bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid hippocampal plasticity supports motor sequence learning
Authors: Jacobacci Florencia , Armony Jorge L. , Yeffal Abraham , Lerner Gonzalo , Amaro Edson , Jovicich Jorge , Doyon Julien , Della-Maggiore Valeria 
Published: September 2020

Significance
Learning predefined sequences of actions is of everyday importance. Recent evidence suggests that improvements in performance associated with learning a motor sequence take place during the quiet rest periods interleaved with practice. This phenomenon known as micro-offline gains (MOGs) is different from offline gains in performance observed overnight. Using a multimodal—functional and structural—MRI approach, here we show that the hippocampus participates in the generation of MOGs through a mechanism reminiscent of memory reactivation. Our findings point to the involvement of the hippocampus in the reactivation of nonhippocampal memories and provide evidence for a possible common mechanism at the basis of the formation of declarative and nondeclarative memories.
The limitations of extending nature’s color palette in correlated, disordered systems
Authors: Jacucci Gianni , Vignolini Silvia , Schertel Lukas 
Published: September 2020

Significance
Scattering from 2D correlated disordered structures is often at the core of matte color appearances in nature. However, the hues related to this mechanism are restricted to UV radiation and the blue part of the visible spectrum. Here we present a numerical study on short-range correlated materials—photonic glasses—without the restriction to a specific light transport regime. We demonstrate that with these materials, saturated angle-independent structural colors cannot be reached in the long-wavelength region of the visible spectrum. In this context, we discuss promising approaches toward 3D isotropic structural colored materials.
SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification
Authors: Rabe Brian A. , Cepko Constance 
Published: September 2020

Significance
This work describes the optimization of a sample preparation and detection pipeline for a SARS-CoV-2 diagnostic test that is rapid and does not require specialized equipment. This pipeline consists of viral inactivation, rendering samples safer to work with, followed by a sensitive 30-min isothermal detection reaction with a color-based red to yellow readout. Sensitivity can be further improved using a simple and inexpensive purification protocol. This pipeline can help address the shortage of testing capacity and can be run in a variety of settings.
Dynamic changes in DICER levels in adipose tissue control metabolic adaptations to exercise
Authors: Brandão Bruna B. , Madsen Søren , Rabiee Atefeh , Oliverio Matteo , Ruiz Gabriel P. , Ferrucci Danilo L. , Branquinho Jéssica L. , Razolli Daniela , Pinto Silas , Nielsen Thomas S. , Festuccia William T. , Martins Adriano S. , Guerra Beatriz A. , Knittel Thiago L. , Søgaard Ditte , Larsen Steen , Helge Jørn W. , Brandauer Josef , Velloso Lício A. , Emanuelli Brice , Kornfeld Jan-Wilhelm , Kahn C. Ronald , Vienberg Sara G. , Zierath Juleen R. , Treebak Jonas T. , Mori Marcelo A. 
Published: September 2020

Significance
Aerobic exercise elicits an integrated metabolic response that involves multiple tissues and confers beneficial effects to metabolic health. Here we found that this integrative response involves energy-sensing pathways in muscle and fat and circulating factors that lead to the upregulation of the type III endoribonuclease DICER in adipose tissue and the consequent increase of microRNAs. Upon upregulation, DICER and the microRNA-203-3p inhibit glucose utilization by fat cells and favor oxidative metabolism. In turn, this supports the exercised muscle with adequate substrate availability. When this pathway is disrupted, whole-body metabolism is affected, and exercise performance is impaired. Thus, adipose tissue DICER integrates signals from the exercising muscle to allow a proper metabolic response to exercise training.
Internet memes we live by (and die by)
Authors: Xie Chaoqun 
Published: September 2020

AbstractIn the internet age, memes are at once products and driving forces of social practices. A meme contains a memetic message and a meme output, and boasts, if guided by a pragmatic way of thinking, several features, including but not limited to salience, frequency, adaptability, argumentativity, sociality, embeddedness, embodiedness, locality, relativity, emotionality and dynamicity. The current global COVID-19 pandemic serves as a fitting and timely touchstone to testify how human beings are surrounded by numerous good and evil memes in the online world, and how internet memes, as can be seen from the illustration of two specific memes, namely, the ‘stay home, stay safe’ meme and the ‘wear a mask’ meme, are impacting human life-worlds, online and offline, with their transformative power, be it constructive or destructive. Moreover, researching how memes plays a decisive part in internet-mediated interaction provides a lens of insight through which ‘deep states’ of human nature of both self and others can be uncovered and through which what Nietzsche called “a revaluation of values” is possible.
Second language immersion impacts native language lexical production and comprehension
Authors: Botezatu Mona Roxana , Kroll Judith F. , Trachsel Morgan I. , Guo Taomei 
Published: September 2020

