bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychometric properties of the Assessment of Positive Occupation 15 final version in individuals with mental disabilities
Authors: Noguchi Takuya , Kyougoku Makoto
Published: January 2018

Purpose: To verify the reliability and validity of the Assessment of Positive Occupation 15 (APO-15) in individuals with mental disabilities living in communities or admitted in hospitals. Methods: A sample of 408 individuals with mental disabilities completed APO-15, the Japanese version of the Recovery Assessment Scale (RAS), the Japanese version of the Self-identified Stage of Recovery Part-B (SISR-B), and the General Health Questionnaire 12 (GHQ-12). We analyzed the psychometric properties of APO-15, including confirmatory factor analysis, entropy, polyserial correlation coefficient, average variance extracted, Cronbach’s α coefficient, Pearson’s product–moment correlation coefficient, item response theory, and cut-off point. Results: This study indicated the validity and reliability of APO-15 in a group of individuals with mental disabilities. The result of this study supported a four-factor model constructing of 15 items; includes a positive relationship, achievement, meaning, and engagement. Validity was supported by various results, i.e. the polyserial correlation and entropy were good, confirmatory factor analysis was a good estimate of the model fit, hypothesis testing was good convergent and discriminant validity, and concurrent validity also good. In addition, reliability was established by various analyses, i.e. the internal consistency reliability was good, and all items of APO-15 demonstrated satisfactory item response. The cut-off point became a 42-point sensitivity (0.770) and demonstrated good results with 1-specificity (0.441). That is, APO-15 can be used to appropriately measure the participation in occupation to promote the well-being of clients. Conclusion: APO-15 demonstrated good psychometric properties in measuring positive occupation in individuals with mental disabilities. APO-15 is an important tool to enable participation in activities that increase well-being in daily living.
Pyknotic chromatin in mitonucleons elevating in syncytia undergo karyorhhexis and karyolysis before coalescing into an irregular chromatin mass: Differentiation of Ishikawa Domes, Part 2
Authors: Fleming Honoree
Published: January 2018

Pyknosis, karyorrhexis and karyolysis, harbingers of programmed cell death in many systems, appear to be driving forces that transform Ishikawa monolayer epithelial cells into differentiated dome cells. The heterochromatin affected by these process is contained in multiple nuclei aggregated in the syncytia that form when Ishikawa monolayers are stimulated to differentiate (Fleming, 2016a). The nuclear aggregates are enveloped in a double membrane staining for the endogenous biotin in mitochondrial carboxylases. The structure called a mitonucleon becomes vacuolated, along with the heterochromatin it envelops, and this structure elevates with the apical membrane of the syncytium 6 to 8 hours into the 20 hour differentiation, becoming increasingly pyknotic. This phase of the differentiation comes to an end when the mitonucleon membranes are breached and nuclei emerging from the aggregated state can be seen to fragment explosively. Fragmented DNA associates with an array of microtubules, filling the large central clearing of the predome. Some chromatin remains unfragmented and can be seen of the edges of the predome clearing. Cell death does not occur. Instead, the fragmented DNA coalesces into an irregular mass within the apical and basal membranes of the predome under which fluid has been accumulating. From the chromatin sheet, nuclei emerge amitotically as described in Part 3 of this series (Fleming, 2016c).
Detecting periodicities with Gaussian processes
Authors: Durrande Nicolas , Hensman James , Rattray Magnus , Lawrence Neil D
Published: January 2018

We consider the problem of detecting and quantifying the periodic component of a function given noise-corrupted observations of a limited number of input/output tuples. Our approach is based on Gaussian process regression which provides a flexible non-parametric framework for modelling periodic data. We introduce a novel decomposition of the covariance function as the sum of periodic and aperiodic kernels. This decomposition allows for the creation of sub-models which capture the periodic nature of the signal and its complement. To quantify the periodicity of the signal, we derive a periodicity ratio which reflects the uncertainty in the fitted sub-models. Although the method can be applied to many kernels, we give a special emphasis to the Matérn family, from the expression of the reproducing kernel Hilbert space inner product to the implementation of the associated periodic kernels in a Gaussian process toolkit. The proposed method is illustrated by considering the detection of periodically expressed genes in the arabidopsis genome.
Reading newspapers on the web with a refined history feature
Authors: Kopetzky Theodorich
Published: January 2018

