bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrochemical impedimetric analysis of different dimensional (0D–2D) carbon nanomaterials for effective biosensing of L-tyrosine
Authors: Roy Souradeep , Sain Sourav , Wadhwa Shikha , Mathur Ashish , Dubey Santosh , Roy Susanta S
Published: October 2021

Electrochemical biosensors employing nano-transduction surfaces are considered highly sensitive to the morphology of nanomaterials. Various interfacial parameters namely charge transfer resistance, double layer capacitance, heterogeneous electron transfer rate and diffusion limited processes, depend strongly on the nanostructure geometry which eventually affects the biosensor performance. The present work deals with a comparative study of electrochemical impedance-based detection of L-tyrosine (or simply tyrosine) by employing carbon nanostructures (graphene quantum dots, single walled carbon nanotubes (CNTs) and graphene) along with tyrosinase as the bio-receptor. Specifically, the role of carbon nanostructures (i.e. 0D, 1D and 2D) on charge transfer resistance is investigated by applying time-varying electric field at the nano-bioelectrode followed by calculating the heterogeneous electron transfer rate, double layer capacitor current and their effects on limits of detection and sensitivities towards tyrosine recognition. A theoretical model based on Randel’s equivalent circuit is proposed to account for the redox kinetics at various carbon nanostructure/enzyme hybrid surfaces. It was observed that, the 1D morphology (single walled CNTs) exhibited lowest charge transfer resistance ∼2.62 kΩ (lowest detection limit of 0.61 nM) and highest electron transfer rate ∼0.35 μm s−1 (highest sensitivity 0.37 kΩ nM−1 mm−2). Our results suggest that a suitable morphology of carbon nanostructure would be essential for efficient and sensitive detection of tyrosine.
Zero valence iron nanocube decoration of graphitic nanoplatelets
Authors: Brack Narelle , Spencer Michelle J S , Mapleback Benjamin , Herries Andy I R , Kappen Peter , Rider Andrew N
Published: October 2021

Graphitic nanoplatelets (GNPs) have been treated using an ultrasonicated ozonolysis procedure to produce stable aqueous dispersions that facilitate deposition of thin films using electrophoretic deposition. The thin GNP films were then coated with zero valence (ZV) iron nanocubes using a pulsed electrodeposition technique. Characterization of the ZV-iron coating with deposition time revealed that the changing magnetic character of the ferromagnetic-graphitic hybrid material was related to the nucleation density and growth of the ZV-iron nanocubes. Density functional theory calculations show a preference for ZV-iron adsorption at the oxygen sites of the GNPs, with ZV-iron displacement of oxygen groups favored in some configurations. Transmission electron microscopy studies confirm ZV-iron growth nucleates preferentially at the graphite nanoplatelet edges and the hybrid material magnetism is affected by the convergent crystalline grain boundaries formed between adjacent ZV-iron nanocubes.
Interacting dark energy from redshift-space galaxy clustering
Authors: Carrilho Pedro , Moretti Chiara , Bose Benjamin , Markovič Katarina , Pourtsidou Alkistis
Published: October 2021

Interacting dark energy models have been proposed as
attractive alternatives to ΛCDM. Forthcoming Stage-IV
galaxy clustering surveys will constrain these models, but they
require accurate modelling of the galaxy power spectrum multipoles
on mildly non-linear scales. In this work we consider a dark
scattering model with a simple 1-parameter extension to wCDM —
adding only A, which describes a pure momentum exchange between
dark energy and dark matter. We then provide a comprehensive
comparison of three approaches of modeling non-linearities, while
including the effects of this dark sector coupling. We base our
modeling of non-linearities on the two most popular perturbation
theory approaches: TNS and EFTofLSS. To test the validity and
precision of the modelling, we perform an MCMC analysis using
simulated data corresponding to a ΛCDM fiducial cosmology
and Stage-IV surveys specifications in two redshift bins, z=0.5
and z=1. We find the most complex EFTofLSS-based model studied to
be better suited at both, describing the mock data up to smaller
scales, and extracting the most information. Using this model, we
forecast uncertainties on the dark energy equation of state, w,
and on the interaction parameter, A, finding σ_w=0.06 and
σ
A
=1.1 b/GeV for the analysis at z=0.5 and σ
w
=0.06
and σ
A
=2.0 b/GeV for the analysis at z=1. In addition, we
show that a false detection of exotic dark energy up to 3σ
would occur should the non-linear modelling be incorrect,
demonstrating the importance of the validation stage for accurate
interpretation of measurements.
Covariant effective action for scalar-tensor theories of gravity
Authors: Aashish Sandeep , Panda Sukanta , Altafhussain Tinwala Abbas , Vidyarthi Archit
Published: October 2021

We develop the calculation of the divergent part of one-loop covariant effective action for scalar fields minimally and non-minimally coupled to gravity using the generalized Schwinger-DeWitt technique. We derive the field-space metric using Vilkovisky's prescription and obtain new terms in the one-loop corrections which are absent in past literature with trivial choices of field-space metric. We further calculate the covariant versions of past results, obtained using the standard approach, by applying Barvinsky and Vilkovisky's extension to the ordinary Schwinger-DeWitt approach. For completeness, we study the one-loop gravitational corrections for a dilaton-extended two-field Starobinsky model and compare with known results.
Stability of scalar perturbations in scalar-torsion f(T,ϕ) gravity theories in the presence of a matter fluid
Authors: Gonzalez-Espinoza Manuel , Otalora Giovanni , Saavedra Joel
Published: October 2021

