bluuebunny/crossref_metadata_2025 huggingface dataset:
Amylase increases energy and nutrient density of Super Cereal Plus porridge as prepared and accepted by Rwandan caregivers
Authors: Broersen Britt , Sinamo Sisay , Nsabimana Jules , Mahamadou Tanimoune , Gatete Edgar , Prigge Shane , Van Hoan Nguyen , de Pee Saskia
Published: October 2018

Adding amylase to Super Cereal Plus (SC+A) improves energy and nutrient intake as porridge energy density reaches 1.0 kcal/g, meeting the recommended ≥0.8 kcal/g for prepared foods for young children. Caregiver response to SC+A in terms of adjusting porridge preparation using printed pictogram instructions was not yet investigated. The study assessed (a) porridge preparation by caregivers; (b) porridge energy density; (c) sensory porridge acceptability; and (d) understanding of preparation instructions. An 8‐day follow‐up intervention study was conducted amongst caregivers of children aged 6–23 months (n = 238) in Rwanda. Caregivers prepared porridge using SC+A whilst referring to printed pictogram instructions at the study site on Days 1 and 8 and received flour for preparation at home on Days 2–7. At the site, data were collected on porridge preparation procedures, energy density, consistency, acceptability, and interviews (n = 12), and focus group discussions (n = 6) were conducted. Mean porridge dry matter (DM) increased from 21.3 ± 4.4% (Day 1) to 25.1 ± 4.8% (Day 8; p < 0.0005). Flour and water were mixed before cooking by 95% of the participants, as per printed instructions. Sensory porridge acceptability was high, and the printed instructions enabled caregivers to prepare an accepted and energy dense porridge. The preferred water/flour volume ratio was 2.5 instead of 3. In conclusion, Rwandan caregivers prepared well‐accepted SC+A porridges with a preferred consistency and mean DM content of 25.1% (1.0 kcal/g), after 1 week practicing at home. This supports introducing SC+A with the tested instructions at scale.
Multiple infections, relatedness and virulence in the anther‐smut fungus castrating Saponaria plants
Authors: Fortuna Taiadjana M. , Namias Alice , Snirc Alodie , Branca Antoine , Hood Michael E. , Raquin Christian , Shykoff Jacqui A. , Giraud Tatiana
Published: October 2018

Multiple infections (co‐occurrence of multiple pathogen genotypes within an individual host) can have important impacts on diseases. Relatedness among pathogens can affect the likelihood of multiple infections and their consequences through kin selection. Previous studies on the castrating anther‐smut fungus Microbotryum lychnidis‐dioicae have shown that multiple infections occur in its host plant Silene latifolia. Relatedness was high among fungal genotypes within plants, which could result from competitive exclusion between unrelated fungal genotypes, from population structure or from interactions between plant and fungal genotypes for infection ability. Here, we aimed at disentangling these hypotheses using M. saponariae and its host Saponaria officinalis, both experimentally tractable for these questions. By analysing populations using microsatellite markers, we also found frequent occurrence of multiple infections and high relatedness among strains within host plants. Infections resulting from experimental inoculations in the greenhouse also revealed high relatedness among strains co‐infecting host plants, even in clonally replicated plant genotypes, indicating that high relatedness within plants did not result merely from plant x fungus interactions or population structure. Furthermore, hyphal growth in vitro was affected by the presence of a competitor growing nearby and by its genetic similarity, although this latter effect was strain‐dependent. Altogether, our results support the hypothesis that relatedness‐dependent competitive exclusion occurs in Microbotryum fungi within plants. These microorganisms can thus respond to competitors and to their level of relatedness.
Genomic signatures of experimental adaptive radiation in Drosophila
Authors: Michalak Pawel , Kang Lin , Schou Mads F. , Garner Harold R. , Loeschcke Volker
Published: October 2018

Abiotic environmental factors play a fundamental role in determining the distribution, abundance and adaptive diversification of species. Empowered by new technologies enabling rapid and increasingly accurate examination of genomic variation in populations, researchers may gain new insights into the genomic background of adaptive radiation and stress resistance. We investigated genomic variation across generations of large‐scale experimental selection regimes originating from a single founder population of Drosophila melanogaster, diverging in response to ecologically relevant environmental stressors: heat shock, heat knock down, cold shock, desiccation and starvation. When compared to the founder population, and to parallel unselected controls, there were more than 100,000 single nucleotide polymorphisms (SNPs) displaying consistent allelic changes in response to selective pressures across generations. These SNPs were found in both coding and noncoding sequences, with the highest density in promoter regions, and involved a broad range of functionalities, including molecular chaperoning by heat‐shock proteins. The SNP patterns were highly stressor‐specific despite considerable variation among line replicates within each selection regime, as reflected by a principal component analysis, and co‐occurred with selective sweep regions. Only ~15% of SNPs with putatively adaptive changes were shared by at least two selective regimes, while less than 1% of SNPs diverged in opposite directions. Divergent stressors driving evolution in the experimental system of adaptive radiation left distinct genomic signatures, most pronounced in starvation and heat‐shock selection regimes.
Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds
Authors: Wille Michelle , Eden John‐Sebastian , Shi Mang , Klaassen Marcel , Hurt Aeron C. , Holmes Edward C.
Published: October 2018

Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA‐sequencing (“meta‐transcriptomics”), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta‐transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red‐necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
BIG regulates stomatal immunity and jasmonate production in Arabidopsis
Authors: Zhang Ruo‐Xi , Ge Shengchao , He Jingjing , Li Shuangchen , Hao Yanhong , Du Hao , Liu Zhongming , Cheng Rui , Feng Yu‐Qi , Xiong Lizhong , Li Chuanyou , Hetherington Alistair M. , Liang Yun‐Kuan
Published: October 2018

Plants have evolved an array of responses that provide them with protection from attack by microorganisms and other predators. Many of these mechanisms depend upon interactions between the plant hormones jasmonate (JA) and ethylene (ET). However, the molecular basis of these interactions is insufficiently understood.

Gene expression and physiological assays with mutants were performed to investigate the role of Arabidopsis BIG gene in stress responses.

BIG transcription is downregulated by methyl JA (MeJA), necrotrophic infection or mechanical injury. BIG deficiency promotes JA‐dependent gene induction, increases JA production but restricts the accumulation of both ET and salicylic acid. JA‐induced anthocyanin accumulation and chlorophyll degradation are enhanced and stomatal immunity is impaired by BIG disruption. Bacteria‐ and lipopolysaccaride (LPS)‐induced stomatal closure is reduced in BIG gene mutants, which are hyper‐susceptible to microbial pathogens with different lifestyles, but these mutants are less attractive to phytophagous insects.

Our results indicate that BIG negatively and positively regulate the MYC2 and ERF1 arms of the JA signalling pathway. BIG warrants recognition as a new and distinct regulator that regulates JA responses, the synergistic interactions of JA and ET, and other hormonal interactions that reconcile the growth and defense dilemma in Arabidopsis.
Cooperative hunting in a predator–prey system with Allee effects in the prey
Authors: Jang Sophia R.‐J. , Zhang Wenjing , Larriva Victoria
Published: October 2018

We propose a continuous‐time predator–prey model with Allee effects in the prey and cooperative hunting in predators to explore their effects on population interactions. If the predator’s reproductive number exceeds one when prey is at its Allee threshold, then although both populations eventually go extinct, the time that it takes to become extinct may be different between cooperation and no cooperation. If the predator’s maximum reproductive number is larger than one, then coexistence occurs for the model of no Allee effect, whereas dynamics of the other model also depend on Allee threshold. There always exists a region of initial population distributions, for which both populations become extinct. When the predator’s maximum reproductive number is smaller than one, then predators go extinct if predators do not engage in cooperative hunting or if the degree of cooperation is small. With intense cooperation, predators may persist. However, the region of initial populations for coexistence is smaller for the model with Allee effects than the model of no Allee effects.

Recommendations for Resource Managers

If predators are specialists and engage in cooperative hunting on a prey population that is subject to Allee effects, then estimate the degree of predator cooperation along with the predator’s reproductive numbers when the prey is at its carrying capacity (termed the predator’s maximum reproductive number) and at Allee threshold.

If both reproductive numbers are larger than one or if the predator’s maximum reproductive number is larger than one, while the other reproductive number is smaller than one, then one should cull predators to avoid prey extinction. The number of predators to be removed will depend on the sizes of the two populations.

