bluuebunny/crossref_metadata_2025 huggingface dataset:
High mobility sputtered InSb film by blue laser diode annealing
Authors: Koswaththage C. J. , Higashizako T. , Okada T. , Sadoh T. , Furuta M. , Bae B. S. , Noguchi T.
Published: April 2019

InSb thin film was deposited on glass by r.f. sputtering using the InSb (atomic ratio of 1:1) target. The film was capped by SiO2 film to prevent the effusion of Sb of low melting point. After that, blue laser beam at 445 nm of controlled power density was irradiated using CW scanning mode. The film was crystalized successfully with keeping the ratio of In and Sb as (1:1). High electron Hall mobility of 1,050 cm2/(Vs) was obtained without degrading under glass. New device applications such as magnetic or infrared sensor system with poly Si TFTs are expected not only on glass but also on flexible panel such as on plastic sheet.
Unsteady MHD slip flow of a ferrofluid over an impulsively stretched vertical surface
Authors: EL-Kabeir S. M. M. , EL-Zahar E. R. , Modather M. , Gorla R. S. R. , Rashad A. M.
Published: April 2019

Investigation of unsteady magnetohydrodynamic (MHD) mixed convective ferrofluid flow over an impulsively stretchable surface is modeled with convective boundary conditions and partial slip impacts. Employing a finite-difference method, the governing non-similar equations are solved computationally. The sway of different considerable parameters on flow and heat transfer are demonstrated in graphical forms and discussed. The results show that the increment in the volume fraction leads to decrease the velocity and the temperature as well as the skin-friction coefficient and Nusselt number. Moreover, in the assisting flow case both the velocity and skin friction coefficient increase as Biot number increases, while they have the opposite behaviour in the opposing flow case. Also, both the temperature and local Nusselt number increase as Biot number increases for assisting and opposing flows.
Fracture characteristics of dissimilar electron-beam welded joints between Cr-Mo steel and austenitic steel AISI 304
Authors: Fouad Yasser , Marouani H.
Published: April 2019

The mechanical and fracture behaviors of electron-beam welded (EBW) joints between Cr-Mo steel (CS) and austenitic stainless steel type AISI 304 (SS) were investigated. A double notch was created at the middle of the weld area with three different notch depth (D) to weld metal width (2W) ratios, D/W = 0.33, 0.42, and 0.5, to study the strength of weld metal compared to that of CS. The weld metal and heat-affected zones (HAZs) were found to be free of defects. The interface region show that Cr23C6 was formed on the stainless steel side, while a martensitic structure was formed on the Cr-Mo steel side. The hardness of the weld metal was higher than that of the rest of the weld metal and the HAZs. Furthermore, the stress concentration (D/W = 0.33) was insufficient to initiate the crack at the notch root, i.e., the strength of CS was lower than that of weld metal with this defect.
Record combination fmax · Vbr of 25 THz·V in AlGaN/GaN HEMT with plasma treatment
Authors: Mi Min-Han , Ma Xiao-Hua , Yang Ling , Lu Yang , Hou Bin , Zhang Meng , Zhang Heng-Shuang , Wu Sheng , Hao Yue
Published: April 2019

A combination of high maximum oscillation frequency (fmax) and breakdown voltage (Vbr) was achieved in AlGaN/GaN high electron mobility transistors (HEMTs) with N2O plasma treatment on the access region. The breakdown voltage is improved from 37 V to 80 V due to the formation of oxide layer in the gate region. A suppressed current collapse is obtained due to plasma treatment on the gate-source and the gate-drain regions. The effect of the present passivation method is almost the same with that of the conventional SiN passivation method, meanwhile it can avoid introducing additional parasitic capacitance due to thinner thickness. The small signal measurement shows that HEMT can yield fT and fmax of 98 and 322 GHz, respectively, higher than that of 70 and 224 GHz for the non-treated HEMT. By using the plasma treatment technique, the HEMT can simultaneously exhibit high fmax and Vbr with a record fmax⋅Vbr of 25 THz⋅V.
Differential reflectance contrast technique in near field limit: Application to graphene
Authors: Lastras-Martínez L. F. , Medina-Escobedo D. , Flores-Rangel G. , Balderas-Navarro R. E. , Ruiz-Cigarrillo O. , Castro-García R. , Morales-Morelos M. del P. , Ortega-Gallegos J. , Losurdo M.
Published: April 2019

We report on differential reflectance contrast (DRC) sub-microscopic images measured of graphene layers exfoliated on a SiO2/Si substrate by using a near field scanning optical microscope (NSOM) with a spatial resolution of 40 nm. In general, high-quality mechanically exfoliated graphene flakes have sizes of some micrometers and exhibit a distribution of different thicknesses; thus an approach to characterize the topography of the flakes in the sub-micrometric regime is fundamental. DRC in the near field limit is a very useful technique to characterize the flakes in the sub-microscopic scale. The DRC signal is obtained by taking the numerical difference between the reflectivity coming from a region with no graphene (substrate) and a region containing a graphene layer. It is shown by a multiple reflection model (graphene/SiO2/Si) and spectroscopic ellipsometry measurements that the optical contrast in such system can be modulated by changing the thickness of the SiO2 layer or/and the wavelength of the incident light. The results open the possibility to use this optical technique for the thicknesses characterization in the sub-micrometer scale of 2D materials.
Control of adiabatic properties using thermal meta-structures
Authors: Lim Taekyung , Ju Sanghyun
Published: April 2019

