bluuebunny/crossref_metadata_2025 huggingface dataset:
Ship Resistance and Propulsion
Authors: Molland Anthony F. , Turnock Stephen R. , Hudson Dominic A.
Published: August 2017

This second edition provides a comprehensive and scientific approach to evaluating ship resistance and propulsion. Written by experts in the field, it includes the latest developments in CFD, experimental techniques, and guidance for the practical estimation of ship propulsive power. It addresses the increasing emphasis on improving energy efficiency and reducing emissions, including the introduction of the Energy Efficiency Design Index (EEDI). The text also includes sufficient published standard series data for hull resistance and propeller performance to enable practitioners to make ship power predictions based on material and data within the book, and numerous fully worked examples illustrate applications for cargo and container ships, tankers, bulk carriers, ferries, warships, work boats, planing craft, yachts, hydrofoils, submarines and AUVs. The book is ideal for practicing naval architects and marine engineers, sea-going officers, small craft designers, undergraduate and postgraduate students, and professionals in transportation, transport efficiency and eco-logistics.
A comprehensive regional clinical and educational ECPR protocol decreases time
to ECMO in patients with refractory out-of-hospital cardiac arrest
Authors: Grunau Brian , Carrier Sarah , Bashir Jamil , Dick William , Harris Luke , Boone Robert , Kalla Dan , Scheuermeyer Frank , Twaites Brian , Straight Ron , Abel James , McDonald Ken , MacRedmond Ruth , Agulnik David , Finkler Joe , MacLeod Jeanne , Christenson Jim , Cheung Anson
Published: August 2017

Objective

Extracorporeal membrane oxygenation within CPR (ECPR) may improve survival
for refractory out-of-hospital cardiac arrest (OHCA). We developed a
prehospital, emergency department (ED), and hospital-based clinical and
educational protocol to improve the key variable of time-to-ECPR
(TTE).

Methods

In a single urban health region we involved key prehospital, clinical, and
administrative stakeholders over a 2-year period, to develop a regional ECPR
program with destination to a single urban tertiary care hospital. We developed
clear and reproducible inclusion criteria and processes, including measures of
program efficiency. We conducted seminars and teaching modules to paramedics
and hospital-based clinicians including monthly simulator sessions, and
performed detailed reviews of each treated case in the form of report cards. In
this before-and-after study we compared patients with ECPR attempted prior to,
and after, protocol implementation. The primary outcome was TTE, defined as the
time of initial professional CPR to establishment of extracorporeal
circulation. We compared the median TTE for patients in the two groups using
the Wilcoxon signed rank test.

Results

Four patients were identified prior to the protocol and managed in an ad
hoc basis; for nine patients the protocol was utilized. Overall favourable
neurological outcomes among ECPR-treated patients were 27%. The median TTE was
136 minutes (IQR 98 - 196) in the pre-protocol group, and 60 minutes (IQR 49 -
81) minutes in the protocol group (p=0.0165).

Conclusion

An organized clinical and educational protocol to initiate ECPR for
patients with OHCA is feasible and significantly reduces the key benchmark of
time-to-ECPR flows.
Of mice and men, nature and nurture, and a few red herrings
Authors: Hauser Marc D.
Published: August 2017

Burkart et al.'s proposal is based on three false premises: (1) theories of the mind are either domain-specific/modular (DSM) or domain-general (DG); (2) DSM systems are considered inflexible, built by nature; and (3) animal minds are deemed as purely DSM. Clearing up these conceptual confusions is a necessary first step in understanding how general intelligence evolved.
The evolution of general intelligence inallanimals and machines
Authors: Holekamp Kay E. , Miikkulainen Risto
Published: August 2017

We strongly agree that general intelligence occurs in many animals but find the cultural intelligence hypothesis of limited usefulness. Any viable hypothesis explaining the evolution of general intelligence should be able to account for it in all species where it is known to occur, and should also predict the conditions under which we can develop machines with general intelligence as well.
Where is the evidence for general intelligence in nonhuman animals?
Authors: Huber Ludwig
Published: August 2017

This commentary contrasts evolutionary plausibility with empirical evidence and cognitive continuity with radiation and convergent evolution. So far, neither within-species nor between-species comparisons on the basis of rigorous experimental and species-appropriate tests substantiate the claims made in the target article. Caution is advisable on meta-analytical comparisons that primarily rely on publication frequencies and overgeneralizations (from murids and primates to other nonhuman animals).
Habit formation generates secondary modules that emulate the efficiency of evolved behavior
Authors: Nordli Samuel A. , Todd Peter M.
Published: August 2017

We discuss the evolutionary implications of connections drawn between the authors' learned “secondary modules” and the habit-formation system that appears to be ubiquitous among vertebrates. Prior to any subsequent coevolution with social learning, we suggest that aspects of general intelligence likely arose in tandem with mechanisms of adaptive motor control that rely on basal ganglia circuitry.
“Birdbrains” should not be ignored in studying the evolution of g
Authors: Pepperberg Irene M.
Published: August 2017