Abstract
We investigated whether the features of the second language (L2) matter when we consider the consequence of short-term L2
immersion on performance in the native language (L1). We compared L1 performance in English-speaking learners of a typologically-dissimilar
L2-Chinese immersed in Chinese while living in Beijing, China and learners of a typologically-similar L2 (Spanish or French) exposed to the
L2 in a classroom setting only. The groups were matched on cognitive abilities. Each group performed a battery of language tasks in English
that assessed the ability to produce and recognize spoken words, as well as to name written words and pseudo-words in the native language.
Immersed learners produced fewer words in their native language, made more semantic errors, and benefited more from higher lexical frequency
when retrieving L1 words relative to classroom learners. Immersed learners also revealed reduced competition from dense phonological
neighborhoods when listening to English words presented in noise, but no difference in English word reading and phonemic decoding
performance compared to classroom learners. Results are consistent with the view that L2 immersion reduces access to the native language,
but suggest that the consequences of L2 immersion on the L1 may be dependent upon the form of cross-language differences.
Mapping terminological variation and ideology in data protection laws
Authors: Pei Jiamin , Cheng Le 
Published: September 2020

Abstract
This study aims to deal with the relationship between terminological variation and ideology by examining the system of
terminology and the defined individual terms in data protection legislation. With two self-compiled corpora incorporating data protection
laws in the United States and the European Union respectively, we adopt a corpus-assisted approach as an effective toolkit to generate a
general profile of the system of legal terminology on the one hand and identify the defined legal terms in the two corpora on the other.
This study, based on Van Dijk’s (1998) multidisciplinary approach to ideology, seeks to unravel
the underlying ideological configurations behind the variation of legal terminology. The findings show that one plausible – though certainly
not definitive – interpretation of the variation in legal terminology in the data protection domain lies in the distinct ideological stances
imposed by such discourse communities as lawmakers, judges as well as the president and the party in power. The ideological investigation of
terminology is a significant aspect of the study of variation phenomena. It is argued that the ideologically variable slants and historical
experiences, as the contextual constraints on the ideological beliefs, may contribute to accounting for the spatial and temporal variation
of legal terminology.
How do supranational terms transfer into national legal systems?
Authors: Biel Łucja , Doczekalska Agnieszka 
Published: September 2020

Abstract
The objective of this paper is to analyse how European Union (EU) supranational terms related to consumer protection
transfer into domestic legal systems of three English-language jurisdictions (the UK, Ireland and Malta) during the transposition of EU
directives. Transposition is a process of incorporating EU directives into national law and capturing supranational terms during their entry
into national legal systems. We adopt a mixed-method approach of corpus linguistics and legal analysis of terms, working with a corpus of
five directives and their UK, Irish and Maltese transposing acts. Distinguishing between a term and a concept level, we propose a
categorisation of transfer techniques arranged along a cline from foreignization to domestication. They involve imports, modifications
(non-denominative and denominative variants), localisations and zero transfer both at the term level and the concept level.
Data driven regularization by projection
Authors: Aspri Andrea , Korolev Yury , Scherzer Otmar 
Published: September 2020

Abstract
We study linear inverse problems under the premise that the forward operator is not at hand but given indirectly through some input-output training pairs. We demonstrate that regularization by projection and variational regularization can be formulated by using the training data only and without making use of the forward operator. We study convergence and stability of the regularized solutions in view of Seidman (1980 J. Optim. Theory Appl.
30 535), who showed that regularization by projection is not convergent in general, by giving some insight on the generality of Seidman’s nonconvergence example. Moreover, we show, analytically and numerically, that regularization by projection is indeed capable of learning linear operators, such as the Radon transform.
Exterior Steklov eigenvalues and modified exterior Steklov eigenvalues in inverse scattering
Authors: Li Yuan 
Published: September 2020

Abstract
The inverse scattering problem for anisotropic media with data measured inside a cavity is considered. We aim to introduce the exterior Steklov eigenvalues (ESEs) and the modified exterior Steklov eigenvalues (MESEs) to detect changes in the material properties of the medium from a knowledge of a modified near field operator each. First, a connection between a modified near field operator and the exterior Steklov eigenvalue problem is established. Then the ESEs are proved to be discrete and lie in the lower half-plane. Since the existence of the ESEs is unknown due to non-self-adjointness, we propose the modified exterior Steklov eigenvalue problem for which infinitely many eigenvalues exist. Based on the factorizations of both the modified near field operator and the auxiliary near field operator, a nonsymmetric version of generalized linear sampling method (GLSM) is employed to compute the ESEs. This method also allows for the computation of the MESEs by adjusting the definitions of some associated operators. Numerical examples are presented to demonstrate the viability of this method and show the potential use of these eigenvalues as new classes of target signatures in nondestructive testing.
Size reduction of boron particles by high-power ultrasound for optimization of bulk MgB2
Authors: Arvapalli Sai Srikanth , Miryala Muralidhar , Jirsa Milos , Murakami Masato 
Published: September 2020