We study the viability conditions for the absence of ghost, gradient and tachyonic instabilities, in scalar-torsion f(T,ϕ) gravity theories in the presence of a general barotropic perfect fluid. To describe the matter sector, we use the Sorkin-Schutz action and then calculate the second order action for scalar perturbations. For the study of ghost and gradient instabilities, we found that the gravity sector keeps decoupled from the matter sector and then applied the viability conditions for each one separately. Particularly, we verified that this theory is free from ghost and gradient instabilities, obtaining the standard results for matter, and for the gravity sector we checked that the corresponding speed of propagation satisfies c_s,g2=1. On the other hand, in the case of tachyonic instability, we obtained the general expressions for the mass eigenvalues and then evaluated them in the scaling matter fixed points of a concrete model of dark energy. Thus, we found a space of parameters where it is possible to have a stable configuration respecting the constraints from the CMB measurements and the BBN constraints for early dark energy. Finally, we have numerically corroborated these results by solving the cosmological equations for a realistic cosmological evolution with phase space trajectories undergoing scaling matter regimes, and then showing that the system presents a stable configuration throughout cosmic evolution.
Kinetic Alfvén waves in a deuterium-tritium fusion plasma with slowing-down distributed α-particles
Authors: Lu Fei-Fei , Liu San-Qiu
Published: October 2021

The dispersion relation and damping rate of kinetic Alfvén waves (KAWs) in a deuterium-tritium fusion plasma with slowing-down distributed α-particles are investigated using the kinetic theory. The variations of wave frequency and damping rate with respect to the α concentration (nα
/n
e) and perpendicular wave number (k
⊥) are studied from a numerical way. The results show that the fluctuation of α concentration slightly affects the frequency and damping rate of KAWs at low nα
/n
e. In addition, the frequency and the damping rate increase as the k
⊥ and the background temperature T
e increase. For comparison, the calculations are performed also in the case of α-particles following an equivalent Maxwellian distribution. For a given k
⊥, the value of the frequency obtained in the slowing-down distribution case is smaller than that obtained in the Maxwellian distribution case. Conversely, the value of the damping rate obtained in the slowing-down distribution case is slightly larger than that obtained in the Maxwellian distribution case.
An analytical model for cross-Kerr nonlinearity in a four-level N-type atomic system with Doppler broadening
Authors: Khoa Dinh Xuan , Bang Nguyen Huy , Le Thuy An Nguyen , Van Phu Nguyen , Van Doai Le
Published: October 2021

We present an analytical model for cross-Kerr nonlinear coefficient in a four-level N-type atomic medium under Doppler broadening. The model is applied to 87Rb atoms to analyze the dependence of the cross-Kerr nonlinear coefficient on the external light field and the temperature of atomic vapor. The analysis shows that in the absence of electromagnetically induced transparency (EIT) the cross-Kerr nonlinear coefficient is zero, but it is significantly enhanced when the EIT is established. It means that the cross-Kerr effect can be turned on/off when the external light field is on or off. Simultaneously, the amplitude and the sign of the cross-Kerr nonlinear coefficient are easily changed according to the intensity and frequency of the external light field. The amplitude of the cross-Kerr nonlinear coefficient remarkably decreases when the temperature of atomic medium increases. The analytical model can be convenient to fit experimental observations and applied to photonic devices.
High-performance coherent population trapping clock based on laser-cooled atoms
Authors: Liu Xiaochi , Ru Ning , Duan Junyi , Yun Peter , Yao Minghao , Qu Jifeng
Published: October 2021

We present a coherent population trapping clock system based on laser-cooled 87Rb atoms. The clock consists of a frequency-stabilized CPT interrogation laser and a cooling laser as well as a compact magneto-optical trap, a high-performance microwave synthesizer, and a signal detection system. The resonance signal in the continuous wave regime exhibits an absorption contrast of ∼ 50%. In the Ramsey interrogation method, the linewidth of the central fringe is 31.25 Hz. The system achieves fractional frequency stability of

2.4
×

10

−
11

/

τ

, which goes down to 1.8 × 10−13 at 20000 s. The results validate that cold atom interrogation can improve the long-term frequency stability of coherent population trapping clocks and holds the potential for developing compact/miniature cold atoms clocks.
Soliton fusion and fission for the high-order coupled nonlinear Schrödinger system in fiber lasers
Authors: Wang Tian-Yi , Zhou Qin , Liu Wen-Jun
Published: October 2021

With the rapid development of communication technology, optical fiber communication has become a key research area in communications. When there are two signals in the optical fiber, the transmission of them can be abstracted as a high-order coupled nonlinear Schrödinger system. In this paper, by using the Hirota’s method, we construct the bilinear forms, and study the analytical solution of three solitons in the case of focusing interactions. In addition, by adjusting different wave numbers for phase control, we further discuss the influence of wave numbers on soliton transmissions. It is verified that wave numbers k
11, k
21, k
31, k
22, and k
32 can control the fusion and fission of solitons. The results are beneficial to the study of all-optical switches and fiber lasers in nonlinear optics.
Development of a gamma-ray imaging detector based on ceramic scintillators with SiPM readout
Authors: Xu L. , Tian Y. , Li Y.
Published: October 2021