The authors evaluate evidence for general intelligence (g) in nonhumans but lean heavily toward mammalian data. They mention, but do not discuss in detail, evidence for g in nonmammalian species, for which substantive material exists. I refer to a number of avian studies, particularly in corvids and parrots, which would add breadth to the material presented in the target article.
General intelligence does not help us understand cognitive evolution
Authors: Shuker David M. , Barrett Louise , Dickins Thomas E. , Scott-Phillips Thom C. , Barton Robert A.
Published: August 2017

Burkart et al. conflate the domain-specificity of cognitive processes with the statistical pattern of variance in behavioural measures that partly reflect those processes. General intelligence is a statistical abstraction, not a cognitive trait, and we argue that the former does not warrant inferences about the nature or evolution of the latter.
Future directions for studying the evolution of general intelligence
Authors: Burkart Judith M. , Schubiger Michèle N. , van Schaik Carel P.
Published: August 2017

The goal of our target article was to lay out current evidence relevant to the question of whether general intelligence can be found in nonhuman animals in order to better understand its evolution in humans. The topic is a controversial one, as evident from the broad range of partly incompatible comments it has elicited. The main goal of our response is to translate these issues into testable empirical predictions, which together can provide the basis for a broad research agenda.
Excitation of terahertz radiation generation by obliquely incident beating lasers on a hot magnetized plasma with step density profile
Authors: Mann K.L. , Sajal V. , Sharma N.K.
Published: August 2017

A scheme of resonant terahertz (THz) radiation generation by non-linear beating of two lasers in hot magnetized plasma with step density profile is investigated. Beating lasers of frequency difference ω1 − ω2 ≈ ωp(~1 THz) is incident obliquely on plasma surface and exerts non-linear ponderomotive force on plasma electrons. The plasma electrons start oscillating in the plane of incidence and give rise to space charge field to maintain plasma neutrality. In turn, both ponderomotive force and space charge field excites a non-linear surface current, responsible for THz radiation generation on the reflection side. The coupling between plasma wave and electromagnetic wave present (inside the plasma as well as on reflection side) becomes stronger in the presence of the transverse DC magnetic field. THz radiation amplitude is optimized at an angle of incidence θ ~ 50–70°.
A Benchmark for Trace Greenhouse Gases in the Arctic Ocean
Authors: Cook Terri
Published: August 2017

Samples of seawater from the North American Arctic show that the region is neither a major source nor sink of methane and nitrous oxide to the overlying atmosphere.
Tracking River Flows from Space
Authors: Gleason Colin , Garambois Pierre-André , Durand Michael
Published: August 2017

Satellite observations, combined with algorithms borrowed from river engineering, could fill large gaps in our knowledge of global river flows where field data are lacking.
A Test Bed for Coastal and Ocean Modeling
Authors: Luettich Jr. Richard , Wright L. , Nichols C. , Baltes Rebecca , Friedrichs Marjorie , Kurapov Alexander , van der Westhuysen Andre , Fennel Katja , Howlett Eoin
Published: August 2017

An ocean modeling program is improving our ability to predict circulation along the U.S. West Coast, dead zones and other coastal ecosystem responses, and storm surges in island environments.
2017 Class of AGU Fellows Announced
Authors: Davidson Eric , Mukasa Samuel
Published: August 2017

The American Geophysical Union is proud to have chosen 61 new Fellows and will honor them at the upcoming 2017 Fall Meeting in New Orleans.
Storm Model Foresaw Tornado Precursor Hours Before Twister Hit
Authors: Cartier Kimberly
Published: August 2017

The experimental Warn-on-Forecast project calculates probabilities of severe weather within at-risk areas smaller than those targeted by current forecasting models.
The Future Hangs in the (Carbon) Balance
Authors: Lunn Jenny
Published: August 2017

A new study suggests that Canada’s boreal forests could absorb more carbon than they release as climate change progresses.
Follow Earthworm Tracks to Better Simulate Water Flow in Soils
Authors: Stanley Sarah
Published: August 2017

Incorporating paths carved by the critters and by tree roots helps scientists align simulations of tropical soils more closely with real-world data.
Blending Satellite Data to Monitor Agricultural Water Use
Authors: Cook Terri
Published: August 2017

A new technique that merges data gathered by multiple satellites can be used to monitor agricultural water use and improve water quality assessments around the globe.
Red/Blue and Peer Review
Authors: Davidson Eric , McNutt Marcia
Published: August 2017

Healthy skepticism has long formed the foundation of the scientific peer review process. Will anything substantively new be gleaned from a red team/blue team exercise?
A Closer Look at an Undersea Source of Alaskan Earthquakes
Authors: Brothers Daniel , Haeussler Peter , East Amy , ten Brink Uri , Andrews Brian , Dartnell Peter , Miller Nathan , Kluesner Jared
Published: August 2017

A systematic survey offers a striking portrait of movement along a 500-kilometer-long undersea section of the Queen Charlotte–Fairweather fault off the coast of southeastern Alaska.
Erratum: Docosahexaenoic acid enrichment in NAFLD is associated with improvements in hepatic metabolism and hepatic insulin sensitivity: a pilot study
Authors: Hodson L , Bhatia L , Scorletti E , Smith D E , Jackson N C , Shojaee-Moradie F , Umpleby M , Calder P C , Byrne C D
Published: August 2017

