bluuebunny/crossref_metadata_2025 huggingface dataset:
Coronin 1C restricts endosomal branched actin to organize ER contact and endosome fission
Authors: Striepen Jonathan F. , Voeltz Gia K.
Published: July 2022

ER contact sites define the position of endosome bud fission during actin-dependent cargo sorting. Disrupting endosomal actin structures prevents retrograde cargo movement; however, how actin affects ER contact site formation and endosome fission is not known. Here we show that in contrast with the WASH complex, actin, its nucleator ARP2/3, and COR1C form a contained structure at the bud neck that defines the site of bud fission. We found that actin confinement is facilitated by type I coronins. Depletion of type I coronins allows actin to extend along the length of the bud in an ARP2/3-dependent manner. We demonstrate that extension of branched actin prevents ER recruitment and stalls buds before fission. Finally, our structure-function studies show that the COR1C’s coiled-coil domain is sufficient to restore actin confinement, ER recruitment, and endosome fission. Together, our data reveal how the dynamics of endosomal actin and activity of actin regulators organize ER-associated bud fission.
NF-κB signaling controls H3K9me3 levels at intronic LINE-1 and hematopoietic stem cell genes in cis
Authors: Pelinski Yanis , Hidaoui Donia , Stolz Anne , Hermetet François , Chelbi Rabie , Diop M’boyba Khadija , Chioukh Amir M. , Porteu Françoise , Elvira-Matelot Emilie
Published: July 2022

Ionizing radiations (IR) alter hematopoietic stem cell (HSC) function on the long term, but the mechanisms underlying these effects are still poorly understood. We recently showed that IR induces the derepression of L1Md, the mouse young subfamilies of LINE-1/L1 retroelements. L1 contributes to gene regulatory networks. However, how L1Md are derepressed and impact HSC gene expression are not known. Here, we show that IR triggers genome-wide H3K9me3 decrease that occurs mainly at L1Md. Loss of H3K9me3 at intronic L1Md harboring NF-κB binding sites motifs but not at promoters is associated with the repression of HSC-specific genes. This is correlated with reduced NFKB1 repressor expression. TNF-α treatment rescued all these effects and prevented IR-induced HSC loss of function in vivo. This TNF-α/NF-κB/H3K9me3/L1Md axis might be important to maintain HSCs while allowing expression of immune genes during myeloid regeneration or damage-induced bone marrow ablation.
Small angles vector magnetometer based on anisotropic ferromagnetic nanofluid functionalized fiber interferometer
Authors: Kumar Ashish , Sahu Subrat , Jha Rajan
Published: July 2022

As factories and vehicles become more automated, accurate and low-latency sensing of motor shaft speed and position is critical for process control, system reliability, and safety. To address these needs, a highly precise and fast vector magnetometer is required that has the capability to detect magnetic field variations also at tiny angles. We present the development of an ultrathin tapered fiber interferometer-based highly accurate sensor suspended in a magnetorheological fluid film, which holds the capability of simultaneously detecting magnetic field intensity and its direction in three-dimensional space. The sensing mechanism counts on the magnetism-regulatable effective index amendment of exciting asymmetric cladding modes in a nonadiabatic biconical tapered fiber interferometer. Based on the azimuth-dependent anisotropic distribution of nanoparticles surrounding the fiber, such a magnetometer has achieved the maximum magnetic field sensitivity of ∼16.4 pm mT−1 at 0° whereas at small angles of ±1° and ±2° the sensitivities are observed of ∼ ±14.6 pm mT−1 and ∼ ±11.7 pm mT−1, respectively over a larger span of 0–567 mT.
A facility for the characterisation of planar multilayer structures with preliminary niobium results
Authors: Turner Daniel A , Malyshev Oleg B , Burt Graeme , Junginger Tobias , Valizadeh Reza , Gurran Lewis
Published: July 2022

The maximum accelerating gradient of superconducting radio frequency cavities are currently reaching their theoretical limits, due to the magnetic field entering the superconductor in the form of vortices. To overcome these limits, thin film coated superconducting materials are required, however these need to be tested to optimise their properties. A system has been designed, built, and commissioned at Daresbury Laboratory that applies a local DC magnetic field parallel to the surface, from one side of a sample, similar to that in cavity operation. A magnetic flux density (up to 600 mT) is generated parallel to the sample surface in the 2 mm gap of a C-shaped ferrite yoke. Two Hall probe sensors are used to measure both the applied and penetrated magnetic field. The system operates in a cryogen free environment, with a minimum temperature of approximately 2.6 K. A Pb foil has been used to characterise the system, and determine how the sample size affects the results. Nb thin film samples have been tested for varying thickness to determine how the depth effects the field of full flux penetration,