Depth of interaction (DOI) measurements can provide
additional position information when long scintillator bars or
scintillator pixels with relatively large thickness are employed in
gamma-ray imaging detectors. In this study, commercially available
GGAG ceramic scintillators were used to fabricate a gamma-ray
imaging detector. The light attenuation, DOI resolution, and
spectroscopic performance of 3.0× 3.0× 48.0 mm3
ceramic bars were evaluated using double-side SiPM readout. The
measured full width at half maximum (FWHM) energy resolution values
ranged between 7.6% and 8.7% at 511 keV. The DOI resolution was
approximately 4 mm (FWHM). A prototype two-layer Compton imaging
detector was fabricated based on 32 ceramic bars and the signals
were readout using four 16-ch application-specific integrated
circuits. The lutetium background was evaluated and a 22Na
point source (0.19 μSv/h 511 keV gamma-ray dose rate at
50 cm) was used to verify the feasibility of using the commercial
GGAG ceramic material in nuclear security applications. The source
can be located within 120 s using a simple back projection
method. The angular resolution measure was estimated as 15∘
(FWHM). A filtered back projection based algorithm improved the
angular resolution (FWHM) to 9.2∘.
Excitons in strained and suspended monolayer WSe2
Authors: Aslan Burak , Yule Colin , Yu Yifei , Lee Yan Joe , Heinz Tony F , Cao Linyou , Brongersma Mark L
Published: October 2021

We study suspended membranes of atomically thin WSe2 as hosts of excitons. We perform optical reflectance measurements to probe the exciton physics and obtain the peak energies for the 1

s

, 2

s

, and 3

s

states of the

A

exciton in suspended WSe2 and consider supported membranes as a reference. We find that elimination of the influence of the dielectric environment enables a strong electron–hole interaction and a concomitant increase in the exciton binding energy in suspended monolayer (1L) WSe2. Based on the experimental results, we calculate the excitonic binding energies by employing the recently developed quantum electrostatic heterostructure model and the commonly employed Rytova–Keldysh potential model. We see that the binding energy of the ground state

A

exciton increases from about 0.3 eV (on a substrate) to above 0.4 eV (suspended). We also exploit the tunability of the excitons in suspended samples via mechanical strain. By applying external gas pressure of 2.72 atm to a 1L suspended over a circular hole of 8 μm diameter, we strain the WSe2 and obtain a reversible 0.15 eV redshift in the exciton resonance. The linewidth of the

A

exciton decreases by more than half, from about 50 to 20 meV under 1.5% biaxial strain at room temperature. This line narrowing is due to the suppression of intervalley exciton–phonon scattering. By making use of the observed strain-dependent optical signatures, we infer the two-dimensional (2D) elastic moduli of 1L and 2L WSe2. Our results exemplify the use of suspended 2D materials as novel systems for fundamental studies, as well as for strong and dynamic tuning of their optical properties.
A two-level preconditioned Helmholtz-Jacobi-Davidson method for the Maxwell eigenvalue problem
Authors: Liang Qigang , Xu Xuejun
Published: October 2021

In this paper, based on a domain decomposition method, we propose an efficient two-level preconditioned Helmholtz-Jacobi-Davidson (PHJD) method for solving the algebraic eigenvalue problem resulting from the edge element approximation of the Maxwell eigenvalue problem. In order to eliminate the components in orthogonal complement space of the eigenvalue, we shall solve a parallel preconditioned system and a Helmholtz projection system together in fine space. After one coarse space correction in each iteration and minimizing the Rayleigh quotient in a small dimensional Davidson space, we finally get the error reduction of this two-level PHJD method as

γ
=
c
(
H
)
(
1
−
C

δ

2

H

2

)

\gamma =c(H)(1-C\frac {\delta ^{2}}{H^{2}})

, where

C
C

is a constant independent of the mesh size

h
h

and the diameter of subdomains

H
H

,

δ
\delta

is the overlapping size among the subdomains, and

c
(
H
)

c(H)

decreasing monotonically to

1
1

as

H
→
0

H\to 0

, which means the greater the number of subdomains, the better the convergence rate. Numerical results supporting our theory are given.
Changes in Life Expectancy and Disability-Free Life Expectancy in Successive Birth Cohorts of Older Cancer Survivors: A Longitudinal Modeling Analysis of the US Health and Retirement Study
Authors: Payne Collin F , Kobayashi Lindsay C
Published: October 2021