Correction to: European Journal of Clinical Nutrition (2017) 71, 973–979; doi:10.1038/ejcn.2017.9; published online 15 March 2017 Updated online 16 August 2017: This article was originally published under a standard EJCN license, but has now been made available under a CC BY 4.0 license. The PDF andHTML versions of the paper have been modified accordingly.
Interleukin‐7 in the transition of bone marrow progenitors to the thymus
Authors: Plumb Adam W , Sheikh Abdalla , Carlow Douglas A , Patton Daniel T , Ziltener Hermann J , Abraham Ninan
Published: August 2017

Interleukin‐7 (IL‐7) is essential for the development of T cells in humans and mice where deficiencies in IL‐7 signaling result in severe immunodeficiency. T cells require IL‐7 at multiple points during development; however, it is unclear when IL‐7 is first necessary. We observed that mice with impaired IL‐7 signaling had a large reduction in the number of early thymic progenitors (ETPs) while mice that overexpress IL‐7 had greatly increased numbers of ETPs. These results indicated that the development of ETPs is sensitive to IL‐7. Bone marrow progenitors of ETP are present in normal numbers in mice with impaired IL‐7 signaling (IL‐7Rα449F) and were efficiently recruited to the thymus. Furthermore, ETPs and their progenitors from IL‐7Rα449F mice did not undergo increased apoptosis and proliferate normally compared to WT cells. Mixed bone marrow chimeras demonstrated that IL‐7 signaling has a cell‐intrinsic role in ETP development but was not required for development of bone marrow progenitors. We have shown a novel role for IL‐7 signaling in the development of ETPs that is distinct from classic mechanisms of IL‐7 regulating survival and proliferation.
Whi7 is an unstable cell-cycle repressor of the Start transcriptional program
Authors: Gomar-Alba Mercè , Méndez Ester , Quilis Inma , Bañó M. Carmen , Igual J. Carlos
Published: August 2017

Start is the main decision point in eukaryotic cell cycle in which cells commit to a new round of cell division. It involves the irreversible activation of a transcriptional program by G1 CDK-cyclin complexes through the inactivation of Start transcriptional repressors, Whi5 in yeast or Rb in mammals. Here we provide novel keys of how Whi7, a protein related at sequence level to Whi5, represses Start. Whi7 is an unstable protein, degraded by the SCFGrr1 ubiquitin-ligase, whose stability is cell cycle regulated by CDK1 phosphorylation. Importantly, Whi7 associates to G1/S gene promoters in late G1 acting as a repressor of SBF-dependent transcription. Our results demonstrate that Whi7 is a genuine paralog of Whi5. In fact, both proteins collaborate in Start repression bringing to light that yeast cells, as occurs in mammalian cells, rely on the combined action of multiple transcriptional repressors to block Start transition.
Electrical control of the anomalous valley Hall effect in antiferrovalley bilayers
Authors: Tong Wen-Yi , Duan Chun-Gang
Published: August 2017

In analogy to all-electric spintronics, all-electric valleytronics, i.e., valley manipulation via electric means, becomes an exciting new frontier as it may bring revolutions in the field of data storage with ultra-high speed and ultra-low power consumption. The existence of the anomalous valley Hall effect in ferrovalley materials demonstrates the possibility of electrical detection for valley polarization. However, in previously proposed valley-polarized monolayers, the anomalous valley Hall effect is controlled by external magnetic fields. Here, through elaborate structural design, we propose the antiferrovally bilayer as an ideal candidate for realizing all-electric valleytronic devices. Using the minimal k·p model, we show that the energy degeneracy between valley indexes in such system can be lifted by electric approaches. Subsequently, the anomalous valley Hall effect strongly depends on the electric field as well. Taking the bilayer VSe2 as an example, all-electric tuning and detecting of anomalous valley Hall effect is confirmed by density-functional theory calculations, indicating that the valley information in such antiferrovalley bilayer can be reversed by an electric field perpendicular to the plane of the system and easily probed through the sign of the Hall voltage.
Discovery from a large-scaled survey of Trichoderma in soil of China
Authors: Chen Kai , Zhuang Wen-Ying
Published: August 2017

The first large-scaled survey of soil-inhabiting Trichoderma is conducted in 23 provinces of China. Twenty-three new species belonging to the green-ascospored clades are discovered. Their phylogenetic positions are determined by sequence analyses of the combined partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit encoding genes. Morphology and culture characteristics are observed, described and illustrated in detail. Distinctions between the new species and their close relatives are compared and discussed. They are named as: T. aggregatum, T. alpinum, T. bannaense, T. breve, T. brevicrassum, T. byssinum, T. chlamydosporicum, T. concentricum, T. ganodermatis, T. hainanense, T. hengshanicum, T. hirsutum, T. hunanense, T. ingratum, T. liberatum, T. linzhiense, T. longisporum, T. polypori, T. pseudodensum, T. simplex, T. solum, T. undatipile and T. zayuense.
Morph specific foraging behavior by a polymorphic raptor under variable light conditions
Authors: Tate Gareth J , Amar Arjun
Published: August 2017

