bluuebunny/crossref_metadata_2025 huggingface dataset:
Ainsley Iggo. 2 August 1924—25 March 2012
Authors: Cervero Fernando
Published: August 2019

Ainsley Iggo's research was focused on the functional properties of sensory receptors in the skin and viscera. He developed a new electrophysiological technique for recording the electrical activity of individual afferent fibres and was the first to record such activity from single unmyelinated afferents, the smallest diameter afferents in sensory nerves. His seminal work contributed to the discovery of nociceptors; the sensory receptors that respond to injury and are at the origin of pain sensation. He also recorded the functional activity of many types of sensory receptor in the skin, muscle and viscera and classified their responses according to their adequate stimuli. These findings gave support to the specificity theory of sensation, particularly of pain. He described the morphology of individually identified receptors, thus providing direct evidence for the long-held assumption that distinct morphological types of skin receptors mediate distinct sensations. Later in life he contributed to studies of sensory neurons in the spinal cord and of the sensory electro-receptors found in animals such as the echidna and the platypus. A native of New Zealand, he moved to the UK in 1950 and spent most of his professional life at the University of Edinburgh, where he created a highly productive research group at the Veterinary School.
A controller for walking derived from how humans recover from perturbations
Authors: Joshi Varun , Srinivasan Manoj
Published: August 2019

Humans can walk without falling despite some external perturbations, but the control mechanisms by which this stability is achieved have not been fully characterized. While numerous walking simulations and robots have been constructed, no full-state walking controller for even a simple model of walking has been derived from human walking data. Here, to construct such a feedback controller, we applied thousands of unforeseen perturbations to subjects walking on a treadmill and collected data describing their recovery to normal walking. Using these data, we derived a linear controller to make the classical inverted pendulum model of walking respond to perturbations like a human. The walking model consists of a point-mass with two massless legs and can be controlled only through the appropriate placement of the foot and the push-off impulse applied along the trailing leg. We derived how this foot placement and push-off impulse are modulated in response to upper-body perturbations in various directions. This feedback-controlled biped recovers from perturbations in a manner qualitatively similar to human recovery. The biped can recover from perturbations over twenty times larger than deviations experienced during normal walking and the biped’s stability is robust to uncertainties, specifically, large changes in body and feedback parameters.
Electrospinning repellents in polyvinyl alcohol-nanofibres for obtaining mosquito-repelling fabrics
Authors: Ciera Lucy , Beladjal Lynda , Van Landuyt Lieve , Menger David , Holdinga Maarten , Mertens Johan , Van Langenhove Lieva , De Clerk Karen , Gheysens Tom
Published: August 2019

Recently, the use of repellents for preventing the transmission of mosquito-borne diseases is getting increasingly more attention. However, most of the current repellents are volatile in nature and must be frequently re-applied as their efficacy is only limited to a short period of time. Therefore, a slow release and abrasion-resistant mechanism is needed for prolonging the protection time of the repellents. The focus of this study is on the direct micro-encapsulation of repellents from an emulsion and integration of already encapsulated repellents into nanofibres via electrospinning. Different repellents were electrospun in polyvinyl alcohol (PVA) nanofibrous structures, namely
p
-menthane-3,8-diol micro-capsules, permethrin, chilli and catnip oil. The repellents were successfully incorporated in the nanofibres and the tensile properties of the resulting samples did not have a significant change. This means that the newly created textiles were identical to current PVA nanofibrous textiles with the added benefit of being mosquito repellent. Principally, all incorporated repellents in the nanofibrous structures showed a significantly reduced number of mosquito landings compared to the control. Consequently, the currently described method resulted in a new and very effective repelling textile material that can be used in the prevention against mosquito-associated diseases.
Gramian solutions and soliton interactions for a generalized (3 + 1)-dimensional variable-coefficient Kadomtsev–Petviashvili equation in a plasma or fluid
Authors: Chen Su-Su , Tian Bo
Published: August 2019

Plasmas and fluids are of current interest, supporting a variety of wave phenomena. Plasmas are believed to be possibly the most abundant form of visible matter in the Universe. Investigation in this paper is given to a generalized (3 + 1)-dimensional variable-coefficient Kadomtsev–Petviashvili equation for the nonlinear phenomena in a plasma or fluid. Based on the existing bilinear form,
N
-soliton solutions in the Gramian are derived, where
N
 = 1, 2, 3…. With
N
 = 3, three-soliton solutions are constructed. Fission and fusion for the three solitons are presented. Effects of the variable coefficients, i.e.
h
(
t
),
l
(
t
),
q
(
t
),
n
(
t
) and
m
(
t
), on the soliton fission and fusion are revealed: soliton velocity is related to
h
(
t
),
l
(
t
),
q
(
t
),
n
(
t
) and
m
(
t
), while the soliton amplitude cannot be affected by them, where
t
is the scaled temporal coordinate,
h
(
t
),
l
(
t
) and
q
(
t
) give the perturbed effects, and
m
(
t
) and
n
(
t
), respectively, stand for the disturbed wave velocities along two transverse spatial coordinates. We show the three parallel solitons with the same direction.
Regularization of the Ostwald supersaturation model for Liesegang bands
Authors: Duley J. M. , Fowler A. C. , Moyles I. R. , O'Brien S. B. G.
Published: August 2019