The population of older cancer survivors in the United States is rapidly growing. However, little is currently known about how the health of older cancer survivors has changed over time and across successive birth cohorts. Using data from the US Health and Retirement Study, we parameterized a demographic microsimulation model to compare partial cohort life expectancy (LE) and disability-free LE for US men and women without cancer and with prevalent and incident cancer diagnoses for 4 successive 10-year birth cohorts, born 1918–1927 to 1948–1957. Disability was defined as being disabled in ≥1 activity of daily living. These cohorts had midpoint ages of 55–64, 65–74, and 75–84 years during the periods 1998–2008 (the “early” period) and 2008–2018 (the “later” period). Across all cohorts and periods, those with incident cancer had the lowest LE, followed by those with prevalent cancer and cancer-free individuals. We observed declines in partial LE and an expansion of life spent disabled among more recent birth cohorts of prevalent-cancer survivors. Our findings suggest that advances in treatments that prolong life for individual cancer patients may have led to population-level declines in conditional LE and disability-free LE across successive cohorts of older cancer survivors.
Rapid evolution of post-zygotic reproductive isolation is widespread in Arctic plant lineages
Authors: Gustafsson A Lovisa S , Gussarova Galina , Borgen Liv , Ikeda Hajime , Antonelli Alexandre , Marie-Orleach Lucas , Rieseberg Loren H , Brochmann Christian
Published: October 2021

Background and Aims

The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbours one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific post-zygotic reproductive isolation (RI) in terms of hybrid sterility has frequently evolved within selfing Arctic species of the genus Draba. Here we assess whether incipient biological species are common in the Arctic flora.

Methods

We conducted an extensive crossing experiment including six species representing four phylogenetically distant families collected across the circumpolar Arctic. We crossed conspecific parental populations representing different spatial scales, raised 740 F1 hybrids to maturity and measured fertility under laboratory conditions. We examined genetic divergence between populations for two of these species (Cardamine bellidifolia and Ranunculus pygmaeus).

Key Results

In five of the six species, we find extensive reduction in pollen fertility and seed set in F1 hybrids; 219 (46 %) of the 477 F1 hybrids generated between parents separated by ≥427 km had <20 % pollen fertility. Isolation with migration (IM) and *BEAST analyses of sequences of eight nuclear genes in C. bellidifolia suggests that reproductively isolated populations of this species diverged during, or even after, the last glaciation. Likewise, Arctic populations of R. pygmaeus were genetically very similar despite exhibiting strongly reduced fertility in crosses, suggesting that RI evolved recently also in this species.

Conclusion

We show that post-zygotic RI has developed multiple times within taxonomically recognized Arctic species belonging to several distantly related lineages, and that RI may have developed over just a few millennia. Rapid and widespread evolution of incipient biological species in the Arctic flora might be associated with frequent bottlenecks due to glacial cycles, and/or selfing mating systems, which are common in the harsh Arctic environment where pollinators are scarce.
Real-Time Ultrasound Imaging of the Tear Trough: Lessons Learned From Functional Anatomy
Authors: Calomeni Mariana , Alfertshofer Michael G , Frank Konstantin , Moellhoff Nicholas , Dennison Rebekah , Bravo Bruna , Schelke Leonie , Velthuis Peter , Green Jeremy B , Cotofana Sebastian
Published: October 2021

Background

The tear trough is one of the most challenging facial regions for soft-tissue filler injections. A thorough understanding of the underlying facial, muscular, and vascular anatomy is crucial to perform safe and effective tear trough injectable treatments.

Objectives

The authors sought to evaluate the location and function of the angular vein in the tear trough in 3 different facial expressions: repose, smiling, and max. orbicularis oculi contraction.

Methods

Twenty study participants with a mean age of 48.3 years and mean BMI of 24.5 kg/m2 were investigated via functional ultrasound imaging. The diameter of the angular vein and the velocity and direction of venous blood flow were analyzed in repose, smiling, and during max. orbicularis oculi contraction.

Results

The angular vein was identified in 100% of the cases to travel inside the orbicularis oculi muscle (intra-muscular course) within the tear trough, whereas the angular artery was not identified in this location. The distance between the angular vein and the inferior orbital rim was (lateral to medial): 4.6 mm, 4.5 mm, 3.9 mm, and 3.8 mm. The caudally directed blood flow was in repose 10.2 cm/s and was 7.3 cm/s at max. orbicularis oculi muscle contraction; however, no blood flow was detectable during smiling.

Conclusions

The diameter and the venous blood flow of the angular vein varied between the 3 tested facial expressions. Based on these anatomical findings, the deep injection approach to the tear trough is recommended due to the intramuscular course of the angular vein.
Enzymatic transformation products of phloretin as potent antiadipogenic compounds
Authors: Jeong Gyeong Han , Cho Jae-Hyeon , Park Eui Kyun , Kim Tae Hoon
Published: October 2021

Enzymatic structure modification of the representative chalcone phloretin (1) with polyphenol oxidase from Agaricus bisporus origin produced 2 new biphenyl-type phloreoxin (2) and phloreoxinone (3), and a previously undescribed (2R)-5,7,3′,5′-tetrahydroxyflavanone (4). The structure of these new oxidized products 2-4 elucidated by interpreting the spectroscopic data (NMR and FABMS) containing the absolute stereochemistry is established by the analysis of the circular dichroism spectrum. Compared to the original phloretin, the new products (2) and (3) showed highly improved antiadipogenic potencies both toward pancreatic lipase and accumulation of 3T3-L1 cells. Also, phloreoxin (2) effectively inhibited the expression of C/EBPβ, PPARγ, and aP2 at the mRNA level in the 3T3 adipocytes. Thus, phloreoxin (2), containing a biphenyl moiety catalyzed by A. bisporus polyphenol oxidase, have the potential to influence the antiadipogenic capacity.
The role of calcium binding to the EF-hand-like motif in bacterial solute-binding protein for alginate import
Authors: Okumura Kenji , Maruyama Yukie , Takase Ryuichi , Mikami Bunzo , Murata Kousaku , Hashimoto Wataru
Published: October 2021