B

f
p

. The design, operation, methods of analysis and first results of this facility will be reported in this paper.
Novel bursting oscillations in a nonlinear gyroscope oscillator
Authors: Oyeleke K S , Olusola O I , Kolebaje O T , Vincent U E , Adeloye A B , McClintock P V E
Published: July 2022

We report the occurrence of bursting oscillations in a gyroscope oscillator driven by low-frequency external period forcing. The bursting patterns arise when either the frequency or amplitude of the excitation force is varied. They take the form of pulse-shaped explosions (PSEs) wherein periodic attractors of lower periodicity disappear due to the loss of asymptotic stability of the equilibrium point between resting and active states. The process involves the appearance of zero eigenvalues and the creation of new attractors of higher periodicity. Both point-cycle and cycle-cycle bursting is seen. It is accompanied by the birth of periodic attractors, ranging from period one to period four, depending on an integer n in the frequency of the parametric driving force. The dynamics of the oscillator is shown to exhibit a fold bifurcation related to critical escape transitions.
Chaotic control of the dynamical behavior of COVID-19 through the electromagnetic fields
Authors: Fathizadeh S , Behnia S , Nemati F , Salimi M , Borjkhani H
Published: July 2022

Investigating the dynamical behavior of a system is an effective method to predict and control its future behavior. Studying the dynamic behavior of a virus can prevent the pathogenicity of a virus and save human lives during the disease epidemic. If the transmission of information from the virus genome to the environment is locked, the pathogenicity of the virus stops. Information transmission can be checked via the investigation of the spin information transport. In the current study, we have characterized the dynamical behavior of the virus by studying the spin transport through its RNA chain to estimate the information transfer path in the system. A voltage generator with adjustable frequency as a control system has been designed using the control theory of chaotic systems. Our aim is disturbing and reduces the transmitted information from viruses to the environment. The external stimuli can propel the system to the locked information transfer situation. Applying an external field noise with a specific frequency range (200–500 GHz) controlled through the external controller system can destroy the information transmitted by the virus to the environment. Disturbance intensity as a control parameter adjusts the external field frequency to push the system to the chaotic behavior which will be able to lock the information transfer and then prevent the spread of the epidemic.
Impact of Se and Te addition on optical characteristics of ternary GeInSb chalcogenide films as promising materials for optoelectronic applications
Authors: El-Metwally E G , Atyia H E , Ismail A M
Published: July 2022

The present study investigates the linear and non-linear optical characteristics of non-crystalline quaternary Ge15In5Sb5Se75 (GIS-Se) and Ge15In5Sb5Te75 (GIS-Te) chalcogenide thin films. The amorphous nature of the studied compositions was confirmed by x-ray diffraction (XRD). The values of transformation temperatures determined by differential thermal analysis (DTA), such as glass transition

T

g

and crystallization

T

c

temperatures, are 524.3 and 639.6 K for GIS-Se and 503.6 and 542.0 K for GIS-Te. The calculated values of glass forming ability (

G
F
A

) and thermal stability (

H

) for GIS-Se are higher than those for GIS-Te. The transmittance

T

(
λ
)

and reflectance

R

(
λ
)

spectrophotometric measurements in the UV–vis. wavelength range (400–2500 nm) are used to estimate the index of refraction

n

and extinction coefficient

k
.

The obtained values of

n

and

k

are found to be thickness independent in the investigated range. Tauc’s extrapolation model was used to determine both Urbach tail (

E

U

) and optical band gap (

E

g

o
p
t

) energies. The values of (

E

U

) are 0.416, 0.526 eV and (

E

g

o
p
t

) are 1.83, 1.31 eV with indirect allowed transitions for GIS-Se and GIS-Te, respectively. The optical conductivity

σ

o
p
t

increased as photon energy (

h
ν

) increased, and it was enhanced in the presence of Te than Se addition. The analysis of the index of refraction (

n

) is used to evaluate the dispersion energy

E

d

,

the high frequency dielectric constant

ε

∞

,

the oscillator strength

S

0

,

the lattice dielectric constant

ε

L

,

the ratio

N
/

m

*

and the optical electronegativity

∅

o
p
t

,

which were found to be higher in GIS-Te than those in GIS-Se composition. The volume (

V
E
L
F

) and surface (

S
E
L
F

) energy loss functions were found to be increased with increasing (

h
ν

) and the presence of Te. Furthermore, the calculated values of nonlinear optical susceptibility