If the maximum reproductive number of predators is smaller than one, then the recommended management plan will depend on the degree of hunting cooperation. If the degree is small, then culling predators can avoid prey extinction. If cooperation is intense, then culling a large number of predators will likely cause predator extinction while removing a small number of predators will yield coexistence.
Evaluating impacts of fish stock enhancement and biodiversity conservation actions on the livelihoods of small‐scale fishers on the Beijiang River, China
Authors: Liu Yiming , Bunting Stuart W. , Luo Shiming , Cai Kunzheng , Yang Qiangqiang
Published: October 2018

Inappropriate development and overexploitation have seriously degraded aquatic resources in China. Stakeholders identified three fish stock enhancement and biodiversity conservation scenarios for the Beijiang River: S1, increased fish restocking; S2, no fishing season and habitat conservation; and S3, strict pollution control. Potential impacts of these actions on the livelihoods of fishers were evaluated using applied economic modeling. Baseline costs and benefits came from logbooks from 30 fishers and a survey of 90 households in three villages. The financial net benefit for a household was US$1583 (￥11,160) annually, representing a 142% and 387% return on capital and operating costs, respectively. Larger catches associated with S1 and S2 generated a net benefit of US$1651 and US$1822, respectively. Strict pollution control resulting in higher catches (+20%) and lower operating costs (−20%) would increase the net benefit by 15.9% to US$1835 annually. Pollution control would benefit other resource users and is a prerequisite for ecological restoration.

Recommendations for Resource Managers

Stringent pollution control measures are essential to conserve aquatic biodiversity and enhance the livelihoods of fishers but will require considerable public and private sector investment.

Enhanced fish stocks in the Beijiang River could benefit poor livelihoods but may not be sufficient to lift households out of poverty, aged fishers require government assistance to diversify their livelihoods, access alternative urban employment, and survive with dignity.

Adopting the economic modeling approach presented here could enable responsible authorities to simultaneously evaluate fish stock enhancement and biodiversity conservation options.

Broader application of the approach presented here could help ensure small‐scale inland fisheries are managed sustainably and aquatic ecosystems are restored and protected by 2020, in line with Target 6 of the United Nations’ Convention on Biological Diversity Strategic Plan for Biodiversity.
The impact of oil price and revenue variations on economic growth in Nigeria
Authors: Omitogun Olawunmi , Longe Adedayo Emmanuel , Muhammad Shehu
Published: October 2018

The study investigates the relationship between oil price, revenue variation and economic growth in Nigeria. The study makes use of a secondary data spanning 1981 and 2016. The Auto‐regressive Distributed Lag was used to analyse the long‐run and short‐run relationship among the variables. The short‐run result shows that oil price and oil revenue positively significantly relates with economic growth, while consumer price index and exchange rate negatively relates with economic growth. In the long‐run, oil price, consumer price index and exchange rate positively relates with economic growth, while oil revenue negatively relates with economic growth. This implies that oil revenue has not been channelled in the direction of enhancing growth in Nigeria, while oil price has been in favour reason been that it determines a larger percentage of the country's revenue. From the findings, the study concludes that variations in oil price and oil revenue are strong determinant factors of economic growth in Nigeria. A major recommendation is that, oil revenue should be restructured towards the strategic sectors of the economy to aid the growth in Nigeria.
Plasma levels of IL‐1Ra are associated with schizophrenia
Authors: Zhou Yi , Peng Wu , Wang Jun , Zhou WenJing , Zhou YanHong , Ying BinWu
Published: October 2018

Aim

Although peripheral low‐grade inflammation and brain‐derived neurotrophic factor (BDNF) levels have been implicated in schizophrenia (SCZ), the interactions between them remain to be fully revealed. We aimed to compare BDNF and cytokines in patients with SCZ and healthy controls (HC). Additionally, we aimed to investigate the association between peripheral levels of cytokines and BDNF in patients with SCZ.

Methods

Plasma levels of BDNF, interferon gamma, interleukin (IL)‐10, IL‐12, IL‐1, IL‐6, IL‐8, tumor necrosis factor alpha, macrophage migration inhibitory factor, IL‐1 receptor antagonist (IL‐1Ra), and CD40 Ligand were compared in 45 SCZ patients and 38 HC using Luminex technology.

Results

Compared to HC, patients had significantly higher IL‐1Ra levels (P = 0.031). We found a strong positive association between BDNF and CD40 Ligand in the patient group (rho = 0.858, P < 0.001) as well as in the HC group (rho = 0.822, P < 0.001), respectively. Furthermore, there was a negative association between BDNF and tumor necrosis factor alpha in patients (rho = −0.429, P = 0.030) as well as in HC (rho = −0.649, P < 0.001).

Conclusion

These results suggest that the cytokine IL‐1Ra may play a role in SCZ pathophysiology. Additionally, the interaction between cytokines and BDNF levels further indicated the diverse actions of these cytokines.
Using Facebook to communicate mammography messages to rural audiences
Authors: Klippert Heidi , Schaper Ana
Published: October 2018

Objective

The purpose of this scholarly project was to answer the following question: What is the highest level of engagement achieved with a mammography campaign on Facebook?