Gram-negative Sphingomonas sp. A1 incorporates acidic polysaccharide alginate into the cytoplasm via a cell-surface alginate-binding protein (AlgQ2)-dependent ATP-binding cassette transporter (AlgM1M2SS). We investigated the function of calcium bound to the EF-hand-like motif in AlgQ2 by introducing mutations at the calcium-binding site. The X-ray crystallography of the AlgQ2 mutant (D179A/E180A) demonstrated the absence of calcium binding and significant disorder of the EF-hand-like motif. Distinct from the wild-type AlgQ2, the mutant was quite unstable at temperature of strain A1 growth, although unsaturated alginate oligosaccharides stabilized the mutant by formation of substrate/protein complex. In the assay of ATPase and alginate transport by AlgM1M2SS reconstructed in the liposome, the wild-type and mutant AlgQ2 induced AlgM1M2SS ATPase activity in the presence of unsaturated alginate tetrasaccharide. These results indicate that the calcium bound to EF-hand-like motif stabilizes the substrate-unbound AlgQ2 but is not required for the complexation of substrate-bound AlgQ2 and AlgM1M2SS.
Dying to cooperate: the role of environmental harshness in human collaboration
Authors: Ibbotson Paul , Jimenez-Romero Cristian , Page Karen M
Published: October 2021

It has been proposed that environmental stress acted as a selection pressure on the evolution of human cooperation. Through agent-based evolutionary modelling, mathematical analysis, and human experimental data we illuminate the mechanisms by which the environment influences cooperative success and decision making in a Stag Hunt game. The modelling and mathematical results show that only cooperative foraging phenotypes survive the harshest of environments but pay a penalty for miscoordination in favourable environments. When agents are allowed to coordinate their hunting intentions by communicating, cooperative phenotypes outcompete those who pursue individual strategies in almost all environmental and payoff scenarios examined. Data from human participants show flexible decision-making in face of cooperative uncertainty, favouring high-risk, high-reward strategy when environments are harsher and starvation is imminent. Converging lines of evidence from the three approaches indicate a significant role for environmental variability in human cooperative dynamics and the species-unique cognition designed to support it.
MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors
Authors: Bonidia Robson P , Domingues Douglas S , Sanches Danilo S , de Carvalho André C P L F
Published: October 2021

One of the main challenges in applying machine learning algorithms to biological sequence data is how to numerically represent a sequence in a numeric input vector. Feature extraction techniques capable of extracting numerical information from biological sequences have been reported in the literature. However, many of these techniques are not available in existing packages, such as mathematical descriptors. This paper presents a new package, MathFeature, which implements mathematical descriptors able to extract relevant numerical information from biological sequences, i.e. DNA, RNA and proteins (prediction of structural features along the primary sequence of amino acids). MathFeature makes available 20 numerical feature extraction descriptors based on approaches found in the literature, e.g. multiple numeric mappings, genomic signal processing, chaos game theory, entropy and complex networks. MathFeature also allows the extraction of alternative features, complementing the existing packages. To ensure that our descriptors are robust and to assess their relevance, experimental results are presented in nine case studies. According to these results, the features extracted by MathFeature showed high performance (0.6350–0.9897, accuracy), both applying only mathematical descriptors, but also hybridization with well-known descriptors in the literature. Finally, through MathFeature, we overcame several studies in eight benchmark datasets, exemplifying the robustness and viability of the proposed package. MathFeature has advanced in the area by bringing descriptors not available in other packages, as well as allowing non-experts to use feature extraction techniques.
FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model
Authors: Lee Dohyeon , Song Giltae
Published: October 2021

Motivation

Over the past decades, vast amounts of genome sequencing data have been produced, requiring an enormous level of storage capacity. The time and resources needed to store and transfer such data cause bottlenecks in genome sequencing analysis. To resolve this issue, various compression techniques have been proposed to reduce the size of original FASTQ raw sequencing data, but these remain suboptimal. Long-read sequencing has become dominant in genomics, whereas most existing compression methods focus on short-read sequencing only.

Results

We designed a compression algorithm based on read reordering using a novel scoring model for reducing FASTQ file size with no information loss. We integrated all data processing steps into a software package called FastqCLS and provided it as a Docker image for ease of installation and execution to help users easily install and run. We compared our method with existing major FASTQ compression tools using benchmark datasets. We also included new long-read sequencing data in this validation. As a result, FastqCLS outperformed in terms of compression ratios for storing long-read sequencing data.

Availability and implementation

FastqCLS can be downloaded from https://github.com/krlucete/FastqCLS.