χ

(
3
)

and nonlinear index of refraction

n

2

for GIS-Se and GIS-Te are 0.195 × 10−12, 2.44 × 10−11 esu and 0.868 × 10−12, 10.19 × 10−11 esu, respectively. The detailed outcomes show that the studied film samples are suitable for various optical applications such as phase-change optical rewritable disks, optical sensors, optoelectronic devices and high-speed optical fibers.
Ferroelectricity induced by the absorption of water molecules on double helix SnIP
Authors: Liu Dan , Wei Ran , Han Lin , Zhu Chen , Dong Shuai
Published: July 2022

We study the ferroelectricity in a one-dimensional (1D) system composed of a double helix SnIP with absorbing water molecules. Our ab initio calculations reveal two factors that are critical to the electrical polarization. The first one is the orientation of polarized water molecules staying in the R2 region of SnIP. The second one is the displacement of I atom which roots from subtle interaction with absorbed water molecules. A reasonable scenario of polarization flipping is proposed in this study. In the scenario, the water molecule is rolling-up with keeping the magnitude of its electrical dipole and changing its direction, meanwhile, the displacement of I atoms is also reversed. Highly tunable polarization can be achieved by applying strain, with 26.5% of polarization enhancement by applying tensile strain, with only 4% degradation is observed with 4% compressive strain. Finally, the direct band gap is also found to be correlated with strain.
On-surface synthesis of one-dimensional carbyne-like nanostructures with sp-carbon
Authors: Gao Wenze , Zhang Chi , Zhou Zheng , Xu Wei
Published: July 2022

Carbyne is an infinite one-dimensional carbon chain comprising of sp-hybridized carbons. Due to its high chemical reactivity and extreme instability, the synthesis and structural diversity of carbyne have been much less investigated in the past decades compared to carbon allotropes built with sp2 hybridized carbons, such as fullerenes, carbon nanotubes, and graphene. The emerging on-surface synthesis strategy provides an extremely promising approach for the fabrication of novel carbyne-like nanostructures with atomic precision. Herein, we summarize recent exciting progress in the synthesis of carbyne-like nanostructures with one-dimensional sp-carbon on surfaces, including polyynes, cumulenes, and organometallic polyynes. We also point out the scientific challenges and prospects, encouraging scientists to explore the fabrication and characterization of single strands of carbyne in this young and promising research field.
Upgrade of the magnetic diagnostic system for restart of HT-6M operation
Authors: Chen Li-Xing , Shen Biao , Chen Da-Long , Luo Zheng-Ping , Zhang Zu-Chao , Chen Ying , Wang Yong , Qian Jin-Ping
Published: July 2022

The HT-6M tokamak at the Thailand Institute of Nuclear Technology has been restarted. In order to ensure the smooth breakdown of plasma and obtain plasma discharge parameters, optimization of the poloidal field coils and upgrade of the magnetic diagnostics are described in this article. A perfect null field (stray field in the main chamber < 10 G) is obtained using an ohmic heating field. To obtain important information about the plasma, an external magnetic diagnostics system is designed and calibrated, including a Rogowski coil (measuring plasma current), a magnetic probe (measuring external field), diamagnetic loops (measuring β
p) and so on. In order to realize high-frequency signal measurement and transmission, a series of frequency responses with the magnetic probe and transmission line are tested. Later, to verify the null field, a fitting code is developed to reconstruct the stray field in the vacuum chamber based on magnetic probe measurements and flux loops. The results show that the error is within 1.5%. This indicates the accuracy of the magnetic measurement system and ensures the preparation for the breakdown of plasma.
Superconductivity and unconventional density waves in vanadium-based kagome materials AV3Sb5
Authors: Chen Hui , Hu Bin , Ye Yuhan , Yang Haitao , Gao Hong-Jun
Published: July 2022

Recently, the discovery of vanadium-based kagome metal AV3Sb5 (A = K, Rb, Cs) has attracted great interest in the field of superconductivity due to the coexistence of superconductivity, non-trivial surface state and multiple density waves. In this topical review, we present recent works of superconductivity and unconventional density waves in vanadium-based kagome materials AV3Sb5. We start with the unconventional charge density waves, which are thought to correlate to the time-reversal symmetry-breaking orders and the unconventional anomalous Hall effects in AV3Sb5. Then we discuss the superconductivity and the topological band structure. Next, we review the competition between the superconductivity and charge density waves under different conditions of pressure, chemical doping, thickness, and strains. Finally, the experimental evidence of pseudogap pair density wave is discussed.
A Wideband Microwave Holography Methodology for Reflector Surface Measurement of Large Radio Telescopes
Authors: Wang Zan , Kong De-Qing , Zhang Hong-Bo , Zhu Xin-Ying , Liu Ze-Xin , Liu Yu-Chen
Published: July 2022