Design and Sample

An Idaho public health department implemented a tailored message mammography campaign on Facebook during Breast Cancer Awareness Month. Target sample for the Facebook campaign were women and men over the age of 40 in rural Idaho.

Measures

Data collected from Facebook were used to measure and stratify engagement into a hierarchy of six levels, with intent to get a mammogram representing the highest level of engagement. A survey measuring women's intent to a get a mammogram was distributed via an online link.

Results

The posts reached 48,503 Facebook users—11,147 of the total reach were unique users. Intent to get a mammogram, the highest level of engagement, was stated both in Facebook comments and on the online survey. Forty‐nine women completed the survey, and 82% of women expressed intent to get a mammogram in the next year.

Conclusion

This project conducted as a program evaluation demonstrates how public health nurses can develop, implement, and evaluate Facebook mammography campaigns in the future.
Disease cycle of Austropuccinia psidii on Eucalyptus globulus and Eucalyptus obliqua leaves of different rust response phenotypes
Authors: Yong W. T. L. , Ades P. K. , Tibbits J. F. G. , Bossinger G. , Runa F. A. , Sandhu K. S. , Taylor P. W. J.
Published: October 2018

Myrtle rust poses a significant biosecurity threat to Australia with potential for long‐term damaging impacts on native flora and plant industries. This study describes the disease cycle of Austropuccinia psidii, the myrtle rust pathogen, in Eucalyptus globulus and Eucalyptus obliqua, two commercially and ecologically important species from different subgenera of Eucalyptus. Ontogeny and morphology of infection structures of A. psidii on plants of both Eucalyptus species with different rust response phenotypes, i.e. completely resistant, hypersensitive and highly susceptible, were investigated. Plants were inoculated with single‐uredinium‐derived urediniospores and examined by scanning electron microscopy. No differences between rust response phenotypes were observed in germination of urediniospores, formation of appressoria or length of germ tubes. The growth of germ tubes had no affinity towards stomata of either species. Histological observations indicated direct penetration by infection pegs through the leaf cuticle and no penetration beyond the epidermis on rust‐resistant E. obliqua. Eucalyptus obliqua plants that were identified as susceptible to A. psidii at 3‐ and 6‐months‐old showed no disease when reinoculated with A. psidii at 12‐months‐old; this indicated possible early acquisition of adult plant resistance to A. psidii in this species. In the susceptible phenotype of E. globulus rust inoculation led to rapid colonization of leaf parenchyma cells with the disease cycle completed within 10 days. These findings provide valuable insights into host–pathogen interactions in the Eucalyptus–A. psidii pathosystem, which might be useful for the development of effective rust control strategies across Eucalyptus subgenera.
Algorithms for computing cubatures based on moment theory
Authors: Collowald Mathieu , Hubert Evelyne
Published: October 2018

Quadrature is an approximation of the definite integral of a function by a weighted sum of function values at specified points, or nodes, within the domain of integration. Gaussian quadratures are constructed to yield exact results for any polynomials of degree or less by a suitable choice of r nodes and weights. Cubature is a generalization of quadrature in higher dimension. In this article, we elaborate algorithms to compute all minimal cubatures for a given domain and a given degree. We propose first algorithm in symbolic computation to characterize all cubatures of a given degree with a fixed number of nodes. The determination of the nodes and weights is then left to the computation of the eigenvectors of the matrix identified at the characterization stage and can be performed numerically. The characterization of cubatures on which our algorithms are based stems from moment theory. We formulate the results there in a basis‐independent way: Rather than considering the moment matrix, the central object in moment problems, we introduce the underlying linear map from the polynomial ring to its dual, the Hankel operator. This makes natural the use of bases of polynomials other than the monomial basis, and proves to be computationally relevant, either for numerical properties or to exploit symmetry.
Routes to parenthood for women with Turner syndrome
Authors: Mascarenhas Mariano , Oliver James , Bhandari Harish M
Published: October 2018

Key content

Turner syndrome (TS) is the most common form of sex chromosome aneuploidy in women.

Most women with TS have primary amenorrhoea, although some women with mosaic TS may have spontaneous menarche but have a significantly reduced ovarian reserve.

Women with TS face higher obstetric and neonatal risks in pregnancy, and pregnancy may be contraindicated for some.

Natural conception can occur in up to 8% of women with TS. For those with TS, assisted reproductive techniques using the woman's own eggs is possible for those with ovarian activity. For women with premature ovarian insufficiency, the use of donor gametes/embryos is possible, or surrogacy is an option for those with an underdeveloped uterus.

