucasian) who currently hear voices completed the Self‐Compassion Scale, Southampton Mindfulness of Voices Questionnaire, Relationships Questionnaire, and Hamilton Programme for Schizophrenia Voices Questionnaire.

Results

Results showed that mindfulness of voices mediated the relationship between self‐compassion and severity of voices, and self‐compassion mediated the relationship between mindfulness of voices and severity of voices. Self‐compassion and mindfulness of voices were significantly positively correlated with each other and negatively correlated with distress and severity of voices.

Conclusion

Mindful relation to voices and self‐compassion are associated with reduced distress and severity of voices, which supports the proposed potential benefits of mindful relating to voices and self‐compassion as therapeutic skills for people experiencing distress by voice hearing.

Practitioner points

Greater self‐compassion and mindfulness of voices were significantly associated with less distress from voices. These findings support theory underlining compassionate mind training.

Mindfulness of voices mediated the relationship between self‐compassion and distress from voices, indicating a synergistic relationship between the constructs.

Although the current findings do not give a direction of causation, consideration is given to the potential impact of mindful and compassionate approaches to voices.
The relationship between learning mathematics and general cognitive ability in primary school
Authors: Cowan Richard , Hurry Jane , Midouhas Emily
Published: August 2017

Three relationships between learning mathematics and general cognitive ability have been hypothesized: The educational hypothesis that learning mathematics develops general cognitive skills, the psychometric hypothesis that differences in general cognitive ability cause differences in mathematical attainment, and the reciprocal influence hypothesis that developments in mathematical ability and general cognitive ability influence each other. These hypotheses are assessed with a sample of 948 children from the Twins Early Development Study who were assessed at 7, 9, and 10 years on mathematics, English, and general cognitive ability. A cross‐lagged path analysis with mathematics and general cognitive ability measures supports the reciprocal influence hypothesis between 7 and 9 and between 9 and 10. A second analysis including English assessments only provides evidence of a reciprocal relationship between 7 and 9.

Statement of Contribution

What is already known on this subject?

The correlations between mathematical attainment, literacy, and measures of general cognitive skills are well established.

The role of literacy in developing general cognitive skills is emerging.

What the present study adds?

Mathematics contributes to the development of general cognitive skills.

General cognitive ability contributes to mathematical development between 7 and 10.

These findings support the hypothesis of reciprocal influence between mathematics and general cognitive ability, at least between 7 and 9.
Anesthetic management for intestinal transplantation: A decade of experience
Authors: Zerillo Jeron , Kim Sang , Hill Bryan , Shapiro David , Lin Hung‐Mo , Burnham Alyssa , Moon Jang , Iyer Kishore , DeMaria Samuel
Published: August 2017

Background

Intestinal transplantation (ITx) is the definitive therapy for patients suffering from intestinal failure. Previously published reports suggest that these cases should be managed perioperatively with the same intensive monitors and techniques as in liver transplantation.

Methods

We retrospectively reviewed the anesthetic management of 67 isolated intestinal, intestinal‐pancreas, and intestinal‐kidney transplants over the previous decade (2005‐2015) in our tertiary care institution.

Results

Patients were typically managed with a single arterial line, a single central venous catheter, and rarely intensive modalities such as a pulmonary artery catheter, a transesophageal echocardiography, a second arterial catheter or central venous catheter, a rapid infusion system, a cell salvage device, or viscoelastic testing. Significant hemodynamic derangements were rare, and the rate of postreperfusion syndrome was 8.96%. Our fluid administration type and volume and transfusion type and volume were similar to previous reports in which more intensive anesthetic management was employed.

Conclusion

We demonstrate that ITx can safely occur without utilizing the intensive resources requisite for a liver transplant.
Improving monitoring tools for spotted wing drosophila, Drosophila suzukii
Authors: Kirkpatrick D.M. , McGhee P.S. , Gut L.J. , Miller J.R.
Published: August 2017

Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) were trapped in the field using colored plastic sphere traps coated with insect Tangle‐trap. Red and black spheres captured significantly more D. suzukii than white spheres. Translucent deli‐cup traps deployed in cherry orchards and baited with yeast, the Alpha Scents lure, or the Scentry lure captured significantly more flies than the Trécé lure and Suzukii bait; all attractants had poor selectivity for D. suzukii. No‐choice evaluations of attractants conducted in field cages corroborated the cherry orchard field study, though translucent deli‐cup traps provisioned with the yeast bait captured significantly more flies than those baited with the Alpha Scents lure. Red sphere traps baited with the Scentry lure captured 3–6× more flies than the deli‐cup trap baited with the same lure, and 3–4× more flies than the deli‐cup trap baited with yeast bait, demonstrating that a trap integrating both visual and olfactory cues is a superior tool for monitoring D. suzukii. Moreover, this simple sticky, dry trap design requires far less labor and maintenance than does a liquid‐based deli‐cup trap.
Semiochemical attractants for the beech leaf‐mining weevil,Orchestes fagi
Authors: Silk P.J. , Mayo P.D. , LeClair G. , Brophy M. , Pawlowski S. , MacKay C. , Hillier N.K. , Hughes C. , Sweeney J.D.
Published: August 2017