In this study, the shapes and materials of thermal meta-structures, which can suppress as much heat propagation as possible in a structure, were investigated using a three-dimensional finite-difference time-domain technique. The heat flux vibrating in the traveling direction could be suppressed using multiple layers of thermal meta-materials. The heat flux transferred through the gap between thermal meta-structures could also be efficiently suppressed by placing even-numbered layers of thermal meta-structures in a zigzag arrangement in a structure. When the air-based thermal meta-structures were increased from one to four layers, the temperature inside the structure could be reduced from 38.9 °C to 25.5 °C. Moreover, when water-, paraffin-, aerogel-, and air-based thermal meta-structures having different thermal conductivities, densities, and specific heat characteristics were applied to the structure, a temperature of 50 °C to one side led to temperatures of 35.7, 33.4, 25.7, and 25.5 °C on the other. In other words, the temperature of the concrete block with air-based and aerogel thermal meta-structures was more than 13 °C lower than that of a conventional concrete block (38.9 °C), confirming that the insulation effect obtained by suppressing heat transfer was significant.
Vitrifying immature equine oocytes impairs their ability to correctly align the chromosomes on the MII spindle
Authors: Ducheyne Kaatje D. , Rizzo Marilena , Daels Peter F. , Stout Tom A. E. , de Ruijter-Villani Marta
Published: April 2019

Vitrified–warmed immature equine oocytes are able to complete the first meiotic division, but their subsequent developmental competence is compromised. Therefore, the present study investigated the effects of vitrifying immature horse oocytes on the chromosome and spindle configuration after IVM. Cumulus–oocytes complexes (COCs) were collected and divided into two groups based on mare age (young ≤14 years; old ≥16 years). COCs were then either directly matured invitro or vitrified and warmed before IVM. Spindle morphology and chromosome alignment within MII stage oocytes were assessed using immunofluorescent staining, confocal microscopy and three-dimensional image analysis. Vitrification reduced the ability of oocytes to reach MII and resulted in ultrastructural changes to the meiotic spindle, including shortening of its long axis, and an increased incidence of chromosomes failing to align properly at the metaphase plate. We hypothesise that aberrant chromosome alignment is an important contributor to the reduced developmental competence of vitrified equine oocytes. Contrary to expectation, oocytes from young mares were more severely affected than oocytes from older mares; we propose that the reduced effect of vitrification on oocytes from older mares is related to pre-existing compromise of spindle assembly checkpoint control mechanisms in these mares.
Evidence of effectiveness in the Cohesive Strategy: measuring and improving wildfire response
Authors: Steelman Toddi , Nowell Branda
Published: April 2019

The United States’ National Cohesive Wildfire Management Strategy aims to achieve greater social and ecological resilience to wildfire. It also raises the question: cohesive for whom and for what purpose? In this article, we address the wildfire response goal and what a cohesive response means. Namely, we define a cohesive response as the ability to co-manage across scales for a more effective wildfire response. Our approach is grounded in the reality of the growing complexity of wildfire – both biophysically and socio-politically. We suggest that suppression and fire operations are necessary, but insufficient in the face of this growing complexity as we seek safer and effective wildfire response. Using network-based concepts and drawing from the literature on socio-ecological resilience, we consider how scales can be matched, what can and should be communicated across scales, and what this means for creating more adaptable institutions for more effective wildfire response. Survey results from 21 fires during the 2013 wildfire season are presented to illustrate relative areas of strength and weakness related to wildfire response and how these measurements can feed into processes to facilitate social learning, adaptation and ultimately more resilient socio-ecological wildfire response institutions.
A review of electrodeposited composite coatings with Ni–B alloy matrix
Authors: Ünal Ersin , Yaşar Abdulkadir , Karahan İsmail Hakki
Published: April 2019

Coating processes are of great importance for protecting the materials used in the industry from the damaging effects of external environments and mechanical forces. There are a wide variety of coating methods, but the electrochemical deposition method within them is one step ahead because of its low cost, easy manufacturability and rapidity. Ni–B coatings have been produced for many years by the electroless deposition method, but electrodeposited Ni–B coatings are a relatively new research topic and attract much attention in recent years. Due to its superior properties Ni–B alloy coatings are successfully used in many industries such as aerospace, automotive, petrochemical, chemical and electronics. Works on reinforcing Ni–B alloys with second phase particles to increase these properties to a better level has been increasing rapidly in recent years. Ni–B alloy and composite coatings were investigated in this study. Furthermore, the bath components, production parameters, contents and properties of Ni–B alloy matrix composite coatings were presented comparatively. It was revealed that reinforcing the Ni–B alloy matrix with ceramic particles affected properties such as crystal structure, morphology, hardness, corrosion and abrasion resistance very seriously.
Monotonicity of the principal eigenvalue for a linear time-periodic parabolic operator
Authors: Liu Shuang , Lou Yuan , Peng Rui , Zhou Maolin
Published: April 2019

