bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship between teaching motivation and teaching behaviour of secondary education teachers in Indonesia (Relación entre la motivación docente y el comportamiento docente en profesores de educación secundaria en Indonesia)
Authors: Irnidayanti Yulia , Maulana Ridwan , Helms-Lorenz Michelle , Fadhilah Nurul
Published: May 2020

Research on teacher motivation is increasing substantially. Several studies have demonstrated the relationship between the motivation and teaching behaviour of teachers. The objective of this study was to investigate the relationship between the perceived motivation of teachers and their actual teaching behaviour in the context of secondary education. A survey on teacher motivation yielded responses from 315 teachers from 28 schools across 13 provinces in Indonesia. These teachers were observed in their classrooms by trained observers using a validated observation scheme. Results of a multilevel analysis indicate that: (1) perceived controlled motivation does not predict actual teaching behaviour; (2) perceived autonomous motivation is a positive predictor of at least some domains of actual teaching behaviour. Higher levels of perceived autonomous motivation are associated with higher scores on classroom management and clarity of instruction. There is also a slight tendency ( p < .10) for autonomous motivation to explain differences in other domains of teaching behaviour, with the exception of activating teaching. This study highlights the importance of autonomous motivation in relation to teaching quality.
Gendered patterns of coping responses with academic sexism in a group of Spanish secondary students (Diferencias de género en las respuestas de afrontamiento del sexismo académico en un grupo de estudiantes españoles de secundaria)
Authors: Sáinz Milagros , Martínez José-Luis , Meneses Julio
Published: May 2020

This study analyses predictors of students’ coping responses to academic sexism. 954 high school students ( M Age = 17; SD Age = 0.90, 57% girls) participated. Boys were therefore more likely to use avoidance responses, whereas girls confronting and help-seeking responses. Likewise, hierarchical regressions suggest that girls and boys and girls whose parents had a high educational level and were without sexist attitudes about women’s higher level of competence in biology and languages were more likely to deploy confronting responses. Similarly, participants who did not embrace stereotypes about boys’ and girls’ higher abilities in some domains were more likely to seek help. Furthermore, boys and girls who believed that girls are better at biology and languages were more likely to develop avoidance responses. Interaction between gender and parental educational level shows that boys with highly educated parents were more likely to avoid the sexism. The present research contributes to the study of factors shaping gender differences in students’ coping with academic sexism. The role played by students’ adherence to stereotyped beliefs about boys’ and girls’ academic abilities is also discussed.
Neuronal activity disrupts myelinated axon integrity in the absence of NKCC1b
Authors: Marshall-Phelps Katy L.H. , Kegel Linde , Baraban Marion , Ruhwedel Torben , Almeida Rafael G. , Rubio-Brotons Maria , Klingseisen Anna , Benito-Kwiecinski Silvia K. , Early Jason J. , Bin Jenea M. , Suminaite Daumante , Livesey Matthew R. , Möbius Wiebke , Poole Richard J. , Lyons David A.
Published: May 2020

Through a genetic screen in zebrafish, we identified a mutant with disruption to myelin in both the CNS and PNS caused by a mutation in a previously uncharacterized gene, slc12a2b, predicted to encode a Na+, K+, and Cl− (NKCC) cotransporter, NKCC1b. slc12a2b/NKCC1b mutants exhibited a severe and progressive pathology in the PNS, characterized by dysmyelination and swelling of the periaxonal space at the axon–myelin interface. Cell-type–specific loss of slc12a2b/NKCC1b in either neurons or myelinating Schwann cells recapitulated these pathologies. Given that NKCC1 is critical for ion homeostasis, we asked whether the disruption to myelinated axons in slc12a2b/NKCC1b mutants is affected by neuronal activity. Strikingly, we found that blocking neuronal activity completely prevented and could even rescue the pathology in slc12a2b/NKCC1b mutants. Together, our data indicate that NKCC1b is required to maintain neuronal activity–related solute homeostasis at the axon–myelin interface, and the integrity of myelinated axons.
Nonadiabatic and Multielectron Effects in the Attoclock Experimental Scheme*
Authors: Xiao Zhi-Lei , Quan Wei , Xu Song-Po , Yu Shao-Gang , Lai Xuan-Yang , Chen Jing , Liu Xiao-Jun
Published: May 2020

The problem of how long it takes for an electron to tunnel from one side of a barrier to the other has been debated for decades and the attoclock is a promising experimental procedure to address this problem. In the attoclock experiment, many physical effects will contribute to the experimental results and it is difficult to extract the tunneling time accurately. We numerically investigate a method of measuring the residual equivalent temporal offset (RETO) induced by the physical effects except for tunneling delay. The Coulomb potential effect, the nonadiabatic effect, the multielectron effect, and the Stark effect are considered in the theoretical model. It is shown that the ratio of the RETO of the target atoms to that of H is insensitive to the wavelength and is linearly proportional to

(
2

I

p

)

−
3

/

2

. This work can help to improve the accuracy of the attoclock technique.
Testing the Universality of Free Fall by Comparing the Atoms in Different Hyperfine States with Bragg Diffraction*
Authors: Zhang Ke , Zhou Min-Kang , Cheng Yuan , Chen Le-Le , Luo Qin , Xu Wen-Jie , Cao Lu-Shuai , Duan Xiao-Chun , Hu Zhong-Kun
Published: May 2020