The beech leaf‐mining weevil,Orchestes fagiL. (Curculionidae:Curculioninae:Rhamphini), a pest of European beech,Fagus sylvaticaL. (Fagaceae), was recently discovered infesting American beech,Fagus grandifoliaEhrh., in Nova Scotia, Canada. AdultO. fagifeed on both young and mature leaves of beech as well as on other species (e.g., raspberry,Rubusspp.), but oviposition and larval feeding are restricted to beech. Females oviposit in young developing beech leaves at the time of bud burst. We characterized volatiles emitted from buds, leaves, and sapwood of American beech and examined their potential as attractants alone or when combined with other weevil pheromones forO. fagi. We predicted that adults would be attracted to volatiles emitted from beech leaves, especially those emitted from bursting beech buds. Gas chromatography/mass spectrometry (GC/MS) analyses of volatiles collected from buds at pre‐ and post‐budburst identified two diterpene hydrocarbons, 9‐geranyl‐p‐cymene (1) and 9‐geranyl‐α‐terpinene (2a), that were emitted in large amounts at the time of bud burst. Compound1significantly increased mean catch of males and totalO. fagi(but not females) on sticky traps compared with unbaited controls. Y‐tube bioassays confirmed attraction of maleO. fagito bursting beech buds and compound1. Attraction of maleO. fagito1, emitted in large quantities from American beech, is likely adaptive because both oviposition and mating ofO. fagicoincide with budburst. Our data suggest that traps baited with1may be useful for monitoring the spread ofO. fagiin North America.
Inga vera trypsin inhibitor interferes in the proteolytic activity and nutritional physiology of Ephestia kuehniella larvae
Authors: Bezerra Cézar da Silva , Oliveira Carolina Turatti , Macedo Maria Lígia Rodrigues
Published: August 2017

Plant peptidase inhibitors provide plants with a defense strategy to inhibit insect digestive enzymes and have been studied as an alternative strategy for pest control as they interfere in normal insect physiology. We evaluated the effects of ingestion of the trypsin inhibitor from Inga vera Willd. (Fabaceae) seeds on the nutritional and digestive physiology of Ephestia kuehniella (Zeller) (Lepidoptera: Pyralidae) larvae. Inga vera trypsin inhibitor (IVTI) reduced the efficiency of the conversion of ingested and digested food in these larvae and increased the metabolic cost, causing an anti‐nutritional effect. In both short‐ and long‐term bioassays, the ingestion of IVTI inactivated most of the insect's trypsin activity, but increased chymotrypsin activity as a compensatory response by the insect; however, protein digestion continued to be partially blocked. Consequently, chymotrypsin‐like enzymes, which were over‐produced in the gut, were excreted more into the frass of IVTI‐fed larvae. As such, the resistance of IVTI to hydrolysis by insect midgut proteases resulted in detrimental effects to larvae. These data provide support for the use of IVTI as a biotechnological tool for pest control.
Low‐dose bortezomib and dexamethasone as primary therapy in elderly patients with Waldenstrӧm macroglobulinemia
Authors: Zhang Ya‐Ping , Yang Xi , Lin Zeng‐Hua , Wang Xin‐Feng , Cao Xin , You Xue‐Fen , Huang Hong‐Ming , Shi Wen‐Yu , Liu Hong
Published: August 2017

Objective

This retrospective study was designed to determine the efficacy and safety of low‐dose bortezomib and dexamethasone (lBD) in elderly Chinese patients with Waldenstrӧm macroglobulinemia (WM).

Methods

Ten patients with WM aged over 60 years received first‐line treatment with lBD.

Results

The median age was 70 years (range, 61‐77 years). The overall response rate was 80%, including 1 patient who achieved a complete response, 1 patient with very good partial response, and 6 patients with a partial response. Median time to response was 1.8 months after treatment with lBD. Six (60%) patients achieved a partial response, including 2 (20%) patients who had a more than 75% reduction in serum immunoglobulin M levels. A rapid reduction in paraprotein was observed in three patients who received plasmapheresis. After a median follow‐up period of 36 months, all patients were still alive and six had no disease progression. The estimated median time to progression was 39 months (range, 15‐60 months). The most common adverse events were anemia, thrombocytopenia, neuropathy, and neutropenia. Peripheral neuropathy was the most common non‐hematological toxicity in six (60%) patients, but did not result in the discontinuation of bortezomib.