We investigate the effect of frequency on the principal eigenvalue of a time-periodic parabolic operator with Dirichlet, Robin, or Neumann boundary conditions. The monotonicity and asymptotic behaviors of the principal eigenvalue with respect to the frequency parameter are established. Our results prove a conjecture raised by Hutson, Michaikow, and Poláčik.
Rank-two Euler systems for symmetric squares
Authors: Büyükboduk Kâzım , Lei Antonio
Published: April 2019

Let

p
≥
7

p\ge 7

be a prime number, and let

f
f

be a normalized eigen-newform with good reduction at

p
p

such that its

p
p

th Fourier coefficient vanishes. We construct a rank-two Euler system attached to the

p
p

-adic realization of the symmetric square motive of

f
f

. Furthermore, we show that the nontriviality is guaranteed by the nonvanishing of the leading term of the relevant

L
L

-value and the nonvanishing of a certain

p
p

-adic period modulo

p
p

.
Quaternionic Artin representations and nontraditional arithmetic statistics
Authors: Rohrlich David
Published: April 2019

We classify and then attempt to count the real quadratic fields (ordered by the size of the totally positive fundamental unit, as in Sarnak’s work) from which quaternionic Artin representations of minimal conductor can be induced. Some of our results can be interpreted as criteria for a real quadratic field to be contained in a Galois extension of

Q

\mathbb {Q}

with controlled ramification and Galois group isomorphic to a generalized quaternion group.
Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication
Authors: Drennan Amanda C. , Krishna Shivaani , Seeger Mark A. , Andreas Michael P. , Gardner Jennifer M. , Sether Emily K. R. , Jaspersen Sue L. , Rayment Ivan
Published: April 2019

Centrosomes and spindle pole bodies (SPBs) are membraneless organelles whose duplication and assembly is necessary for bipolar mitotic spindle formation. The structural organization and functional roles of major proteins in these organelles can provide critical insights into cell division control. Spc42, a phosphoregulated protein with an N-terminal dimeric coiled-coil (DCC), assembles into a hexameric array at the budding yeast SPB core, where it functions as a scaffold for SPB assembly. Here, we present in vitro and in vivo data to elucidate the structural arrangement and biological roles of Spc42 elements. Crystal structures reveal details of two additional coiled-coils in Spc42: a central trimeric coiled-coil and a C-terminal antiparallel DCC. Contributions of the three Spc42 coiled-coils and adjacent undetermined regions to the formation of an ∼145 Å hexameric lattice in an in vitro lipid monolayer assay and to SPB duplication and assembly in vivo reveal structural and functional redundancy in Spc42 assembly. We propose an updated model that incorporates the inherent symmetry of these Spc42 elements into a lattice, and thereby establishes the observed sixfold symmetry. The implications of this model for the organization of the central SPB core layer are discussed.
A framework for space-efficient variable-order Markov models
Authors: Cunial Fabio , Alanko Jarno , Belazzougui Djamal
Published: April 2019

Motivation

Markov models with contexts of variable length are widely used in bioinformatics for representing sets of sequences with similar biological properties. When models contain many long contexts, existing implementations are either unable to handle genome-scale training datasets within typical memory budgets, or they are optimized for specific model variants and are thus inflexible.

Results

We provide practical, versatile representations of variable-order Markov models and of interpolated Markov models, that support a large number of context-selection criteria, scoring functions, probability smoothing methods, and interpolations, and that take up to four times less space than previous implementations based on the suffix array, regardless of the number and length of contexts, and up to ten times less space than previous trie-based representations, or more, while matching the size of related, state-of-the-art data structures from Natural Language Processing. We describe how to further compress our indexes to a quantity related to the redundancy of the training data, saving up to 90% of their space on very repetitive datasets, and making them become up to 60 times smaller than previous implementations based on the suffix array. Finally, we show how to exploit constraints on the length and frequency of contexts to further shrink our compressed indexes to half of their size or more, achieving data structures that are a hundred times smaller than previous implementations based on the suffix array, or more. This allows variable-order Markov models to be used with bigger datasets and with longer contexts on the same hardware, thus possibly enabling new applications.