We perform a precision atom interferometry experiment to test the universality of free fall. Our experiment employs the Bragg atom interferometer with 87Rb atoms either in hyperfine state

F
=
1
,

m

F

=
0

or

F
=
2
,

m

F

=
0

, and the wave packets in these two states are diffracted by one pair of Bragg beams alternatively, which is helpful for suppressing common-mode systematic errors. We obtain an Eötvös ratio

η

1
−
2

=

0.9
±
2.7

×

10

−
10

, and set a new record on the precision with improvement of nearly 5 times. This measurement also provides constraint on the difference of the diagonal terms of the mass-energy operator.
Tunable Dielectric Properties of Carbon Nanotube@Polypyrrole Core-Shell Hybrids by the Shell Thickness for Electromagnetic Wave Absorption
*
Authors: Wang De-Ting , Wang Xian-Chao , Zhang Xiao , Yuan Hao-Ran , Chen Yu-Jin
Published: May 2020

Carbon nanotube@polypyrrole (CNT@PPy) hybrids have been successfully fabricated via a simple in situ chemical oxidation polymerization. The thickness of the PPy shell can be finely controlled in the range of 3.0–6.4 nm. The dielectric loss of core-shell hybrids can be tuned by the shell thickness, resulting in a well-matched characteristic impedance that can enhance electromagnetic wave (EMW) absorption performance. Minimum reflection loss of the hybrid with moderate PPy shell thickness can reach −51.4 dB at 11.8 GHz with a matching thickness of merely 2 mm. Furthermore, the minimum reflection loss values of the hybrid are below −30 dB even at thickness in the range of 1.4–1.9 mm, endowing the possibility of practical application of the hybrids in electromagnetic wave absorption field.
Molecular Dynamics Simulation of Effects of Stretching and Compressing on Thermal Conductivity of Aligned Silicon Oxygen Chains*
Authors: Xu Wen-Xue , Liang Xin-Gang
Published: May 2020

The effects of stretching and compressing on the thermal conductivity (TC) of silicon oxygen chain are studied by means of non-equilibrium molecular dynamics simulation. It is found that stretching can improve TC, and compressing may reduce the TC and can also increase the TC. This mechanism is explained based on the variation of phonon group velocity and the specific heat per volume with stretching and compressing. The distributions of bond angle and bond length under different normalized chain lengths are given. It is found that the bond length and bond angle in the skeleton chain would deviate from their original position. In addition, the phonon density of states (PDOSs) of silicon and oxygen atoms in the chains under different normalized chain lengths are analyzed. The overall trend is that the TC increases and the peaks of PDOSs move towards higher frequency with increasing stretch strain.
Wettability and Surface Energy of Hydrogen- and Oxygen-Terminated Diamond Films*
Authors: Ma Zi-Cheng , Gao Nan , Cheng Shao-Heng , Liu Jun-Song , Yang Ming-Chao , Wang Peng , Feng Zhi-Yuan , Wang Qi-Liang , Li Hong-Dong
Published: May 2020

The contact angle and surface energy values of diamond are systemically investigated in terms of surface treatments (hydrogen- and oxygen-terminations), structure feature (single crystal diamonds and polycrystalline diamond films), crystal orientation ((100), (111) and mixed (100)/(111) orientations), different fluids (probes of polar deionized water and nonpolar di-iodomethane). It is found that the hydrophobic/hydrophilic characteristic and surface energy values of diamond are mainly determined by the surface hydrogen/oxygen termination, and less related to the structural features and crystal orientation. Based on the contact angle values with polar water and nonpolar di-iodomethane, the surface energies of diamond are estimated to be about 43 mJ/m2 for hydrogen-termination and about 60 mJ/m2 for oxygen-termination. Furthermore, the varying surface roughness of diamond and fluids with different polarities examined determine the variation of contact angles as well as the surface energy values. These results would be helpful for a more detailed understanding of the surface properties of diamond films for further applications in a broad number of fields, such as optical and microwave windows, biosensors, and optoelectronic devices, etc.
Pressure-Induced Metallization and Structural Phase Transition in the Quasi-One-Dimensional TlFeSe2*
Authors: Liu Zi-Yi , Dong Qing-Xin , Shan Peng-Fei , Wang Yi-Yan , Dai Jian-Hong , Jana Rajesh , Chen Ke-Yu , Sun Jian-Ping , Wang Bo-Sen , Yu Xiao-Hui , Liu Guang-Tong , Uwatoko Yoshiya , Sui Yu , Yang Huai-Xin , Chen Gen-Fu , Cheng Jin-Guang
Published: May 2020

We report a comprehensive high-pressure study on the monoclinic TlFeSe2 single crystal, which is an antiferromagnetic insulator with quasi-one-dimensional crystal structure at ambient pressure. It is found that TlFeSe2 undergoes a pressure-induced structural transformation from the monoclinic phase to an orthorhombic structure above P
c ≈ 13 GPa, accompanied with a large volume collapse of ΔV/V
0 = 8.3%. In the low-pressure monoclinic phase, the insulating state is easily metallized at pressures above 2 GPa; while possible superconductivity with