Conclusions

Our findings show that lBD is an effective and tolerable treatment regimen for elderly patients with WM.
Retreatment and prolonged therapy with subcutaneous bortezomib in patients with relapsed multiple myeloma: A randomized, controlled, phase III study
Authors: Terpos Evangelos , Gobbi Marco , Potamianou Anna , Lahaye Marjolein , Couturier Catherine , Cavo Michele
Published: August 2017

Objectives

This randomized, international, multicenter, open‐label phase III study investigated the effects of experimental retreatment with subcutaneous bortezomib plus dexamethasone (VD) followed by prolonged bortezomib therapy vs standard VD retreatment in patients with relapsed/refractory multiple myeloma.

Methods

Patients were randomized (2:1) to receive either experimental (n = 53) or standard (n = 27) retreatment, stratified by the number of prior therapy lines.

Results

The study was terminated prematurely with insufficient enrollment to adequately compare the retreatment therapies; results should be considered descriptive. After a median follow‐up of 21.2 and 20.0 months in the experimental and standard arms, respectively, the median progression‐free survival (primary endpoint) was 7.2 months (95% confidence interval 5.7‐9.0) vs 7.8 months (4.9‐11.7). The overall response rate was 66% and 52% for experimental and standard retreatment regimens, respectively. Thrombocytopenia was the most common and most differentially observed grade ≥3 adverse event (experimental: 9% vs standard: 22%). Any‐grade peripheral neuropathies (including peripheral sensory neuropathies) were reported in 23% vs 37% of patients.

Conclusions

This study showed no significant benefit with experimental vs standard VD retreatment therapy. Further investigations are required to determine whether the experimental retreatment regimen is a suitable alternative to the current standard retreatment regimen.
Attention‐Deficit/Hyperactivity Disorder (ADHD): Interaction between socioeconomic status and parental history of ADHD determines prevalence
Authors: Rowland Andrew S. , Skipper Betty J. , Rabiner David L. , Qeadan Fares , Campbell Richard A. , Naftel A. Jack , Umbach David M.
Published: August 2017

Background

Many studies have reported a higher prevalence of Attention‐Deficit/Hyperactivity Disorder (ADHD) among disadvantaged populations, but few have considered how parental history of ADHD might modify that relationship. We evaluated whether the prevalence of ADHD varies by socioeconomic status (SES) and parental history of ADHD in a population‐sample of elementary school children age 6–14 years.

Methods

We screened all children in grades 1–5 in 17 schools in one North Carolina (U.S.) county for ADHD using teacher rating scales and 1,160 parent interviews, including an ADHD structured interview (DISC). We combined parent and teacher ratings to determine DSM‐IV ADHD status. Data analysis was restricted to 967 children with information about parental history of ADHD. SES was measured by family income and respondent education.

Results

We found an interaction between family income and parental history of ADHD diagnosis (p = .016). The SES gradient was stronger in families without a parental history and weaker among children with a parental history. Among children without a parental history of ADHD diagnosis, low income children had 6.2 times the odds of ADHD (95% CI 3.4–11.3) as high income children after adjusting for covariates. Among children with a parental history, all had over 10 times the odds of ADHD as high income children without a parental history but the SES gradient between high and low income children was less pronounced [odds ratio (OR) = 1.4, 95% CI 0.6–3.5].

Conclusions

Socioeconomic status and parental history of ADHD are each strong risk factors for ADHD that interact to determine prevalence. More research is needed to dissect the components of SES that contribute to risk of ADHD. Future ADHD research should evaluate whether the strength of other environmental risk factors vary by parental history. Early identification and interventions for children with low SES or parental histories of ADHD should be explored.
Imitation inhibition in children with Tourette syndrome
Authors: Brandt Valerie Cathérine , Moczydlowski Agnes , Jonas Melanie , Boelmans Kai , Bäumer Tobias , Brass Marcel , Münchau Alexander
Published: August 2017

Objective

Echopraxia, that is, the open and automatic imitation of other peoples’ actions, is common in patients with Gilles de la Tourette syndrome, autism spectrum disorder, and also those with frontal lobe lesions. While systematic reaction time tasks have confirmed increased automatic imitation in the latter two groups, adult patients with Tourette syndrome appear to compensate for automatic imitation tendencies by an overall slowing in response times. However, whether children with Tourette syndrome are already able to inhibit automatic imitation tendencies has not been investigated.

