bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Solid‐State Fermentation by Lactobacillus plantarum on the Cooking Quality, Microstructure, and Physicochemical Properties of Brown Rice
Authors: Li Yongfu , Cheng Xin , Shi Feng , Wang Li , Li Yanan , Chen Zhengxing
Published: October 2018

Brown rice (BR) is nutritious but difficult to cook, which limits its consumption. In this study, a novel processing technology, solid‐state fermentation (SSF), is developed to improve the cooking quality of BR. After SSF treatment with Lactobacillus plantarum JYI‐3913, BR hardness (821.20 g) decreased by 36.91%, and its cooking time (19.69 min) is reduced by 29.07% compared to untreated BR (1301.72 g and 27.76 min, respectively). In addition, some small gullies and holes appear on the BR grain cortex, and the connections between the starch particles become looser. Cellulose and hemicellulose in BR exhibit a certain degree of degradation. Furthermore, the molecular structures of BR starch granules are damaged; the long chains of amylopectin are partially broken; the crystal structure of starch is partially destroyed; gelatinization enthalpy is decreased; and the setback value of starch is decreased. All of these characteristics make the BR easier to cook, and the cooked BR presents an improved taste and slower retrogradation. The results show that applied SSF treatment improves the cooking quality of BR.
Dispersion relation for hadronic light-by-light scattering: pion pole
Authors: Hoferichter Martin , Hoid Bai-Long , Kubis Bastian , Leupold Stefan , Schneider Sebastian P.
Published: October 2018

Abstract

The pion-pole contribution to hadronic light-by-light scattering in the anomalous magnetic moment of the muon (g − 2)
μ
is fully determined by the doubly-virtual pion transition form factor. Although this crucial input quantity is, in principle, directly accessible in experiment, a complete measurement covering all kinematic regions relevant for (g −2)
μ
is not realistic in the foreseeable future. Here, we report in detail on a reconstruction from available data, both space- and time-like, using a dispersive representation that accounts for all the low-lying singularities, reproduces the correct high- and low-energy limits, and proves convenient for the evaluation of the (g − 2)
μ
loop integral. We concentrate on the systematics of the fit to e
+
e
− → 3π data, which are key in constraining the isoscalar dependence, as well as the matching to the asymptotic limits. In particular, we provide a detailed account of the pion transition form factor at low energies in the time- and space-like region, including the error estimates underlying our final result for the pion-pole contribution,

$$ {a}_{\mu}^{\uppi^0-\mathrm{pole}}={62.6}_{-2.5}^{+3.0}\times {10}^{-11} $$

a
μ

π
0

−
pole

=

62.6

−
2.5

+
3.0

×

10

−
11

, and demonstrate how forthcoming singly-virtual measurements will further reduce its uncertainty.
Genetics of autosomal recessive intellectual disability
Authors: Jamra Rami
Published: October 2018

In the last few years, next-generation sequencing has led to enormous progress in deciphering monogenic forms of intellectual disability. Autosomal dominant intellectual disability (ADID) and X chromosomal intellectual disability (XLID) have been the focus of research. Apart from metabolic disorders, autosomal recessive intellectual disability (ARID) is still behind, probably because it is more heterogeneous and less prevalent in industrial populations. The prevalence of ARID in a cohort of affected children of an outbred population is estimated to be about 10%, with an upward tendency in still unclarified cases. The risk for ARID in children of first cousins or closer is a magnitude higher than for children of unrelated parents. Taken together, it seems that children of related parents are at a 2 to 3 times higher risk for ID. There are no prevalent ARID genes, pathways, or protein complexes and the functions of the affected proteins are very diverse and limited not only to neurological aspects. Thus, in a regular case, there is no reasoning for picking a few genes for a first diagnostic step, and a genetic diagnosis of ID in general, and ARID specifically, is better made using large panels or exome sequencing. In addition, in the last few months, evidence has been growing that many ARID genes are pleiotropic and that the resulting phenotypes may have a broad spectrum. For an exhaustive deciphering of the genetics of ARID, we suggest research at the level of single genes rather than large meta-analyses.
Is a “straight to test” strategy a pragmatic alternative to the conventional two-week wait referral pathway for colorectal cancer in an ethnically diverse hospital catchment area? A single-centre case series
Authors: Katifi Hannah N. , Slesser Alistair AP. , Roden Lorna , Patel Trushma , Agarwal Tushar
Published: October 2018

ABSTRACT

Introduction:

In a climate of rising pressure to ameliorate cancer services, a “straight to test” (STT) model whereby two-week wait (TWW) colorectal referrals undergo an investigative procedure prior to an outpatient assessment has been explored as a method to expedite the clinical pathway. We aim to evaluate the potential for its application in an ethnically diverse region and assess whether this model improves the time to diagnosis compared to the conventional route.

Presentation of cases:

Between September and October 2016, we performed a prospective comparative case series of 132 consecutive TWW colorectal referrals to a district general hospital. Following a two-stage triage process, 24 patients were allocated to a STT group and 108 patients were assessed in clinic first. The times to the first investigation, endoscopic procedure and established diagnosis were compared between the two groups.

Discussion:

The median time to the first investigation was 13.5 days in the STT group versus 24 days in the non-STT group (p < 0.001). A diagnosis was established at a median time of 14 days for the STT group versus 25 days in the non-STT group (p < 0.001). 62/132 (47%) of all TWW referrals were excluded from STT owing to language barriers and medical grounds.