T
c

onset

∼
2

K is found to emerge above 30 GPa in the high-pressure phase. Such a great tunability of TlFeSe2 under pressure indicates that the ternary AFeSe2 system (A = Tl, K, Cs, Rb) should be taken as an important platform for explorations of interesting phenomena such as insulator-metal transition, dimensionality crossover, and superconductivity.
Negative Magnetoresistance in Antiferromagnetic Topological Insulator EuSn2As2
*
Authors: Chen Huan-Cheng , Lou Zhe-Feng , Zhou Yu-Xing , Chen Qin , Xu Bin-Jie , Chen Shui-Jin , Du Jian-Hua , Yang Jin-Hu , Wang Hang-Dong , Fang Ming-Hu
Published: May 2020

The measurements of magnetization, longitudinal and Hall resistivities are carried out on the intrinsic antiferromagnetic (AFM) topological insulator EuSn
2
As
2. It is confirmed that our EuSn
2
As
2
crystal is a heavily hole doping A-type AFM metal with the Néel temperature T
N = 24 K, with a metamagnetic transition from an AFM to a ferromagnetic (FM) phase occurring at a certain critical magnetic field for the different field orientations. Meanwhile, we also find that the carrier concentration does not change with the evolution of magnetic order, indicating that the weak interaction between the localized magnetic moments from Eu
2+ 4f
7
orbits and the electronic states near the Fermi level. Although the quantum anomalous Hall effect (AHE) is not observed in our crystals, it is found that a relatively large negative magnetoresistance (−13%) emerges in the AFM phase, and exhibits an exponential dependence upon magnetic field, whose microscopic origin is waiting to be clarified in future research.
Analogue Soliton with Variable Mass in Super-Conducting Quantum Interference Devices*
Authors: Yang Ying , Tian Ze-Hua , Jing Ji-Liang
Published: May 2020

It is difficult to investigate the behavior of solitons in realistic inhomogeneity media in experiment due to inhomogeneity of the media and noise from the unwanted coupling. We propose to use a waveguide-like transmission line which is based on direct-current super-conducting quantum interference devices to simulate behavior of solitons because we find that the behavior of the node flux in this transmission is similar to that of solitons with variable mass.
Magnetoelastic properties and behaviour of 4C pyrrhotite, Fe7S8, through the Besnus transition
Authors: Haines C R S , Dutton S E , Volk M W R , Carpenter M A
Published: May 2020

Pyrrhotite, Fe7S8, is a commonly occurring carrier of magnetic remanence and has a low temperature transition, the Besnus transition, involving a change in spin state. Variations of the thermodynamic, magnetic and elastic properties through this transition at ∼33 K in a natural sample of 4C pyrrhotite have been tested against a group theoretical model for coupling between order parameters relating to Fe/vacancy ordering (irrep U
1(1/2,0,1/4)) and magnetic ordering (irreps m

Γ

4

+

and m

Γ

5

+

). Magnetoelastic coupling is weak but the pre-existing microstructure of ferroelastic and magnetic domains, that develop as a consequence of Fe/vacancy and ferrimagnetic ordering during slow cooling in nature (P63/mmc → C2′/c′), causes subtle changes in the low temperature transition (C2′/c′ → P

1

¯

). The Besnus transition involves a rotation of magnetic moments out of the a–c plane of the monoclinic structure, but it appears that the transition temperature might vary locally according to whether it is taking place within the pre-existing domain walls or in the domains that they separate. Evidence of metamagnetic transitions suggests that the magnetic field–temperature phase diagram will display some interesting diversity. Low temperature magnetic transitions in minerals of importance to the palaeomagnetism community have been used to identify the presence of magnetite and haematite in rocks and the Besnus transition is diagnostic of the existence of pyrrhotite, Fe7S8.
Basic magnetic properties of magnetoactive elastomers of mixed content
Authors: Becker T I , Stolbov O V , Borin D Yu , Zimmermann K , Raikher Yu L
Published: May 2020

The results of theoretical and experimental investigations of the polymer composites that belong to a class of magnetoactive elastomers with mixed magnetic content (MAEs-MC) are presented. The fundamental distinction of such composites from ordinary magnetoactive elastomers is that the magnetic filler of MAEs-MC comprises both magnetically soft (MS) particles of size 3–5 µm and magnetically hard (MH) particles whose size is an order of magnitude greater. Since MH particles of the magnetic filler are mixed into a composition in a non-magnetised state, this can ensure preparation of samples with fairly homogeneous distribution of the filler. The ‘initiation’ process of a synthesised MAE-MC is done by its magnetisation in a strong magnetic field that imparts to the sample unique magnetic and mechanical properties. In this work, it is shown that the presence of MS particles around larger MH particles, firstly, causes an augmentation of magnetic moments, which the MH particles acquire during initiation, and secondly, enhances the magnetic susceptibility and remanent magnetisation of MAEs-MC. These magnetic parameters are evaluated on the basis of the macroscopic magnetostatics from the experimental data of spatial scanning of the field over the space around MAEs-MC made in the shape of a spheroid. A set of samples with a fixed MH and varying MS volume contents that are initiated in two different fields, is used. The developed mesoscopic model of magnetic interactions between the MH and MS phases is able to explain the experimentally observed dependencies of the magnetic parameters on the concentration of the MS phase. The problem is solved numerically under the assumption that the elastic matrix of MAEs-MC is rigid, i.e. the mutual displacements of the particles are negligible. The model helps to elucidate the interaction of the magnetic phases and to establish that the MS phase plays thereby a dual role. On the one hand, the MS phase screens out the field acting inside MH particles, and on the other hand, it forms mesoscopic magnetic bridges between adjoining MH particles, which in turn enhance their field. The combined interplay of these contributions defines the resulting material properties of MAEs-MC on the macroscopic scale.
A study on microstructure and erosion-corrosion performance of Fe–Cr–Ni–B alloy
Authors: Yi Da-Wei , Li Chong , Shi Yu-Pu , Chen Jin
Published: May 2020