Method

Fifteen children with Tourette syndrome and 15 healthy children (aged 7–12 years) performed an imitation inhibition paradigm. Participants were asked to respond to an auditory cue by lifting their index finger or their little finger. Participants were simultaneously presented with either compatible or incompatible visual stimuli.

Results

Overall responses in children with Tourette syndrome were slower than in healthy children. Although responses were faster in compatible than in incompatible trials in both groups, this ‘interference effect’ was smaller in children with Tourette syndrome.

Conclusions

Children with Tourette syndrome have a smaller interference effect than healthy children, indicating an enhanced ability to behaviourally control automatic imitation tendencies at the cost of reacting slower. The results suggest that children with Tourette syndrome already employ different or additional inhibition strategies compared to healthy children.
Characterization of intrinsic material properties of a model lipoproteic emulsion gel by oscillatory and creep compliance rheometry
Authors: Okada Kyle S. , Kuo Wan‐Yuan , Lee Youngsoo
Published: August 2017

The effects of varying formulation and processing parameters on rheological properties in a model lipid/protein‐based emulsion gel were studied. Heat‐set model lipoproteic emulsion gels were prepared with varying levels of protein, lipid, and NaCl contents and high pressure homogenization treatments. Small deformation oscillatory rheometry, creep compliance, and pore size analysis experiments were used to characterize intrinsic structural properties, matrix interactions, and microstructure. Creep compliance behavior of the gel system was successfully modeled by a four‐component Burgers model. Shear storage and loss moduli and Newtonian viscosity increased while instantaneous compliance, retarded compliance, and pore size decreased with increasing protein or fat content or homogenization pressure. The data obtained in this study provide information on factors affecting protein network structure and strength, properties may be useful for creating desirable attributes in lipid/protein‐based foods with a further optimization process.

Practical applications

This research evaluates the effects of formulation and processing factors on the properties of a protein/fat‐based food system. These properties may be related to sodium mobility and salty taste perception. This research provides information on strategies that can be used to control factors influencing the physical properties of protein/fat‐based food systems targeting sodium reduction.
Single‐cell sequencing unveils the lifestyle and CRISPR‐based population history of Hydrotalea sp. in acid mine drainage
Authors: Medeiros J. D. , Leite L. R. , Pylro V. S. , Oliveira F. S. , Almeida V. M. , Fernandes G. R. , Salim A. C. M. , Araújo F. M. G. , Volpini A. C. , Oliveira G. , Cuadros‐Orellana S.
Published: August 2017

Acid mine drainage (AMD) is characterized by an acid and metal‐rich run‐off that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early‐stage AMD sample. These cells belong to the genus Hydrotalea and are closely related to Hydrotalea flava. The phylogeny and average nucleotide identity analysis suggest that all single amplified genomes (SAGs) form two clades that may represent different strains. These cells have the genomic potential for denitrification, copper and other metal resistance. Two coexisting CRISPR‐Cas loci were recovered across SAGs, and we observed heterogeneity in the population with regard to the spacer sequences, together with the loss of trailer‐end spacers. Our results suggest that the genomes of Hydrotalea sp. strains studied here are adjusting to a quickly changing selective pressure at the microhabitat scale, and an important form of this selective pressure is infection by foreign DNA.
Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Authors: Chan Kin Onn , Alexander Alana M. , Grismer L. Lee , Su Yong‐Chao , Grismer Jesse L. , Quah Evan S. H. , Brown Rafe M.
Published: August 2017

Accurately delimiting species boundaries is a nontrivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly used species delimitation methods (SDMs) and a population genomics approach based on genomewide single‐nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genomewide SNPs to identify putative species boundaries by implementing noncoalescent and coalescent‐based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA‐BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
The cereal pathogen Fusarium pseudograminearum produces a new class of active cytokinins during infection
Authors: Sørensen Jens Laurids , Benfield Aurelie H. , Wollenberg Rasmus Dam , Westphal Klaus , Wimmer Reinhard , Nielsen Mikkel Rank , Nielsen Kristian Fog , Carere Jason , Covarelli Lorenzo , Beccari Giovanni , Powell Jonathan , Yamashino Takafumi , Kogler Herbert , Sondergaard Teis Esben , Gardiner Donald Max
Published: August 2017