Fertility preservation is possible for affected women with good ovarian reserve and offers an opportunity to achieve pregnancy when they are physically and psychologically ready.

Learning objectives

To understand the underlying pathophysiology of the impact of TS on reproductive life.

To be aware of the specific risks women with TS face during pregnancy.

To be able to counsel women with TS regarding their available options for parenthood.

Ethical issues

Does refusing fertility treatment to women with TS who have contraindications to pregnancy violate patient autonomy, or is it unethical to proceed with fertility treatment because it risks maternal death?

Can girls with TS who have not yet reached the legal age of consent undergo oocyte freezing (if post‐pubertal) or ovarian tissue freezing (if pre‐pubertal)?
Pseudoginsenoside‐F11 alleviates oligomeric β‐amyloid‐induced endosome‐lysosome defects in microglia
Authors: Yao Xue C. , Xue Xue , Zhang Hao T. , Zhu Ming M. , Yang Xiao W. , Wu Chun F. , Yang Jing Y.
Published: October 2018

Amyloid accumulation in the brain is the major pathological hallmark of Alzheimer disease (AD). Amyloid beta (Aβ) is cleared by the endosomal‐autophagy‐lysosomal system, which is impaired in AD pathogenesis by an unknown mechanism. Pseudoginsenoside‐F11 (PF11), an ocotillol‐type ginsenoside, has been demonstrated to decrease the level of Aβ in APP/PS1 mouse brain and to protect neurons by inhibiting the activation of microglia in vitro. The present study showed that PF11 was capable of increasing the uptake and degradation of oligomeric Aβ in cultured microglia. Oligomeric Aβ (oAβ) interrupted the autophagy‐lysosomal degradative system by regulating the nuclear translocation of transcription factor EB (TFEB), a master factor in lysosomal biogenesis. Conversion of Rab5 to Rab7, which is important for the mechanism of cargo progression from early to late endosomes, was also interrupted by high‐concentration oAβ. Notably, in the PF11‐treated microglial cells, a dramatic increase of the lysosome‐associated proteins and enzyme expression were observed, along with the intracellular pH steady state, indicating the improvement of lysosomal function. In addition, PF11 induced TFEB nuclear translocation in microglia treated with high‐concentration oAβ. Furthermore, PF11 was able to restore Rab conversion, suggesting an effective role of PF11 in the maturation of endosomes. These data provide evidence that PF11 can reverse the dysfunction of the endosomal‐lysosomal system induced by high‐concentration oAβ in microglia, and this might be the main mechanism by which PF11 facilitates oAβ clearance. Accordingly, we propose that PF11 should be considered as a potential agent for treating AD.
Contribution of rat embryonic stem cells to xenogeneic chimeras in blastocyst or 8‐cell embryo injection and aggregation
Authors: Okumura Hiroki , Nakanishi Anna , Toyama Satoshi , Yamanoue Mai , Yamada Kana , Ukai Akane , Hashita Tadahiro , Iwao Takahiro , Miyamoto Tomomi , Tagawa Yoh‐ichi , Hirabayashi Masumi , Miyoshi Ichiro , Matsunaga Tamihide
Published: October 2018

The ultimate goal of regenerative medicine is the transplantation of a target organ generated by the patient's own cells. Recently, a method of organ generation using pluripotent stem cells (PSCs) and blastocyst complementation was reported. This approach is based on chimeric animal generation using an early embryo and PSCs, and the contribution of PSCs to the target organ is key to the method's success. However, the contribution rate of PSCs in target organs generated by different chimeric animal generation methods remains unknown. In this study, we used 8‐cell embryo aggregation, 8‐cell embryo injection, and blastocyst injection to generate interspecies chimeric mice using rat embryonic stem (ES) cells and then investigated the differences in the contribution rate of the rat ES cells. The rate of chimeric mouse generation was the highest using blastocyst injection, followed in order by 8‐cell embryo injection and 8‐cell embryo aggregation. However, the contribution rate of rat ES cells was the highest in chimeric neonates generated by 8‐cell embryo injection, and the difference was statistically significant in the liver. Live functionality was confirmed by analyzing the expression of rat hepatocyte‐derived drug‐metabolizing enzyme. Collectively, these findings indicate that the 8‐cell embryo injection method is the most suitable for generation of PSC‐derived organs via chimeric animal generation, particularly for the liver.
A Synergistic Optimal Design for Trajectory Tracking of Underactuated Manipulators
Authors: Bastos Guaraci
Published: October 2018