Current web browser offer a history feature. Interestingly, this feature can still be refined. In this paper such a refinement is presented: the history of the seen. With this refinement not only clicked links are considered for the history but also links which only have been displayed to user. This is under the assumption that a link not followed will be less interesting in the future. By making the presentation of such links more inconspicuous, the cognitive burden on the users is reduced. A prototype implementation is shown for news sites, where not following a link the first time usually means that the link will not be followed in the future as well.
Influence of onabotulinumtoxin A on testes of the growing rat
Authors: Breikaa Randa M. , Mosli Hisham A , Abdel-Naim Ashraf B.
Published: January 2018

Onabotulinumtoxin A (onabotA) is gaining wide medical use in children. However, little is known about its potential testicular effects. The present study was planned to investigate the influence of its injection on the maturing testicular structures in rats. Immature rats were injected in the peritesticular area by onabotA with three doses of (10, 20 and 40 U/kg) three times in a two-week interval. The effect of these injections on fertility indices (sperm parameters, semen quality and testosterone levels) was examined. In addition, levels of antisperm antibodies and several apoptosis parameters were investigated. DNA content in form of ploidy was compared to control group via flow cytometric analysis. Histopathological examination was carried out to confirm the findings. OnabotA-injected groups showed decreased sperm count and semen quality, while sperm vitality, morphology and testosterone levels were not significantly affected. Furthermore, DNA flow cytometric analysis confirmed delayed sperm maturation. Apoptosis markers were significantly increased by the injections. In conclusion, onabotA use in growing rats adversely affected sperm count and maturation. However, it had no significant effects on sperm morphology or vitality. OnabotA testicular effects are mediated, at least partly, by apoptosis.
A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands
Authors: Lameris Thomas K , Bennett Joseph R , Blight Louise K , Giesen Marissa , Janssen Michael H , Schaminée Joop JHJ , Arcese Peter
Published: January 2018

We used 116-years of floral and faunal records from Mandarte Island, British Columbia, Canada, to estimate the indirect effects of humans on plant communities via their effects on the population size of a surface-nesting, colonial seabird, the Glaucous-winged gull (Larus glaucescens). Comparing current to historical records revealed 18 extirpations of native plant species (32% of species historically present), 31 exotic species introductions, and one case of exotic introduction followed by extirpation. Contemporary surveys indicated that native species cover declined dramatically from 1986 to 2006, coincident with the extirpation of ‘old-growth’ conifers. Because vegetation change co-occurred with an increasing gull population locally and regionally, we also tested predictions from the hypothesis that the presence and activities of seabirds help to explain those changes. Specifically, we predicted we would observe high nutrient loading and exotic plant species richness and cover on nearby islands with versus without gull colonies as a consequence of competitive dominance in species adapted to high soil nitrogen and trampling. As predicted, we found that native plant species cover and richness were lower, and exotic species cover and richness higher, on islands with versus without gull colonies. In addition, we found that soil carbon and nitrogen on islands with nesting gulls were positively related to soil depth and exotic species richness and cover across plots and islands. Our results suggest that gulls have the potential to drive rapid change in insular plant communities by increasing nutrients and disturbing vegetation. Because human activities have contributed to long-term change in gull populations, our results further suggest compelling, indirect links between human management decisions and plant community composition on islands of the Georgia Basin.
Assigning Hippocampus guttulatus recruits to the populations of origin using microsatellites: results from a field study in the Ria Formosa (south Portugal)
Authors: Andrade José P , Madeira Céline , Correia Miguel , Palma Jorge
Published: January 2018

The deployment of Artificial Holdfast Units (AHU) has been demonstrated as an effective tool for creating holdfast and sheltering conditions for Hippocampus guttulatus in the Ria Formosa (South Portugal). Preliminary results obtained with a pilot-scale AHU showed a high settlement rate, with recorded densities of up to 13.1 individuals.m-2. With the present study, we aim to understand weather the AHU’s contributed to attract new H. guttulatus recruits or concentrate those previously existing in these areas. Prior to the deployment of the AHU’s in a total of four focal sites, a sample of the skin filaments was collected from each H. guttulatus (n= 70) sighted in those locations. The same sampling protocol was later carried out on the recruits (n=14) sighted in one pilot-scale AHU since its deployment. Upon DNA extraction the variation of 13 highly polymorphic microsatellite loci isolated for H. guttulatus (or obtained by cross-amplification in H. hippocampus) has been analyzed. PCR reactions with labeled primers were performed using standard procedures and amplified products were run on an ABI PRISM 3130 XL Genetic Analyser©. Based on the genetic data, ONCOR software package was used to estimate the population of origin of recruits. Preliminary results indicate that more than 90% of the recruits at the AHU were assigned to the sites located up to 500 meter apart. No assignment has been demonstrated for the other sampled locations, situated further away from the AHU.
Strategic decision-making by chimpanzees (Pan troglodytes), bonobos (Pan paniscus) and children in a Snowdrift-Game task
Authors: Sanchez-Amaro Alejandro , Duguid Shona , Call Josep , Tomasello Michael
Published: January 2018