The fungal pathogen Fusarium pseudograminearum causes important diseases of wheat and barley. During a survey of secondary metabolites produced by this fungus, a novel class of cytokinins, herein termed Fusarium cytokinins, was discovered. Cytokinins are known for their growth‐promoting and anti‐senescence activities, and the production of a cytokinin mimic by what was once considered as a necrotrophic pathogen that promotes cell death and senescence challenges the simple view that this pathogen invades its hosts by employing a barrage of lytic enzymes and toxins. Through genome mining, a gene cluster in the F. pseudograminearum genome for the production of Fusarium cytokinins was identified and the biosynthetic pathway was established using gene knockouts. The Fusarium cytokinins could activate plant cytokinin signalling, demonstrating their genuine hormone mimicry. In planta analysis of the transcriptional response to one Fusarium cytokinin suggests extensive reprogramming of the host environment by these molecules, possibly through crosstalk with defence hormone signalling pathways.
Investigation of the diversity of effector genes in the banana pathogen, Fusarium oxysporum f. sp. cubense, reveals evidence of horizontal gene transfer
Authors: Czislowski Elizabeth , Fraser‐Smith Sam , Zander Manuel , O'Neill Wayne T. , Meldrum Rachel A. , Tran‐Nguyen Lucy T. T. , Batley Jacqueline , Aitken Elizabeth A. B.
Published: August 2017

It is hypothesized that the virulence of phytopathogenic fungi is mediated through the secretion of small effector proteins that interfere with the defence responses of the host plant. In Fusarium oxysporum, one family of effectors, the Secreted In Xylem (SIX) genes, has been identified. We sought to characterize the diversity and evolution of the SIX genes in the banana‐infecting lineages of F. oxysporum f. sp. cubense (Foc). Whole‐genome sequencing data were generated for the 23 genetic lineages of Foc, which were subsequently queried for the 14 known SIX genes (SIX1–SIX14). The sequences of the identified SIX genes were confirmed in a larger collection of Foc isolates. Genealogies were generated for each of the SIX genes identified in Foc to further investigate the evolution of the SIX genes in Foc. Within Foc, variation of the SIX gene profile, including the presence of specific SIX homologues, correlated with the pathogenic race structure of Foc. Furthermore, the topologies of the SIX gene trees were discordant with the topology of an infraspecies phylogeny inferred from EF‐1α/RPB1/RPB2 (translation elongation factor‐1α/RNA polymerase II subunit I/RNA polymerase II subunit II). A series of topological constraint models provided strong evidence for the horizontal transmission of SIX genes in Foc. The horizontal inheritance of pathogenicity genes in Foc counters previous assumptions that convergent evolution has driven the polyphyletic phylogeny of Foc. This work has significant implications for the management of Foc, including the improvement of diagnostics and breeding programmes.
Cyclic and intermittent very low‐protein diet can have beneficial effects against advanced diabetic nephropathy in Wistar fatty (fa/fa) rats, an animal model of type 2 diabetes and obesity
Authors: Kitada Munehiro , Ogura Yoshio , Suzuki Taeko , Monnno Itaru , Kanasaki Keizo , Watanabe Ai , Koya Daisuke
Published: August 2017

A low‐protein diet (LPD), particularly, very low‐protein diet (VLPD) is expected for reno‐protection in advanced chronic kidney disease, including diabetic nephropathy. We previously also demonstrated that a VLPD clearly improved advanced diabetic nephropathy in a type 2 diabetes and obesity rat. However, clinically, an everyday long‐term VLPD contributes to poor adherence, which may be related to controvertial results of an LPD on the suppression for diabetic nephropathy, and has nutritional issues, such as sarcopenia or protein‐energy wasting. The aim of this study is to elucidate the reno‐protective effect of a cyclic and intermittent VLPD, not an everyday VLPD, against the advanced experimental diabetic nephropathy. Diabetic male Wistar fatty (fa/fa) rats (WFRs) were treated with a standard diet (STD; 23.84% protein) or a cyclic and intermittent VLPD (5.77% protein) consisting of an STD for 3 days and a VLPD for 4 days a week for 20 weeks beginning at 24 weeks of age. A cyclic and intermittent VLPD significantly improved renal hypertrophy, and significantly decreased urinary albumin and liver‐type fatty acid binding protein (L‐FABP) excretion without changes in body weight or exacerbation of HbA1c levels in diabetic rats. Additionally, diabetes‐induced renal injuries including fibrosis, tubular cell damage and inflammation were significantly ameliorated by a cyclic and intermittent VLPD in diabetic rats. Thus, based on our experimental data, a cyclic and intermittent VLPD may be a dietary regimen that is easy to continue and has less risk of malnutrition, compared to an everyday long‐term VLPD, against advanced diabetic nephropathy.
The Generalized Integration Challenge in Metaethics
Authors: Schroeter Laura , Schroeter François
Published: August 2017