Conclusion:

A STT approach minimises the time from TWW referral to investigations and diagnosis for patients with suspected colorectal cancer. Application of a STT model may be limited by local population factors including language issues and a high prevalence of medical comorbidity.

Highlights:
Food- and diet-based validations of a Nestlé Nutrient Profiling System for reformulation in two nationally representative surveys
Authors: Vieux Florent , Privet Lisa , Masset Gabriel
Published: October 2018

The Nestlé Nutritional Profiling System (NNPS) has been developed to guide food and beverage reformulation. The WHO published guidelines to develop and validate nutrient profiling systems. The objective was to conduct validation tests of the NNPS following principles of the WHO guidelines. French (Individual and National Survey on food Consumption 2006–2007) and the USA (National Health and Nutrition Examination Surveys 2011–2012) nationally representative dietary surveys were used. NNPS outcomes (PASS, FAIL, out-of-scope) of foods were compared with the validated UK Ofcom nutrient profiling system outcomes. Contributions of NNPS outcomes to energy intakes were compared between diets nutritional quality classes defined by two methods: based on a food-based quality indicator (Programme National Nutrition Santé Guideline Score in France, Healthy Eating Index 2010 in the USA) or on a combination of three nutrient-based indicators (mean adequacy ratio, mean excess ratio and energy density). In both countries, food items with a NNPS FAIL outcome had a lower nutritional quality according to the UK Ofcom, with an overall agreement between the two systems of 75·7 % in France and 68·8 % in the USA. In both countries, a high (respectively, low) contribution of NNPS PASS (respectively, NNPS FAIL) was positively associated with diet healthiness. Absolute associations were stronger between the contribution of NNPS FAIL products and measures of diet healthiness. Foods and beverages reaching NNPS standards appeared to have a higher nutritional quality and would be more likely to contribute to healthier diets, mainly linked to a reduction of nutrients to limit.
Temporary Constitutional Amendments as a Means to Undermine the Democratic Order: Insights from the Israeli Experience
Authors: Dishon Nadav
Published: October 2018

This article focuses on the adoption of temporary measures within the generally rigid constitutional sphere. Commentators frequently contemplate the extent to which temporary constitutional measures are adequate and necessary within a constitution that is meant to be perpetuated. Some writers are in favour of temporary constitutionalism, claiming that it allows flexibility and relieves the counter-majoritarian problem. Others emphasise the devastating impact of intense implementation of temporary measures on the status and legitimacy of the constitution.

The article contends that as beneficial as temporary constitutionalism may be in some circumstances, its use should be scrutinised with great suspicion, especially when it is employed in weak constitutional regimes. In outlining the history of temporary constitutionalism in the State of Israel, the article illustrates how temporary constitutional amendments can be harnessed to undermine the democratic order. The Israeli use of temporary constitutionalism since 2009 reveals a new under-explored manifestation of ‘abusive constitutionalism’, referred to here as ‘abusive temporary constitutionalism’. With abusive temporary constitutionalism, incumbents can entrench their power against their opponents while avoiding both public accountability and judicial review of their actions. Drawing on the Israeli experience, the article outlines several signifiers (i.e. distinctive markers) which will allow judges in the future to monitor and suppress the development of the abusive employment of temporary constitutional amendments.
The medium-term effect of natural compost on the spectroscopic properties of humic acids of Czech soils
Authors: Enev V. , Doskočil L. , Kubíková L. , Klučáková M.
Published: October 2018

In the current work, humic acids (HAs) isolated from natural compost and unamended and amended soils in a medium-time field experiment were characterized to evaluate the effects of the amendment at rates of 124, 239 and 478 t/ha on their chemical, compositional and structural features. The impact of the application of compost on their properties was observed over 3 years. Humic acids were characterized using spectral methods and elemental analysis. Humic acid isolated from compost was predominantly aliphatic, with a larger content of nitrogen and low degree of aromaticity and humification. The typical maximum (280/345 nm) of HA obtained from compost lies within the T (tryptophan-like) region, which can be ascribed to proteinaceous organic materials. On the other hand, the HAs obtained from amended soil were mainly aromatic in character, with a larger distribution of oxygen-containing functional groups, molecular weight and greater aromaticity. Fluorophores of HAs obtained from amended soil lie within the C (humic-like) region with typical maxima centred in the range 430–450/500–540 nm, occurring usually in HAs isolated from soil, peat and lignite. According to ultra-violet/visible and Fourier-transform infrared (FTIR) spectroscopy, the larger oxygen contents of these HAs are associated with the substitution of aromatic rings by oxygen-containing functional groups such as carboxylic, hydroxyls and ethers. On the basis of FTIR spectra, it was shown that HAs obtained from amended soil 2 and 3 years after compost application were enriched by peptid, aromatic and polysaccharide compounds absorbing at 1540, 1515 and 1040/cm, respectively.
Shedding of Angiostrongylus costaricensis larvae in the faeces of Swiss mice experimentally infected with different infective doses
Authors: Hermes C.C. , Benvegnú E. , Costa M.M. , Rodriguez R. , Vieira M.I.B.
Published: October 2018