Colour polymorphism may be maintained within a population by disruptive-selection. One hypothesis proposes that different morphs are adapted to different ambient light conditions, with lighter morphs having a selective advantage in bright conditions and darker morphs having advantages in darker conditions. The mechanism for this advantage is proposed to be through enhanced crypsis via background-matching. We explore this hypothesis in a polymorphic raptor, the black sparrowhawk Accipiter melanoleucus, which exhibits a discrete dark and white-morph. We use GPS-tracking data to contrast the foraging behaviour and habitat selection of morphs. As predicted, we found that light-levels influenced foraging behaviour in different ways for morphs: Dark-morphs showed a decrease in foraging with increasing light-levels; whereas no relationship was found for white-morphs. Furthermore, we found differential-degrees of habitat selection, with dark-morphs selecting more enclosed habitats compared to white-morphs. This suggests that different morphs may be better adapted to foraging under different light-conditions, potentially playing a role in maintaining colour polymorphism in this species. Our results may also help explain why dark-morphs predominate in this study region, which experiences high rainfall and lower light-levels during the breeding-period. This study suggests that avian morphs may allocate/partition foraging activity by weather conditions/habitat, which maximise their concealment from prey.
A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species
Authors: van Dam Peter , Fokkens Like , Ayukawa Yu , van der Gragt Michelle , ter Horst Anneliek , Brankovics Balázs , Houterman Petra M. , Arie Tsutomu , Rep Martijn
Published: August 2017

The genome of Fusarium oxysporum (Fo) consists of a set of eleven ‘core’ chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, and a chromosome that shows all the hallmarks of a pathogenicity chromosome comprised two contigs. A central part of this chromosome contains all identified candidate effector genes, including homologs of SIX6, SIX9, SIX11 and SIX13. We show that SIX6 contributes to virulence of Forc. Through horizontal chromosome transfer (HCT) to a non-pathogenic strain, we also show that the accessory chromosome containing the SIX gene homologs is indeed a pathogenicity chromosome for cucurbit infection. Conversely, complete loss of virulence was observed in Forc016 strains that lost this chromosome. We conclude that also a non-wilt-inducing Fo pathogen relies on effector proteins for successful infection and that the Forc pathogenicity chromosome contains all the information necessary for causing root rot of cucurbits. Three out of nine HCT strains investigated have undergone large-scale chromosome alterations, reflecting the remarkable plasticity of Fo genomes.
Unilateral stimulation of the lateral division of the dorsal telencephalon induces synaptic plasticity in the bilateral medial division of zebrafish
Authors: Wu Yao-Ju , Chen Yu-Lan , Tang Tso-Hao , Ng Ming-Chong , Amstislavskaya Tamara G. , Tikhonova Maria A. , Yang Yi-Ling , Lu Kwok-Tung
Published: August 2017

This study was aimed to evaluate the synaptic plasticity in projections from the dorsal lateral region (Dl) to the bilateral dorsal medial region (Dm) of the zebrafish telencephalon. The results showed that unilateral electrical stimulation of the Dl evokes a negative field potential (FP) in both the contralateral and ipsilateral side of the Dm. We tested synaptic plasticity, including high-frequency stimulation-induced LTP (HFS-LTP) and low-frequency stimulation-induced LTD (LFS-LTD). We demonstrated that HFS-induced bilateral LTP is NMDAR-dependent by the application of an NMDAR antagonist, DL-AP5 (30 μM, suprafused for 10 min), which blocked the HFS-induced LTP in both the contralateral and ipsilateral Dm. In addition, LTP was restored after DL-AP5 was washed out by continuous aCSF suprafusion. These results suggested that the potentiation is NMDAR-dependent. Either LFS (1 Hz for 20 min) or applying the mGluR agonist, DHPG (40 μM, suprafused for 10 min) successfully induced bilateral LTD for at least 1 h. Furthermore, both the contralateral fEPSP and LTP vanished after ablation of the anterior commissure. In conclusion, the results of the present study suggested that the projection between the Dl and contralateral Dm in the telencephalon of zebrafish is via the anterior commissure and possesses synaptic plasticity.
The influence of attention and reward on the learning of stimulus-response associations
Authors: Vartak Devavrat , Jeurissen Danique , Self Matthew W. , Roelfsema Pieter R.
Published: August 2017

We can learn new tasks by listening to a teacher, but we can also learn by trial-and-error. Here, we investigate the factors that determine how participants learn new stimulus-response mappings by trial-and-error. Does learning in human observers comply with reinforcement learning theories, which describe how subjects learn from rewards and punishments? If yes, what is the influence of selective attention in the learning process? We developed a novel redundant-relevant learning paradigm to examine the conjoint influence of attention and reward feedback. We found that subjects only learned stimulus-response mappings for attended shapes, even when unattended shapes were equally informative. Reward magnitude also influenced learning, an effect that was stronger for attended than for non-attended shapes and that carried over to a subsequent visual search task. Our results provide insights into how attention and reward jointly determine how we learn. They support the powerful learning rules that capitalize on the conjoint influence of these two factors on neuronal plasticity.
Corrosion resistance and bioactivity enhancement of MAO coated Mg alloy depending on the time of hydrothermal treatment in Ca-EDTA solution
Authors: Kim Seo-Young , Kim Yu-Kyoung , Ryu Moon-Hee , Bae Tae-Sung , Lee Min-Ho
Published: August 2017