Chimpanzees must be able to coordinate with others even when conflicts of interest are present. The “Snowdrift-Game” provides a model to understand how organisms coordinate and make decisions under conflict situations. By investigating whether and how chimpanzees solve this dilemma we can gain insight into the mechanisms of cooperation. Moreover, by comparing chimpanzees with their closest relatives, bonobos and humans, we can understand the evolutionary context of decision making in this situation. We presented pairs of captive chimpanzees (N=10; Mage= 20.5 years) and bonobos (N=6, Mage=13.7 years) housed at the Leipzig Zoo in Germany as well as 20 children dyads from the same city, with an adapted version of the Snowdrift games. In our task, subjects were faced with an unequal reward distribution. In the critical condition the higher reward was acquired by letting a partner act, with the risk that if neither partner acted the rewards would be lost after a period of thirty seconds. Both chimpanzees and children were highly successful at coordinating their actions to solve the dilemma (bonobo data is currently under collection). They almost never lost the rewards because at least one partner was willing to pay the cost of getting the decreased reward, to avoid coordination failure (no reward). Both species behaved strategically as they waited longer for their partner to act when this would lead to a higher reward. However, evidence from their resource distributions, their action latencies and their communicative acts suggests that children behaved more strategic than chimpanzees. Our results demonstrate that both species can successfully coordinate their actions in conflict situations although they differ in the way they achieve coordination.
Banggai cardinalfish (Pterapogon kauderni) populations (stocks) around Banggai Island, a geometric and classical morphometric approach
Authors: Ndobe Samliok , Moore Abigail
Published: January 2018

Background. The identification and characterisation of appropriate management units (stocks) is important as a basis for responsible fisheries management as well as conservation of within species biodiversity. The Banggai cardinalfish Pterapogon kauderni (F.P. Koumans,1933), a mouthbrooding apogonid with Endangered status (IUCN Red List) has been shown to have a high level of genetic population structure across the endemic distribution in the Banggai Archipelago. With a life-cycle making recovery frrm extirpation extremely unlikely, this indicates a need to conserve each reproductively isolated population (stock), in particular to support zonation of Banggai Island in the context of the proposed district marine protected area. Genetic and morphological variations are often but not always related, and ideally both should be used in stock identification. However there were no data on classical or geometric morphometric characteristics of P. kauderni populations. Methods. Adult P. kauderni for classical and geometric morphometric analyses were collected randomly at six sites on Banggai Island (31-34 adult fish/site, total 193). Eleven morphometric parameters were measured and 10 dimensionless ratios were compared using the ANOVA function in Microsoft Excel 2007. A landmark set for P. kauderni was developed. Each specimen was photographed, digitised (tps.dig and tps.util). Characteristics of the six populations were analysed using Canonical Variate Analysis (CVA) and Discriminant Function Analysis (DFA) in MorphoJ geometric morphometric software to identify significant between-site variation. The results were compared with genetic, geophysical, bio-ecological and socio-economic data to determine meaningful stocks or management units. Results. Except for one site pair (Monsongan and Tinakin Laut) we found significant or highly significant differences between sites (sub-populations) in morphometric characteristics, as well as from the CVA and DFA results. The greatest morphometric difference was between sub-populations at the north (Popisi) and southeast (Matanga) extremities of the Banggai Island P. kauderni distribution. The Popisi population was characterised by short/high head shape, Matanga by a more hydrodynamic shape (elongated with a more pointed head). The findings were consonant with genetic study results. We propose a population model with four closed populations and one metapopulation resulting in five P. kauderni stocks around Banggai Island. Discussion. Observed patterns of morphometric variation could be related to geographical spread (radiation or North-South gradient), habitat-driven selection or growth patterns, stochastic events, or a combination. Such fine-scale characterisation calls for intra-species conservation, with implications for the management of this restricted range ornamental fish around Banggai Island and throughout the P. kauderni endemic distribution.
The investigation of polymorph transition of erlotinib salts
Authors: Maruszak Wioleta , Łaszcz Marta , Trzcińska Kinga , Łuniewski Wojciech , Bańkowski Krzysztof , Jatczak Kamil
Published: January 2018