The microstructure and erosion-corrosion performance of Fe–Cr–Ni–B alloy were studied. The experimental results were analyzed by hardness tester, energy spectrum analyzer, scanning electron microscope, X-ray diffraction analyzer. The results show that the Fe–Cr–Ni–B alloy consists of martensite and borocarbides [M2(B, C) and M7(B, C)3], and M2(B,C) and M7(B,C)3 borocarbides both have more chromium and less nickel than the matrix. After heat treatment, the hardness of the alloy reaches 52.3HRC. For the test alloys, the higher rotating speed test condition results in higher erosion-corrosion weight loss, and the erosion-corrosion weight loss increases first and then decreases with the increase of the impingement angle. Compared with Cr28 high chromium cast iron, in the erosion-corrosion surface of Fe–Cr–Ni–B alloy, the borocarbides are slightly broken, so, the Fe–Cr–Ni–B alloy exhibits excellent erosion-corrosion resistance under the borocarbide protection.
Evaluation of high-resolution rapid refresh (HRRR) forecasts for extreme precipitation
Authors: Yue Haowen , Gebremichael Mekonnen
Published: May 2020

This study evaluates the accuracy of short-range (1-h to 18-hr lead-time) forecasts from the High-Resolution Rapid Refresh (HRRR) model for five extreme storms in the United States: (1) the September 21–23, 2016, frontal storms in Iowa, (2) the April 28-May 1, 2017, frontal storms in the Southern Midwestern US, (3) the August 25–31, 2017, Hurricane Harvey storms in Texas, (4) the September 13–17, 2018, Hurricane Florence storms in the Carolinas, and (5) the September 4–6, 2019, Hurricane Dorian storms in the Carolinas. The evaluation was carried out by comparison with gauge-corrected Multi-Radar/Multi-Sensor (MRMS-GC) products. In terms of temporal variability, there was a good agreement between the forecasted and observed precipitation on an hourly basis. Thus, the HRRR products provide relatively reliable forecasts. However, the forecasts were mostly biased: they tend to overestimate rainfall for both hurricanes, underestimate rainfall for tropical storms in Iowa, and produce almost unbiased estimates for the frontal storms in Southern Midwestern US. In terms of spatial pattern, the forecasts are able to capture the spatial pattern of hurricanes, however, they produce too many, localized, high-rain intensities for the frontal storms than what the observations show. With regard to the effect of lead times, the 1-h lead forecasts have often lower accuracy than the other lead-time forecasts, while there was no much systematic difference in accuracy among the 2-h to 18-h lead-time forecasts. The bias estimates in the forecast are also examined at different spatial scales, ranging from 2 km × 2 km all the way to 128 km × 128 km. The results show that the bias estimated at smaller spatial scales vary within a large range, mostly within the range of −100% to +100%, indicating that the bias estimates obtained at large scale (hundreds of km grids) are not applicable to bias estimates at small scales, and vice versa. Local-bias correction approaches are therefore preferable over global bias-correction approaches.
Literature and Anthropology
Authors: Brandel Andrew
Published: May 2020

Literature is often understood to be one of anthropology’s most recurrent and provocative companions in thought. The relationship between the two has taken a number of different and variously interrelated forms. Perhaps the most familiar of these is the theorization of the anthropologist’s status as a writer; this work tends to take its cue from certain strands of postmodernism and invokes literary techniques as tools through which to address concerns around representation and the evocation of lived experience. A second important, if often overlooked, area of research involves the study of concrete literary practices including reading, writing, performing, sharing, and listening, whether by means of ethnographic fieldwork or anthropological modes of textual analysis. Finally, there are the myriad relationships that anthropologists have maintained with particular literary figures or texts, which have proven essential to their thinking and to their lives.
Sexual selection on size and shape in Japanese beetles (Popillia japonica)
Authors: Kelly Clint D
Published: May 2020

The mobility hypothesis argues that species in which males compete for mates in scrambles often exhibit female-biased size dimorphism because smaller male body size should increase male mobility and success in searching for mates. Sexual dimorphism can be further exaggerated if fecundity or sexual selection concurrently selects for larger female size. Scramble competition can select for trait characteristics that optimize locomotion; for example, long and slender wings should be favored if aerial speed is important to mating success. I tested these predictions in the scrambling Japanese beetle (Popillia japonica), a female-biased size dimorphic insect pest that is invasive to North America. Multivariate selection analyses support the prediction that smaller body size and larger wings in males benefit their mating success. My analyses also revealed significant selection for larger wings in females but, contrary to prediction, direct sexual selection favors smaller body size in females. These results support the mobility hypothesis and partially explain the evolution of female-biased size dimorphism in this species. Sexual selection favored rounder bodies in females and more tapered bodies in males, whereas, in both sexes, the effect of wing shape appears less important to fitness than wing size.
Using conceptual modeling to improve genome data management
Authors: Pastor Óscar , León Ana Palacio , Reyes José Fabián Román , García Alberto Simón , Casamayor Juan Carlos Rodenas
Published: May 2020