In a previous paper, we analysed the Keller–Rubinow formulation of Ostwald's supersaturation theory for the formation of Liesegang rings or Liesegang bands, and found that the model is ill-posed, in the sense that after the termination of the first crystal front growth, secondary bands form, as in the experiment, but these are numerically found to be a single grid space wide, and thus an artefact of the numerical method. This ill-posedness is due to the discontinuity in the crystal growth rate, which itself reflects the supersaturation threshold inherent in the theory. Here we show that the ill-posedness can be resolved by the inclusion of a relaxation mechanism describing an impurity coverage fraction, which physically enables the transition in heterogeneous nucleation from precipitate-free impurity to precipitate-covered impurity.
Boolean logic by convective obstacle flows
Authors: Bartlett S. J. , Yung Y. L.
Published: August 2019

We present a potential new mode of natural computing in which simple, heat-driven fluid flows perform Boolean logic operations. The system comprises a two-dimensional single-phase fluid that is heated from below and cooled from above, with two obstacles placed on the horizontal mid-plane. The obstacles remove all vertical momentum that flows into them. The horizontal momentum extraction of the obstacles is controlled in a binary fashion, and constitutes the 2-bit input. The output of the system is a thresholded measure of the energy extracted by the obstacles. Due to the existence of multiple attractors in the phase space of this system, the input–output relationships are equivalent to those of the OR, XOR or NAND gates, depending on the threshold and obstacle separation. The ability to reproduce these logical operations suggests that convective flows might have the potential to perform more general computations, despite the fact that they do not involve electronics, chemistry or multiple fluid phases.
Contextual priors do not modulate action prediction in children with autism
Authors: Amoruso Lucia , Narzisi Antonio , Pinzino Martina , Finisguerra Alessandra , Billeci Lucia , Calderoni Sara , Fabbro Franco , Muratori Filippo , Volzone Anna , Urgesi Cosimo
Published: August 2019

Bayesian accounts of autism suggest that this disorder may be rooted in an impaired ability to estimate the probability of future events, possibly owing to reduced priors. Here, we tested this hypothesis within the action domain in children with and without autism using a behavioural paradigm comprising a familiarization and a testing phase. During familiarization, children observed videos depicting a child model performing actions in diverse contexts. Crucially, within this phase, we implicitly biased action-context associations in terms of their probability of co-occurrence. During testing, children observed the same videos but drastically shortened (i.e. reduced amount of kinematics information) and were asked to infer action unfolding. Since during the testing phase movement kinematics became ambiguous, we expected children's responses to be biased to contextual priors, thus compensating for perceptual uncertainty. While this probabilistic effect was present in controls, no such modulation was observed in autistic children, overall suggesting an impairment in using contextual priors when predicting other peoples' actions in uncertain environments.
Quantifying maladaptation during the evolution of sexual dimorphism
Authors: Matthews Genevieve , Hangartner Sandra , Chapple David G. , Connallon Tim
Published: August 2019

Females and males have distinct trait optima, resulting in selection for sexual dimorphism. However, most traits have strong cross-sex genetic correlations, which constrain evolutionary divergence between the sexes and lead to protracted periods of maladaptation during the evolution of sexual dimorphism. While such constraints are thought to be costly in terms of individual and population fitness, it remains unclear how severe such costs are likely to be. Building upon classical models for the ‘cost of selection’ in changing environments (
sensu
Haldane), we derived a theoretical expression for the analogous cost of evolving sexual dimorphism; this cost is a simple function of genetic (co)variances of female and male traits and sex differences in trait optima. We then conducted a comprehensive literature search, compiled quantitative genetic data from a diverse set of traits and populations, and used them to quantify costs of sexual dimorphism in the light of our model. For roughly 90% of traits, costs of sexual dimorphism appear to be modest, and comparable to the costs of fixing one or a few beneficial substitutions. For the remaining traits (approx. 10%), sexual dimorphism appears to carry a substantial cost—potentially orders of magnitude greater than costs of selection during adaptation to environmental changes.
Redesigned upstream processing enables a 24-hour workflow from E. coli cells to cell-free protein synthesis
Authors: Levine Max Z. , So Byungcheol , Mullin Alissa C. , Watts Katharine R. , Oza Javin P.
Published: August 2019