Erlotinib is a reversible tyrosine kinase inhibitor, which acts on the epidermal growth factor receptor (EGFR) and is used to treat non-small cell lung cancer (NSCLC), pancreatic cancer and several other types of cancer [1]. It is known that erlotinib forms different salts which can exist in multiple crystalline solid forms. This important property known as a polymorphism may have an impact on physical and chemical stability of the drug substance (API), processability during manufacturing in the final drug product and bioavailability of the drug to the patient. Changes in the crystal structure of API can lead to the undesired changes in properties. Hence, the control of the polymorphic form is essential during the drug substance manufacture and requires a thorough understanding of solid-state changes that may occur in pharmaceutical materials. To achieve a comprehensive understanding of solid-state transformations different analytical techniques are applied. In our studies the variable–temperature powder X-ray diffraction (VT–PXRD), differential scanning calorimetry (DSC), thermogravimetry (TGA), Fourier transformed infrared (FTIR), attenuated total reflectance (ATR) and Raman spectroscopy were used to investigate the correlation between the thermal behavior and structural transformations of polymorphic forms of erlotinib salts. VT-PXRD method has detected the temperature range of the existence of polymorphic transitions, spectroscopy methods have characterized intramolecular vibrations and thermal methods have provided information on the transition and melting temperature and relationships between polymorphic forms.
Development and validation of gas chromatography methods for the control of volatile impurities in the pharmaceutical substance dutasteride
Authors: Groman Aleksandra , Stolarczyk Elżbieta U. , Jatczak Marta , Lipiec-Abramska Elżbieta
Published: January 2018

Dutasteride, N-[2,5-Bis(trifluoromethyl)phenyl]-3-oxo-4-aza-5α-androst-1-ene-17β-carboxamide, is an active pharmaceutical ingredient (API) which inhibits the conversion of testosterone to dihydrotestosterone. Dutasteride as a 5-reductase inhibitor is useful for the treatment of benign prostatic hyperplasia (BPH) and prostate cancer. Because of a large variety of solvents and reagents used in the synthesis, it was necessary to develop new, sensitive and selective gas chromatography (GC) methods. The optimization of the methods consisted in selecting different types of sample injection and detection as well as optimization of experimental conditions that allowed to meet the appropriate range (10-120% of the specification limit) and suitable detection limits (LOD) of compounds. Significant differences in the volatility of these compounds forced the division into volatile solvents (methanol, acetonitrile, dichloromethane, ethyl acetate, heptane and toluene) analyzed with the use of the gas chromatography with headspace (GC-HS) and less volatile compounds (pyridine, dimethylformamide, 1,4-dioxane, acetic acid, ethylene glycol, 4-dimethylaminopyridine) analyzed with the use of gas chromatography with direct injection (GC-FID). Benzene, carbon tetrachloride and 1,2-dichloroethane are potential contaminants of toluene and dichloromethane, thus the control of these solvents was a limit test procedure. Due to the low specification limits for benzene (2 ppm), carbon tetrachloride (4 ppm) and 1,2-dichloroethane (5 ppm) it was neccesery to use gas chromatography with mass spectrometry detection (GC-MS).

All three new methods were validated according to the requirements of the ICH (International Conference on Harmonization) validation guideline Q2R1 and the guideline for residual solvents Q3C. Specificity, precision, accuracy, linearity, limits of detection and quantitation and robustness were determined and the results meeting the acceptance criteria were obtained.
Healthy and disturbed sleep: from the laboratory to actigraphy
Authors: Penzel Thomas , Fietze Ingo
Published: January 2018