In this study, a two-step surface treatment was developed to restrain the rapid primary degradation of a biodegradable Mg alloy and to improve their biocompatibility. Micro arc oxidation (MAO) coating was performed in alkaline electrolytes such as 1.0 M NaOH with 0.1 M glycerol and 0.1 M Na3PO4. Hydrothermal treatment was performed in 0.1 M Ca-EDTA (C10H12CaN2Na2O8) and 0.5 M NaOH solution at 90 °C for different times (6, 12, 24, and 48 h). The film morphology and chemical properties were evaluated by XRD and FE-SEM. The electrochemical and corrosion behaviors were examined in the simulated body fluid, and cytotoxicity was assessed using MC3T3-E1 cells. After MAO coating, an oxide layer containing $${\bf{P}}{{\bf{O}}}_{4}^{3-}$$
P

O

4

3
−

formed on the surface. During the hydrothermal treatment in Ca-EDTA solution, calcium phosphate and Mg(OH)2 were produced via a reaction between $${\bf{P}}{{\bf{O}}}_{4}^{3-}$$
P

O

4

3
−

on the surface and Ca2+ in solution. The layer with ceramics and oxides was grown on the surface with increasing hydrothermal treatment time, and improved the surface corrosion resistance. The 24 h hydrothermal-treated group showed the lowest immersion corrosion rate and high cell viability. Therefore, this treatment was the most favorable surface modification for improving the initial corrosion resistance and bioactivity of the biodegradable Mg alloy.
Extracellular redox sensitivity of Kv1.2 potassium channels
Authors: Baronas Victoria A. , Yang Runying Y. , Kurata Harley T.
Published: August 2017

Kv1.2 is a prominent potassium channel subtype in the nervous system and serves as an important structural template for investigation of ion channel function. However, Kv1.2 voltage-dependence exhibits dramatic cell-to-cell variability due to a gating mode shift that is regulated by an unknown mechanism. We report that this variable behavior is regulated by the extracellular redox environment. Exposure to reducing agents promotes a shift in gating properties towards an ‘inhibited’ gating mode that resists opening, and causes channels to exhibit pronounced use-dependent activation during trains of repetitive depolarizations. This sensitivity to extracellular redox potential is absent in other Kv1 channels, but is apparent in heteromeric channels containing Kv1.2 subunits, and overlaps with the reported physiological range of extracellular redox couples. Mutagenesis of candidate cysteine residues fails to abolish redox sensitivity. Therefore, we suggest that an extrinsic, redox-sensitive binding partner imparts these properties.
Seasonal singing of a songbird living near the equator correlates with minimal changes in day length
Authors: Quispe Rene , Protazio João Marcelo Brazão , Gahr Manfred
Published: August 2017

Behaving in accordance with natural cycles is essential for survival. Birds in the temperate regions use the changes of day length to time their behavior. However, at equatorial latitudes the photoperiod remains almost constant throughout the year, and it is unclear which cues songbirds use to regulate behaviors, such as singing. Here, we investigated the timing of dawn-song of male silver-beaked tanagers in the equatorial lowland Amazonas over two years. In this region, birds experience around nine minutes of annual day length variation, with sunrise times varying by 32 minutes over the year. We show that the seasonal timing of dawn-song was highly regular between years, and was strongly correlated with slight increases in day length. During the singing season the daily dawn-song onset was precisely aligned to variations in twilight time. Thus, although photoperiodic changes near the equator are minimal, songbirds can use day length variation to time singing.
Simulation of Quantum Dynamics of Excitonic Systems at Finite Temperature: an efficient method based on Thermo Field Dynamics
Authors: Borrelli Raffaele , Gelin Maxim F.
Published: August 2017

Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on Thermo Field Dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. The solution of Thermo Field Dynamics equations with a novel technique for the propagation of Tensor Trains (Matrix Product States) is implemented and discussed. The methodology is applied to the study of the exciton dynamics in the Fenna-Mathews-Olsen complex using a realistic structured spectral density to model the electron-phonon interaction. The results of the simulations highlight the effect of specific vibrational modes on the exciton dynamics and energy transfer process, as well as call for careful modeling of electron-phonon couplings.
Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein
Authors: Lourenço José , Watkins Eleanor R. , Obolski Uri , Peacock Samuel J. , Morris Callum , Maiden Martin C. J. , Gupta Sunetra
Published: August 2017

Populations ofStreptococcus pneumoniae(SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of thegroESLoperon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions betweengroESLand a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
Photo-flocculation of microbial mat extracellular polymeric substances and their transformation into transparent exopolymer particles: Chemical and spectroscopic evidences
Authors: Shammi Mashura , Pan Xiangliang , Mostofa Khan M. G. , Zhang Daoyong , Liu Cong-Qiang
Published: August 2017