Cell-free protein synthesis (CFPS) platforms have undergone numerous workflow improvements to enable diverse applications in research, biomanufacturing, point-of-care detection, therapeutics, and education using affordable laboratory equipment and reagents. The Escherichia coli cell extract-based platform, being one of the most affordable and versatile CFPS platforms, has been broadly adopted. In spite of the promise of simplicity, the cell-free platform remains technically nuanced, posing challenges to reproducible implementation and broad adoption. Additionally, while the CFPS reaction itself can be implemented on-demand, the upstream processing of cells to generate crude cell lysate remains time-intensive, representing one of the largest sources of cost associated with the biotechnology. To circumvent the lengthy and tedious upstream workflow, we have redesigned the processes by developing a long-lasting autoinduction media formulation for cell-free that obviates human intervention between inoculation and harvest. Cell-free autoinduction (CFAI) media supports these advantages through the production of highly robust cell extracts from high cell density cultures nearing stationary phase of growth. Growth of cells to high density and autoinduction of T7 RNAP expression can be achieved by incubation overnight, eliminating the need for user intervention for the entirety of the process. The total mass of cells obtained is substantially increased, which directly results in a 400% increase in total extract volume obtained compared to past workflows. Based on these advances, we outline a new upstream processing workflow that allows researchers to go from cells on a streak plate to completing CFPS reactions within 24 hours while maintaining robust reaction yields of sfGFP (>1 mg/ml). We hope this advance will improve the time and cost-efficiency for existing CFPS researchers, increase the simplicity and reproducibility, and reduce the barrier-to-entry for new researchers interested in implementing CFPS.
Are tropical reptiles really declining? A six-year survey of snakes in Drake Bay, Costa Rica, and the role of temperature, rain and light
Authors: Barquero-González Jose Pablo , Stice Tracie L. , Gómez Gianfranco , Monge-Nájera Julián
Published: August 2019

Introduction

studies in the last two decades have found declining snake populations in both temperate and tropical sites, including informal reports from Drake Bay, Costa Rica.

Objective

to investigate if reports of decreasing snake populations in Drake Bay had a real basis, and if environmental factors, particularly temperature, rain and light, have played a role in that decrease.

Methods

we worked at Drake Bay from 2012 through 2017 and made over 4000 h of transect counts. Using head flashlights we surveyed a transect covered by lowland tropical rainforest at an altitude of 12–38 m above sea level, near the Agujas River, mostly at 1930–2200 hours. We counted all the snakes that we could see along the transect.

Results

snake counts increase from August to September and then decline rapidly. The May snakes/rainfall peaks coincide, but the second snake peak occurs one month before the rain peak; we counted more snakes in dry nights, with the exception of Imantodes cenchoa which was equally common despite rain conditions. We saw less Leptodeira septentrionalis on bright nights, but all other species were unaffected. Along the six years, the number of species with each diet type remained relatively constant, but the number of individuals declined sharply for those that feed on amphibians and reptiles. We report Rhadinella godmani, a highland species, at 12–38 m of altitude.

Conclusion

night field counts of snakes in Drake Bay, Costa Rica, show a strong decline from 2012 through 2017.
Dynamics of the energy seascape can explain intra-specific variations in sea-crossing behaviour of soaring birds
Authors: Nourani E. , Vansteelant W. M. G. , Byholm P. , Safi K.
Published: August 2019

Thermal soaring birds extract energy from the atmosphere to achieve energetically low-cost movement. When encountering regions that are energetically costly to fly over, such as open seas, they attempt to adjust the spatio-temporal pattern of their passage to maximize energy extraction from the atmosphere over these ecological barriers. We apply the concept of energy landscapes to investigate the spatio-temporal dynamics of energy availability over the open sea for soaring flight. We specifically investigated how the “energy seascape” may shape age-specific sea-crossing behaviour of European honey buzzards Pernis apivorus over the Mediterranean Sea in autumn. We found uplift potential over the sea to be the main determinant of sea-crossing length, rather than wind conditions. Considering this variable as a proxy for available energy over the sea, we constructed the energy seascape for the autumn migration season using forty years of temperature data. Our results indicate that early-migrating adult buzzards are likely to encounter adverse energy subsidence over the Mediterranean, whereas late-migrating juveniles face less adverse flight conditions, and even conditions conducive to soaring flight. Our study provides evidence that the dynamics of the energy landscape can explain intra-specific variation in migratory behaviour also at sea.
NADPH consumption by L-cystine reduction creates a metabolic vulnerability upon glucose deprivation
Authors: Joly James H. , Delfarah Alireza , Phung Philip S. , Parrish Sydney , Graham Nicholas A.
Published: August 2019