Most reflector surface holographic measurements of a large radio telescope utilize a geostationary satellite as the signal source. The shortcoming is that those measurements could only be done at a limited elevation angle due to the satellite’s relatively stationary state. This paper proposed a new wideband microwave holographic measurement method based on radio sources to achieve full-elevation-angle measurement with small size reference antenna. In theoretical derivation, the time delay and phase change due to path length and device difference between the antenna under test and reference antenna are compensated first. Then the correct method of wideband holography effect, which is because of antenna pattern differing under different wavelengths when receiving a wideband signal, is presented. To verify the proposed methodology, a wideband microwave holographic measurement system is established, the data processing procedure is illustrated, and the reflector surface measurement experiments on a 40 m radio telescope at different elevation angles are conducted. The result shows that the primary reflector surface root-mean-square at around elevation angles of 28°, 44°, 49°, and 75° are respectively 0.213 mm, 0.170 mm, 0.188 mm, and 0.199 mm. It is basically consistent with the real data, indicating that the proposed wideband microwave holography methodology is feasible.
Economic optimization of acceptance interval in conformity assessment: 1. Process with no systematic effect
Authors: Shirono Katsuhiro , Tanaka Hideyuki , Koike Masayoshi
Published: July 2022

In inspections for conformity assessment, an acceptance interval smaller than the tolerance interval is often determined in order to reduce the risk of consumers obtaining non-conforming items in the market. The presence of non-conforming items in the market impairs the evaluation of items by customers and may have an impact on revenue by decreasing prices. However, setting too small an acceptance interval reduces the revenue from the process by decreasing the number of the items available in the market. We thus propose a method to determine the optimum acceptance interval in conformity assessment by means of maximization of the revenue from processes. For this purpose, we give a mathematical model for the price of an item and its cost in the production process. Through theoretical analysis and simulations, it is shown that a parameter in the price model is the key in the optimization. In this paper we report a method for processes where no systematic effect component of measurement uncertainty exists, and in part 2 of this series we will report an extended method in which systematic effects are taken into consideration.
A digital framework for realising the SI—a proposal for the metre
Authors: Lewis Andrew J , Yacoot Andrew , Milton Martin J T , Lancaster Andrew J
Published: July 2022

A current focus of the international metrology community is the digitalisation of documents, certificates and services in response to initiatives underway throughout industry and to the requirement to follow the principles of data being Findable, Accessible, Interoperable, and Reusable. We propose the key elements of a digital framework for the SI metre, at the point of realisation, showing how it may be implemented in practice. We give examples of direct benefits of this approach, which may be extended to other SI units.
Swimming in density-stratified fluid: study on a flapping foil
Authors: Kandel Prabal , Deng Jian
Published: July 2022

It is of interest to investigate how a swimming animal performs in a density-stratified fluid. This paper studies a simplified swimmer, a pitching NACA0015 airfoil, considering its locomotion in both homogeneous, or unstratified, and stratified fluid flows. A direct comparison is made between these two conditions through two-dimensional numerical simulations. Our numerical results show that the stratification modifies the dynamics of the pitching foil in both its wake structures and the drag force, or thrust, as well as its propulsive performance. We suggest that the effects of stratification on flapping performance or propulsive efficiency can be categorized according to the Froude number, or the level of stratification. First, in the range of high Froude numbers, notable modification of the flow structure can be observed, which however does not greatly affect the propulsive performance. Second, at a very low Froude number, i.e., Fr = 1, the propulsive efficiency drops markedly compared to its homogeneous counterpart, attributed to the pronounced internal waves induced by the strong stratification. Moreover, at a moderate Froude number Fr = 2, we find an increase in the propulsive efficiency, which can be explained by the unique variation in the wake structure. At A
D = 2.50, the propulsive efficiency peaks at Fr = 2, with its efficiency 18.3% higher than its homogeneous counterpart, exhibiting a favourable influence of the stratification on a swimmer.
Non-state climate governance, corporate leadership, and governance performance: evidence from the US electric utility sector
Authors: Ba Yuhao
Published: July 2022

COP26 highlighted near-term emissions reductions in addition to longer-term net-zero. At the same time, shifts in political landscapes around the world have furthered the salience of climate action led by non-state actors such as business interests, civil society and nonprofits, and local and regional communities. Despite the promise, performance of non-state climate action remains unclear and requires further empirical validation. The current study focuses on corporate entities and explores the potential effect of corporate leadership on climate governance (CG) performance. Our aim is to advance the literature on non-state CG by offering empirical evidence of the less-studied effectiveness of non-state CG leadership. Echoing previous research, our study identifies a contingent perspective on the effect of corporate leadership on CG performance. Specifically, through the context of utilities’ energy efficiency programming in the U.S. and a multilevel research design, we find suggestive evidence that when the moderating effect of citizens’ support is considered, corporate leadership could potentially positively affect CG performance. Additionally, we demonstrate that a CG system’s operational uncertainty can complicate the effect of corporate leadership on performance whereas a pro-environmental citizenry can enhance such effect.
miRNA induced 3D bioprinted-heterotypic osteochondral interface
Authors: Celik Nazmiye , Kim Myoung Hwan , Yeo Miji , Kamal Fadia , Hayes Daniel J , Ozbolat Ibrahim T
Published: July 2022