Upon exposure to sunlight extracellular polymeric substances (EPS) were partially transformed into transparent exopolymer particles (TEP) and unstable flocs of different sizes without the addition of any precursors. Parallel factor (PARAFAC) modelling of the sample fluorescence spectra identified humic-like and protein-like or tyrosine-like components in both untreated and irradiated EPS samples. After 58 hours of solar irradiation, humic-like substances were entirely decomposed, while the regenerated protein-like substance from EPS was the key component in the irradiated samples. Degradation and reformation of EPS occurred which was confirmed by the results of size exclusion chromatography, dissolved organic carbon, total protein and total polysaccharide analyses. Irradiated EPS was composed of –COOH or C = O (amide I band) and –NH and –CN (amide II band), while Fourier transform infrared spectroscopy (FTIR) of TEP revealed more acidic –COOH and –C–O groups, indicating typical acidic protein-like TEP. The regenerated protein-like substances could form complexes with free metals originating from degraded EPS in irradiated samples, which could be responsible for the formation of TEP/floc in the aqueous media. These results suggest that TEP/floc formation from EPS could occur by a complexation mechanism between dissolved organic matter and metals, thereby causing ionic charge neutralisation upon sunlight exposure.
Accelerating next generation sequencing data analysis with system level optimizations
Authors: Kathiresan Nagarajan , Temanni Ramzi , Almabrazi Hakeem , Syed Najeeb , Jithesh Puthen V. , Al-Ali Rashid
Published: August 2017

Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default ’on-demand’ mode of CPU frequency is over-clocked by using ’performance-mode’ to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.
Evaluation of the new Chinese Disseminated Intravascular Coagulation Scoring System in critically ill patients: A multicenter prospective study
Authors: Wu Yingying , Luo Lili , Niu Ting , Han Yue , Feng Ying , Ding Qiulan , Huang Ruibin , Zhang Xiaohui , Feng Jianming , Hou Ming , Peng Jun , Li Yan , Zhou Yuhong , Su Lei , Yang Linhua , Zhou Zeping , Xue Feng , Gu Jian , Zhu Tienan , Wang Xiaomin , Deng Jun , Mei Heng , Hu Yu
Published: August 2017

Disseminated intravascular coagulation (DIC) is a common life-threatening complication in critically ill patients. The diagnostic scoring systems of DIC enable a more prompt and accurate diagnosis of DIC, such as the International Society on Thrombosis and Haemostasis (ISTH), the Japanese Association for Acute Medicine (JAAM) and the Japanese Ministry of Health and Welfare (JMHW). This study prospectively evaluated the newly proposed Chinese DIC Scoring System (CDSS), which was conducted at 18 centers in China during a one-year period. Receiver operating characteristic (ROC) curves showed that, for diagnosis of DIC and for prediction of the 28-day all-cause mortality, the CDSS had larger areas under the ROC curve (AUCs) than the ISTH and the JAAM in different groups. The CDSS also had larger AUC than the JMHW for the ISTH DIC in non-infectious diseases. All of the AUCs of the CDSS were greater than 0.8, accompanied with both high sensitivity and high specificity. Furthermore, the CDSS score was an independent predictor of mortality (odds ratio, 1.882; p < 0.001), and could reflect the illness severity (p < 0.001 for Spearman’s rank correlations with the scores of severity). In conclusion, the CDSS is worthy of promotion with a better diagnostic and prognostic value for DIC.
Serum and urine 1H NMR-based metabolomics in the diagnosis of selected thyroid diseases
Authors: Wojtowicz Wojciech , Zabek Adam , Deja Stanislaw , Dawiskiba Tomasz , Pawelka Dorota , Glod Mateusz , Balcerzak Waldemar , Mlynarz Piotr
Published: August 2017

Early detection of nodular thyroid diseases including thyroid cancer is still primarily based on invasive procedures such as fine-needle aspiration biopsy. Therefore, there is a strong need for development of new diagnostic methods that could provide clinically useful information regarding thyroid nodular lesions in a non-invasive way. In this study we investigated 1H NMR based metabolic profiles of paired urine and blood serum samples, that were obtained from healthy individuals and patients with nodular thyroid diseases. Estimation of predictive potential of metabolites was evaluated using chemometric methods and revealed that both urine and serum carry information sufficient to distinguish between patients with nodular lesions and healthy individuals. Data fusion allowed to further improve prediction quality of the models. However, stratification of tumor types and their differentiation in relation to each other was not possible.
Growth differentiation factor 15 promotes blood vessel growth by stimulating cell cycle progression in repair of critical-sized calvarial defect
Authors: Wang Shaoyi , Li Mengyu , Zhang Wenjie , Hua Hongfei , Wang Ningtao , Zhao Jun , Ge Jing , Jiang Xinquan , Zhang Zhiyuan , Ye Dongxia , Yang Chi
Published: August 2017