Abdominal angiostrongyliasis is an endemic zoonosis in southern Brazil caused by the nematode Angiostrongylus costaricensis, which uses terrestrial molluscs as intermediate hosts and wild rodents as final hosts. Humans can be infected by ingesting infectious A. costaricensis larvae. To date, correlations between shedding of first-stage larvae (L1) and different infective doses of third-stage larvae (L3) have not been elucidated. The aim of this study was to assess L1 faecal shedding levels in Swiss mice experimentally infected with different doses of A. costaricensis L3 and to determine whether infective doses are related to mortality. Thirty-two male Swiss mice were divided evenly into a non-infected control (NI-Con); low-dose infection (LD-Inf); medium-dose infection (MD-Inf) and high-dose infection (HD-Inf) groups infected with 0, 5, 15 and 30 A. costaricensis L3, respectively. Faecal samples were collected from each animal, starting at day 20 post infection. HD-Inf mice had greater faecal L1 shedding levels than LD-Inf mice, but not a significantly shortened survival. In conclusion, infective doses of A. costaricensis L3 affect L1 shedding levels without altering mortality in Swiss mice.
In situlong-term monitoring of cardiac activity of two bivalve species from the White Sea, the blue musselMytilus edulisand horse musselModiolus modiolus
Authors: Bakhmet Igor N. , Sazhin Andrey , Maximovich Nikolay , Ekimov Dmitry
Published: October 2018

Cardiac activity of two White Sea Bivalvia species –Mytilus edulisandModiolus modiolus– was monitoredin situfor one full calendar year every 4 days. During the year, we also assessed the temperature and salinity of the ambient seawater (at intervals of 1 min), measured phytoplankton concentration (every 4 days) and checked the reproductive status of the molluscs (every 2 weeks). Our field study showed a significant linear correlation between the molluscs’ heart rates and the temperature of the ambient seawater. However, during specific periods of the year, we observed that phytoplankton composition or reproductive status became the dominant influence over cardiac activity. Phytoplankton concentrations were generally found to be low throughout the entire year, but two peak periods of drastically elevated phytoplankton concentration were found (April and May), and during April the peak heart rates of the blue mussels significantly increased. Spawning time took place in the middle of June, and at this time the cardiac activity of the molluscs did not change in spite of a 4°C temperature increase in the ambient seawater. Monitoring of the heart rates of the real intertidal blue mussels (animals located at the middle part of intertidal) revealed periodic fluctuations in cardiac activity that correlated strongly with tidal fluctuations. Cardiac activity inM. modioluswas significantly lower than inM. edulisfrom 9 May to 25 November. On the basis of our data, we concluded that the molluscs’ cardiac activity can serve not only as an indicator of the animals’ physiological conditions, but also as an indicator of changes in ambient factors.
Relationships of phosphorus concentration in reproductive organs with soil phosphorus availability for tropical rain-forest trees on Mount Kinabalu, Borneo
Authors: Tsujii Yuki , Kitayama Kanehiro
Published: October 2018

Bornean rain forests on phosphorus (P)-poor soils exhibit a high P-use efficiency in the production of reproductive organs (i.e. the inverse of P concentration in reproductive-organ litter). The mechanism underpinning this high P-use efficiency is not known, but is hypothesized to result from dilution of P in a given type of reproductive organ and/or a shift of the community composition of flower/fruit types with decreasing P availability. These hypotheses were tested using eight forests with different soil P availabilities on Mount Kinabalu, Borneo. Mean P concentration per forest by genus in inflorescences was significantly positively correlated with P availability, while that in seeds or pericarps was not significantly correlated. This trend was consistent across 21 genera that we analysed, suggesting that P concentration in seeds is maintained in exchange with the dilution of P in inflorescences. The composition of fruit types in tree community was estimated based on the relative abundances of genera in each forest. The relative abundance of capsulate species, which required less P in pericarps, tended to increase in tree community with decreasing P availability. Therefore, both mechanisms were involved in P-use efficiency. This work provides an insight into the reproductive adaptation of trees to P deficiency.
How hybrid is blog data? A comparison between speech, writing and blog data in Swedish
Authors: Wiktorsson Maria
Published: October 2018

The new forms of written online communication offer a great resource for researchers interested in language variation and use, but more large-scale systematic research into the nature of the data is needed. For instance, Swedish blog data is often described as more informal and spoken in nature than traditional edited written material but overall systematic comparisons are lacking. This short communication contributes systematic comparisons between blog data and spoken and written registers by comparing measures such as type/token ratios and word frequencies. Type/token ratios of blog texts are found to lie between those for interactive speech and formal edited writing, whereas the distribution of words from different frequency bands is closer to the written material. Comparison of the ten most frequent word forms indicates that blog data resembles formal edited writing from a structural perspective, but also suggests that further studies into features of personal involvement may provide additional insights.
Orbit Determination Using Pulsar Timing Data and Orientation Vector
Authors: Zhang Hua , Jiao Rong , Xu Luping
Published: October 2018