Supplementary information

Supplementary data are available at Bioinformatics online.
scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets
Authors: Yuan Musu , Chen Liang , Deng Minghua
Published: October 2021

Motivation

Single-cell RNA-seq (scRNA-seq) has been widely used to resolve cellular heterogeneity. After collecting scRNA-seq data, the natural next step is to integrate the accumulated data to achieve a common ontology of cell types and states. Thus, an effective and efficient cell-type identification method is urgently needed. Meanwhile, high-quality reference data remain a necessity for precise annotation. However, such tailored reference data are always lacking in practice. To address this, we aggregated multiple datasets into a meta-dataset on which annotation is conducted. Existing supervised or semi-supervised annotation methods suffer from batch effects caused by different sequencing platforms, the effect of which increases in severity with multiple reference datasets.

Results

Herein, a robust deep learning-based single-cell Multiple Reference Annotator (scMRA) is introduced. In scMRA, a knowledge graph is constructed to represent the characteristics of cell types in different datasets, and a graphic convolutional network serves as a discriminator based on this graph. scMRA keeps intra-cell-type closeness and the relative position of cell types across datasets. scMRA is remarkably powerful at transferring knowledge from multiple reference datasets, to the unlabeled target domain, thereby gaining an advantage over other state-of-the-art annotation methods in multi-reference data experiments. Furthermore, scMRA can remove batch effects. To the best of our knowledge, this is the first attempt to use multiple insufficient reference datasets to annotate target data, and it is, comparatively, the best annotation method for multiple scRNA-seq datasets.

Availability and implementation

An implementation of scMRA is available from https://github.com/ddb-qiwang/scMRA-torch.

Supplementary information

Supplementary data are available at Bioinformatics online.
Volitional control of individual neurons in the human brain
Authors: Patel Kramay , Katz Chaim N , Kalia Suneil K , Popovic Milos R , Valiante Taufik A
Published: October 2021

Brain–machine interfaces allow neuroscientists to causally link specific neural activity patterns to a particular behaviour. Thus, in addition to their current clinical applications, brain–machine interfaces can also be used as a tool to investigate neural mechanisms of learning and plasticity in the brain. Decades of research using such brain–machine interfaces have shown that animals (non-human primates and rodents) can be operantly conditioned to self-regulate neural activity in various motor-related structures of the brain. Here, we ask whether the human brain, a complex interconnected structure of over 80 billion neurons, can learn to control itself at the most elemental scale—a single neuron.

We used the unique opportunity to record single units in 11 individuals with epilepsy to explore whether the firing rate of a single (direct) neuron in limbic and other memory-related brain structures can be brought under volitional control. To do this, we developed a visual neurofeedback task in which participants were trained to move a block on a screen by modulating the activity of an arbitrarily selected neuron from their brain.

Remarkably, participants were able to volitionally modulate the firing rate of the direct neuron in these previously uninvestigated structures. We found that a subset of participants (learners), were able to improve their performance within a single training session. Successful learning was characterized by (i) highly specific modulation of the direct neuron (demonstrated by significantly increased firing rates and burst frequency); (ii) a simultaneous decorrelation of the activity of the direct neuron from the neighbouring neurons; and (iii) robust phase-locking of the direct neuron to local alpha/beta-frequency oscillations, which may provide some insights in to the potential neural mechanisms that facilitate this type of learning.

Volitional control of neuronal activity in mnemonic structures may provide new ways of probing the function and plasticity of human memory without exogenous stimulation. Furthermore, self-regulation of neural activity in these brain regions may provide an avenue for the development of novel neuroprosthetics for the treatment of neurological conditions that are commonly associated with pathological activity in these brain structures, such as medically refractory epilepsy.
Brain injections of glial cytoplasmic inclusions induce a multiple system atrophy-like pathology
Authors: Teil Margaux , Dovero Sandra , Bourdenx Mathieu , Arotcarena Marie-Laure , Camus Sandrine , Porras Gregory , Thiolat Marie-Laure , Trigo-Damas Ines , Perier Celine , Estrada Cristina , Garcia-Carrillo Nuria , Morari Michele , Meissner Wassilios G , Herrero María Trinidad , Vila Miquel , Obeso Jose A , Bezard Erwan , Dehay Benjamin
Published: October 2021

Synucleinopathies encompass several neurodegenerative diseases, which include Parkinson's disease, dementia with Lewy bodies and multiple system atrophy. These diseases are characterized by the deposit of α-synuclein aggregates in intracellular inclusions in neurons and glial cells. Unlike Parkinson’s disease and dementia with Lewy bodies, where aggregates are predominantly neuronal, multiple system atrophy is associated with α-synuclein cytoplasmic inclusions in oligodendrocytes. Glial cytoplasmic inclusions are the pathological hallmark of multiple system atrophy and are associated with neuroinflammation, modest demyelination and, ultimately, neurodegeneration.

To evaluate the possible pathogenic role of glial cytoplasmic inclusions, we inoculated glial cytoplasmic inclusion-containing brain fractions obtained from multiple system atrophy patients into the striatum of non-human primates. After a 2-year in vivo phase, extensive histochemical and biochemical analyses were performed on the whole brain.

We found loss of both nigral dopamine neurons and striatal medium spiny neurons, as well as loss of oligodendrocytes in the same regions, which are characteristics of multiple system atrophy. Furthermore, demyelination, neuroinflammation and α-synuclein pathology were also observed. These results show that the α-synuclein species in multiple system atrophy-derived glial cytoplasmic inclusions can induce a pathological process in non-human primates, including nigrostriatal and striatofugal neurodegeneration, oligodendroglial cell loss, synucleinopathy and gliosis.