Abstract
Critical current density, J
c, in superconductors is strongly connected with size of defects in the material. Frequently, the smaller defects, the higher J
c. In this work, we tried to reduce the size of cheap commercial boron precursor powder using high energy ultra-sonication in ethanol media. The resulting powder was then utilized in synthesizing bulk MgB2 via sintering at 775 °C. Effect of boron powder ultra-sonication on superconducting properties of the bulk MgB2 was studied and discussed. SEM of ultra-sonicated boron showed fine particles with sharp edges (high-energy surfaces), irregular shapes and clustering of fine particles occurred for longer ultra-sonication durations. XRD proved a high quality of MgB2 with only small traces of MgO. Around 36% improvement in Jc
at 20 K and Tc
close to 39 K were observed in MgB2 bulk prepared with boron ultra-sonicated for 15 min. Microstructure studies showed numerous nanometre sized MgB2 grains in the bulk. Other bulks (made of boron ultra-sonicated longer, for 30, 45, and 60 min) have larger grains. It resulted in slightly lower J
c, anyway, still by 22% higher than in reference bulk. The present results demonstrate that the high performance bulk MgB2 can be achieved without reduction in T
c via employing a cheap boron, reduced in size by high-energy ultra-sonication.
Chondrobags: A high throughput alginate-fibronectin micromass platform for in vitro human cartilage formation
Authors: Witte Kimia , de Andrés María C , Wells Julia , Dalby Matthew J , Salmeron-Sanchez Manuel , Oreffo Richard O C 
Published: September 2020

Abstract
The maintenance and expansion of the cells required for formation of tissue-engineered cartilage has, to date, proven difficult. This is, in part, due to the initial solid phase extracellular matrix demanded by the cells inhabiting this avascular tissue. Herein, we engineer an innovative alginate-fibronectin microfluidic-based carrier construct (termed a chondrobag) equipped with solid phase presentation of growth factors that support skeletal stem cell chondrogenic differentiation while preserving human articular chondrocyte phenotype. Results demonstrate biocompatibility, cell viability, proliferation and tissue-specific differentiation for chondrogenic markers SOX9, COL2A1 and ACAN. Modulation of chondrogenic cell hypertrophy, following culture within chondrobags loaded with TGF-β1, was confirmed by down-regulation of hypertrophic genes COL10A1 and MMP13. MicroRNAs involved in the chondrogenesis process, including miR-140, miR-146b and miR-138 were observed. Results demonstrate the generation of a novel high-throughput, microfluidic-based, scalable carrier that supports human chondrogenesis with significant implications therein for cartilage repair-based therapies.
Limitations of paraxial approximation to model elec-tron acceleration by a laser pulse in vacuum in the presence of an axial magnetic field
Authors: Singh Kunwar Pal , Malik Anil K 
Published: September 2020

Abstract
We model electron acceleration using paraxial approximation (PA) and seventh order correction description (O7) of a laser field in vacuum in the presence of an axial magnetic field. The effect of initial momentum, laser intensity, spot size, and initial position of electron on optimum value of magnetic field and electron energy for linearly and circularly polarized laser pulse has been investigated. We show that PA fails to obtain correct values of optimum magnetic field and electron energy. The amplitude of oscillations of the electron increases with time in the presence of axial magnetic field and PA fails to correctly take into account focusing and defocusing of laser and obtain correct results.
Seasonal coordination of leaf hydraulics and gas exchange in a wintergreen fern
Authors: Prats Kyra A , Brodersen Craig R 
Published: September 2020

AbstractWintergreen fern Polystichum acrostichoides has fronds that are photosynthetically active year-round, despite diurnal and seasonal changes in soil moisture, air temperature and light availability. This species can fix much of its annual carbon during periods when the deciduous canopy is open. Yet, remaining photosynthetically active year-round requires the maintenance of photosynthetic and hydraulic systems that are vulnerable to freeze–thaw cycles. We aimed to determine the anatomical and physiological strategies P. acrostichoides uses to maintain positive carbon gain, and the coordination between the hydraulic and photosynthetic systems. We found that the first night below 0 °C led to 25 % loss of conductivity (PLC) in stipes, suggesting that winter-induced embolism occurred. Maximum photosynthetic rate and chlorophyll fluorescence declined during winter but recovered by spring, despite PLC remaining high; the remaining hydraulic capacity was sufficient to supply the leaves with water. The onset of colder temperatures coincided with the development of a necrotic hinge zone at the stipe base, allowing fronds to overwinter lying prostrate and maintain a favourable leaf temperature. Our conductivity data show that the hinge zone did not affect leaf hydraulics because of the flexibility of the vasculature. Collectively, these strategies help P. acrostichoides to survive in northeastern forests.
Built to change: dominance strategy changes with life stage in a primitively eusocial bee
Authors: Orlova Margarita , Treanore Erin , Amsalem Etya 
Published: September 2020