With advances in genomic sequencing technology, a large amount of data is publicly available for the research community to extract meaningful and reliable associations among risk genes and the mechanisms of disease. However, this exponential growth of data is spread in over thousand heterogeneous repositories, represented in multiple formats and with different levels of quality what hinders the differentiation of clinically valid relationships from those that are less well-sustained and that could lead to wrong diagnosis. This paper presents how conceptual models can play a key role to efficiently manage genomic data. These data must be accessible, informative and reliable enough to extract valuable knowledge in the context of the identification of evidence supporting the relationship between DNA variants and disease. The approach presented in this paper provides a solution that help researchers to organize, store and process information focusing only on the data that are relevant and minimizing the impact that the information overload has in clinical and research contexts. A case-study (epilepsy) is also presented, to demonstrate its application in a real context.
Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra
Authors: Weis Caroline , Horn Max , Rieck Bastian , Cuénod Aline , Egli Adrian , Borgwardt Karsten
Published: May 2020

Motivation

Microbial species identification based on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a standard tool in clinical microbiology. The resulting MALDI-TOF mass spectra also harbour the potential to deliver prediction results for other phenotypes, such as antibiotic resistance. However, the development of machine learning algorithms specifically tailored to MALDI-TOF MS-based phenotype prediction is still in its infancy. Moreover, current spectral pre-processing typically involves a parameter-heavy chain of operations without analyzing their influence on the prediction results. In addition, classification algorithms lack quantification of uncertainty, which is indispensable for predictions potentially influencing patient treatment.

Results

We present a novel prediction method for antimicrobial resistance based on MALDI-TOF mass spectra. First, we compare the complex conventional pre-processing to a new approach that exploits topological information and requires only a single parameter, namely the number of peaks of a spectrum to keep. Second, we introduce PIKE, the peak information kernel, a similarity measure specifically tailored to MALDI-TOF mass spectra which, combined with a Gaussian process classifier, provides well-calibrated uncertainty estimates about predictions. We demonstrate the utility of our approach by predicting antibiotic resistance of three clinically highly relevant bacterial species. Our method consistently outperforms competitor approaches, while demonstrating improved performance and security by rejecting out-of-distribution samples, such as bacterial species that are not represented in the training data. Ultimately, our method could contribute to an earlier and precise antimicrobial treatment in clinical patient care.

Availability and implementation

We make our code publicly available as an easy-to-use Python package under https://github.com/BorgwardtLab/maldi_PIKE.
Identifying diagnosis-specific genotype–phenotype associations via joint multitask sparse canonical correlation analysis and classification
Authors: Du Lei , Liu Fang , Liu Kefei , Yao Xiaohui , Risacher Shannon L , Han Junwei , Guo Lei , Saykin Andrew J , Shen Li ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: May 2020

Motivation

Brain imaging genetics studies the complex associations between genotypic data such as single nucleotide polymorphisms (SNPs) and imaging quantitative traits (QTs). The neurodegenerative disorders usually exhibit the diversity and heterogeneity, originating from which different diagnostic groups might carry distinct imaging QTs, SNPs and their interactions. Sparse canonical correlation analysis (SCCA) is widely used to identify bi-multivariate genotype–phenotype associations. However, most existing SCCA methods are unsupervised, leading to an inability to identify diagnosis-specific genotype–phenotype associations.

Results

In this article, we propose a new joint multitask learning method, named MT–SCCALR, which absorbs the merits of both SCCA and logistic regression. MT–SCCALR learns genotype–phenotype associations of multiple tasks jointly, with each task focusing on identifying one diagnosis-specific genotype–phenotype pattern. Meanwhile, MT–SCCALR cannot only select relevant SNPs and imaging QTs for each diagnostic group alone, but also allows the selection of those shared by multiple diagnostic groups. We derive an efficient optimization algorithm whose convergence to a local optimum is guaranteed. Compared with two state-of-the-art methods, MT–SCCALR yields better or similar canonical correlation coefficients and classification performances. In addition, it owns much better discriminative canonical weight patterns of great interest than competitors. This demonstrates the power and capability of MTSCCAR in identifying diagnostically heterogeneous genotype–phenotype patterns, which would be helpful to understand the pathophysiology of brain disorders.

Availability and implementation

The software is publicly available at https://github.com/dulei323/MTSCCALR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Benchmarking gene ontology function predictions using negative annotations
Authors: Warwick Vesztrocy Alex , Dessimoz Christophe
Published: May 2020

Motivation

With the ever-increasing number and diversity of sequenced species, the challenge to characterize genes with functional information is even more important. In most species, this characterization almost entirely relies on automated electronic methods. As such, it is critical to benchmark the various methods. The Critical Assessment of protein Function Annotation algorithms (CAFA) series of community experiments provide the most comprehensive benchmark, with a time-delayed analysis leveraging newly curated experimentally supported annotations. However, the definition of a false positive in CAFA has not fully accounted for the open world assumption (OWA), leading to a systematic underestimation of precision. The main reason for this limitation is the relative paucity of negative experimental annotations.