The present data pave the way for using this experimental model for MSA research and therapeutic development.
Dementia in the older population is associated with neocortex content of serum amyloid P component
Authors: Ellmerich Stephan , Taylor Graham W , Richardson Connor D , Minett Thais , Schmidt Amand Floriaan , Brayne Carol , Matthews Fiona E , Ince Paul G , Wharton Stephen B , Pepys Mark B ,   Cognitive Function and Ageing Study, Brayne Carol , Matthews Fiona E , Robinson Louise , Comas-Herrera Adelina , Woods Bob , Stephan Blossom , Parry Bronwyn , Jagger Carol , Clare Linda , Dening Tom , Barnes Linda , Forster Gill , McKeith Ian , Wittenberg Raphael , Wharton Stephen B , Pendlebury Sarah , Harrison Simon , Arthur Antony , Weller Roy , Pickering-Brown Stuart , Ince Paul G
Published: October 2021

Despite many reported associations, the direct cause of neurodegeneration responsible for cognitive loss in Alzheimer’s disease and some other common dementias is not known. The normal human plasma protein, serum amyloid P component, a constituent of all human fibrillar amyloid deposits and present on most neurofibrillary tangles, is cytotoxic for cerebral neurones in vitro and in experimental animals in vivo. The neocortical content of serum amyloid P component was immunoassayed in 157 subjects aged 65 or more with known dementia status at death, in the large scale, population-representative, brain donor cohort of the Cognitive Function and Ageing Study, which avoids the biases inherent in studies of predefined clinico-pathological groups. The serum amyloid P component values were significantly higher in individuals with dementia, independent of serum albumin content measured as a control for plasma in the cortex samples. The odds ratio for dementia at death in the high serum amyloid P component tertile was 5.24 (95% confidence interval 1.79–15.29) and was independent of Braak tangle stages and Thal amyloid-β phases of neuropathological severity. The strong and specific association of higher brain content of serum amyloid P component with dementia, independent of neuropathology, is consistent with a pathogenetic role in dementia.
Persistent sodium currents in SCN1A developmental and degenerative epileptic dyskinetic encephalopathy
Authors: Gorman Kathleen M , Peters Colin H , Lynch Bryan , Jones Laura , Bassett Dani S , King Mary D , Ruben Peter C , Rosch Richard E
Published: October 2021

Pathogenic variants in the voltage-gated sodium channel gene (SCN1A) are amongst the most common genetic causes of childhood epilepsies. There is considerable heterogeneity in both the types of causative variants and associated phenotypes; a recent expansion of the phenotypic spectrum of SCN1A associated epilepsies now includes an early onset severe developmental and epileptic encephalopathy with regression and a hyperkinetic movement disorder. Herein, we report a female with a developmental and degenerative epileptic-dyskinetic encephalopathy, distinct and more severe than classic Dravet syndrome. Clinical diagnostics indicated a paternally inherited c.5053G>T; p. A1685S variant of uncertain significance in SCN1A. Whole-exome sequencing detected a second de novo mosaic (18%) c.2345G>A; p. T782I likely pathogenic variant in SCN1A (maternal allele). Biophysical characterization of both mutant channels in a heterologous expression system identified gain-of-function effects in both, with a milder shift in fast inactivation of the p. A1685S channels; and a more severe persistent sodium current in the p. T782I. Using computational models, we show that large persistent sodium currents induce hyper-excitability in individual cortical neurons, thus relating the severe phenotype to the empirically quantified sodium channel dysfunction. These findings further broaden the phenotypic spectrum of SCN1A associated epilepsies and highlight the importance of testing for mosaicism in epileptic encephalopathies. Detailed biophysical evaluation and computational modelling further highlight the role of gain-of-function variants in the pathophysiology of the most severe phenotypes associated with SCN1A.
Striatal BOLD and midfrontal theta power express motivation for action
Authors: Algermissen Johannes , Swart Jennifer C , Scheeringa René , Cools Roshan , den Ouden Hanneke E M
Published: October 2021

Action selection is biased by the valence of anticipated outcomes. To assess mechanisms by which these motivational biases are expressed and controlled, we measured simultaneous EEG-fMRI during a motivational Go/NoGo learning task (N = 36), leveraging the temporal resolution of EEG and subcortical access of fMRI. VmPFC BOLD encoded cue valence, importantly predicting trial-by-trial valence-driven response speed differences and EEG theta power around cue onset. In contrast, striatal BOLD encoded selection of active Go responses and correlated with theta power around response time. Within trials, theta power ramped in the fashion of an evidence accumulation signal for the value of making a “Go” response, capturing the faster responding to reward cues. Our findings reveal a dual nature of midfrontal theta power, with early components reflecting the vmPFC contribution to motivational biases, and late components reflecting their striatal translation into behavior, in line with influential recent “value of work” theories of striatal processing.
Laterality hotspots in the striatum
Authors: Korponay Cole , Stein Elliot A , Ross Thomas J
Published: October 2021