X-ray Pulsar Navigation (XPNAV) uses the Time Difference of Arrival (TDOA) of the pulsar signal between the spacecraft and Solar System Barycentre (SSB) to determine position. In this paper, a novel method to improve the performance of XPNAV via exploiting the pulsar position vector is proposed. First, the field of view of the collimator is utilised to find the pulsar orientation direction. Then, a searching strategy based on the modified Powell method under given coordinate frames is proposed. We also mathematically prove the existence of the extreme value of the searching strategy. Subsequently, an observation model based on the pulsar radiation vector is presented and applied to formulate the observation function together with pulsar time transfer function. Finally, an Adaptive Divided Difference Filter (ADDF) algorithm is introduced to iteratively estimate the position and velocity of the spacecraft. Numerical simulations show that the vector searching method is feasible and the pulsar radiation direction can improve the navigation performance by 75%. The simulation results also show that the ADDF performs better than Unscented Kalman Filtering (UKF) and DDF in position estimation.
Attentional Control as a Predictor of Response to Psychological Treatment for Depression and Relapse up to 1 year After Treatment: A Pilot Cohort Study
Authors: Buckman J.E.J. , Saunders R. , Fearon P. , Leibowitz J. , Pilling S.
Published: October 2018

Background:Identifying depressed patients unlikely to reach remission and those likely to relapse after reaching remission is of great importance, but there are few pre-treatment factors that can help clinicians predict prognosis and together these explain relatively little variance in treatment outcomes. Attentional control has shown promise in studies to date, but has not been investigated prospectively in routine clinical settings with depressed patients.Aims:This study aimed to pilot the use of a brief self-report measure of attentional control in routine care and investigate the associations between attentional control, psychological treatment response and relapse to depression up to 1 year post-treatment.Method: Depressed patients were recruited from two primary care psychological treatment (IAPT) services and completed the Attentional Control Scale (ACS) alongside routine symptom measures at every therapy session. Participants were tracked and followed up for 1 year post-treatment.Results: Baseline ACS scores were associated with remission and residual depressive symptoms post-treatment, and relapse within 12 months of ending treatment, all independent of pre-treatment depressive symptom severity, and the latter also independent of residual symptoms.Conclusion: A self-report measure of attentional control can potentially be used to predict levels of depressive symptoms post-treatment and can contribute to predicting risk of relapse to depression in IAPT services, without affecting rates of therapy completion/drop-out or data completion of standard IAPT measures. However, this pilot study had a small overall sample size and a very small number of observed relapses, so replication in a larger study is needed before firm conclusions can be made.
The development and evaluation of the Depth and Duration of Awareness Coding Scheme (D-DACS)
Authors: Higginson Sally , Mansell Warren
Published: October 2018

Recent advances in transdiagnostic cognitive therapy such as Method of Levels therapy have utilized perceptual control theory (PCT). The current study reports the development and preliminary investigations of the psychometric properties of a newly developed coding scheme – the Depth and Duration of Awareness Coding Scheme (D-DACS) – which utilizes PCT to code a client's awareness of their present moment experiences, counterproductive strategies (arbitrary control), goal conflict and higher-level goals. Fifty participants’ first therapy sessions were coded according to the D-DACS. For the purposes of inter-rater reliability analysis, 25% of sessions were co-coded and inter-rater reliability of the D-DACS was found to fall in the good range. Findings for the convergent validity of the D-DACS were mixed with the finding of a significant association between the D-DACS primary indices and a more global and subjective index of awareness as measured by the D-DACS, but a lack of association between the D-DACS primary indices and self-report measures that were somewhat conceptually related. Support for the predictive validity of the D-DACS primary indices in relation to the prediction of change in symptoms for a subset of the sample who returned for a second session (n = 35) was not found. Limitations to the D-DACS as it stands and to the current study are discussed. Considerations for future research that address such limitations are also discussed.
Anisotropic Physical Properties of Mafic and Ultramafic Rocks From an Oceanic Core Complex
Authors: Bayrakci G. , Falcon‐Suarez I. H. , Minshull T. A. , North L. , Barker A. , Zihlmann B. , Rouméjon S. , Best A. I.
Published: October 2018

We analyzed the physical properties of altered mafic and ultramafic rocks drilled at the Atlantis Massif (Mid‐Atlantic Ridge, 30°N; Integrated Ocean Discovery Program Expeditions 304‐305 and 357). Our objective was to find a physical property that allows direct distinction between these lithologies using remote geophysical methods. Our data set includes the density, the porosity,PandSwave velocities, the electrical resistivity, and the permeability of mafic and ultramafic samples under shallow subsurface conditions (confining pressure up to 50 MPa equivalent to ~2‐km depth). In shallow subsurface conditions, mafic and ultramafic samples showed distinct differences in the density, the seismic wave velocities, and the electrical resistivity (mafic samples: 2,840 to 2,860 kg/m3, 5.92 to 6.70 km/s, and 60 to 221 Ω m; ultramafic samples: 2,370 to 2,790 kg/m3, 3.36 and 3.62 km/s, and 8 to 44 Ω m). However, we observed an overlap between physical properties of mafic and ultramafic rocks when we compared our measurements with those acquired from similar environments. The anisotropic homogeneous electrical resistivity inversion shows transverse isotropy symmetry, which is typical of a foliated microstructure. In both the inversion results and the thin sections, the direction of high resistivity axes of ultramafic rock samples is systematically perpendicular to the equivalent axes in mafic rock samples analyzed in this study. Our sample scale study suggests that electrical resistivity anisotropy may allow us to distinguish mafic and ultramafic lithologies via controlled source electromagnetic surveys. When surface conduction is negligible, the electrical resistivity can be used as proxy for permeability.
Simulating the 128‐ka Antarctic Climate Response to Northern Hemisphere Ice Sheet Melting Using the Isotope‐Enabled HadCM3
Authors: Holloway Max D. , Sime Louise C. , Singarayer Joy S. , Tindall Julia C. , Valdes Paul J.
Published: October 2018