Results

This article introduces a new, OWA-compliant, benchmark based on a balanced test set of positive and negative annotations. The negative annotations are derived from expert-curated annotations of protein families on phylogenetic trees. This approach results in a large increase in the average information content of negative annotations. The benchmark has been tested using the naïve and BLAST baseline methods, as well as two orthology-based methods. This new benchmark could complement existing ones in future CAFA experiments.

Availability and Implementation

All data, as well as code used for analysis, is available from https://lab.dessimoz.org/20_not.

Supplementary information

Supplementary data are available at Bioinformatics online.
Privacy-preserving construction of generalized linear mixed model for biomedical computation
Authors: Zhu Rui , Jiang Chao , Wang Xiaofeng , Wang Shuang , Zheng Hao , Tang Haixu
Published: May 2020

Motivation

The generalized linear mixed model (GLMM) is an extension of the generalized linear model (GLM) in which the linear predictor takes random effects into account. Given its power of precisely modeling the mixed effects from multiple sources of random variations, the method has been widely used in biomedical computation, for instance in the genome-wide association studies (GWASs) that aim to detect genetic variance significantly associated with phenotypes such as human diseases. Collaborative GWAS on large cohorts of patients across multiple institutions is often impeded by the privacy concerns of sharing personal genomic and other health data. To address such concerns, we present in this paper a privacy-preserving Expectation–Maximization (EM) algorithm to build GLMM collaboratively when input data are distributed to multiple participating parties and cannot be transferred to a central server. We assume that the data are horizontally partitioned among participating parties: i.e. each party holds a subset of records (including observational values of fixed effect variables and their corresponding outcome), and for all records, the outcome is regulated by the same set of known fixed effects and random effects.

Results

Our collaborative EM algorithm is mathematically equivalent to the original EM algorithm commonly used in GLMM construction. The algorithm also runs efficiently when tested on simulated and real human genomic data, and thus can be practically used for privacy-preserving GLMM construction. We implemented the algorithm for collaborative GLMM (cGLMM) construction in R. The data communication was implemented using the rsocket package.

Availability and implementation

The software is released in open source at https://github.com/huthvincent/cGLMM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Floral development and anatomy of two species ofAechmea(Bromeliaceae, Bromelioideae)
Authors: Santa-Rosa Sandra , Versieux Leonardo M , Rossi Monica Lanzoni , Martinelli Adriana Pinheiro
Published: May 2020

Aechmea (Bromeliaceae) is a large genus with controversial systematics and distinct flower shapes and pollinators. We explored floral anatomy and development in two Aechmea spp. belonging to different subgenera to contribute useful information on reproductive biology and taxonomy. We examined floral buds using scanning electron and light microscopy to characterize the development of septal nectaries, petal appendages, ovules, stamens and carpels. In A. gamosepala, we confirmed that the petal appendages develop late, whereas in A. correia-araujoi they develop earlier during floral development. Petal appendage formation included positional changes, possibly affecting floral attributes and visitation by insects, rather than vertebrates. Nectar is released through three basal orifices distally on the ovary, and here we document the link between the nectary region, through discrete canals, upward to the conduplicate lobes of the wet stigma. Improved understanding of the floral development and morphology of Aechmea may help to explain the existence of polymorphic flowers in this genus and may have implications for studies on interactions with pollinators and systematics.
Sex-dependent autosomal effects on clinical progression of Alzheimer’s disease
Authors: Fan Chun Chieh , Banks Sarah J , Thompson Wesley K , Chen Chi-Hua , McEvoy Linda K , Tan Chin Hong , Kukull Walter , Bennett David A , Farrer Lindsay A , Mayeux Richard , Schellenberg Gerard D , Andreassen Ole A , Desikan Rahul , Dale Anders M
Published: May 2020

Sex differences in the manifestations of Alzheimer’s disease are under intense investigation. Despite the emerging importance of polygenic predictions for Alzheimer’s disease, sex-dependent polygenic effects have not been demonstrated. Here, using a sex crossover analysis, we show that sex-dependent autosomal genetic effects on Alzheimer’s disease can be revealed by characterizing disease progress via the hazard function. We first performed sex-stratified genome-wide associations, and then applied derived sex-dependent weights to two independent cohorts. Relative to sex-mismatched scores, sex-matched polygenic hazard scores showed significantly stronger associations with age-at-disease-onset, clinical progression, amyloid deposition, neurofibrillary tangles, and composite neuropathological scores, independent of apolipoprotein E. Models without using hazard weights, i.e. polygenic risk scores, showed lower predictive power than polygenic hazard scores with no evidence for sex differences. Our results indicate that revealing sex-dependent genetic architecture requires the consideration of temporal processes of Alzheimer’s disease. This has strong implications not only for the genetic underpinning of Alzheimer’s disease but also for how we estimate sex-dependent polygenic effects for clinical use.
Persistence of Clinically Significant Portal Hypertension After Eradication of Hepatitis C Virus in Patients With Advanced Cirrhosis
Authors: Díez Cristina , Berenguer Juan , Ibañez-Samaniego Luis , Llop Elba , Pérez-Latorre Leire , Catalina María V , Hontañón Víctor , Jiménez-Sousa María A , Aldámiz-Echevarría Teresa , Martínez Javier , Calleja José Luis , Albillos Agustín , Bellón José M , Resino Salvador , González-García Juan , Bañares Rafael
Published: May 2020