The consequences of metabolic reprogramming in cancer can include an increased dependence on metabolic substrates such as glucose for survival. As such, the vulnerability of cancer cells to glucose deprivation creates an attractive opportunity for therapeutic intervention. Because it is not possible to starve tumors of glucosein vivo, we sought to identify the mechanisms regulating cancer cell death upon glucose deprivation and then design combinations of inhibitors to mimic glucose deprivation-induced cell death. Using metabolomic profiling, we found that cells undergoing glucose deprivation-induced cell death exhibited dramatic accumulation of intracellular L-cysteine and its oxidized dimer, L-cystine, and depletion of the antioxidant glutathione. Building on this observation, we show that glucose deprivation-induced cell death is driven not by lack of glucose but rather by L-cystine import. Following glucose deprivation, the import of L-cystine and subsequent reduction to L-cysteine depleted both NADPH and glutathione, thereby allowing toxic accumulation of reactive oxygen species. Consistent with this model, we found that the glutamate/cystine antiporter, xCT, was required for sensitivity to glucose deprivation. We searched for glycolytic enzymes whose expression is essential for survival of cancer cells with high xCT expression and identified the glucose transporter GLUT1. We therefore tested a drug combination co-targeting GLUT1 and glutathione synthesis and found that these drugs induced synthetic lethal cell death in high xCT-expressing cell lines susceptible to glucose deprivation. These results indicate that co-targeting GLUT1 and glutathione synthesis is a potential therapeutic approach in tumors dependent on glucose for survival.
Neutrophilic granule protein is a novel murine LPS antagonist
Authors: Hong Jaewoo , Qu Peng , Wuest Todd R. , Lin P. Charles
Published: August 2019

NGP was previously reported as a granular protein of neutrophils in mouse but the function has not been known clearly. We found the presence of the possible signal peptide in NGP and we hypothesized this protein is being secreted to the blood stream. Since this protein has sequence similarity with an antimicrobial protein cathelicidin, we observed the aspect of inflammation of NGP. Interestingly, NGP interacts with the complex of LPS and LBP and blocked the inflammatory function of NGP. This inhibitory effect of NGP was through the inhibition of LPS-LBP complex to interact with TLR4 molecule. Furthermore, the inhibitory function of NGP could be repeated on the inflammatory effect of LPS in both in vitro and in vivo. With these findings, we report NGP is a novel secretory protein to mask LPS and inhibits its function.
Measurement of skeletal muscle fiber contractility with high-speed traction microscopy
Authors: Rausch M , Böhringer D , Steinmann M , Schubert DW , Schrüfer S , Mark C , Fabry B
Published: August 2019

We describe a technique for simultaneous quantification of the contractile forces and cytosolic calcium dynamics of muscle fibers embedded in three-dimensional biopolymer gels. We derive a scaling law for linear elastic matrices such as basement membrane extract hydrogels (Matrigel) that allows us to measure contractile force from the shape of the relaxed and contracted muscle cell and the Young’s modulus of the matrix, without further knowledge of the matrix deformations surrounding the cell and without performing computationally intensive inverse force reconstruction algorithms. We apply our method to isolated mouse flexor digitorum brevis (FDB) fibers that are embedded in 10 mg/ml Matrigel. Upon electrical stimulation, individual FDB fibers show twitch forces of 0.37 µN ± 0.15 µN and tetanic forces (100 Hz stimulation frequency) of 2.38 µN ± 0.71 µN, corresponding to a tension of 0.44 kPa ± 0.25 kPa and 2.53 kPa ± 1.17 kPa, respectively. Contractile forces of FDB fibers increase in response to caffeine and the troponin-calcium-stabilizer Tirasemtiv, similar to responses measured in whole muscle. From simultaneous high-speed measurements of cell length changes and cytosolic calcium concentration using confocal line scanning at a frequency of 2048 Hz, we show that twitch and tetanic force responses to electric pulses follow the low-pass filtered calcium signal. In summary, we present a technically simple high speed and high throughput method for measuring contractile forces and cytosolic calcium dynamics of single muscle fibers. We expect that our method will help to reduce preparation time, costs, and the number of sacrificed animals needed for experiments such as drug testing.