Availability and implementation

https://github.com/jnalanko/VOMM

Supplementary information

Supplementary data are available at Bioinformatics online.
Fostering researcher identity in STEM distance education: impact of a student-led on-line case study
Authors: Marvasi Massimiliano , Sebastian Galindo , Lorenzo Silva-Lugo Jose
Published: April 2019

Researcher identity can be defined as the totality of traits such as confidence, logical thinking and having both the ability to design experiments, interpret results, and the desire to seek and succeed in authentic research. Therefore, the development of students' researcher identity can be supported by authentic research experiences embedded in introductory courses. Distance courses are increasingly more appealing to students and institutions, and there is a need to assess to what extent web-based education can provide opportunities to foster researcher identity. In an attempt to offer authentic research opportunities in a course with partially web-delivered content and to foster a research identity, we developed an outbreak case study—group project (OCS-GP) that is an investigation of a mock outbreak of illness. Participants were divided into groups tasked with conceiving an outbreak scenario and then identifying the cause and the source of the outbreak. The case studies were open-ended and designed to provide students with authentic learning experiences. Development of a researcher identity was evaluated in this exploratory study via reflective tests: participants in the OCS-GP demonstrated more willingness to conduct research, when compared with those who completed a similar outbreak case study but as individual assignment (OCS-IA).
Two lytic transglycosylases of Xanthomonas campestris pv. campestris associated with cell separation and type III secretion system, respectively
Authors: Wang Lin , Yang Li-Yan , Gan Yong-Liang , Yang Feng , Liang Xue-Lian , Li Wan-Lian , Bo-Le Jiang
Published: April 2019

The lytic transglycosylases (LTs) are important enzymes that degrade peptidoglycan of the bacterial cell wall and affect many biological functions. We present here that XC_0706 and XC_3001 are annotated as the LTs in Xanthomonas campestris pv. campestris. XC_0706 is associated with virulence and plays a pivotal role in cell division. Mutation on XC_3001 reduced hypersensitive response induction and the translocation of type III effector, but did not affect the function of the type II secretion system. Further studies showed that multiple LTs genes contribute to efficiency of the type III secretory system in X. campestris pv. campestris.
“Now I Write Songs”: Growth and Reciprocity After Long-Term Nursing Home Placement
Authors: Allison Theresa A , Smith Alexander K
Published: April 2019

Background and Objectives

Nursing home residents have a need for activities that are meaningful, yet mandated scheduled activities remain poorly characterized. In order to understand how scheduled activities provide meaning for nursing home residents, we conducted a study of daily life in a nursing home with a robust activities program.

Research Design and Methods

This 2-year, longitudinal ethnographic study embedded an ethnographer into the activities department of a 430-bed, not-for-profit, faith-based nursing home. Forty-three interviews and more than 250 hr of participant-observation were conducted, with a focus on creative arts and religious activities. Thirty-two residents and 15 activities staff were followed more than 12–23 months. Data were coded concurrently, and emerging themes challenged through purposive recruitment until thematic saturation was reached.

Results

Scheduled activities in the nursing home offered opportunities for learning and personal growth regardless of functional or cognitive disability. Three major themes emerged. Artistic development included new self-identification as a musician, painter, or sculptor through arts programming. Intellectual and spiritual growth involved the use of activities to support ongoing practice and study. Reciprocity occurred as residents used the arts to remain contributing members of their institutional society, reciprocating with the institution that housed them.

Discussion and Implications

Nursing home scheduled activities can facilitate the transformation of identity from resident or patient to the normalized social roles of artist, Torah scholar, and productive member of society.
Systems in Play: Simon Nicholson’s Design 12 Course, University of California, Berkeley, 1966
Authors: Stott Timothy
Published: April 2019

In 1966, British artist, designer and educator Simon Nicholson (1934–1990) offered a lower division course, Design 12, at the College of Environmental Design, UC Berkeley. Controversially, Nicholson promoted play as the principal method of design and invited children to assess students’ projects on the Berkeley campus and in local schools, parks, playgrounds and hospitals. This article presents Design 12 as an important example of environmental design pedagogy in the USA, which uniquely attempted to synthesize British post-war constructivism with ‘design science’ and adventure play. The result was a course that placed play at the centre of design pedagogy, where it could combine intuition with systems building to promote ‘involved science’ and co-construction.
Clinical trials in end-stage renal disease—priorities and challenges
Authors: Kovesdy Csaba P
Published: April 2019

Patients with end-stage renal disease (ESRD) experience extremely high morbidity and mortality and there are virtually no therapeutic interventions besides dialysis treatment that are proven in properly designed randomized controlled trials (RCTs) to improve patients’ outcomes. Historically, the number of RCTs performed in the ESRD population has been very low compared with other medical subspecialties, and several of the few large RCTs have yielded inconclusive or negative results, dampening enthusiasm for future investment in similar trials. Recent initiatives promoting a focus on patient-centered outcomes and more active patient and caregiver involvement in the planning and conduct of clinical trials may result in more clinically relevant RCTs and broader participation from patients representing the diversity of the ESRD population. The adoption of novel clinical trial design elements characteristic of pragmatic clinical trials and platform trials could help improve both the internal and external validity of RCTs in ESRD, ultimately resulting in the adoption of therapeutic interventions that can be rapidly translated to clinical practice.
INSTI-Based Triple Regimens in Treatment-Naïve HIV-Infected Patients Are Associated With HIV-RNA Viral Load Suppression at Ultralow Levels
Authors: Lambert-Niclot Sidonie , Boyd Anders , Fofana Djeneba , Valin Nadia , Wirden Marc , Meynard Jean-Luc , Palich Romain , Agher Rachid , Valantin Marc-Antoine , Calvez Vincent , Katlama Christine , Girard Pierre-Marie , Marcelin Anne-Geneviève , Morand-Joubert Laurence
Published: April 2019

Background

During antiretroviral therapy (ART), HIV-1-infected patients may present with ultralow (UL) HIV-RNA viral loads (VLs) below quantification levels of current assays. Reasons for UL-VL detection and its relation to virological rebound (VR) are unclear.