An integrated and general methodology is required to define an ideal relation between input controls and structural parameters of a system in trajectory tracking problems. For underactuated manipulators, a synergistic optimal design should be able to reduce elastic deformations, mass of the structure, and actuation forces. The key advantage of such integrated approach is the capability to search in a feasible design space, to account for many dynamic couplings in an early design stage, and to avoid simplifying assumptions which would induce to suboptimal design. Particularly, some advances considering underactuated manipulators are the possibility to treat nonminimum phase systems, then lighter structures could be selected, since bounded and smoother solution can be generated. A synergistic consideration, in order to find the desired requirements and realize the specified task through an optimal control problem, is in evidence, where a generalization of an inverse dynamics problem is defined. A planar underactuated manipulator is considered for the methodology application.
Interaction of hydrogen with hafnium dioxide grown on silicon dioxide by the atomic layer deposition technique
Authors: Kolkovsky Vladimir , Scholz Sebastian , Kolkovsky Valery , Schmidt Jan-Uwe , Heller Rene
Published: October 2018

The electrical and structural properties of thin hafnia films grown by the atomic layer deposition technique were investigated before and after different annealing steps as well as after a dc H plasma treatment. By using the nuclear reaction analysis, the authors demonstrated that high concentrations of hydrogen (about 1–2 at. %) could be observed even in as-grown hafnia layers. An additional hydrogenation of the samples with atomic H led to a significant shift of the flatband voltage. This shift could be explained by the introduction of positively charged H-related defects which were found to be stable at room temperature. By comparing the experimental findings with the theory and the data from muon spin spectroscopy, they tentatively ascribed these defects to interstitial H in HfO2.
Highly parallel scanning tunneling microscope based hydrogen depassivation lithography
Authors: Randall John N. , Owen James H. G. , Lake Joseph , Saini Rahul , Fuchs Ehud , Mahdavi Mohammad , Moheimani S. O. Reza , Schaefer Benjamin Carrion
Published: October 2018

Hydrogen depassivation lithography (HDL) carried out by a scanning tunneling microscope has sub-nm resolution and the potential to create atomically precise patterns. However, as a serial write tool, it is subject to Tennant’s law which fairly accurately predicts an extremely low areal throughput in line with their experimental results. In order to improve the throughput, the authors explore the feasibility of an approach to develop a highly parallel exposure system, which preserves the ability to perform truly atomically precise patterning. The obvious way to increase scanning probe lithography throughput is to increase the number of probes. In this paper, they compare existing multiple scanning probe systems [D. S. Ginger, H. Zhang, and C. A. Mirkin, Angew. Chem. Int. Ed. 43, 30 (2004) and P. Vettiger et al., Microelectronic 46, 11 (1999)] with their proposed highly parallel, MEMS-based scanners with three degrees of freedom (3 DoF) movement. Additionally, since HDL is a version of e-beam lithography, they examine the problems encountered by the attempts to go parallel with conventional e-beam lithography and why highly parallel HDL avoids these physical and engineering problems. While there are still some engineering challenges to be met, the path to massively parallel HDL tip arrays is relatively straightforward. They believe that 3 DoF MEMS-based independently controlled scanners could be placed with a density of 10 100/cm2. That density range implies 7 × 106 tips on a 300 mm wafer. However, they do want to make clear that they do not contend that even this level of parallelism will make HDL a contender for producing CMOS consumer electronics.
Leveraging audiovisual speech perception to measure anticipatory coarticulation
Authors: Redford Melissa A. , Kallay Jeffrey E. , Bogdanov Sergei V. , Vatikiotis-Bateson Eric
Published: October 2018

A noninvasive method for accurately measuring anticipatory coarticulation at experimentally defined temporal locations is introduced. The method leverages work in audiovisual (AV) speech perception to provide a synthetic and robust measure that can be used to inform psycholinguistic theory. In this validation study, speakers were audio-video recorded while producing simple subject-verb-object sentences with contrasting object noun rhymes. Coarticulatory resistance of target noun onsets was manipulated as was metrical context for the determiner that modified the noun. Individual sentences were then gated from the verb to sentence end at segmental landmarks. These stimuli were presented to perceivers who were tasked with guessing the sentence-final rhyme. An audio-only condition was included to estimate the contribution of visual information to perceivers' performance. Findings were that perceivers accurately identified rhymes earlier in the AV condition than in the audio-only condition (i.e., at determiner onset vs determiner vowel). Effects of coarticulatory resistance and metrical context were similar across conditions and consistent with previous work on coarticulation. These findings were further validated with acoustic measurement of the determiner vowel and a cumulative video-based measure of perioral movement. Overall, gated AV speech perception can be used to test specific hypotheses regarding coarticulatory scope and strength in running speech.
Perceived Barriers and Sources of Support for Undergraduate Female Students’ Persistence in the Sport Management Major
Authors: Sauder Molly Hayes , Mudrick Michael , DeLuca Jaime R.
Published: October 2018