Sleep presents a third of human life and a healthy and restorative sleep is indispensable for a good performance during daytime. Human functions follow circadian rhythms and follow the need to relax and recover from daytime stressors. According to human senses and abilities this relaxation and recovery period is concentrated on nighttime. Sleep is shutting off senses and follow a dedicated program for recovery with light sleep, deep sleep and rapid eye movement sleep with different functions linked to these sleep phases and with different consequences for the physical and mental functions. Unfortunately in patients with sleep disorders this recovery program is disturbed. In order to identify reasons and in order to explore physical and mental problems related to this, sleep studies had been developed and are conducted in sleep medicine centers. Sleep medicine centers perform a cardiorespiratory polysomnography. During cardiorespiratory polysomnography brain functions and sleep stages are quantifed through assessing electroencephalography (EEG), electrooculography (EOG), electromyography (EMG) on the head and on the legs, electrocardiography (ECG), respiratory airflow, respiratory effort, oxygen concentration (SaO2), body position, and body movements. Because going to bed to find sleep is a behavioral action as well, we record video and sound in addition. This is done under laboratory conditions in a controlled and supervised setting, called sleep medicine center. Sleep disorders can be identified and are classified into six categories: insomnia, hypersomnia of central origin, sleep related breathing disorders, sleep related movement disorders, sleep-wake rhythm disorders, and parasomnias. In addition secondary sleep disorders due to medical or mental problems or due to substances or drugs are known as well. Due to the high prevalence of sleep disorders and sleep complaints there is an urgent need to develop and introduce simplified tools to identify sleep problems. For some sleep disorders protable recorder systems were developed. This is the case for sleep disordered breathing. For insomnia problems and sleep-wake rhythm disorders actigraphy systems are used. Only based on the recording of movement and motion using statistical analysis it is possible to distinguish sleep and wake with a good accuracy and reliability. This method is used to study sleep duration as well as sleep fragmentation to some extent. A study on sleep duration and impaired sleep in ballet dancers over a period of 60 days prior to a major premiere event is presented.
Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current
Authors: Doblin Martina A , Petrou Katherina , Sinutok Sutinee , Seymour Justin R , Messer Lauren F , Brown Mark V , Norman Louiza , Everett Jason D , McInnes Allison S , Ralph Peter J , Thompson Peter A , Hassler Christel S
Published: January 2018

The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC) region to sample microbes in a cyclonic (cold-core) eddy (CCE) and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2 to 10 times greater Shannon index) in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67%) by larger micro-plankton (≥ 20 µm), as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN-A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a ‘greening’ effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si) and iron amendment , whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially mitigate the negative consequences of increased stratification due to ocean warming, but also increase the biological demand for iron that is necessary to sustain the growth of large-celled phototrophs and potentially support the diversity of diazotrophs over longer time-scales.
Occurrence of twin embryos in the eastern bluebird
Authors: Bailey Robyn L. , Clark Gerald E.
Published: January 2018

We report the first record of presumed twinning in eastern bluebird (Sialia sialis) and provide a review of all previously reported twinning events in wild birds. A nest containing twin eastern bluebird nestlings was monitored in 2013 in central Pennsylvania and reported to the Cornell Lab of Ornithology’s NestWatch program, a national program where volunteers submit data on wild nesting birds. A presumed double-yolked egg of a free-living eastern bluebird pair hatched successfully, and twin nestlings lived for 11 days in a nest box shared by three siblings. Due to the rarity of twinning in wild birds, engaging the public to monitor large numbers of nests is the most likely approach to documenting twinning in wild populations, and citizen science provides the infrastructure for individuals to share observations.
Behavior of biomarkers during pregnancy and lactation through a biological multi-paradigm model. BECOME study protocol
Authors: Aguilar-Cordero María José , Baena-García Laura , Rodríguez-Blanque Raquel , Sánchez-García Juan Carlos , Capel-Tuñón Manuel Isidoro , Sánchez-López Antonio Manuel
Published: January 2018