Repair of large bone defects remains a challenge for surgeons, tissue engineering represents a promising approach. However, the use of this technique is limited by delayed vascularization in central regions of the scaffold. Growth differentiation factor 15(GDF15) has recently been reported to be a potential angiogenic cytokine and has an ability to promote the proliferation of human umbilical vein endothelial cells(HUVECs). Whether it can be applied for promoting vascularized bone regeneration is still unknown. In this study, we demonstrated that GDF15 augmented the expression of cyclins D1 and E, induced Rb phosphorylation and E2F-1 nuclear translocation, as well as increased HUVECs proliferation. Furthermore, we also observed that GDF15 promoted the formation of functional vessels at an artificially-induced angiogenic site, and remarkably improved the healing in the repair of critical-sized calvarial defects. Our results confirm the essential role of GDF15 in angiogenesis and suggest its potential beneficial use in regenerative medicine.
Exploration of the Brain in Rest: Resting-State Functional MRI Abnormalities in Patients with Classic Galactosemia
Authors: van Erven Britt , Jansma Bernadette M. , Rubio-Gozalbo M. Estela , Timmers Inge
Published: August 2017

Patients with classic galactosemia, a genetic metabolic disorder, encounter cognitive impairments, including motor (speech), language, and memory deficits. We used functional magnetic resonance imaging to evaluate spontaneous functional connectivity during rest to investigate potential abnormalities in neural networks. We characterized networks using seed-based correlation analysis in 13 adolescent patients and 13 matched controls. Results point towards alterations in several networks, including well-known resting-state networks (e.g. default mode, salience, visual network). Particularly, patients showed alterations in networks encompassing medial prefrontal cortex, parietal lobule and (pre)cuneus, involved in spatial orientation and attention. Furthermore, altered connectivity of networks including the insula and superior frontal gyrus -important for sensory-motor integration and motor (speech) planning- was demonstrated. Lastly, abnormalities were found in networks involving occipital regions, linked to visuospatial capacities and working memory. Importantly, across several seeds, altered functional connectivity to the superior frontal cortex, anterior insula, parietal lobule and the (pre)cuneus was observed in patients, suggesting special importance of these brain regions. Moreover, these alterations correlated with neurocognitive test results, supporting a relation with the clinical phenotype. Our findings contribute to improved characterization of brain impairments in classic galactosemia and provide directions for further investigations.
RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis
Authors: Cui Xiaogang , Marshall Brett , Shi Ning , Chen Shi-You , Rekaya Romdhane , Liu Hong-Xiang
Published: August 2017

RNA-Seq is a powerful tool in transcriptomic profiling of cells and tissues. We recently identified many more taste buds than previously appreciated in chickens using molecular markers to stain oral epithelial sheets of the palate, base of oral cavity, and posterior tongue. In this study, RNA-Seq was performed to understand the transcriptomic architecture of chicken gustatory tissues. Interestingly, taste sensation related genes and many more differentially expressed genes (DEGs) were found between the epithelium and mesenchyme in the base of oral cavity as compared to the palate and posterior tongue. Further RNA-Seq using specifically defined tissues of the base of oral cavity demonstrated that DEGs between gustatory (GE) and non-gustatory epithelium (NGE), and between GE and the underlying mesenchyme (GM) were enriched in multiple GO terms and KEGG pathways, including many biological processes. Well-known genes for taste sensation were highly expressed in the GE. Moreover, genes of signaling components important in organogenesis (Wnt, TGFβ/ BMP, FGF, Notch, SHH, Erbb) were differentially expressed between GE and GM. Combined with other features of chicken taste buds, e.g., uniquely patterned array and short turnover cycle, our data suggest that chicken gustatory tissue provides an ideal system for multidisciplinary studies, including organogenesis and regenerative medicine.
Dynamics and detection of the Newton-Wigner time delays at interfaces using a swivelling method
Authors: Floch Albert Le , Emile Olivier , Ropars Guy , Agrawal Govind P.
Published: August 2017

Evanescent waves are ubiquitous at interfaces with optical, seismic or acoustic waves, and also with electron, neutron or atom beams. Newton was the first to suspect that both small time delays and spatial shifts exist during total internal reflection. However, these effects are so tiny that the spatial shifts were only observed in 1947 in optics, whereas the time delay values predicted by the Wigner model in the 10−14 s range in optics had to await femtosecond lasers to be detected with difficulty. The spatial shifts have been isolated in many areas but the time delays, though fundamental, generally remain out of reach, particularly with particles. In textbooks usually both quantities are supposed to be simply linked. Here we report, using swivelling detectors, that the spatial and temporal measurements are intimately intermingled, especially in the so-called cyclical regime. Indeed, while the spatial shift does not depend on the type of detection, the measured time delay can be positive, negative or zero, but controllable. We also discuss how such intricate measurements of spatial and temporal effects allow crucial time penalties to be eliminated in guided soliton propagation, and should be used to unambiguously identify the Newton-Wigner time delays for particles.
RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout
Authors: Paneru Bam Dev , Al-Tobasei Rafet , Kenney Brett , Leeds Timothy D. , Salem Mohamed
Published: August 2017