The engineering of osteochondral interfaces remains a challenge. MicroRNAs (miRs) have emerged as significant tools to regulate the differentiation and proliferation of osteogenic and chondrogenic formation in the human musculoskeletal system. Here, we describe a novel approach to osteochondral reconstruction based on the three-dimensional (3D) bioprinting of miR-transfected adipose-derived stem cell (ADSC) spheroids to produce a heterotypic interface that addresses the intrinsic limitations of the traditional approach to inducing zonal differentiation via the use of diffusible cytokines. We evaluated the delivery of miR-148b for osteogenic differentiation and the codelivery of miR-140 and miR-21 for the chondrogenic differentiation of ADSC spheroids. Our results demonstrated that miR-transfected ADSC spheroids exhibited upregulated expression of osteogenic and chondrogenic differentiation related gene and protein markers, and enhanced mineralization and cell proliferation compared to spheroids differentiated using a commercially-available differentiation medium. Upon confirmation of the osteogenic and chondrogenic potential of miR-transfected ADSC spheroids, using aspiration-assisted bioprinting, these spheroids were 3D bioprinted into a dual-layer heterotypic osteochondral interface with a stratified arrangement of distinct osteogenic and chondrogenic zones. The proposed approach holds great promise for the biofabrication of stratified tissues, not only for the osteochondral interfaces presented in this work, but also for other composite tissues and tissue interfaces, such as, but not limited to, the bone-tendon-muscle interface and craniofacial tissues.
Tribological behavior of cellulose nanostructured films
Authors: Fuenmayor Carmen , da Silva Dimas A , Klock Umberto , Lengowski Elaine C , de Andrade Alan S , Bonfatti Eraldo A , Trejo Jhonattan , Nuñez Yamid , Palma Oriana , de Cademartori Pedro Henrique G , de Muniz Graciela Ines B
Published: July 2022

This work aimed to study the tribological behavior of films composed of mixtures of nanofibrillated cellulose (NFC) and microcrystalline cellulose (MCC) at different concentrations. A micro-abrasive wear resistance analysis is presented as part of the tribological properties. Tribological behavior was observed against wear and tear in dry conditions. Mean surface roughness (Ra) was directly influenced by MCC concentrations in films, reaching values up to three times higher at concentrations of 30% MCC compared to films without MCC. The specific wear rate (k) of the films was inversely proportional to the MCC concentrations, observing that for low concentrations of MCC (5%), the wear reduction was only 7% for films without MCC. In concentrations of 10% MCC, the wear rate reduced by 52%, but in concentrations of 30% MCC, the reduction was up to 95%. The specific wear rate obtained was favorable and comparable to films of synectic origin. This shows that NFC/MCC composites may offer tribological advantages such as reinforcement coatings on different materials.
Climate change effects on understory plant phenology: implications for large herbivore forage availability
Authors: Brown Casey L , Coe Priscilla K , Clark Darren A , Wisdom Michael J , Rowland Mary M , Averett Joshua P , Johnson Bruce K
Published: July 2022

Consistent with a warming climate, the timing of key phenological phases (i.e. phenophases) for many plant species is shifting, but the direction and extent of these shifts remain unclear. For large herbivores such as ungulates, altered plant phenology can have important nutritional and demographic consequences. We used two multi-year datasets collected during 1992–1996 and 2015–2019 of understory plant phenology in semi-arid forested rangelands in northeastern Oregon, United States, to test whether the duration of phenophases for forage species has changed over time for three plant functional groups (forbs, graminoids, and shrubs). Duration of spring green-up was approximately 2 weeks shorter in the later years for forbs (19 ± 3.8 d) and graminoids (13.2 ± 2.8 d), and senescence was 3 weeks longer for graminoids (25.1 ± 5.1) and shrubs (22.0 ± 4.6). Average peak flowering date was 3.1 ± 0.2 d earlier per decade for understory forage species with approximately 1/3 of the species (35%) exhibiting earlier peak flowering dates over time. Variation in late-winter precipitation had the greatest effect on the duration of understory green-up, whereas variation in summer precipitation had a greater effect on duration of the senescent period. Collectively, these results indicate climate-related progression towards shorter periods of peak plant productivity, and earlier and longer periods of plant senescence, the combination of which substantially reduces the temporal window of forage available in growing forms most usable to herbivores. This work adds a needed component to the climate change literature, by describing links between shifting climate variables, multiple phases of understory plant phenology, and possible nutritional consequences for herbivores under a warming climate.
Continuous-Time Modeling of the Bidirectional Relationship Between Incidental Affect and Physical Activity
Authors: Ruissen Geralyn R , Beauchamp Mark R , Puterman Eli , Zumbo Bruno D , Rhodes Ryan E , Hives Benjamin A , Sharpe Brinkley M , Vega Julio , Low Carissa A , Wright Aidan G C
Published: July 2022