Male undergraduate sport management majors substantially outnumber females, suggesting that the path to a career in the sport industry is male dominated and gender stereotypes may exist. Simultaneously, there is a dearth of research on females’ experiences while enrolled in higher education and within sport management career development. Through qualitative focus groups conducted at two institutions with female sport management majors, this research sought to understand the barriers and sources of support that female students perceive while engaged in this academic discipline. The authors identified four themes—otherness, roles and credibility, prior experiences, and people of influence—all of which help illuminate the lived experience of gender bias among women in the sport management major and generate suggestions for the creation of more inclusive environments that foster persistence.
The PARE Project: A Short Course-Based Research Project for National Surveillance of Antibiotic-Resistant Microbes in Environmental Samples
Authors: Genné-Bacon Elizabeth A. , Bascom-Slack Carol A.
Published: October 2018

Course-based research experiences (CREs) have been proposed as an inclusive model to expose all students, including those at institutions without a strong research infrastructure, to research at an early stage. Converting an entire semester-long course can be time consuming for instructors and expensive for institutions, so we have developed a short CRE that can be implemented in a variety of life science course types. The Prevalence of Antibiotic Resistance in the Environment (PARE) project uses common microbiology methods and equipment to engage students in nationwide surveillance of environmental soil samples to document the prevalence of antibiotic-resistant bacteria. The project has been implemented at institutions ranging from community colleges to doctoral-granting institutions in 30 states plus Puerto Rico. Programmatic feedback was obtained from instructors over three iterations, and revisions were made based on this feedback. Student learning was measured by pre/post assessment in a subset of institutions. Outcomes indicate that students made significant gains in the project learning goals. Journal of Microbiology & Biology Education
The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources
Authors: Perez-Samper Gemma , Cerulus Bram , Jariani Abbas , Vermeersch Lieselotte , Barrajón Simancas Nuria , Bisschops Markus M. M. , van den Brink Joost , Solis-Escalante Daniel , Gallone Brigida , De Maeyer Dries , van Bael Elise , Wenseleers Tom , Michiels Jan , Marchal Kathleen , Daran-Lapujade Pascale , Verstrepen Kevin J.
Published: October 2018

The lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox of
S. cerevisiae
combined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.
Genome-Wide Characterization of the Fur Regulatory Network Reveals a Link between Catechol Degradation and Bacillibactin Metabolism in Bacillus subtilis
Authors: Pi Hualiang , Helmann John D.
Published: October 2018

Many bacteria synthesize high-affinity iron chelators (siderophores). Siderophore-mediated iron acquisition is an efficient and widely utilized strategy for bacteria to meet their cellular iron requirements. One prominent class of siderophores uses catecholate groups to chelate iron.
B. subtilis
bacillibactin, structurally similar to enterobactin (made by enteric bacteria), is a triscatecholate siderophore that is hydrolyzed to monomeric units after import to release iron. However, the ultimate fates of these catechol compounds and their potential toxicities have not been defined previously. We performed genome-wide identification of Fur binding sites
in vivo
and uncovered a connection between catechol degradation and bacillibactin metabolism in
B. subtilis
. Besides its role in the detoxification of environmental catechols, the catechol 2,3-dioxygenase encoded by
catDE
also protects cells from intoxication by endogenous bacillibactin-derived catechol metabolites under iron-limited conditions. These findings shed light on the degradation pathway and precursor recycling of the catecholate siderophores.
Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge
Authors: Wei Sean Ting-Shyang , Wu Yu-Wei , Lee Tzong-Huei , Huang Yi-Shiang , Yang Cheng-Yu , Chen Yi-Lung , Chiang Yin-Ru
Published: October 2018

Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor
de novo
synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.
Effectiveness of plant-based diets in promoting well-being in the management of type 2 diabetes: a systematic review
Authors: Toumpanakis Anastasios , Turnbull Triece , Alba-Barba Isaura
Published: October 2018