Statement of significance

We describe a high speed, high throughput method for the simultaneous measurement of contractile force and cytoplasmic calcium dynamics following electrical pulse stimulation of muscle fibers embedded in a 3-dimensional biopolymer matrix. In contrast to the classical approach of attaching muscle fibers to a force-transducer, our method allows for a highly efficient, parallel analysis of large numbers of fibers under different treatment conditions.
In situ activation and heterologous production of a cryptic lantibiotic from a plant-ant derived Saccharopolyspora species
Authors: Vikeli Eleni , Widdick David A. , Batey Sibyl F. , Heine Daniel , Holmes Neil A. , Bibb Mervyn J. , Martins Dino J. , Pierce Naomi E. , Hutchings Matthew I. , Wilkinson Barrie
Published: August 2019

Most clinical antibiotics are derived from actinomycete natural products (NPs) discovered at least 60 years ago. Repeated rediscovery of known compounds led the pharmaceutical industry to largely discard microbial NPs as a source of new chemical diversity but advances in genome sequencing revealed that these organisms have the potential to make many more NPs than previously thought. Approaches to unlock NP biosynthesis by genetic manipulation of the strain, by the application of chemical genetics, or by microbial co-cultivation have resulted in the identification of new antibacterial compounds. Concomitantly, intensive exploration of coevolved ecological niches, such as insect-microbe defensive symbioses, has revealed these to be a rich source of chemical novelty. Here we report the novel lanthipeptide antibiotic kyamicin generated through the activation of a cryptic biosynthetic gene cluster identified by genome mining Saccharopolyspora species found in the obligate domatia-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. Heterologous production and purification of kyamicin allowed its structural characterisation and bioactivity determination. Our activation strategy was also successful for the expression of lantibiotics from other genera, paving the way for a synthetic heterologous expression platform for the discovery of lanthipeptides that are not detected under laboratory conditions or that are new to nature.

Importance

The discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here we report an activation strategy that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression.
Diversity of responses of soil saprobic fungi to recurring heat events
Authors: Szymczak Aleksandra , Ryo Masahiro , Rillig Matthias C.
Published: August 2019

As a consequence of ongoing climate change, the frequency of extreme heat events is expected to increase. Recurring heat pulses may disrupt functions supported by soil microorganisms, thus affecting the entire ecosystem. However, most perturbation experiments only test effects of single heat events, and therefore it remains largely unknown how soil microorganisms react to repeated pulse events. Here we present data from a lab experiment exposing 32 filamentous fungi, originally isolated from the same soil, to sequential heat perturbations. Soil saprobic fungi isolates were exposed to one or two heat pulses: mild (35°C/2h), strong (45°C/1h), or both in sequence (35°C/2h+45°C/1h), and we assessed growth rate. Out of the 32 isolates 13 isolates showed an antagonistic response, 3 isolates a synergistic response and 16 isolates responded in an additive manner. These differences in species responses to the thermal environment may contribute to species coexistence, and such dissimilarities in thermal perturbation responses may be a key aspect influencing ecosystem services that soil saprobic fungi support.
Direct observation of independently moving replisomes in Escherichia coli
Authors: Japaridze Aleksandre , Gogou Christos , Kerssemakers Jacob W. J. , Nguyen Huyen My , Dekker Cees
Published: August 2019

The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in E. coli cells with an increased width. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move independently from the origin to the terminus of replication along each of the two arms of the circular chromosome, providing direct support for the so-called train-track model, and against a factory model for replisomes. The origin of replication duplicates near midcell, initially splitting to random directions and subsequently towards the poles. The probability of successful segregation of chromosomes significantly decreases with increasing cell width, indicating that chromosome confinement by the cell boundary is an important driver of DNA segregation. Our findings resolve long standing questions in bacterial chromosome organization.
Genetic Associations in Four Decades of Multi-Environment Trials Reveal Agronomic Trait Evolution in Common Bean
Authors: MacQueen Alice H. , White Jeffrey W. , Lee Rian , Osorno Juan M. , Schmutz Jeremy , Miklas Phillip N. , Myers Jim , McClean Phillip E. , Juenger Thomas E.
Published: August 2019

Multi-environment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET datasets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for over 70 years in the United States and Canada, consisting of 20 to 50 entries each year at 10 to 20 locations. The CBDN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association (GWAS) using best linear unbiased predictions (BLUPs) derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2M SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. The first use of mash on an agricultural dataset discovered two genomic regions with pleiotropic effects on multiple phenotypes, likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that by applying multiple statistical genomic approaches on data mined from MET phenotypic data sets, significant genetic effects that define genomic regions associated with crop improvement can be discovered.
Potential Utility of Routine Programmatic Data in Monitoring National and State-Level HIV Epidemic in Nigeria: Data Triangulation Analysis
Authors: Henry Debem , Yakubu Aminu , Ahmed Mukhtar , Jerry Gwamna , Ibrahim Dalhatu
Published: August 2019