Warmer than present Antarctic and Southern Ocean temperatures during the last interglacial, approximately 128,000 years ago, have been attributed to changes in north‐south ocean heat transport, causing opposing hemispheric temperature anomalies. We investigate the magnitude of Antarctic warming and Antarctic ice core isotopic enrichment in response to Northern Hemisphere meltwater input during the early last interglacial. A 1,600‐year HadCM3 simulation driven by 0.25 Sv of meltwater input reproduces 50–60% of the peak Southern Ocean summer sea surface temperature anomaly, sea ice retreat, and ice core isotope enrichment. We also find a robust increase in the proportion of cold season precipitation during the last interglacial, leading to lower isotopic values at the Antarctic ice core sites. These results suggest that a HadCM3 simulation including 0.25 Sv for 3,000–4,000 years would reconcile the last interglacial observations, providing a potential solution for the last interglacial missing heat problem.
Distinct Influences of Land Cover and Land Management on Seasonal Climate
Authors: Singh Deepti , McDermid Sonali P. , Cook Benjamin I. , Puma Michael J. , Nazarenko Larissa , Kelley Maxwell
Published: October 2018

Anthropogenic land use and land cover change is primarily represented in climate model simulations through prescribed transitions from natural vegetation to cropland or pasture. However, recent studies have demonstrated that land management practices, especially irrigation, have distinct climate impacts. Here we disentangle the seasonal climate impacts of land cover change and irrigation across areas of high agricultural intensity using climate simulations with three different land surface scenarios: (1) natural vegetation cover/no irrigation, (2) year 2000 crop cover/no irrigation, and (3) year 2000 crop cover and irrigation rates. We find that irrigation substantially amplifies land cover‐induced climate impacts but has opposing effects across certain regions. Irrigation mostly causes surface cooling, which substantially amplifies land cover change‐induced cooling in most regions except over Central, West, and South Asia, where it reverses land cover change‐induced warming. Despite increases in net surface radiation in some regions, this cooling is associated with enhancement of latent relative to sensible heat fluxes by irrigation. Similarly, irrigation substantially enhances the wetting influence of land cover change over several regions including West Asia and the Mediterranean. The most notable contrasting impacts of these forcings on precipitation occur over South Asia, where irrigation offsets the wetting influence of land cover during the monsoon season. Differential changes in regional circulations and moist static energy induced by these forcings contribute to their precipitation impacts and are associated with differential changes in surface and tropospheric temperature gradients and moisture availability. These results emphasize the importance of including irrigation forcing to evaluate the combined impacts of land surface changes for attributing historical climatic changes and managing future impacts.
Large‐Scale Intrusion of Circumpolar Deep Water on Antarctic Margin Recorded by Stylasterid Corals
Authors: King Theresa M. , Rosenheim Brad E. , Post Alexandra L. , Gabris Theresa , Burt Taylor , Domack Eugene W.
Published: October 2018

We present centennial‐scale radiocarbon (14C) records archived by deep sea stylasterid corals from the outer shelf and upper slope of the Antarctic margin. These novel stylasterids (Errina spp.) were collected from the western Ross Sea shelf (500 m) and slope (1,700 m), as well as the eastern Wilkes Land shelf (670 m). We provide two corals from each region and document an abrupt reversal of 14C ages in the upper (younger) part of each coral. We test the statistical robustness of each record and demonstrate the significance of the age reversals, as well as the ability of these corals to record environmental change. We discuss a variety of possible drivers for this 14C reversal and conclude that it is most likely an encroachment of 14C‐depeleted Circumpolar Deep Water (CDW). This water mass has regionally intruded onto the Antarctic margin in recent decades, facilitating loss of grounded Antarctic ice; which has implications for global sea level, deep‐water formation, and carbon sequestration in the Southern Ocean. Thus, understanding the past variability of CDW on the margin is vital to better constrain climate change trajectories in the near future. We estimate large‐scale encroachment of CDW onto the shelf likely commencing after 1830 CE (±120 year). We present possible drivers for the intrusion, but highlight the need for additional chronologic constraint. This study not only demonstrates the utility of a novel coral taxon but also presents the paleoceanographic community with a testable hypothesis concerning a recent, widespread CDW intrusion.
Reprogramming mechanisms influence the maturation of hematopoietic progenitors from human pluripotent stem cells
Authors: Heo Hye-Ryeon , Song Haengseok , Kim Hye-Ryun , Lee Jeong Eun , Chung Young Gie , Kim Woo Jin , Yang Se-Ran , Kim Kye-Seong , Chun Taehoon , Lee Dong Ryul , Hong Seok-Ho
Published: October 2018