This prospective study of 34 patients with HCV cirrhosis (17 HIV positive) with baseline clinically significant portal hypertension (CSPH; HVPG ≥10 mmHg) and SVR after DAA therapy showed that disappearance of CSPH (primary endpoint) is a rare event (6/18 patients; 18%), indicating a persistent risk of clinical progression or death.
Towards Rivalry or Concert? A China–US Financial Competition Triumvirate
Authors: Zhang Falin
Published: May 2020

Given the pivotal role of finance in interstate relations as a prominent source of international power, China–US financial competition, or even confrontation, could be more intense and devastating than trade conflict. It hence merits greater policy and academic attention and communication between the two states. This article takes stock of a triumvirate of Chinese views regarding China’s financial rise and potential China–US financial competition that has empirical and epistemological dimensions. Empirically, it signifies three major issue areas: Renminbi (RMB) strategies and dollar hegemony; the China–US financial imbalance and debt relations; and US dominance of global financial governance and ‘Zhongguo Fangan’—Chinese Solutions. RMB strategies to break dollar hegemony include a further three areas: International Monetary System reform; RMB internationalisation; and financial opening-up. Epistemologically, the empirical analyses present a triumvirate of embedded and interweaved angles: normative and universal; technical and micro level; and power and nationalist. Based on a triumvirate of perspectives, it argues that China’s financial rise is variously limited in relevant fields, and that China–US financial competition also varies according to different issue areas associated with different financial powers, and thus calls for a reductionist, field-specific, and pluralistic approach to managing China–US financial competition.
EmailDetective: An Email Authorship Identification And Verification Model
Authors: Fang Yong , Yang Yue , Huang Cheng
Published: May 2020

Emails are often used to illegal cybercrime today, so it is important to verify the identity of the email author. This paper proposes a general model for solving the problem of anonymous email author attribution, which can be used in email authorship identification and email authorship verification. The first situation is to find the author of an anonymous email among the many suspected targets. Another situation is to verify if an email was written by the sender. This paper extracts features from the email header and email body and analyzes the writing style and other behaviors of email authors. The behaviors of email authors are extracted through a statistical algorithm from email headers. Moreover, the author’s writing style in the email body is extracted by a sequence-to-sequence bidirectional long short-term memory (BiLSTM) algorithm. This model combines multiple factors to solve the problem of anonymous email author attribution. The experiments proved that the accuracy and other indicators of proposed model are better than other methods. In email authorship verification experiment, our average accuracy, average recall and average F1-score reached 89.9%. In email authorship identification experiment, our model’s accuracy rate is 98.9% for 10 authors, 92.9% for 25 authors and 89.5% for 50 authors.
The prognostic value of soluble suppression of tumourigenicity 2 and galectin-3 for sinus rhythm maintenance after cardioversion due to persistent atrial fibrillation in patients with normal left ventricular systolic function
Authors: Wałek Paweł , Gorczyca Iwona , Grabowska Urszula , Spałek Michał , Wożakowska-Kapłon Beata
Published: May 2020

Aims

Soluble suppression of tumourigenicity 2 (sST2) and galectin-3 are involved in cardiac fibrosis, inflammation, and remodelling. However, the place of sST2 and galectin-3 in predicting the outcomes of electrical cardioversion of atrial fibrillation (AF) is uncertain. We evaluated whether these biomarkers could predict sinus rhythm (SR) maintenance after cardioversion of persistent AF in patients with normal left ventricular systolic function.

Methods and results

The study included 80 patients with persistent AF, who underwent cardioversion from February 2016 to August 2018. The blood concentrations of sST-2 and galectin-3 were measured with ELISA and the ASPECT-PLUS assays. Clinical and electrocardiographic follow-up was performed at months 1, 6, and 12. Patients who maintained SR at 12 months had significantly lower concentrations of sST2, measured by ELISA and ASPECT-PLUS assays, than the remaining patients (16.9 ± 9.8 vs. 28 ± 22.9 ng/mL; P < 0.001; 28.7 ± 13.4 vs. 40 ± 25.1 ng/mL; P = 0.003); the concentration of galectin-3 did not differ between these patients. Multivariable logistic regression showed that log-transformed sST2 ELISA was a significant predictor of SR maintenance at 12 months [odds ratio 0.14; 95% confidence interval (CI) 0.03–0.58; P = 0.006]. On receiver-operating characteristic curve analysis, the areas under the curve for the concentration of sST2 was 0.752 (95% CI 0.634–0.870; P < 0.001). The concentrations of sST2 measured with the two assays were strongly correlated (rho = 0.8; CI 95% 0.7–0.87; P = 0.001).