Nigeria relies on data from periodic resource-intensive surveys such as antenatal HIV seroprevalence sentinel surveys (ANC-HSS) and population-based National AIDS and Reproductive Health Surveys (NARHS) for its HIV control efforts. Nigeria has not explored the use of readily available routine programmatic data (RPD) to easily inform and monitor epidemic control efforts at local settings in near real time. This study aimed to determine the utility of RPDs (Prevention of Mother-To-Child Transmission [PMTCT] and HIV Testing and Counseling [HTC]) as a proxy for monitoring HIV epidemic in Nigeria. Using World Health Organization 12 step triangulation procedures, we compared state-level seropositivity data from PMTCT and HTC programs to HIV prevalence data from NARHS and ANC-HSS reports in relevant pairs from 2010 to 2014 in Nigeria. The study population was pregnant women and general population. We abstracted relevant data from PEPFAR Nigeria data source and published national survey reports. We compared visual (scatterplots and maps) patterns and trends, and performed Pearson correlation and univariate linear regression models of the estimates for best matched/contiguous years for which data were available. Correlation between PMTCT2014 and ANC-HSS2014 was positive and significant (R=0.7,p<0.001). ANC-HSS2014 and HTC2014 were slightly correlated (R=0.4,p<0.05). Significant correlation was observed between ANC-HSS2010 and PMTCT2013 (R=0.8,p<0.001) and between ANC-HSS2010 and HTC2013 (R=0.6, p<0.001). All RPD sources and ANC-HSS indicated a decreasing trend in national HIV prevalence in Nigeria. PMTCT2014 data showed strong capability of predicting HIV prevalence in ANC-HSS2014 in regression model (B=2.09,p<0.0001). Use of routine PMTCT data in monitoring HIV prevalence among women of reproductive age could be more valid and reliable in local settings than the use of HTC data. Use of RPD to monitor national and sub-national-level HIV epidemic in between national surveys in Nigeria could maximize program resources, and promote a more responsive and efficient actions toward epidemic control.
Adaptation and competition in deteriorating environments
Authors: Limberger Romana , Fussmann Gregor F.
Published: August 2019

Evolution might rescue populations from extinction in changing environments. Using experimental evolution with microalgae, we investigated if competition influences adaptation to an abiotic stressor, and vice versa, if adaptation to abiotic change influences competition. In a first set of experiments, we propagated monocultures of five species with and without increasing salt stress for ~180 generations. When assayed in monoculture, two of the five species showed signatures of adaptation, that is, lines with a history of salt stress had higher population growth rates at high salt than lines without prior exposure to salt. When assayed in mixtures of species, however, only one of these two species had increased population size at high salt, indicating that competition can alter how adaptation to abiotic change influences population dynamics. In a second experiment, we cultivated two species in monocultures and in pairs, with and without increasing salt. While we found no effect of competition on adaptation to salt, our experiment revealed that evolutionary responses to salt can influence competition. Specifically, one of the two species had reduced competitive ability in the no-salt environment after long-term exposure to salt stress. Collectively, our results highlight the complex interplay of adaptation to abiotic change and competitive interactions.
Casein Kinase 1 dynamics underlie the PER2 circadian phosphoswitch
Authors: Philpott Jonathan M. , Narasimamurthy Rajesh , Ricci Clarisse G. , Freeberg Alfred M. , Hunt Sabrina R. , Yee Lauren E. , Pelofsky Rebecca S. , Tripathi Sarvind , Virshup David M. , Partch Carrie L.
Published: August 2019

Post-translational control of PERIOD stability by Casein Kinase 1δ and ε (CK1) plays a key regulatory role in metazoan circadian rhythms. Despite the deep evolutionary conservation of CK1 in eukaryotes, little is known about its regulation and the factors that influence substrate selectivity on functionally antagonistic sites in PERIOD that directly control circadian period. Here we describe a molecular switch involving a highly conserved anion binding site in CK1. This switch controls conformation of the activation loop to define substrate selectivity on mammalian PER2, thereby directly regulating its stability. Integrated experimental and computational studies shed light on the allosteric linkage between two anion binding sites that dynamically regulate kinase activity. We show that period-altering kinase mutations from humans toDrosophiladifferentially modulate this activation loop switch to elicit predictable changes in PER2 stability, providing a foundation to understand and further manipulate CK1 regulation of circadian rhythms.
Separating the signal from the noise in metagenomic cell-free DNA sequencing
Authors: Burnham Philip , Gomez-Lopez Nardhy , Heyang Michael , Cheng Alexandre Pellan , Lenz Joan Sesing , Dadhania Darshana , Lee John Richard , Suthanthiran Manikkam , Romero Roberto , De Vlaminck Iwijn
Published: August 2019