Background

Previous research suggests that there is a bidirectional relationship between incidental affect (i.e., how people feel in day-to-day life) and physical activity behavior. However, many inconsistencies exist in the body of work due to the lag interval between affect and physical activity measurements.

Purpose

Using a novel continuous-time analysis paradigm, we examined the temporal specificity underlying the dynamic relationship between positive and negative incidental affective states and moderate-to-vigorous physical activity (MVPA).

Methods

A community sample of adults (n = 126, Mage = 27.71, 51.6% Male) completed a 14-day ambulatory assessment protocol measuring momentary positive and negative incidental affect six times a day while wearing a physical activity monitor (Fitbit). Hierarchical Bayesian continuous-time structural equation modeling was used to elucidate the underlying dynamics of the relationship between incidental affective states and MVPA.

Results

Based on the continuous-time cross-effects, positive and negative incidental affect predicted subsequent MVPA. Furthermore, engaging in MVPA predicted subsequent positive and negative incidental affect. Incidental affective states had a greater relative influence on predicting subsequent MVPA compared to the reciprocal relationship. Analysis of the discrete-time coefficients suggests that cross-lagged effects increase as the time interval between measurements increase, peaking at about 8 h between measurement occasions before beginning to dissipate.

Conclusions

The results provide support for a recursive relationship between incidental affective states and MVPA, which is particularly strong at 7–9 hr time intervals. Future research designs should consider these medium-term dynamics, for both theory development and intervention.
Identification of Putative Causal Relationships Between Type 2 Diabetes and Blood-Based Biomarkers in East Asians by Mendelian Randomization
Authors: Zhang Haoyang , Xiu Xuehao , Yang Yuedong , Yang Yuanhao , Zhao Huiying
Published: July 2022

Observational studies have revealed phenotypic associations between type 2 diabetes (T2D) and many biomarkers. However, causality between these conditions in East Asians is unclear. We leveraged genome-wide association study (GWAS) summary statistics on T2D (n = 77,418 cases; n = 356,122 controls) from the Asian Genetic Epidemiology Network (sample recruited during 2001–2011) and GWAS summary statistics on 42 biomarkers (n = 12,303–143,658) from BioBank Japan (sample recruited during 2003–2008) to investigate causal relationships between T2D and biomarkers. Applications of Mendelian randomization approaches consistently revealed genetically instrumented associations of T2D with increased serum potassium levels (liability-scale β = 0.04–0.10; P = 6.41 × 10−17–9.85 × 10−5) and decreased serum chloride levels (liability-scale β = −0.16 to −0.06; P = 5.22 × 10−27–3.14 × 10−5), whereas these 2 biomarkers showed no causal effects on T2D. Heritability Estimation Using Summary Statistics (ρ-HESS) and summary-data–based Mendelian randomization highlighted 27 genomic regions and 3 genes (α-1,3-mannosyl-glycoprotein 2-β-N-acetylglucosaminyltransferase (MGAT1), transducing-like enhancer (TLE) family member 1, transcriptional corepressor (TLE1), and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR)) that interactively associated with the shared genetics underlying T2D and the 2 biomarkers. Thus, T2D may causally affect serum potassium and chloride levels among East Asians. In contrast, the relationships of potassium and chloride with T2D are not causal, suggesting the importance of monitoring electrolyte disorders for T2D patients.
Resolving single-cell copy number profiling for large datasets
Authors: Ruohan Wang , Yuwei Zhang , Mengbo Wang , Xikang Feng , Jianping Wang , Shuai Cheng Li
Published: July 2022

The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, an efficient method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map (DCM), capturing the similarities between any two bins along the genome. Then, SeCNV partitions the genome into segments by minimizing the structural entropy from the DCM. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e. the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50 000 cells) within 4 min, while other tools fail to finish within the time limit, i.e. 120 h. We apply SeCNV to single-nucleus sequencing datasets from two breast cancer patients and acoustic cell tagmentation sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
Authors: Wittig Alice , Miranda Fábio , Hölzer Martin , Altenburg Tom , Bartoszewicz Jakub M , Beyvers Sebastian , Dieckmann Marius A , Genske Ulrich , Giese Sven H , Nowicka Melania , Richard Hugues , Schiebenhoefer Henning , Schmachtenberg Anna-Juliane , Sieben Paul , Tang Ming , Tembrockhaus Julius , Renard Bernhard Y , Fuchs Stephan
Published: July 2022

The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast.