Methods

HIV-1-infected, ART-naïve patients followed at 2 university hospitals were included. All participants had an HIV-RNA >200 copies/mL at ART initiation and achieved a VL <50 copies/mL during ART. UL-VL was determined by the presence/absence of polymerase chain reaction signal detected using a commercially available assay (COBAS, TaqMan, Roche). Random-effects Poisson regression was used for assessing determinants of UL-VL not detected overtime and conditional risk set analysis for VR (1 VL > 200 copies/mL or 2 VL > 50 copies/mL) while accounting for frequency of VL measurements.

Results

Between 2009 and 2013, 717 patients initiated ART containing 2 nucleos(-t)ide reverse transcriptase inhibitors (NRTIs) plus a non-NRTI (29.4%), a protease inhibitor (58.4%), or an integrase-strand transfer inhibitor (INSTI; 12.1%). During a median (interquartile range) 3.4 (2.3–4.6) years, 676 (94.3%) patients achieved UL-VL not detected. In multivariable analysis, UL-VL not detected overtime was associated with younger age (P < .001), female gender (P = .04), lower baseline VL (P < .001), baseline CD4+ >500 vs <350/mm3 (P < .001), and INSTI-containing ART (P = .009). One hundred thirty-one (18.3%) patients had VR during follow-up, which was independently associated with a CD4/CD8 ratio <0.8 during follow-up (P = .01) and time spent with UL-VL not detected (P < .001). When UL-VL not detected occurred for ≥50% of the follow-up duration (n = 290), faster time to reach UL-VL not detected (P < .001), faster CD4+ T-cell count increase (P = .03), and faster CD4/CD8 ratio increase (P = .001) were observed.

Conclusions

VL suppression at an ultralow level is associated with INSTI-class ART initiation. Extensive VL suppression below ultralow detection could improve immune reconstitution.
Relief of Neuropathic Pain Through Epidermal Growth Factor Receptor Inhibition: A Randomized Proof-of-Concept Trial
Authors: Kersten Christian , Cameron Marte G , Bailey Andrew G , Fallon Marie T , Laird Barry J , Paterson Vicki , Mitchell Rory , Fleetwood-Walker Sue M , Daly Fergus , Mjåland Svein
Published: April 2019

Objective

Case reports and a case series have described relief of neuropathic pain (NP) after treatment with epidermal growth factor receptor inhibitors (EGFR-Is). These observations are supported by preclinical findings. The aim of this trial was to explore a potential clinical signal supporting the therapeutic efficacy of EGFR-Is in NP.

Methods

In a proof-of-concept trial using a randomized, double-blind, placebo-controlled design, 14 patients with severe, chronic, therapy-resistant NP due to compressed peripheral nerves or complex regional pain syndrome were randomized to receive a single infusion of the EGFR-I cetuximab and placebo in crossover design, followed by a single open-label cetuximab infusion.

Results

The mean reduction in daily average pain scores three to seven days after single-blinded cetuximab infusion was 1.73 points (90% confidence interval [CI] = 0.80 to 2.66), conferring a 1.22-point greater reduction than placebo (90% CI = –0.10 to 2.54). Exploratory analyses suggested that pain reduction might be greater in the 14 days after treatment with blinded cetuximab than after placebo. The proportion of patients who reported ≥50% reduction in average pain three to seven days after cetuximab was 36% (14% after placebo), and comparison of overall pain reduction suggests a trend in favor of cetuximab. Skin rash (grade 1–2) was the most frequent side effect (12/14, 86%).

Conclusions

This small proof-of-concept evaluation of an EGFR-I against NP did not provide statistical evidence of efficacy. However, substantial reductions in pain were reported, and confidence intervals do not rule out a clinically meaningful treatment effect. Evaluation of EGFR-I against NP therefore warrants further investigation.
New diagnosis for Allodaposuchus precedens, the type species of the European Upper Cretaceous clade Allodaposuchidae
Authors: Narváez Iván , Brochu Christopher A , De Celis Ane , Codrea Vlad , Escaso Fernando , Pérez-García Adán , Ortega Francisco
Published: April 2019