Cell-free DNA (cfDNA) in blood, urine and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. Here, we report Low Biomass Background Correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term.
Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
Authors: Zhang Xiao-Ou , Gingeras Thomas R. , Weng Zhiping
Published: August 2019

Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because Alu elements are highly repetitive, it has been difficult to identify the Pol III–transcribed elements and quantify their expression levels. In this study, we generated high-resolution, long-genomic-span RAMPAGE data in 155 biosamples all with matching RNA-seq data and built an atlas of 17,249 Pol III–transcribed Alu elements. We further performed an integrative analysis on the ChIP-seq data of 10 histone marks and hundreds of transcription factors, whole-genome bisulfite sequencing data, ChIA-PET data, and functional data in several biosamples, and our results revealed that although the human-specific Alu elements are transcriptionally repressed, the older, expressed Alu elements may be exapted by the human host to function as cell-type–specific enhancers for their nearby protein-coding genes.
A tolbutamide–metformin salt based on antidiabetic drug combinations: synthesis, crystal structure analysis and pharmaceutical properties
Authors: Jia Lina , Wu Songgu , Gong Junbo
Published: August 2019

A drug–drug anhydrous pharmaceutical salt containing tolbutamide {systematic name: 3-butyl-1-[(4-methylbenzene)sulfonyl]urea, TOL, C12H18N2O3S} and metformin (systematic name: 1-carbamimidamido-N,N-dimethylmethanimidamide, MET, C4H11N5) was created based on antidiabetic drug combinations to overcome the poor pharmaceutical properties of the parent drugs. Proton transfer and the proportion of the two components were confirmed by 1H NMR spectroscopy and single-crystal X-ray diffraction analysis. Comprehensive characterization of the new pharmaceutical salt crystal, 2-[(dimethylamino)(iminiumyl)methyl]guanidine (butylcarbamoyl)[(4-methylbenzene)sulfonyl]azanide, C4H12N5
+·C12H17N2O3S−, was performed and showed enhancement of the pharmaceutical properties, such as lower hygroscopicity and greater accelerated stability than the parent drug MET, and higher solubility and dissolution rate than TOL. The property alterations were correlated with the crystal packing features and potential hydrogen-bonding sites through observed changes in the crystal structures.
Deciphering the hydrogen-bonding scheme in the crystal structure of triphenylmethanol: a tribute to George Ferguson and co-workers
Authors: Rodríguez Tzompantzi Tomasa , Amaro Hernández Aldo Guillermo , Meza-León Rosa Luisa , Bernès Sylvain
Published: August 2019

The crystal structure of triphenylmethanol, C19H16O, has been redetermined using data collected at 295 and 153 K, and is compared to the model published by Ferguson et al. over 25 years ago [Ferguson et al. (1992). Acta Cryst. C48, 1272–1275] and that published by Serrano-González et al., using neutron and X-ray diffraction data [Serrano-González et al. (1999). J. Phys. Chem. B, 103, 6215–6223]. As predicted by these authors, the hydroxy groups are involved in weak intermolecular hydrogen bonds in the crystal, forming tetrahedral tetramers based on the two independent molecules in the asymmetric unit, one of which is placed on the threefold symmetry axis of the R\overline{3} space group. However, the reliable determination of the hydroxy H-atom positions is difficult to achieve, for two reasons. Firstly, a positional disorder affects the full asymmetric unit, which is split over two sets of positions, with occupancy factors of ca 0.74 and 0.26. Secondly, all hydroxy H atoms are further disordered, either by symmetry, or through a positional disorder in the case of parts placed in general positions. We show that the correct description of the hydrogen-bonding scheme is possible only if diffraction data are collected at low temperature. The prochiral character of the hydrogen-bonded tetrameric supramolecular clusters leads to enantiomorphic three-dimensional graphs in each tetramer. The crystal is thus a racemic mixture of sup
S and sup
R motifs, consistent with the centrosymmetric nature of the R\overline{3} space group.
Effect of supply-chain resilience on firm performance and competitive advantage
Authors: Abeysekara Nadeesha , Wang Haijun , Kuruppuarachchi Duminda
Published: August 2019

Purpose

The purpose of this paper is to investigate the extent to which firms in the Sri Lankan apparel industry practice supply-chain-resilience (SCRes) capabilities and examine whether SCRes practices affect the performance and competitive advantage of those firms.

Design/methodology/approach

Uses a conceptual framework to assess SCRes capabilities and to investigate their impact on firm performance and competitive advantage. Uses partial least squares structural equation modeling (PLS-SEM) to quantitatively analyze questionnaire data collected from 89 Sri Lankan apparel manufacturers.

Findings

In the presence of SCRes capabilities in the apparel industry, this study finds that supply-chain risk-management culture positively affects SCRes capabilities, namely re-engineering, agility and collaboration. Agility shows the greatest influence on firm performance and competitive advantage.