Availability and implementation

CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar.

Supplementary information

Supplementary data are available at Bioinformatics online.
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis
Authors: Wang Yizhuo , Flowers Christopher R , Li Ziyi , Huang Xuelin
Published: July 2022

In the era of big data, machine learning techniques are widely applied to every area in biomedical research including survival analysis. It is well recognized that censoring, which is a common missing issue in survival time data, hampers the direct usage of these machine learning techniques. Here, we present CondiS, a web toolkit with graphical user interface to help impute the survival times for censored observations and predict the survival times for future enrolled patients. CondiS imputes a censored survival time based on its distribution conditional on its observed part. When covariates are available, CondiS-X incorporates this information to further increase the imputation accuracy. Users can also upload data of newly enrolled patients and predict their survival times. As the first web-app tool with an imputation function for censored lifetime data, CondiS web can facilitate conducting survival analysis with machine learning approaches.

Availability and implementation

CondiS is an open-source application implemented with Shiny in R, available free at: https://biostatistics.mdanderson.org/shinyapps/CondiS/.

Supplementary information

Supplementary data are available at Bioinformatics online.
DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia
Authors: Fu Xiaoming , Zhou Xinyi , Gu Dongyang , Cao Zhixing , Grima Ramon
Published: July 2022

DelaySSAToolkit.jl is a Julia package for modelling reaction systems with non-Markovian dynamics, specifically those with time delays. These delays implicitly capture multiple intermediate reaction steps and hence serve as an effective model reduction technique for complex systems in biology, chemistry, ecology and genetics. The package implements a variety of exact formulations of the delay stochastic simulation algorithm.

Availability and implementation

The source code and documentation of DelaySSAToolkit.jl are available at https://github.com/palmtree2013/DelaySSAToolkit.jl.
IIFDTI: predicting drug–target interactions through interactive and independent features based on attention mechanism
Authors: Cheng Zhongjian , Zhao Qichang , Li Yaohang , Wang Jianxin
Published: July 2022

Motivation

Identifying drug–target interactions is a crucial step for drug discovery and design. Traditional biochemical experiments are credible to accurately validate drug–target interactions. However, they are also extremely laborious, time-consuming and expensive. With the collection of more validated biomedical data and the advancement of computing technology, the computational methods based on chemogenomics gradually attract more attention, which guide the experimental verifications.

Results

In this study, we propose an end-to-end deep learning-based method named IIFDTI to predict drug–target interactions (DTIs) based on independent features of drug–target pairs and interactive features of their substructures. First, the interactive features of substructures between drugs and targets are extracted by the bidirectional encoder–decoder architecture. The independent features of drugs and targets are extracted by the graph neural networks and convolutional neural networks, respectively. Then, all extracted features are fused and inputted into fully connected dense layers in downstream tasks for predicting DTIs. IIFDTI takes into account the independent features of drugs/targets and simulates the interactive features of the substructures from the biological perspective. Multiple experiments show that IIFDTI outperforms the state-of-the-art methods in terms of the area under the receiver operating characteristics curve (AUC), the area under the precision-recall curve (AUPR), precision, and recall on benchmark datasets. In addition, the mapped visualizations of attention weights indicate that IIFDTI has learned the biological knowledge insights, and two case studies illustrate the capabilities of IIFDTI in practical applications.

Availability and implementation

The data and codes underlying this article are available in Github at https://github.com/czjczj/IIFDTI.

Supplementary information

Supplementary data are available at Bioinformatics online.
How Did Levels of Psychological Distress and Perceptions of Workplace Support amongst Children’s Social Work Staff Change during the Covid-19 Pandemic?
Authors: Jones Rebecca K , Wilkins David , Bezeczky Zoe , Thompson Sarah
Published: July 2022