Allodaposuchus precedens is a basal member of Eusuchia, which was established almost a century ago on a set of cranial and postcranial fragmentary remains from the lower Maastrichtian of Vălioara, Romania. It was the first described member and type species of Allodaposuchidae, a recently described European clade representing one of the nearest outgroups to Crocodylia. Although our understanding of the group has expanded in recent years through the description of new forms, a review of Al. precedens is needed. The detailed revision of the classical material from Vălioara, including cranial and postcranial remains, and a comparison with the nearly complete skull from the Romanian synchronous locality of Oarda de Jos, allows us to emend the diagnosis for Al. precedens.
Cambridge radio sonobuoys and the seismic structure of oceanic crust
Authors: Mason Melvyn , White Robert S.
Published: April 2019

The Cambridge University Department of Geodesy and Geophysics pioneered the development of radio sonobuoys which could be used from a single ship to study the structure of the submarine crust. By contrast, contemporaneous marine seismic research, mainly in the USA, used more expensive techniques requiring the use of two ships. For nearly three decades from the early 1950s several generations of Cambridge sonobuoys were used as the primary tool to study the structure of the oceanic crust and the adjacent continental margins by seismic refraction methods, until superseded by ocean-bottom seismographs. An early result was to confirm the ubiquity across the world of relatively thin (compared with continental crust), probably volcanic, oceanic crust. This in turn underpinned the subsequent recognition of seafloor spreading and plate tectonics.
Skilled musicians are indeed subject to the McGurk effect
Authors: Politzer-Ahles Stephen , Pan Lei
Published: April 2019

The McGurk effect is an illusion whereby speech sounds are often mis-categorized when the auditory cues in the stimulus conflict with the visual cues from the speaker's face. A recent study claims that ‘skilled musicians are not subject to’ this effect. It is not clear, however, if this is intended to mean that skilled musicians do not experience the McGurk effect at all, or if they just experience it to a lesser magnitude than non-musicians. The study also does not statistically demonstrate either of these conclusions, as it does report a numerical (albeit non-significant) McGurk effect for musicians and does not report a significant difference between musicians' and non-musicians’ McGurk effect sizes. This article reports a pre-registered, higher-power replication of that study (using twice the sample size and changing from a between- to a within-participants manipulation). Contrary to the original study's conclusion, we find that musicians do show a large and statistically significant McGurk effect and that their effect is no smaller than that of non-musicians.
Studies on chain shuttling polymerization reaction of nonbridged half-titanocene and bis(phenoxy-imine) Zr binary catalyst system
Authors: Xu Qinwen , Gao Rong , Liu Dongbing
Published: April 2019

In this contribution, olefin block copolymers were produced via chain shuttling polymerization (CSP), using a new combination of catalysts and a chain shuttling agent (CSA) diethylzinc (ZnEt
2
). The binary catalyst system included nonbridged half-titanocene catalyst, Cp*TiCl
2
(O-2,6-
i
Pr
2
C
6
H
3
) (Cat
A
) and bis(phenoxy-imine) zirconium, {
η
2
-1-[C(H)=NC
6
H
11
]-2-O-3-
t
Bu-C
6
H
3
}
2
ZrCl
2
(Cat
B
), as well as co-catalyst methylaluminoxane (MAO). In contrast to dual-catalyst system in the absence of CSA, the blocky structure was obtained in the presence of CSA and rationalized from rheological studies. The binary catalyst system could cause the CSP reaction to occur in the presence of CSA ZnEt
2
, which yielded broad distribution ethylene/1-octene copolymers (
M
w
/
M
n
: 35.86) containing block polymer chains with high
M
w
. The presented dual-catalytic system was applied for the first time in CSP and has a potential to be extended to produce a library of olefin block copolymers that can be used as advanced additives for thermoplastics.
Nest defence behavioural reaction norms: testing life-history and parental investment theory predictions
Authors: Thys Bert , Lambreghts Yorick , Pinxten Rianne , Eens Marcel
Published: April 2019

Predation is the primary source of reproductive failure in many avian taxa and nest defence behaviour against predators is hence an important aspect of parental investment. Nest defence is a complex trait that might consistently differ among individuals (personality), while simultaneously vary within individuals (plasticity) according to the reproductive value of the offspring. Both complementary aspects of individual variation can influence fitness, but the causality of links with reproductive success remains poorly understood. We repeatedly tested free-living female great tits (Parus major) for nest defence (hissing) behaviour across the nesting cycle, by presenting them with a model predator. Hissing behaviour was highly repeatable but, despite population-level plasticity, we found no support for individual differences in plasticity. Path analysis revealed that repeatable differences in hissing behaviour had no direct effect on nest success or fledgling number. However, our best supported path-model showed that more fiercely hissing females laid smaller clutches, with clutch size in turn positively influencing fledgling number, suggesting that females are most likely facing a trade-off between investment in nest defence and reproduction. Strong stabilizing selection for optimal plasticity, in combination with life-history trade-offs, might explain the high repeatability of nest defence and its link with reproductive success.
New logic facilitated identification of novel phage recombinase function units
Authors: Chang Yizhao , Wang Qian , Su Tianyuan , Qi Qingsheng
Published: April 2019