AbstractAccess to reproduction is determined by an individual’s dominance rank in many species and is achieved through aggression and/or dominance signaling. In eusocial insects, one or several dominant females (queens) monopolize reproduction but to what extent queens rely on aggression and signaling remains obscure. Aggression is costly and its efficiency depends on the group size, whereas signaling may reduce the risks and costs of aggression. Both strategies are used to regulate reproduction in social taxa, with aggression being more common in small social groups, compared to signaling in larger societies. Here, we examine the use of aggression and chemical signaling in a social species (Bombus impatiens) where the dominant queen interacts with increasing numbers of workers as she ages. We found that the queen’s strategy to monopolize reproduction changes with life stage, shifting from overt aggression to chemical signaling as the queen gets older. Particularly, old queens exhibited a higher ratio of short to long cuticular hydrocarbons compared to young queens, an endogenous shift that was attributed to age, as all egg-laying queens were fecund and kept with the same number of workers. Our findings contribute to the understanding of reproductive dominance in the context of an individual’s life history.
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation
Authors: Saha Chayan Kumar , Sanches Pires Rodrigo , Brolin Harald , Delannoy Maxence , Atkinson Gemma Catherine 
Published: September 2020

Abstract

Summary
Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin–antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.

Availability and implementation
FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.

Supplementary information
Supplementary data are available at Bioinformatics online.
SCHNEL: scalable clustering of high dimensional single-cell data
Authors: Abdelaal Tamim , de Raadt Paul , Lelieveldt Boudewijn P F , Reinders Marcel J T , Mahfouz Ahmed 
Published: September 2020

Abstract

Motivation
Single cell data measures multiple cellular markers at the single-cell level for thousands to millions of cells. Identification of distinct cell populations is a key step for further biological understanding, usually performed by clustering this data. Dimensionality reduction based clustering tools are either not scalable to large datasets containing millions of cells, or not fully automated requiring an initial manual estimation of the number of clusters. Graph clustering tools provide automated and reliable clustering for single cell data, but suffer heavily from scalability to large datasets.

Results
We developed SCHNEL, a scalable, reliable and automated clustering tool for high-dimensional single-cell data. SCHNEL transforms large high-dimensional data to a hierarchy of datasets containing subsets of data points following the original data manifold. The novel approach of SCHNEL combines this hierarchical representation of the data with graph clustering, making graph clustering scalable to millions of cells. Using seven different cytometry datasets, SCHNEL outperformed three popular clustering tools for cytometry data, and was able to produce meaningful clustering results for datasets of 3.5 and 17.2 million cells within workable time frames. In addition, we show that SCHNEL is a general clustering tool by applying it to single-cell RNA sequencing data, as well as a popular machine learning benchmark dataset MNIST.

Availability and implementation
Implementation is available on GitHub (https://github.com/biovault/SCHNELpy). All datasets used in this study are publicly available.

Supplementary information
Supplementary data are available at Bioinformatics online.
The effect of kinship in re-identification attacks against genomic data sharing beacons
Authors: Ayoz Kerem , Aysen Miray , Ayday Erman , Cicek A Ercument 
Published: September 2020

Abstract

Motivation
Big data era in genomics promises a breakthrough in medicine, but sharing data in a private manner limit the pace of field. Widely accepted ‘genomic data sharing beacon’ protocol provides a standardized and secure interface for querying the genomic datasets. The data are only shared if the desired information (e.g. a certain variant) exists in the dataset. Various studies showed that beacons are vulnerable to re-identification (or membership inference) attacks. As beacons are generally associated with sensitive phenotype information, re-identification creates a significant risk for the participants. Unfortunately, proposed countermeasures against such attacks have failed to be effective, as they do not consider the utility of beacon protocol.

Results
In this study, for the first time, we analyze the mitigation effect of the kinship relationships among beacon participants against re-identification attacks. We argue that having multiple family members in a beacon can garble the information for attacks since a substantial number of variants are shared among kin-related people. Using family genomes from HapMap and synthetically generated datasets, we show that having one of the parents of a victim in the beacon causes (i) significant decrease in the power of attacks and (ii) substantial increase in the number of queries needed to confirm an individual’s beacon membership. We also show how the protection effect attenuates when more distant relatives, such as grandparents are included alongside the victim. Furthermore, we quantify the utility loss due adding relatives and show that it is smaller compared with flipping based techniques.