Somatic cell nuclear transfer (SCNT) or the forced expression of transcription factors can be used to generate autologous pluripotent stem cells (PSCs). Although transcriptomic and epigenomic comparisons of isogenic human NT-embryonic stem cells (NT-ESCs) and induced PSCs (iPSCs) in the undifferentiated state have been reported, their functional similarities and differentiation potentials have not been fully elucidated. Our study showed that NT-ESCs and iPSCs derived from the same donors generally displayed similar in vitro commitment capacity toward three germ layer lineages as well as proliferative activity and clonogenic capacity. However, the maturation capacity of NT-ESC-derived hematopoietic progenitors was significantly greater than the corresponding capacity of isogenic iPSC-derived progenitors. Additionally, donor-dependent variations in hematopoietic specification and commitment capacity were observed. Transcriptome and methylome analyses in undifferentiated NT-ESCs and iPSCs revealed a set of genes that may influence variations in hematopoietic commitment and maturation between PSC lines derived using different reprogramming methods. Here, we suggest that genetically identical iPSCs and NT-ESCs could be functionally unequal due to differential transcription and methylation levels acquired during reprogramming. Our proof-of-concept study indicates that reprogramming mechanisms and genetic background could contribute to diverse functionalities between PSCs.
Laser-induced vapour nanobubbles improve drug diffusion and efficiency in bacterial biofilms
Authors: Teirlinck Eline , Xiong Ranhua , Brans Toon , Forier Katrien , Fraire Juan , Van Acker Heleen , Matthijs Nele , De Rycke Riet , De Smedt Stefaan C. , Coenye Tom , Braeckmans Kevin
Published: October 2018

Hindered penetration of antibiotics through biofilms is one of the reasons for the alarming increase in bacterial tolerance to antibiotics. Here, we investigate the potential of laser-induced vapour nanobubbles (VNBs) formed around plasmonic nanoparticles to locally disturb biofilm integrity and improve antibiotics diffusion. Our results show that biofilms of both Gram-negative (Burkholderia multivorans, Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) bacteria can be loaded with cationic 70-nm gold nanoparticles and that subsequent laser illumination results in VNB formation inside the biofilms. In all types of biofilms tested, VNB formation leads to substantial local biofilm disruption, increasing tobramycin efficacy up to 1-3 orders of magnitude depending on the organism and treatment conditions. Altogether, our results support the potential of laser-induced VNBs as a new approach to disrupt biofilms of a broad range of organisms, resulting in improved antibiotic diffusion and more effective biofilm eradication.
Synthesis and assembly of colloidal cuboids with tunable shape biaxiality
Authors: Yang Yang , Chen Guangdong , Thanneeru Srinivas , He Jie , Liu Kun , Nie Zhihong
Published: October 2018

The design and assembly of monodisperse colloidal particles not only advances the development of functional materials, but also provides colloidal model systems for understanding phase behaviors of molecules. This communication describes the gram-scale synthesis of highly uniform colloidal cuboids with tunable dimension and shape biaxiality and their molecular mesogen-like assembly into various mesophasic structures in pristine purity. The synthesis relies on the nanoemulsion-guided generation of ammonium sulfate crystals that template the subsequent silica coating. The shape of the cuboidal particles can be tuned from square platelike, to biaxial boardlike, and to rodlike by independently controlling the length, width and thickness of the particles. We demonstrated the assembly of the cuboidal colloids into highly pure mesoscopic liquid crystal phases, including smectic A, biaxial smectic A, crystal B, discotic, and columnar phases, as well as established a correlation between mesophasic formation and colloidal biaxiality in experiments.
Network integration of multi-tumour omics data suggests novel targeting strategies
Authors: do Valle Ítalo Faria , Menichetti Giulia , Simonetti Giorgia , Bruno Samantha , Zironi Isabella , Durso Danielle Fernandes , Mombach José C. M. , Martinelli Giovanni , Castellani Gastone , Remondini Daniel
Published: October 2018

We characterize different tumour types in search for multi-tumour drug targets, in particular aiming for drug repurposing and novel drug combinations. Starting from 11 tumour types from The Cancer Genome Atlas, we obtain three clusters based on transcriptomic correlation profiles. A network-based analysis, integrating gene expression profiles and protein interactions of cancer-related genes, allows us to define three cluster-specific signatures, with genes belonging to NF-κB signaling, chromosomal instability, ubiquitin-proteasome system, DNA metabolism, and apoptosis biological processes. These signatures have been characterized by different approaches based on mutational, pharmacological and clinical evidences, demonstrating the validity of our selection. Moreover, we define new pharmacological strategies validated by in vitro experiments that show inhibition of cell growth in two tumour cell lines, with significant synergistic effect. Our study thus provides a list of genes and pathways that could possibly be used, singularly or in combination, for the design of novel treatment strategies.
Weaker plant-enemy interactions decrease tree seedling diversity with edge-effects in a fragmented tropical forest
Authors: Krishnadas Meghna , Bagchi Robert , Sridhara Sachin , Comita Liza S.
Published: October 2018