The role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes. Ninety microRNAs showed differential expression between families with divergent phenotypes, and their expression was strongly associated with variation in phenotypes. A total of 204 single nucleotide polymorphisms (SNPs) present in 3′ UTR of target genes either destroyed or created novel illegitimate microRNA target sites; of them, 78 SNPs explained significant variation in the aforementioned 5 muscle traits. Majority of the phenotype-associated SNPs were present in microRNA-binding sites of genes involved in energy metabolism and muscle structure. These findings suggest that variation in microRNA expression and/or sequence variation in microRNA binding sites in target genes play an important role in mediating differences in fish growth and muscle quality phenotypes.
GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana
Authors: Ramegowda Venkategowda , Gill Upinder Singh , Sivalingam Palaiyur Nanjappan , Gupta Aarti , Gupta Chirag , Govind Geetha , Nataraja Karaba N. , Pereira Andy , Udayakumar Makarla , Mysore Kirankumar S. , Senthil-Kumar Muthappa
Published: August 2017

Drought transcriptome analysis of finger millet (Eleusine coracana) by cDNA subtraction identified drought responsive genes that have a potential role in drought tolerance. Through virus-induced gene silencing (VIGS) in a related crop species, maize (Zea mays), several genes, including a G-BOX BINDING FACTOR 3 (GBF3) were identified as candidate drought stress response genes and the role of GBF3 in drought tolerance was studied in Arabidopsis thaliana. Overexpression of both EcGBF3 and AtGBF3 in A. thaliana resulted in improved tolerance to osmotic stress, salinity and drought stress in addition to conferring insensitivity to ABA. Conversely, loss of function of this gene increased the sensitivity of A. thaliana plants to drought stress. EcGBF3 transgenic A. thaliana results also suggest that drought tolerance of sensitive plants can be improved by transferring genes from far related crops like finger millet. Our results demonstrate the role of GBF3 in imparting drought tolerance in A. thaliana and indicate the conserved role of this gene in drought and other abiotic stress tolerance in several plant species.
Naturally acquired antibody response to Plasmodium falciparum describes heterogeneity in transmission on islands in Lake Victoria
Authors: Idris Zulkarnain Md , Chan Chim W. , Kongere James , Hall Tom , Logedi John , Gitaka Jesse , Drakeley Chris , Kaneko Akira
Published: August 2017

As markers of exposure anti-malaria antibody responses can help characterise heterogeneity in malaria transmission. In the present study antibody responses to Plasmodium falciparum AMA-1, MSP-119 and CSP were measured with the aim to describe transmission patterns in meso-endemic settings in Lake Victoria. Two cross-sectional surveys were conducted in Lake Victoria in January and August 2012. The study area comprised of three settings: mainland (Ungoye), large island (Mfangano) and small islands (Takawiri, Kibuogi, Ngodhe). Individuals provided a finger-blood sample to assess malaria infection by microscopy and PCR. Antibody response to P. falciparum was determined in 4,112 individuals by ELISA using eluted dried blood from filter paper. The overall seroprevalence was 64.0% for AMA-1, 39.5% for MSP-119, and 12.9% for CSP. Between settings, seroprevalences for merozoite antigens were similar between Ungoye and Mfangano, but higher when compared to the small islands. For AMA-1, the seroconversion rates (SCRs) ranged from 0.121 (Ngodhe) to 0.202 (Ungoye), and were strongly correlated to parasite prevalence. We observed heterogeneity in serological indices across study sites in Lake Victoria. These data suggest that AMA-1 and MSP-119 sero-epidemiological analysis may provide further evidence in assessing variation in malaria exposure and evaluating malaria control efforts in high endemic area.
How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study
Authors: Kong Xiaotian , Sun Huiyong , Pan Peichen , Li Dan , Zhu Feng , Chang Shan , Xu Lei , Li Youyong , Hou Tingjun
Published: August 2017

Janus kinase 2 (JAK2) has been regarded as an essential target for the treatment of myeloproliferative neoplasms (MPNs). BBT594 and CHZ868, Type-II inhibitors of JAK2, illustrate satisfactory efficacy in preclinical MPNs and acute lymphoblastic leukemia (ALL) models. However, the L884P mutation of JAK2 abrogates the suppressive effects of BBT594 and CHZ868. In this study, conventional molecular dynamics (MD) simulations, umbrella sampling (US) simulations and MM/GBSA free energy calculations were employed to explore how the L884P mutation affects the binding of BBT594 and CHZ868 to JAK2 and uncover the resistance mechanism induced by the L884P mutation. The results provided by the US and MD simulations illustrate that the L884P mutation enhances the flexibility of the allosteric pocket and alters their conformations, which amplify the conformational entropy change (−TΔS) and weaken the interactions between the inhibitors and target. Additionally, the structural analyses of BBT594 and CHZ868 in complex with the WT JAK2 illustrate that the drug tail with strong electronegativity and small size located in the allosteric pocket of JAK2 may enhance anti-resistance capability. In summary, our results highlight that both of the changes of the conformational entropies and enthalpies contribute to the L884P-induced resistance in the binding of two Type-II inhibitors into JAK2 kinase.