Phage recombinase function unit (PRFU) contains one single strand annealing protein (SSAP) and one 5’-3’ exonuclease (EXO). Well-known PRFU such as lambda-Red or Rac RecET has been proved to be useful tool in the recombineering ofEscherichia colibut had limited efficiency in distant species. Therefore, PRFUs from closely related species were often searched and developed as specific genetic tools. However, there are still many bacteria with few PRFU identified. Here, we hypothesised that the occurrence of PRFU might be related to specific strains. Based on this assumption, we managed to identify 59 unique sets of PRFUs in over 23 species of the genusCorynebacterium, a taxonomic group that were reported to be lacking in such system. The identified PRFUs were then classified to show their similarities and relation to species based on both sequential and structural information. Representative PRFUs were verified to be highly effective in mediating recombineering using ssDNA or dsDNA substrates. Analysis of the functional PRFUs indicated that they share similar local genome contexts, which might suggest their common origin. Our findings reveal the relation of PRFUs, species and strains and provide novel candidate genetic manipulation tools in genusCorynebacterium.

Author Summary

GenusCorynebacteriumis a taxonomic group with highly diversified species that are of medical, veterinary, or biotechnological relevance. However, being lack of genetic tools limits the study of these species. Our new verified phage recombinase function units (PRFUs) in this genus that are highly effective in mediating recombineering will provide new candidate genetic tools in this genus. Besides, reference genomes were often used for genome study and data mining. While for the mobile genetic elements, their transferable characteristic may affect their occurrence among genomes. Here we provide evidence for this idea by showing that the occurrence of PRFU is strain related but not species related. This may be helpful for the functional genomics study of mobile genetic elements among genomes.
The Cupin Protein, Dehydratase Pac13 is a Homodimer
Authors: Zhang Rundong
Published: April 2019

Cupin proteins share a double-stranded β-helix fold, form one of the largest superfamilies and possess remarkable functional diversity. They usually form homooligomeric states. Michailidou et al. recently reported that a cupin protein Pac13, which is a dehydratase mediating the formation of the 3’-deoxy nucleoside of pacidamycins, is an unusual, small monomer. However, a careful analysis of the biophysical and structural data provided by the authors clearly indicates that Pac13 is a homodimer.
Neurophysiological correlates of collective perceptual decision-making
Authors: Baumgart Kristina G. , Byvshev Petr , Sliby Alexa-Nicole , Strube Andreas , König Peter , Wahn Basil
Published: April 2019

Humans frequently coordinate with others in daily life. A recent study on perceptual decision-making showed that dyad members with similar individual performances attain a higher joint performance than the better dyad member (i.e., a collective benefit). However, little is known about the physiological basis of these results. Here, we replicate this earlier work and also investigate the neurophysiological correlates of decision-making using EEG.

In a two interval forced choice task, co-actors individually indicated presence of a target stimulus with a higher contrast and then indicated their confidence on a rating scale. Viewing the individual ratings, dyads made a joint decision. Replicating earlier work, we found a positive correlation between the similarity of individual performances and collective benefit.

We analyzed event related potentials (ERPs) in three phases (i.e., stimulus onset, response, and feedback) using explorative cluster mass permutation tests. At stimulus onset, ERPs were significantly linearly related to our manipulation of contrast differences, validating our manipulation of task difficulty. For individual and joint responses, we found a significant centro-parietal error-related positivity for correct versus incorrect responses, which suggests that accuracy is already evaluated at the response level. At feedback presentation, we found a significant late positive fronto-central potential elicited by incorrect joint responses, suggesting a stronger emotional response to negative as compared to positive feedback. In sum, these results demonstrate that response- and feedback-related components elicited by an error-monitoring system differentially integrate conflicting information exchanged during the joint decision-making process.
Endophytic Virome
Authors: Das Saurav , Barooah Madhumita , Thakur Nagendra
Published: April 2019

Endophytic microorganisms are well established for their mutualistic relationship and plant growth promotion through production of different metabolites. Bacteria and fungi are the major group of endophytes which were extensively studied. Virus are badly named for centuries and their symbiotic relationship was vague. Recent development of omics tools especially next generation sequencing has provided a new perspective towards the mutualistic viral relationship. Endogenous virus which has been much studied in animal and are less understood in plants. In this study, we described the endophytic viral population of tea plant root. Viral population (9%) were significantly less while compared to bacterial population (90%). Viral population of tea endophytes were mostly dominated by endogenous pararetroviral sequences (EPRV) derived from Caulimoviridae and Geminiviridae. Subclassification of Caulimoviridae showed the dominance of Badnavirus (42%), Caulimovirus (29%), Soymovirus (3%), Tungrovirus (3%), while Geminviridae was only represented by genus Bagmovirus. Interestingly, the endophytic virome sequence from root also showed the presence of phage virus from order Caudovirales. Identified sequence from Caudovirales were Myoviridae and Siphoviridae. Sequence comparison with viral population of soil and root showed the possibility of horizontal transfer of Caudovirales from soil to root environment. This study will expand the knowledge on endogenous viruses especially for tea plant. This study will also help us to understand the symbiotic integration of viral particle with plant which could be used in broader sense to tackle different agronomic problems.