In fragmented forests, tree diversity declines near edges but the ecological processes underlying this loss of diversity remain poorly understood. Theory predicts that top-down regulation of seedling recruitment by insect herbivores and fungal pathogens contributes to maintaining tree diversity in forests, but it is unknown whether proximity to forest edges compromises these diversity-enhancing biotic interactions. Here we experimentally demonstrate that weakened activity of fungal pathogens and insect herbivores reduced seedling diversity, despite similar diversity of seed rain, during recruitment near forest edges in a human-modified tropical landscape. Only at sites farthest from forest edges (90–100 m) did the application of pesticides lower seedling diversity relative to control plots. Notably, lower seedling diversity corresponded with weaker density-dependent mortality attributable to insects and fungi during the seed-to-seedling transition. We provide mechanistic evidence that edge-effects can manifest as cryptic losses of crucial biotic interactions that maintain diversity.
Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Authors: Brochmann P. R. , Hesketh A. , Jana B. , Brodersen G. H. , Guardabassi L.
Published: October 2018

Previous studies on bacterial response to antibiotics mainly focused on susceptible strains. Here we characterized the transcriptional responses of distinct cephalosporin-resistant bacteria of public health relevance to cefotaxime (CTX), a cephalosporin widely used in clinical practice. Adaptation to therapeutic concentrations of CTX (30 µg/ml) was investigated by RNA sequencing in mid-exponential phase cultures of a methicillin-resistant Staphylococcus aureus (MRSA) and two genetically diverse E. coli producing CTX-M-15 or CMY-2 β-lactamase following genome sequencing and annotation for each strain. MRSA showed the most notable adaptive changes in the transcriptome after exposure to CTX, mainly associated with cell envelope functions. This reprogramming coincided with a transient reduction in cell growth, which also occurred in the CMY-2-producing E. coli but not in the CTX-M-15-producing strain. Re-establishment of growth in the CMY-2 producer proceeded without any notable adaptive transcriptional response, while limited reprogramming of gene transcription was observed in the CTX-M-15 producer. Our data show that the transcriptional response of CTX-resistant bacteria to CTX depends on the bacterial species, level of resistance and resistance determinant involved. Gene products induced in the presence of CTX may play an essential role for bacterial survival during therapy and merit further investigation as possible targets for potentiating CTX.
The c-Jun and JunB transcription factors facilitate the transit of classical Hodgkin lymphoma tumour cells through G1
Authors: Zhang Jingxi , Wu Zuoqiao , Savin Anton , Yang Mihye , Hsu Ying-Han R. , Jantuan Eugeniu , Bacani Julinor T. C. , Ingham Robert J.
Published: October 2018

Classical Hodgkin Lymphoma (cHL) is primarily a B cell lymphoid neoplasm and a member of the CD30–positive lymphomas. cHL and the other CD30–positive lymphomas are characterized by the elevated expression and/or constitutive activation of the activator protein-1 (AP-1) family transcription factors, c-Jun and JunB; however, the specific roles they play in the pathobiology of cHL are unclear. In this report we show that reducing either c-Jun or JunB expression with short-hairpin RNAs (shRNAs) reduced the growth of cHL cell lines in vitro and in vivo, primarily through impairing cell cycle transition through G1. We further investigated the effect of c-Jun and JunB knock-down on proliferation in another CD30–positive lymphoma, anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL). We found that JunB knock-down in most ALK+ ALCL cell lines examined also resulted in reduced proliferation that was associated with a G0/G1 cell cycle defect. In contrast, c-Jun knock-down in multiple ALK+ ALCL cell lines had no effect on proliferation. In summary, this study directly establishes that both c-Jun and JunB play roles in promoting HRS cell proliferation. Furthermore, we demonstrate there are similarities and differences in c-Jun and JunB function between cHL and ALK+ ALCL.
Substantial diagnostic impact of blood culture independent molecular methods in bloodstream infections: Superior performance of PCR/ESI-MS
Authors: Makristathis Athanasios , Harrison Nicole , Ratzinger Franz , Kussmann Manuel , Selitsch Brigitte , Forstner Christina , Hirschl Alexander M. , Burgmann Heinz
Published: October 2018

This study analyzed the performance of different molecular technologies along with blood culture (BC) in the diagnosis of bloodstream infections (BSI) in patients from internal medicine wards - including intensive care units (ICUs) - and the emergency room. Patients with systemic inflammatory response syndrome were prospectively included. BCs and EDTA whole blood were obtained simultaneously. The latter was analyzed by PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS; IRIDICA BAC BSI assay, Abbott) and by SeptiFast (Roche). Cases were classified as BSI according to adapted European Centre for Disease Prevention and Control criteria. Out of 462 analyzed episodes, 193 with valid test results fulfilled the inclusion criteria and were further evaluated. Sixty-nine (35.8%) were classified as BSI. PCR/ESI-MS showed a significantly better overall performance than BC (p = 0.004) or SeptiFast (p = 0.034). Only in patients from the ICU the performance of SeptiFast was comparable to that of PCR/ESI-MS. Mainly due to the negative effect of antimicrobial pre-treatment on BC results, the cumulative performance of each of the molecular tests with BC was significantly higher than that of BC alone (p < 0.001). SeptiFast and in particular the broad-range pathogen detection system PCR/ESI-MS proved to be an essential addition to BC-based diagnostics in BSI.
Deep learning enables automated scoring of liver fibrosis stages
Authors: Yu Yang , Wang Jiahao , Ng Chan Way , Ma Yukun , Mo Shupei , Fong Eliza Li Shan , Xing Jiangwa , Song Ziwei , Xie Yufei , Si Ke , Wee Aileen , Welsch Roy E. , So Peter T. C. , Yu Hanry
Published: October 2018