Background Despite of advances in research, at the moment, various points related to the physiology of gestation and the etiology of severe diseases that can be developed in the course of it remain unknown. One of those aspects is the behavior of biomarkers (triglycerides, prolactin, glucose and cholesterol) during pregnancy, which experience a gradual increase in their levels until they reach the peak of hypertriglyceridemia, a few days before delivery. Several studies have reported that biomarkers experience a higher elevation in diabetic and obese pregnant women and in those women who suffer preeclampsia. The description of their behavior in different population of pregnant women (healthy women and women at risk) would identify the relation of these with some of the alterations that occurs more frequently during pregnancy. Objective The aim of this study is to develop a multi-paradigm biological model of systems to determine triglyceride, prolactin, glucose and cholesterol levels during pregnancy and its relation with lactogenesis in healthy and risk pregnant women. Methods A prospective cohort study will take place with women during pregnancy and lactation. Participating women will be divided into two groups. One group will be integrated by healthy women and the other group by pregnant women with a risk medical history. The personal, family and a detailed medical history will be collected in each group. A study of all the variables which influence the level of the mentioned biomarkers (triglycerides, cholesterol, glucose and prolactin) will be done. The universe consists in 4,300 women, who constitute the historical average deliveries during the semester in the city of Granada (Spain). The sample collection will be made in medical office’s pregnancy control in Granada’s hospitals, in their respective health centers and during the second half of 2015. The sample will be stratified and probabilistic. Peculiarities of pregnant women will be taken into account when calculating the size of the study sample. This sample will be made up of 224 women who comply with the inclusion criteria and that have signed the informed consent. To achieve the project objectives an organization comprising six theoretical and practical phases enabling the scientific development of the project. During the first phase, the technical and administrative preparation of the project is constructed. Thereafter, the work is divided into two action areas which encompass the collection and data modeling. The creation of a biological multi-paradigm computer simulation model of the levels of biomarkers in different months of pregnancy and in the various pathologies of pregnant women can be very effective to know the risks that involve high levels of lipids for the mother and for the baby.
Geometric model of image formation in Scheimpflug cameras
Authors: Sinharoy Indranil , Rangarajan Prasanna , Christensen Marc P.
Published: January 2018

We present a geometric model of image formation in Scheimpflug cameras that is most general. Scheimpflug imaging is commonly used is scientific and medical imaging either to increase the depth of field of the imager or to focus on tilted object surfaces. Existing Scheimpflug imaging models do not take into account the effect of pupil magnification (i.e. the ratio of the exit pupil diameter to the entrance pupil diameter), which we have found to affect the type of distortions experienced by the image-field upon lens rotations. In this work, we have also derived the relationship between the object, lens and sensor planes in Scheimpflug configuration, which is very similar in form with the standard Gaussian imaging equation, but applicable for imaging systems in which the lens plane and the sensor plane are arbitrarily oriented with respect to each other. Since the conventional rigid camera, in which the sensor and lens planes are constrained to be parallel to each other, is a special case of the Scheimpflug camera, our model also applies to imaging with conventional cameras.
Incorporation of an invasive plant into a native insect herbivore food web
Authors: Schilthuizen Menno , Santos Pimenta Lúcia P , Lammers Youri , Steenbergen Peter J , Flohil Marco , Beveridge Nils G.P. , van Duijn Pieter T , Meulblok Marjolein M , Sosef Nils , van de Ven Robin , Werring Ralf , Beentjes Kevin K , Meijer Kim , Vos Rutger A , Vrieling Klaas , Gravendeel Barbara , Choi Young , Verpoorte Robert , Smit Chris , Beukeboom Leo W
Published: January 2018

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird cherry), with similar proportions of specialists and generalists. While herbivory on P. padus remained stable over the past century, that on P. serotina gradually doubled. We show that P. serotina may have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetle Gonioctena quinquepunctata, recently shifted from native Sorbus aucuparia to P. serotina, we find divergent host preferences on Sorbus- versus Prunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character of P. serotina.
Upward nitrate transport by phytoplankton in oceanic waters: balancing nutrient budgets in oligotrophic seas
Authors: Villareal Tracy A , Pilskaln Cynthia H. , Montoya Joseph P. , Dennett Mark
Published: January 2018