Striatal loci are connected to both the ipsilateral and contralateral frontal cortex. Normative quantitation of the dissimilarity between striatal loci’s hemispheric connection profiles and its spatial variance across the striatum, and assessment of how interindividual differences relate to function, stands to further the understanding of the role of corticostriatal circuits in lateralized functions and the role of abnormal corticostriatal laterality in neurodevelopmental and other neuropsychiatric disorders. A resting-state functional connectivity fingerprinting approach (n = 261) identified “laterality hotspots”—loci whose profiles of connectivity with ipsilateral and contralateral frontal cortex were disproportionately dissimilar—in the right rostral ventral putamen, left rostral central caudate, and bilateral caudal ventral caudate. Findings were replicated in an independent sample and were robust to both preprocessing choices and the choice of cortical atlas used for parcellation definitions. Across subjects, greater rightward connectional laterality at the right ventral putamen hotspot and greater leftward connectional laterality at the left rostral caudate hotspot were associated with higher performance on tasks engaging lateralized functions (i.e., response inhibition and language, respectively). In sum, we find robust and reproducible evidence for striatal loci with disproportionately lateralized connectivity profiles where interindividual differences in laterality magnitude are associated with behavioral capacities on lateralized functions.
Sex Differences in Human Immunodeficiency Virus Persistence and Reservoir Size During Aging
Authors: Gianella Sara , Rawlings Stephen A , Dobrowolski Curtis , Nakazawa Masato , Chaillon Antoine , Strain Matthew , Layman Laura , Caballero Gemma , Scully Eileen , Scott Brianna , Pacis Caitleen , Weber Kathleen M , Landay Alan , Anderson Christy , Karn Jonathan
Published: October 2021

Background

Sex differences in human immunodeficiency virus (HIV) reservoir dynamics remain underexplored.

Methods

Longitudinal samples from virally suppressed midlife women (n = 59, median age 45 years) and age-matched men (n = 31) were analyzed retrospectively. At each time point, we measured sex hormones (by means of enzyme-linked immunosorbent assay) and cellular HIV DNA and RNA (by means of digital droplet polymerase chain reaction). Number of inducible HIV RNA+ cells, which provides an upper estimate of the replication-competent reservoir, was quantified longitudinally in a different subset of 14 women, across well-defined reproductive stages. Mixed-effects models included normalized reservoir outcomes and sex, time since antiretroviral therapy (ART) initiation, and the sex-by-time interaction as predictors.

Results

At ART initiation, women and men had median (interquartile range [IQR]) CD4+ T-cell counts of 204/μL (83–306/μL) versus 238/μL (120–284/μL), respectively; median ages of 45 (42–48) versus 47 (43–51) years; and median follow-up times of 79.2/μL (60.5–121.1/μL) versus 66.2/μL (43.2–80.6/μL) months. We observed a significant decline of total HIV DNA over time in both men and women (P < .01). However, the rates of change differed significantly between the sexes (P < .01), with women having a significantly slower rate of decline than men, more pronounced with age. By contrast, the levels of inducible HIV RNA increased incrementally over time in women during reproductive aging (P < .01).

Conclusions

In contrast to men, in whom the HIV reservoir steadily declines with aging, the HIV reservoir in women is more dynamic. Total HIV DNA (including intact and defective genomes) declines more slowly in women than in men, while the inducible HIV RNA+ reservoir, which is highly enriched in replication-competent virus, increases in women after menopause.
Inflammatory Bowel Disease-related Behaviours [IBD-Bx] Questionnaire: Development, Validation and Prospective Associations with Fatigue
Authors: Walentynowicz Marta , van de Pavert Iris , Fierens Liselotte , Coenen Sofie , Vlaeyen Johan W S , von Leupoldt Andreas , Van Oudenhove Lukas , Vermeire Séverine , Van Assche Gert , Ferrante Marc , Van Diest Ilse
Published: October 2021

Background and Aims

Disease-related behaviours that may maintain or worsen symptom burden remain largely unexplored in inflammatory bowel disease [IBD]. In this study, we developed and validated an instrument assessing IBD-related, modifiable behaviours and explored which behaviours prospectively correlate with fatigue, a debilitating and common symptom in IBD.

Methods

Initially, 72 items reflecting IBD-related behaviours were generated based on literature review and input from clinicians and people diagnosed with IBD. During wave 1, 495 IBD patients rated to what extent each behaviour was applicable to them. Additionally, disease activity, fatigue, IBD-related concerns and psychological variables were assessed. During a follow-up visit 4–12 weeks later [wave 2], a random selection of 92 patients from wave 1 completed the measures assessing the IBD-related behaviours, disease activity and fatigue once more.

Results

A principal component analysis with oblique rotation revealed seven components in the 72 IBD behaviours, which could be interpreted as: [1] Avoiding food and activities, [2] Access to toilets, [3] Avoidance of sex, [4] Cognitive avoidance, [5] Not sharing with others, [6] Alternative treatments and [7] Disease management. Each component was reduced to three to five representative items, resulting in a final, 25-item IBD-Bx questionnaire showing good concurrent validity [alphas > 0.63] and reliability. Almost all components were cross-sectionally related to levels of fatigue. Avoiding food and activities and Access to toilets significantly predicted fatigue at wave 2 when controlling for baseline fatigue.

Conclusions

The IBD-Bx is a valid and reliable questionnaire of IBD-related behaviours, some of which predict future fatigue burden.