Diet interventions have suggested an association between plant-based diets and improvements in psychological well-being, quality of life and glycated hemoglobin (HbA1c) control in populations with diabetes. The aims of this review are to systematically analyze the available literature on plant-based diet interventions targeting diabetes in adults and to clearly define the benefits on well-being of such interventions. This is a systematic review of controlled trials. A computerized systematic literature search was conducted in the following electronic databases: Allied and Complementary Medicine, Cochrane Central Register of Controlled Trials, Cumulative Index to Nursing and Allied Health Literature, E-Journals, Excerpta Medica Database, MEDLINE, Health Management Information Consortium, PsycARTICLES, PsycINFO, PubMed, SocINDEX and Web of Science. The search strategy retrieved 1240 articles, of which 11 met the inclusion criteria (n=433; mean sample age 54.8 years). Plant-based diets were associated with significant improvement in emotional well-being, physical well-being, depression, quality of life, general health, HbA1c levels, weight, total cholesterol and low-density lipoprotein cholesterol, compared with several diabetic associations’ official guidelines and other comparator diets. Plant-based diets can significantly improve psychological health, quality of life, HbA1c levels and weight and therefore the management of diabetes.
Use of an electronic patient-reported outcome measure in the management of patients with advanced chronic kidney disease: the RePROM pilot trial protocol
Authors: Kyte Derek , Bishop Jon , Brettell Elizabeth , Calvert Melanie , Cockwell Paul , Dutton Mary , Eddington Helen , Hadley Gabby , Ives Natalie J , Jackson Louise J , Stringer Stephanie , Valente Marie
Published: October 2018

Introduction

Chronic kidney disease (CKD) affects up to 16% of adults in the UK. Patient quality of life is particularly reduced in end-stage renal disease and is strongly associated with increased hospitalisation and mortality. Thus, accurate and responsive healthcare is a key priority. Electronic patient-reported outcome measures (ePROMs) are online questionnaires which ask patients to self-rate their health status. Evidence in oncology suggests that the use of ePROM data within routine care, alongside clinical information, may enhance symptom management and improve patient outcomes. However, National Health Service (NHS)-based ePROM research in CKD is lacking. This pilot trial will assess the feasibility of undertaking a full-scale randomised controlled trial (RCT) in patients with CKD within the NHS.

Methods and analysis

The renal ePROM pilot trial is an investigator-led single-centre, open-label, two-arm randomised controlled pilot trial of 66 participants ≥18 years with advanced CKD. Participants will be randomised to receive either usual care or usual care supplemented with an ePROM intervention. Participants within the intervention arm will be asked to submit monthly self-reports of their health status using the ePROM system. The system will provide tailored information to patients in response to each report and notify the clinical team of patient deterioration. The renal clinical team will monitor for ePROM notifications and will respond with appropriate action, in line with standard clinical practice. Measures of study feasibility, participant quality of life and CKD severity will be completed at 3 monthly intervals. Health economic outcomes will be assessed. Clinicians will record treatment decision-making. Acceptability and feasibility of the protocol will be assessed alongside outcome measure and intervention compliance rates. Qualitative process evaluation will be conducted.

Ethics and dissemination

The findings will inform the design of a full-scale RCT and the results will be submitted for publication in peer-reviewed journals. The study has ethical approval.

Trial registration numbers

ISRCTN12669006; Pre-results.
Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin
Authors: He Zhen , Gharaibeh Raad Z , Newsome Rachel C , Pope Jllian L , Dougherty Michael W , Tomkovich Sarah , Pons Benoit , Mirey Gladys , Vignard Julien , Hendrixson David R , Jobin Christian
Published: October 2018

Objective

Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined.

Design

Germ-free (GF) ApcMin/+mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis.

Results

GF ApcMin/+mice colonised with human clinical isolate C. jejuni81–176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni.

Conclusion

Human clinical isolate C. jejuni 81–176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.
Obesity, equity and choice
Authors: Wilkinson Timothy M
Published: October 2018

Obesity is often considered a public health crisis in rich countries that might be alleviated by preventive regulations such as a sugar tax or limiting the density of fast food outlets. This paper evaluates these regulations from the point of view of equity. Obesity is in many countries correlated with socioeconomic status and some believe that preventive regulations would reduce inequity. The puzzle is this: how could policies that reduce the options of the badly off be more equitable? Suppose we distinguish: (1) the badly off have poor options from (2) the badly off are poor at choosing between their options (ie, have a choosing problem). If obesity is due to a poverty of options, it would be perverse to reduce them further. Some people in public health say that preventive regulations do not reduce options but, I shall argue, they are largely wrong. So the equity case for regulations depends on the worst off having a choosing problem. It also depends on their having a choosing problem that makes their choices against their interests. Perhaps they do. I ask, briefly, what the evidence has to say about whether the badly off choose against their interests. The evidence is thin but implies that introducing preventive regulations for the sake of equity would be at least premature.