Conclusion

Soluble suppression of tumourigenicity 2, but not galectin-3, can be used to predict SR maintenance after cardioversion of AF in patients with normal left ventricular systolic function. The measurements of sST2 concentrations with the rapid lateral flow and enzyme-linked immunoassays were consistent.
A comparison of self-reported to cotinine-detected smoking status among adults in Georgia
Authors: Williams Julianne , Rakovac Ivo , Loyola Enrique , Sturua Lela , Maglakelidze Nino , Gamkrelidze Amiran , Mauer-Stender Kristina , Mikkelsen Bente , Breda João
Published: May 2020

Background

Self-reported measures of tobacco use may have limited validity, particularly among some populations. This study aims to validate self-reported smoking measures among Georgian adults participating in the 2016 STEPS survey using cotinine biomarker measurements, and to explore potential differences according to sociodemographic characteristics. Additionally, this paper examines how the estimated prevalence of smoking in the population varies according to measurement type.

Methods

Using the WHO standardized STEPS methodology, adults self-reported their smoking status. In a later stage of the survey, a subset of participants provided a urine sample, which was tested for cotinine. Using each participant’s objective cotinine measurement and their self-reported smoking status, we calculated the sensitivity, specificity and positive predictive value of self-reported smoking. Next, we calculated the estimated prevalence of smokers according to the type of measurement.

Results

Results indicated high sensitivity (83.37%, 95% CI: 76.79–88.37%) among males and relatively low sensitivity (38.60% CI: 29.23–48.90%) among females. According to self-report, the prevalence of smokers was 26.44% (23.61–29.48%), while according to cotinine detection, the prevalence of smokers was 32.27% (29.16–35.55%). Among all subgroups, the self-reported prevalence of smoking was significantly lower than the cotinine-detected prevalence.

Conclusions

To the best of our knowledge, this is the first time that the validity of the STEPS self-reported tobacco indicator has been tested. Self-reported measures of smoking status may lead to an under-estimation of smoking prevalence among Georgian adults, especially women. These findings suggest that integration of biochemical measures of smoking into tobacco use studies may be an important investment.
The extent of continental material in oceans: C-Blocks and the Laxmi Basin example
Authors: Geoffroy L , Guan H , Gernigon L , Foulger G R , Werner P
Published: May 2020

We propose a tectonic interpretation for the outer-SDRs (SDRs: Seaward-Dipping Reflectors) and Pannikar central ridge in the aborted Laxmi Basin west of India from wide-angle seismic reflection data. The outer-SDRs comprise syn-tectonic extrusives (lavas and/or volcaniclastics) emplaced above passively exhumed mid-to-lower mafic crust of continental origin. They erupted following sudden lithosphere weakening associated with isolation of a continental block (a ‘C-Block’). Continuous magmatic addition during crustal extension allowed stretching of the lower crust whilst maintaining constant or even increasing thickness. A similar process occurred at both conjugate margins allowing bulk, pure-shear plate separation and formation of linear magnetic anomalies. The Laxmi example can explain enigmatic features observed in mature oceans such as presence of distal buoyant plateaus of thick continental crust away from the margins.
Coding in medically assisted reproduction: the status of the implementation of the Single European Code for reproductive cells and tissues†
Authors:   The ESHRE Special Interest Group Safety and Quality in ART, Alteri Alessandra, , Vermeulen Nathalie , Rugescu Ioana Adina , Nogueira Daniela , Veleva Zdravka , D’Angelo Arianna , Tilleman Kelly
Published: May 2020

STUDY QUESTION

To evaluate the implementation of the coding systems in medically assisted reproduction (MAR) centres in the European Union (EU).

SUMMARY ANSWER

Our data show that a significant number of MAR centres use the Single European Code (SEC), but it also shows certain limitations to the coding.

WHAT IS KNOWN ALREADY

Traceability and identification of tissue and cells used for clinical application are extremely important as it is one of the key aspects of quality and safety both for the donors and the recipients. Patients as well as tissues and cells move across the European continent and far beyond, hence a uniform coding system was very much needed. The coding of tissues and cells from human origin was already embedded in the EU directives 2004/23/EC. The use of the Single European Code (SEC) on tissues and cells was enforced in 2017 for tissues and cells distributed within the EU or exported from the EU. The SEC ensures standardization within the EU, allowing the integration of the two existing codes (ISBT-128 and Eurocode) within the SEC structure. Likewise, in the MAR field, the SEC was launched in order to ensure the traceability of reproductive tissues and cells. Gametes and embryos from partner donation as well as reproductive cells and tissues of allogeneic donation were excluded from the SEC as long as they remain in the centre of origin.

STUDY DESIGN, SIZE, DURATION

A cross-sectional survey aimed to gain insight into the use of SEC by MAR centres was conducted between 5 November and 15 December 2018.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The online survey was distributed among the ESHRE members.

MAIN RESULTS AND THE ROLE OF CHANCE

The survey results highlight the strengths and weaknesses in the practical use of the SEC. The data from the survey showed that the SEC code is something that is known in the MAR field. Our data showed that over half of the respondents were using the SEC in their centre. On the other hand, there is also criticism about the use of SEC in MAR, especially that the added value for traceability and identification in ART is found to be rather limited.

LIMITATIONS, REASONS FOR CAUTION

The survey response rate was rather low (4.84%). The view of the use of SEC discussed in this paper still provides insight into the use of the SEC in several MAR centres.

WIDER IMPLICATIONS OF THE FINDINGS

The survey highlights some knowledge gaps concerning coding. This information can be used to develop tools to increase knowledge of the SEC.

STUDY FUNDING/COMPETING INTEREST(S)

There was no external funding for this study. The authors declare that they have no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.