Research limitations/implications

This study is limited to the apparel industry sector (a manufacturing sector) in Sri Lanka to maintain the uniformity of the research constructs.

Practical implications

Results imply that management should pay more attention to enhancing SCRMC and prioritizing their SCRes capabilities.

Originality/value

This study is the first to assess SCRes capabilities in the apparel-manufacturing sector and examine the impact of SCRes capabilities on firm performance and competitive advantage.
Cornwall Foundation Trust’s capacity to implement the government’s children and young people’s mental health strategy
Authors: Macpherson Reynold , Vann Barbara
Published: August 2019

Purpose

The purpose of this paper evaluates the capacity of the Cornwall Foundation Trust (CFT) of the National Health Service (NHS) to implement the UK Government’s children and young people’s mental health strategy through its school-based integrated health centre (SBIHC) delivery model.

Design/methodology/approach

This evaluation uses six case studies of SBIHCs to indicate the general effectiveness of this delivery model and its capacity to implement the three core proposals of the Government’s strategy. The core proposals are: to encourage all schools and colleges to identify and train a designated senior lead (DSL) for mental health; to fund new mental health support teams (MHSTs); and to develop strategies to meet the proposed four-week waiting time for access to specialist NHS mental health services.

Findings

This evaluation found that the Duchy Health Charity and CFT piloted a new delivery model in three SBIHCs from 2009 that successfully integrated health and educational services to children and adolescents, including general health and well-being and sexual and mental health and, more recently, integrated welfare services.

Research limitations/implications

The main research implication is that longitudinal case studies of organisational innovations can reveal the subtleties of educational management in context and potentially inform advances elsewhere consistent with national policy developments.

Practical implications

The main practical implication is that the SBIHCs at Penair Community School, Budehaven Community School, Hayle Community School, Looe Community Academy, Treviglas Community Academy and Wadebridge Community School should each be recognised as a “trailblazer site” in the implementation of the Government’s children and young people’s mental health strategy.

Social implications

Mandatory secondary education is the last opportunity that the UK society has to embed knowledge, skills and attitudes needed for the life-long self-management of health. The CFT’s SBIHC model trialled since 2009 has successfully integrated health and educational services to children and adolescents, including general health and well-being and sexual and mental health and, more recently, integrated welfare services.

Originality/value

This evaluation research is unique. It reports that the CFT’s SBIHC model is the first and only organisational innovation at a system level in the UK that has successfully integrated health and education services to children and adolescents.
The road already traveled: communication advice for higher education leaders
Authors: McNaughtan Jon L. , DePue Brooke Wilson , McNaughtan Elisabeth D.
Published: August 2019

Purpose

Turnover of presidents in colleges and universities occurs frequently and new presidents are rarely trained to handle communication with the range of stakeholders involved in a campus community, which is one of the most complex tasks their job requires. New presidents need guidance and insight to prepare them for this vital aspect of campus leadership. The paper aims to discuss this issue.

Design/methodology/approach

This paper analyzes interviews with sitting presidents and vice presidents of communication at flagship universities in the USA to identify themes and best practices for presidential communication.

Findings

Analysis of interviews resulted in five consistent recommended practices: be informed about your issue and audience; utilize multiple communication channels; know when to speak; identify and use a communication team; and when you speak, use your own authentic voice.

Originality/value

Limited research exists on the communication process and skills needed to effectively lead colleges and universities. While incoming presidents often lack backgrounds and training in communication strategies, such strategies are required to effectively engage both internal and external audiences. The study provides new leaders with tips from seasoned leaders to enhance their communication strategies.
International students’ experiences in a flipped classroom environment
Authors: Nachatar Singh Jasvir Kaur , Nagpal Swati , Inglis Susan , Jacob-John Jubin
Published: August 2019

Purpose

The purpose of this paper is to explore undergraduate international students’ experiences in a flipped classroom environment in an Australian university.

Design/methodology/approach

In total, 32 in-depth interviews were conducted with undergraduate international students at one Australian university by three researchers.

Findings

The learning experiences of international students in a flipped classroom environment include increased flexibility in learning; enhanced engagement with content and; more confident participation in face-to-face workshops. In addition, the analysis further illustrates that international students intrinsically develop soft skills (e.g. increased confidence and communication skills), learning skills (e.g. research and critical thinking) and employability skills (e.g. time management and accountability).

Research limitations/implications

These findings focus only on the positive learning experiences of undergraduate international students in one Australian university.

Originality/value

The study contributes to the literature by identifying learning experiences of undergraduate international students in a flipped classroom environment and the connection with their development of soft skills, learning skills and employability skills.