The Generalized Integration Challenge (GIC) is the task of providing, for a given domain of discourse, a simultaneously acceptable metaphysics, epistemology and metasemantics and showing them to be so. In this paper, we focus on a metaethical position for which (GIC) seems particularly acute: the brand of normative realism which takes normative properties to be (i) mind‐independent and (ii) causally inert. The problem is that these metaphysical commitments seem to make normative knowledge impossible. We suggest that bringing metasemantics into play can help to resolve this puzzle. We propose an independently plausible metasemantic constraint on reference determination and show how it can provide a plausible response to (GIC) for this brand of normative realism.
Distinct DC subsets regulate adaptive Th1 and 2 responses during Trichuris muris infection
Authors: Demiri M. , Müller‐Luda K. , Agace W. W. , Svensson‐Frej M.
Published: August 2017

Low‐ and high‐dose infections with the murine large intestinal nematode Trichuris muris are associated with induction of adaptive Th1 and Th2 responses, respectively, in mesenteric lymph nodes (MLN). Classical dendritic cells (cDC) accumulate in the large intestinal mucosa and MLN upon T. muris infection, yet their role in driving adaptive responses to infection remains largely unknown. We performed low‐ and high‐dose T. muris infections of mice deficient in defined cDC subsets to investigate their role in induction of adaptive immune responses. Mice lacking IRF4‐dependent cDC failed to clear a high‐dose infection and displayed impaired Th2 responses. Conversely, mice lacking IRF8‐dependent cDC cleared a low‐dose infection and displayed an impaired Th1 response while increased production of Th2 cytokines. Finally, mice lacking both IRF4‐ and IRF8‐dependent cDC were able to generate a Th2 response and clear a low‐dose infection. Collectively, these results suggest that IRF4‐ and IRF8‐dependent cDC act antagonistically during T. muris infection, and demonstrate that intestinal Th2 responses can be generated towards T. muris in the absence of IRF4‐dependent cDC.
Single layer centrifugation of fresh dromedary camel semen improves sperm quality and in vitro fertilization capacity compared with simple sperm washing
Authors: Malo C , Crichton EG , Morrell JM , Pukazhenthi BS , Skidmore JA
Published: August 2017

Contents

Single layer centrifugation (SLC) through a colloid is a tool for selecting viable mammalian spermatozoa but has not been used previously for fresh dromedary camel sperm. Semen from six camels (2 ejaculates/male) was diluted 1:5 (v:v) or 1:10 (v:v) in a Tris–citrate–fructose buffer for mechanical liquefaction by gentle pipetting. Following liquefaction, semen was processed either by SLC or by centrifugation without a colloid (control). Total and progressive motilities, CASA kinematics, vitality and acrosome integrity (eosin–nigrosin) and plasma membrane integrity (Hypo‐osmotic swelling test; HOST), and fertilizing ability in a heterologous assay (zona‐free goat oocytes) were evaluated. Both total (p = .003) and progressive motilities (p = .003) were higher in SLC‐processed than in control semen samples, irrespective of dilution. Positive HOST values increased when using colloid in 1:5 (p = .001) and 1:10 dilution (p = .010). Colloid‐selected sperm had higher penetration rates than controls (p < .001 and p = .02 for 1:5 and 1:10 dilutions, respectively). However, only the SLC sperm at 1:5 dilution showed higher percentages of pronuclear formation (p = .02) than controls. Dilution effect was only significant for total motility before in vitro fertilization, with higher values for the 1:5 dilution (p = .033). The recovery rates of motile sperm between dilutions were similar (26.1% vs 35.4%; p = .226). In conclusion, SLC is a promising tool for selecting functional dromedary camel sperm and warrants more research.
Effects of service number on conception rate in Japanese Black cattle
Authors: Irikura N , Uematsu M , Kitahara G , Osawa T , Sasaki Y
Published: August 2017