Current liver fibrosis scoring by computer-assisted image analytics is not fully automated as it requires manual preprocessing (segmentation and feature extraction) typically based on domain knowledge in liver pathology. Deep learning-based algorithms can potentially classify these images without the need for preprocessing through learning from a large dataset of images. We investigated the performance of classification models built using a deep learning-based algorithm pre-trained using multiple sources of images to score liver fibrosis and compared them against conventional non-deep learning-based algorithms - artificial neural networks (ANN), multinomial logistic regression (MLR), support vector machines (SVM) and random forests (RF). Automated feature classification and fibrosis scoring were achieved by using a transfer learning-based deep learning network, AlexNet-Convolutional Neural Networks (CNN), with balanced area under receiver operating characteristic (AUROC) values of up to 0.85–0.95 versus ANN (AUROC of up to 0.87–1.00), MLR (AUROC of up to 0.73–1.00), SVM (AUROC of up to 0.69–0.99) and RF (AUROC of up to 0.94–0.99). Results indicate that a deep learning-based algorithm with transfer learning enables the construction of a fully automated and accurate prediction model for scoring liver fibrosis stages that is comparable to other conventional non-deep learning-based algorithms that are not fully automated.
Postprandial glycaemia-lowering effect of a green tea cultivar Sunrouge and cultivar-specific metabolic profiling for determining bioactivity-related ingredients
Authors: Wasai Masafumi , Fujimura Yoshinori , Nonaka Haruna , Kitamura Ryo , Murata Motoki , Tachibana Hirofumi
Published: October 2018

Although the major green tea catechins can inhibit the activity of carbohydrate-hydrolyzing enzymes, there is a paucity of information describing the potential of other green tea ingredients and numerous green tea cultivars. Herein, we reveled that a green tea cultivar Sunrouge significantly suppressed the postprandial blood glucose level in mice. Unlike the most representative Japanese green tea cultivar, Yabukita, the suppression by Sunrouge was observed clearly during the initial period after oral dosing of starch. Sunrouge also strongly inhibited the carbohydrate-hydrolyzing enzymes α-glucosidase and α-amylase when compared with that of Yabukita and many other cultivars. Liquid chromatography–mass spectrometry (LC–MS)-based metabolic profiling (MP) of 42 Japanese green tea cultivars was performed. Multivariate statistical analysis enabled visualization of the differences among cultivars with respect to their ability to inhibit carbohydrate-hydrolyzing activities. Analysis of metabolites, contributing to the discrimination and prediction of the bioactivity of cultivars, showed that O-methylated catechins, epicatechin-3-O-(3-O-methyl) gallate (ECG3”Me) and epigallocatechin-3-O-(3-O-methyl) gallate (EGCG3”Me), were newly identified α-glucosidase inhibitors. Such ability was also observed in epigallocatechin-3-O-gallate (EGCG), epicatechin-3-O-gallate (ECG), delphinidin-3-O-glucoside and myricetin-3-O-glucoside. The amounts of these compounds in Sunrouge were higher than that in many other cultivars. These results suggest that Sunrouge has high potential for suppressing the elevation of the postprandial blood glucose level, and an MP approach may become a valuable strategy for evaluating the anti-hyperglycemic activity of green tea and for screening its active ingredients.
Phosphoinositide 3-kinase-delta could be a biomarker for eosinophilic nasal polyps
Authors: Kim Jong Seung , Jeong Jae Seok , Lee Kyung Bae , Kim So Ri , Choe Yeong Hun , Kwon Sam Hyun , Cho Seong Ho , Lee Yong Chul
Published: October 2018

Nasal polyps (NP) cause diverse clinical symptoms of chronic rhinosinusitis (CRS). Chronic inflammation of sinonasal mucosa is known to be crucial in NP formation. We aimed to define the implications of phosphoinositide 3-kinase (PI3K)-δ in nasal inflammation associated with NP by analyzing NP tissue obtained from CRS patients. Results showed that expression of p110δ, a regulatory subunit of PI3K-δ, in NP tissue was increased compared to control tissue. Increased p110δ expression was closely correlated with more severe CRS features. Interestingly, p110δ expression was increased in eosinophilic NP, which are closely related to more complicated clinical courses of the disease. Furthermore, CRS patients possessing NP with higher p110δ expression displayed more eosinophils in NP tissue and blood, higher levels of IL-5 in NP tissue, and more severe features of the disease. Therefore, PI3K-δ may contribute to the formation of NP, especially eosinophilic NP associated with more severe clinical presentations and radiological features.
Pay-off scarcity causes evolution of risk-aversion and extreme altruism
Authors: Evans R. M. L.
Published: October 2018

All organisms descend from populations with limited resources, so it is clear why evolution should select strategies that win resources at the expense of competitors. Less obvious is how altruistic behaviours evolve, whereby an individual helps others despite expense to itself. Modelling simple agents using evolutionary game theory, it is shown that steady states of extreme altruism can evolve when pay-offs are very rare compared with death. In these states, agents give away most of their wealth. A new theorem for general evolutionary models shows that, when pay-offs are rare, evolution no longer selects strategies to maximize income (average pay-off), but to minimize the risk of missing-out entirely on a rare resource. Principles revealed by the model are widely applicable, where the game represents rare life-changing events: disasters or gluts.