Significance Statement

Virus were badly named for centuries and mostly known for their disease-causing abilities. But recent development of omics tools has focused another facet which is symbiotic. This paper discusses about viral community identified from shotgun sequence of tea root samples which are endogenous in origin. Interestingly, we also identified sequences of phage virus from Caudovirales family which possibly have transmitted from soil. Here we also compared the soil virome community with tea virome to establish the hypothesis. This research will broaden the current knowledge on symbiotic relationship of virus and plant.
Modeling place cells and grid cells in multi-compartment environments: hippocampal-entorhinal loop as a multisensory integration circuit
Authors: Li Tianyi , Arleo Angelo , Sheynikhovich Denis
Published: April 2019

Hippocampal place cells and entorhinal grid cells are thought to form a representation of space by integrating internal and external sensory cues. Experimental studies show that different subsets of place cells are controlled by vision, self-motion or a combination of both. Moreover, recent studies in environments with a high degree of visual aliasing suggest that a continuous interaction between place cells and grid cells can result in a deformation of hexagonal grids or in a progressive loss of visual cue control. The computational nature of such a bidirectional interaction remains unclear. In this work we present a neural network model of a dynamic loop between place cells and grid cells. The model is tested in two recent experimental paradigms involving double-room environments that provide conflicting evidence about visual cue control over self-motion-based spatial codes. Analysis of the model behavior in the two experiments suggests that the strength of hippocampal-entorhinal dynamical loop is the key parameter governing differential cue control in multi-compartment environments. Construction of spatial representations in visually identical environments requires weak visual cue control, while synaptic plasticity is regulated by the mismatch between visual- and self-motion representations. More gener-ally our results suggest a functional segregation between plastic and dynamic processes in hippocampal processing.
Disruption of large-scale electrophysiological networks in stroke patients with visuospatial neglect
Authors: Ros Tomas , Michela Abele , Meyer Anaïs , Bellman Anne , Vuadens Philippe , Zermatten Victorine , Saj Arnaud , Vuilleumier Patrik
Published: April 2019

Stroke frequently produces attentional dysfunctions including symptoms of hemispatial neglect, which is characterized by a breakdown of awareness for the contralesional hemispace. Recent studies with functional MRI (fMRI) suggest that hemineglect patients display abnormalintra-andinter-hemisphericfunctional connectivity. However, since stroke is a vascular disorder and fMRI signals remain sensitive to non-neuronal (i.e. vascular) coupling, more direct demonstrations of neural network dysfunction in hemispatial neglect are warranted. Here, we utilize electroencephalogram (EEG) source imaging to uncover differences in resting-state network organization between patients with right-hemispheric stroke (N = 15) and age-matched, healthy controls (N = 27), and determine the relationship between hemineglect symptoms and brain network organization. We estimatedintra-andinter-regional differences in cortical communication, by calculating the spectral power and amplitude envelope correlations (AEC) of narrow-band EEG oscillations. We firstly observed focal frequency-slowing within the right posterior cortical regions, reflected in relative delta/theta power increases and alpha/beta/gamma decreases. Secondly, nodes within the right temporal and parietal cortex consistently displayed anomalous intra- and inter- hemispheric coupling, stronger in delta and gamma bands, and weaker in theta, alpha, and beta bands. Finally, a significant association was observed between the severity of left-hemispace search deficits (e.g. cancellation test omissions) and reduced functional connectivity within the alpha and beta bands. In sum, our novel results validate the hypothesis of large-scale cortical network disruption following stroke, and reinforce the proposal that abnormal brain oscillations may be intimately involved in the pathophysiology of visuospatial neglect.
A global perspective on microbial diversity in the terrestrial deep subsurface
Authors: Soares A. , Edwards A. , An D. , Bagnoud A. , Bomberg M. , Budwill K. , Caffrey S. M. , Fields M. , Gralnick J. , Kadnikov V. , Momper L. , Osburn M. , Moreau J.W. , Moser D. , Mu A. , Purkamo L. , Rassner S. M. , Sheik C. S. , Sherwood Lollar B. , Toner B. M. , Voordouw G. , Wouters K. , Mitchell A. C.
Published: April 2019

While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earth’s bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to ∼1.8% in the deep subseafloor1–3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities4–6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. Anin-silicocontamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
Nuclear gene transformation in a dinoflagellate
Authors: Sprecher Brittany N. , Zhang Huan , Lin Senjie
Published: April 2019

The lack of a robust gene transformation tool that allows functional testing of the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of fundamental biology in this ecologically important and evolutionarily unique lineage. Here we report the development of a dinoflagellate expression vector, an electroporation protocol, and successful expression of introduced genes in the dinoflagellateOxyrrhis marina. This protocol, involving the use of Lonza’s Nucleofector and a codon optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.