Contents

The conception rate (CR) of Japanese Black cattle has been decreasing since 1990. The objectives of this study were to compare CR by artificial insemination (AI) number, and to assess the interaction between AI number and possible factors related to CR in Japanese Black cattle. Records of 11,182 AI records for 6,741 heifers and 61,302 AI records for 13,139 cows on 977 farms were analysed. The average CR of heifers was 47.0%, and CR at the first, second and third AI was higher than at the fourth or subsequent AI (p < 0.05). The average CR of cows was 47.8%, and their CR at first and second AI was higher than the fourth or subsequent AI (p < 0.05). Data analysis with CR as the dependent variable revealed significant interactions of AI number with interval from calving to first AI and AI season. Cows first serviced at ≤48 days post‐partum had lower CR than those at ≥90 days at first AI (p < 0.05), but the interval from calving to first AI did not affect CR at second AI. Cows serviced in the autumn had a higher CR at first AI than those serviced in the spring and winter (p < 0.05); however, there was no seasonal difference in CR at the second AI. In summary, CR began to decrease from the fourth AI in heifers and the third AI in cows. The AI season and the interval from calving to first AI significantly affected CR only at the first AI.
Small Domain Estimation of Business Statistics by Using Multivariate Skew Normal Models
Authors: Ferrante Maria Rosaria , Pacei Silvia
Published: August 2017

Small domain business statistics are becoming important for better planning business policies. We focus on the estimation of the averages of value added and labour cost in small domains. To take into account the positive skewness in the distribution of outcomes and the correlation between them, we propose a bivariate skew normal small area model. Estimates are obtained from real survey data. The performance of the estimator proposed is evaluated on the basis of both survey data and a synthetic firm population. Results show that the model proposed increases the estimates’ reliability and that the estimates obtained make it possible to perform detailed regional economic studies.
Heritability estimates of endurance‐related phenotypes: A systematic review and meta‐analysis
Authors: Miyamoto‐Mikami E. , Zempo H. , Fuku N. , Kikuchi N. , Miyachi M. , Murakami H.
Published: August 2017

The aim of this study was to clarify heritability estimates for endurance‐related phenotypes and the underlying factors affecting these estimates. A systematic literature search was conducted for studies reporting heritability estimates of endurance‐related phenotypes using the PubMed database (up to 30 September 2016). Studies that estimated the heritability of maximal oxygen uptake (), submaximal endurance phenotypes, and endurance performance were selected. The weighted mean heritability for endurance‐related phenotypes was calculated using a random‐effects model. A total of 15 studies were selected via a systematic review. Meta‐analysis revealed that the weighted means of the heritability of absolute values and those adjusted for body weight and for fat‐free mass were 0.68 (95% CI: 0.59‐0.77), 0.56 (95% CI: 0.47‐0.65), and 0.44 (95% CI: 0.13‐0.75), respectively. There was a significant difference in the weighted means of the heritability of across these different adjustment methods (P < .05). Moreover, there was evidence of statistical heterogeneity in the heritability estimates among studies. Meta‐regression analysis revealed that sex could partially explain the heterogeneity in the heritability estimates adjusted by body weight. For submaximal endurance phenotypes and endurance performance, the weighted mean heritabilities were 0.49 (95% CI: 0.33‐0.65) and 0.53 (95% CI: 0.27‐0.78), respectively. There was statistically significant heterogeneity in the heritability estimates reported among the studies, and we could not identify the specific factors explaining the heterogeneity. Although existing studies indicate that genetic factors account for 44%‐68% of the variability in endurance‐related phenotypes, further studies are necessary to clarify these values.
From the generalized reflection law to the realization of perfect anomalous reflectors
Authors: Díaz-Rubio Ana , Asadchy Viktar S. , Elsakka Amr , Tretyakov Sergei A.
Published: August 2017

Nonlocal metasurface for perfect anomalous reflection demonstrates a new possibility for controlling electromagnetic energy flow.
Large polarons in lead halide perovskites
Authors: Miyata Kiyoshi , Meggiolaro Daniele , Trinh M. Tuan , Joshi Prakriti P. , Mosconi Edoardo , Jones Skyler C. , De Angelis Filippo , Zhu X.-Y.
Published: August 2017

Charge carriers in both hybrid and all-inorganic lead halide perovskites form large polarons.
Human blood T
fr
cells are indicators of ongoing humoral activity not fully licensed with suppressive function
Authors: Fonseca Valter R. , Agua-Doce Ana , Maceiras Ana Raquel , Pierson Wim , Ribeiro Filipa , Romão Vasco C. , Pires Ana Rita , da Silva Susana Lopes , Fonseca João Eurico , Sousa Ana E. , Linterman Michelle A. , Graca Luis
Published: August 2017

Circulating human T follicular regulatory (T
fr
) cells are distinct from tissue T
fr
cells.
Removal of Soluble Strontium via Incorporation into Biogenic Carbonate Minerals by Halophilic Bacterium Bacillus sp. Strain TK2d in a Highly Saline Solution
Authors: Horiike Takumi , Dotsuta Yuma , Nakano Yuriko , Ochiai Asumi , Utsunomiya Satoshi , Ohnuki Toshihiko , Yamashita Mitsuo
Published: August 2017