In oceanic gyres, primary producers are numerically dominated by small (1-5 µm diameter) pro- and eukaryotic cells that primarily utilize recycled nutrients produced by rapid grazing turnover in a highly efficient microbial loop. Continuous losses of nitrogen to depth by sinking, either as single cells, aggregates or fecal pellets, are balanced by both nitrate inputs at the base of the euphotic zone and nitrogen-fixation. This input of N (new nitrogen) to balance export losses (the biological pump) is a fundamental aspect of nitrogen cycling and central to understanding carbon fluxes in the ocean. In the Pacific Ocean, detailed nitrogen budgets at the time-series station HOT require upward transport of nitrate from the nutricline (80-100 m) into the surface layer (~0-40 m) to balance productivity and export needs. However, concentration gradients are negligible and cannot support the fluxes. Physical processes can inject nitrate into the base of the euphotic zone, but the mechanisms for transporting this nitrate into the surface layer across many 10s of m in highly stratified systems are unknown. In these seas, vertical migration by the very largest 102-103 µm diameter) phytoplankton is common as a survival strategy to obtain nitrogen from sub-euphotic zone depths. This vertical migration is driven by buoyancy changes rather than by flagellated movement and can provide upward nitrogen transport as nitrate (mM concentrations) in the cells. However, the contribution of vertical migration to nitrate transport has been difficult to quantify over the required basin scales. In this study, we use towed optical systems and isotopic tracers to show that migrating diatom (Rhizosolenia) mats are widespread in the N. Pacific Ocean from 140°W to 175°E and together with other migrating phytoplankton (Ethmodiscus, Halosphaera, Pyrocystis, and solitary Rhizosolenia) can mediate time-averaged transport of N (235 µmol N m-2 d-1) equivalent to eddy nitrate injections (242 µmol NO3- m-2 d-1). This upward biotic transport can close nitrate budgets in the upper 250 m of the central Pacific Ocean and together with diazotrophy creates a surface zone where biological nutrient inputs rather than physical processes dominate the new N flux. In addition to these numerically rare large migrators, there is extensive evidence in the literature of ascending behavior in small phytoplankton that contributes to upward flux as well. Although passive downward movement has dominated models of phytoplankton flux, there is now sufficient evidence to require a rethinking of this paradigm. Quantifying these fluxes is a challenge for the future and requires a reexamination of individual phytoplankton sinking rates as well as methods for capturing and enumerating ascending phytoplankton in the sea.
Supertrees based on the subtree prune-and-regraft distance
Authors: Whidden Chris , Zeh Norbert , Beiko Robert G
Published: January 2018

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of simulated benchmark datasets, we show that SPR supertrees are more similar to correct species histories under plausible rates of LGT than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera; a small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT.
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
Authors: Rodriguez-R Luis M , Konstantinidis Konstantinos T
Published: January 2018

Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic under- or over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu
How apparent competition and predator responses led to the decline of Arctic ground squirrels in the boreal forests of the southwest Yukon
Authors: Werner Jeffery R , Gillis Elizabeth A , Boonstra Rudy , Krebs Charles J
Published: January 2018

Throughout much of North America’s boreal forest, the cyclical fluctuations of snowshoe hare populations (Lepus americanus) may cause other herbivores to become entrained in similar cycles. Alternating apparent competition and indirect mutualism via prey switching are the mechanisms behind this interaction. Our purpose is to document a change in the role of indirect interactions between sympatric populations of hares and arctic ground squirrels (Urocitellus parryii plesius), and to emphasize the influence of predation for controlling ground squirrel numbers. We used mark-recapture to estimate the population densities of both species over a 25-year period that covered two snowshoe hare cycles. We analysed the strength of association between snowshoe hare and ground squirrel numbers and changes in the seasonal and annual population growth rates of ground squirrels over time. A hyperbolic curve best describes the per capita rate of increase of ground squirrels relative to their population size, with a single stable equilibrium and a lower critical threshold below which populations drift to extinction. The crossing of this unstable boundary resulted in the subsequent uncoupling of ground squirrel and hare populations following the decline phase of their cycles in 1998. The implications are that this sustained Type II predator response led to the local extinction of ground squirrels. Arctic ground squirrels may also have exhibited an Allee effect caused by the disruption of social signalling of approaching predators when few individuals are left in a colony.
Gene expression profile of sodium channel subunits in the anterior cingulate cortex during experimental paclitaxel-induced neuropathic pain in mice
Authors: Masocha Willias
Published: January 2018

Paclitaxel, a chemotherapeutic agent, causes neuropathic pain whose supraspinal pathophysiology is not fully understood. Dysregulation of sodium channel expression, studied mainly in the periphery and spinal cord level, contributes to the pathogenesis of neuropathic pain. We examined gene expression of sodium channel subunits by real time PCR in the anterior cingulate cortex (ACC) at day 7 post first administration of paclitaxel, when mice had developed paclitaxel-induced thermal hyperalgesia. The ACC was chosen because increased activity in the ACC has been observed during neuropathic pain. In the ACC of control animals the Ct values for Nav1.4, Nav1.5, Nav1.7, Nav1.8 and Nav1.9 were above 30 and/or not detectable in some samples. Thus, comparison in mRNA expression between control and paclitaxel treated animals was done for Nav1.1, Nav1.2, Nav1.3, Nav1.6, Nax as well as Navβ1-Navβ4. Paclitaxel treatment significantly increased the mRNA expression of Nav1.1, Nav1.2, Nav1.6 and Nax, but not Nav1.3, sodium channel alpha subunits compared to vehicle-treated controls. Amongst the sodium channel beta subunits treatment with paclitaxel significantly increased the expression of Navβ1 and Navβ3, but not Navβ2 and Navβ4, compared to vehicle-treated controls. These findings suggest that during PINP there is differential upregulation of sodium channels in the ACC, which might contribute to the increased neuronal activity observed in the area during neuropathic pain.
Conserved queen pheromones in bumblebees: A reply to Amsalem et al.
Authors: Holman Luke , van Zweden Jelle S , Caliari Oliveira Ricardo , van Oystaeyen Annette , Wenseleers Tom
Published: January 2018