Radioactive strontium (
90
Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant after a nuclear accident. Since the removal of
90
Sr using general adsorbents (e.g., zeolite) is not efficient at high salinity, a suitable alternative immobilization method is necessary. Therefore, we incorporated soluble Sr into biogenic carbonate minerals generated by urease-producing microorganisms from a saline solution. An isolate,
Bacillus
sp. strain TK2d, from marine sediment removed >99% of Sr after contact for 4 days in a saline solution (1.0 × 10
−3
mol liter
−1
of Sr, 10% marine broth, and 3% [wt/vol] NaCl). Transmission electron microscopy and energy-dispersive X-ray spectroscopy showed that Sr and Ca accumulated as phosphate minerals inside the cells and adsorbed at the cell surface at 2 days of cultivation, and then carbonate minerals containing Sr and Ca developed outside the cells after 2 days. Energy-dispersive spectroscopy revealed that Sr, but not Mg, was present in the carbonate minerals even after 8 days. X-ray absorption fine-structure analyses showed that a portion of the soluble Sr changed its chemical state to strontianite (SrCO
3
) in biogenic carbonate minerals. These results indicated that soluble Sr was selectively solidified into biogenic carbonate minerals by the TK2d strain in highly saline environments.

IMPORTANCE
Radioactive nuclides (
134
Cs,
137
Cs, and
90
Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant accident. Since the removal of
90
Sr using general adsorbents, such as zeolite, is not efficient at high salinity, a suitable alternative immobilization method is necessary. Utilizing the known concept that radioactive
90
Sr is incorporated into bones by biomineralization, we got the idea of removing
90
Sr via incorporation into biominerals. In this study, we revealed the ability of the isolated ureolytic bacterium to remove Sr under high-salinity conditions and the mechanism of Sr incorporation into biogenic calcium carbonate over a longer duration. These findings indicated the mechanism of the biomineralization by the urease-producing bacterium and the possibility of the biomineralization application for a new purification method for
90
Sr in highly saline environments.
Antibiofilm Effect of Poly(Vinyl Alcohol-
co
-Ethylene) Halamine Film against Listeria innocua and Escherichia coli O157:H7
Authors: Cossu Andrea , Si Yang , Sun Gang , Nitin Nitin
Published: August 2017

Bacterial biofilm formation is linked to several infections and foodborne disease outbreaks. To address this challenge, there is an unmet need to develop rechargeable antimicrobial materials that can provide continuous sanitation of contact surfaces, especially in the food industry. This study was aimed at evaluating a novel rechargeable antimicrobial polymer formed using poly(vinyl alcohol-
co
-ethylene) (PVA-
co
-PE) with halamine functionality to prevent biofilm formation with repeated exposure to high loads of bacteria and organic content and also to aid in inactivation of preformed biofilms upon contact with this novel material. The antibiofilm activity of this rechargeable antimicrobial material was evaluated using a combination of fluorescence and scanning electron microscopy techniques and biofilm metabolic activity analyses. The results determined on the basis of imaging and metabolic activity measurements demonstrated that halamine-functionalized polymer films significantly reduced
Listeria innocua
and
Escherichia coli
O157:H7 biofilm formation. This novel polymeric material maintained its antibiofilm activity with repeated cycles of extended exposure to high levels of bacterial load. These polymeric films were recharged using bleach and cleaned using mechanical sonication after each cycle of extended incubation with bacteria. Halamine-functionalized polymeric material also exhibited significant antibacterial activity against preformed biofilms on a model surface. In summary, our results demonstrate the potential of this antimicrobial material to provide continuous sanitation of surfaces and applications for inactivating preformed biofilms without extensive use of resources, including water and heat. This polymeric material may be used as a replacement for existing polymeric materials or as a coating on diverse materials.

IMPORTANCE
Conventional sanitizers can have limited efficacy in inactivating biofilms in areas with limited accessibility and buildup of organic biomass. Furthermore, none of the current approaches provide continuous sanitation of surfaces. There is a significant unmet need to develop and validate materials that can prevent biofilm formation as well as inactivate preformed biofilms. In this study, the efficacy of a copolymer film containing
N
-halamine against biofilms of
L. innocua
and
E. coli
O157:H7 was evaluated. The polymer film showed strong inhibitory activity against pregrown biofilm or prevented the growth of a new biofilm. The polymer film also maintained its antibiofilm activity after multiple cycles of exposure to high titers of bacterial load with recharging of the polymer film using bleach at intermediate steps between the cycles. Overall, the results demonstrate the potential of a novel antimicrobial material to inhibit and treat biofilms in food industry applications.