In a recent study, Amsalem et al. performed experiments with Bombus impatiens bumblebees to test the hypothesis that saturated cuticular hydrocarbons are evolutionarily conserved signals used to regulate reproductive division of labour in many Hymenopteran social insects. They concluded that the cuticular hydrocarbon pentacosane (C25), previously identified as a queen pheromone in a congeneric bumblebee, does not affect worker reproduction in B. impatiens. Here we identify some significant shortcomings of Amsalem et al.’s study that make its conclusions unreliable. In particular, inappropriate statistical tests were used, and a reanalysis of their dataset found that C25 substantially reduced and delayed worker egg laying in B. impatiens. Additionally, the study’s low sample sizes (mean n per treatment = 13.6, range: 4-23) give it low power, not 99% power as claimed, meaning that some its non-significant results may be false negatives. Additionally, several confounding effects may have affected the results of both experimental manipulations in the study
A horizon scan of future threats and opportunities for pollinators and pollination
Authors: Brown Mark JF , Dicks Lynn V , Paxton Robert J , Baldock Katherine C R , Barron Andrew B , Chauzat Marie-Pierre , Freitas Breno M , Goulson Dave , Jepsen Sarina , Kremen Claire , Li Jilian , Neumann Peter , Pattemore David E , Potts Simon G , Schweiger Oliver , Seymour Colleen L , Stout Jane C
Published: January 2018

Background. Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines. Methods. Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades. Results. Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings. Discussion. While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations.
Some like it hot: A differential response to changing temperatures by the malaria vectors Anopheles funestus and An. gambiae s.l.
Authors: Charlwood Jacques D
Published: January 2018

Background: With the possible implications of global warming, the effect of temperature on the dynamics of malaria vectors in Africa has become a subject of increasing interest. Information from the field is, however, relatively sparse. We describe the effect of ambient temperature over a five-year period on the dynamics of An. funestus and An. gambiae s.l., collected from a single village in southern Mozambique where temperatures varied from a night-time minimum of 6oC in the cool season to a daytime maximum of 35oC in the hot season. Results: Mean daily air temperatures varied from 34o C to 20oC and soil temperatures varied from 26 o C to 12 o C. Diurnal variation was greatest in the cooler months of the year and were greater in air temperatures than soil temperatures. During the study 301, 705 female An. funestus were collected in 6043 light-trap collections, 161, 466 in 7397 exit collections and 16, 995 in 1315 resting collections. The equivalent numbers for An. gambiae s.l. are 72, 475 in light-traps, 33, 868 in exit collections and 5, 333 from indoor resting collections. Numbers of mosquito were greatest in the warmer months. Numbers of An. gambiae s.l. went through a one hundredfold change (from a mean of 0.14 mosquitoes a night to 14) whereas numbers of An. funestus merely doubled (from a mean of 20 to 40 a night). The highest environmental correlations and mosquito numbers were between mean air temperature (r2 = 0.52 for An. funestus and 0.77 for An. gambiae s.l.). Numbers of mosquito collected were not related to rainfall with lags of up to four weeks. Numbers of both gravid and unfed An. gambiae complex females in exit collections continued to increase at all temperatures recorded but gravid females of An. funestus decreased at temperatures above 28oC. Overall the numbers of gravid and unfed An. funestus collected in exit collections were not correlated (p = 0.07). For an unknown reason the number of An. gambiae s.l. fell below monitoring thresholds during the study. Conclusions: Mean air temperature was the most important environmental parameter affecting both vectors in this part of Mozambique. Numbers of An. gambiae s.l. increased at all temperatures recorded whilst An. funestus appeared to be adversely affected by temperatures of 28oC and above. These differences may influence the distribution of the vectors as the planet warms.