Covid-19 brought about drastic changes in day-to-day life and working practices, and had a profound impact on the mental health and well-being of the general population. Certain professional groups have also been particularly affected. This study sought to explore how levels of psychological distress and perceptions of workplace support amongst social work staff changed during the pandemic. We present the results from a series of surveys conducted in four local authorities (LAs) in England, before and during the Covid-19 pandemic. Social workers and other social care staff (n = 62) were asked about their experiences of psychological distress, using the twelve-item General Health Questionnaire. Overall, we found the proportion of staff reporting elevated levels of psychological distress increased and, in line with previous studies involving social workers, was high relative to the general population. Yet, most staff also said they had high levels of support from managers and colleagues, whilst a small proportion reported an increased perception of workplace support during the pandemic, compared to before. We consider these findings in relation to Organisational Support Theory and reflect on the ability of LAs to provide effective support for social care staff.
Resilience and Resistance in the Community Sector: Organisational Challenges and Responses by the Australian DFV Sector in the Time of COVID-19 Pandemic
Authors: Clarke Joanne , Morley Christine , Warren Shane , Carrington Kerrie , Vitis Laura , Ryan Vanessa , Ball Matthew
Published: July 2022

The COVID-19 pandemic led to increases in family violence in Australia and elsewhere. In response, organisations in the domestic and family violence (DFV) sector, had to adapt to the emerging public health measures and worked collaboratively to protect the most vulnerable in the community. These services, including courts, rapidly transformed their methods of service delivery that are likely to continue for some time. But what have been the implications/impacts of these rapid changes on the DFV service sector in Australia? How have these impacts informed the future needs of the DFV sector? And what is needed to strengthen this community sector of the future? This article reports on the findings of a national research project examining the impacts of COVID-19 on the DFV service sector and the adaptations and innovations that emerged in response. The study highlights that the surge in demand for services put pressure on an already overwhelmed workforce/service sector and provided an opportunity for front line workers to contribute to building a robust sector to respond to future crisis events. These findings have significant implications for future DFV sector service delivery, and for the social work profession as a whole.
In vivo quantitative imaging of hippocampal inflammation in autoimmune neuroinflammatory conditions: a systematic review
Authors: Nwaubani P , Cercignani M , Colasanti A
Published: July 2022

The hippocampus is a morphologically complex region of the brain limbic system centrally involved in important cognitive, affective, and behavioural regulatory roles. It has exquisite vulnerability to neuroinflammatory processes, with some of its subregions found to be specific sites of neuroinflammatory pathology in ex-vivo studies. Optimizing neuroimaging correlates of hippocampal neuroinflammation would enable the direct study of functional consequences of hippocampal neuroinflammatory pathology, as well as the definition of therapeutic end-points for treatments targeting neuroinflammation, and their related affective or cognitive sequelae. However, in vivo traditional imaging of the hippocampus and its subregions is fraught with difficulties, due to methodological challenges deriving from its unique anatomical characteristics. The main objective of this review is to provide a current update on the characterization of quantitative neuroimaging correlates of hippocampal neuroinflammation by focusing on three prototypical autoimmune neuro-inflammatory conditions [multiple sclerosis (MS), systemic lupus erythematosus (SLE), and autoimmune encephalitis (AE)]. We focused on studies employing TSPO-targeting positron emission tomography (PET), quantitative magnetic resonance imaging (MRI), and spectroscopy techniques assumed to be sensitive to neuroinflammatory tissue changes. We found 18 eligible studies (14, 2, and 2 studies in MS, AE, and SLE, respectively). Across conditions, the largest effect was seen in TSPO PET and diffusion-weighted MRI studies. No study examined neuroinflammation-related changes at the hippocampal subfield level. Overall, results were largely inconsistent due to heterogeneous imaging methods, small sample sizes, and different population studies. We discuss how these data could inform future study design and conclude by suggesting further methodological directions aimed at improving the precision and sensitivity of neuroimaging techniques to characterize hippocampal neuroinflammatory pathology in the human brain.
Estimating Analytical Errors of Glomerular Filtration Rate Measurement
Authors: Ognissanti Damiano , Andresen Bergström Moa , Theodorsson Elvar , Larsson Anders , Nordin Gunnar , Hammarsten Ola
Published: July 2022

Background

Few studies are available on how to optimize time points for sampling and how to estimate effects of analytical uncertainty when glomerular filtration rate (GFR) is calculated.

Methods

We explored the underlying regression mathematics of how analytical variation of a kidney filtration marker affects 1-compartment, slope-and-intercept GFR calculations, using 2 or 3 time points following a bolus injection, and used this to examine the results from 731 routine 3-point iohexol plasma clearance measurements.

Results

GFR calculations inflated analytical uncertainty if the time points were taken too late after the bolus injection and too close after each other. The uncertainty in GFR calculation was, however, the same as the analytical uncertainty if optimal time points were used. The middle of the 3 samples was of little value. The first sample should be taken as early as possible after the distribution phase. Sampling before the patient specific half-life of the kidney filtration marker resulted in an exponential error inflation whereas no error inflation was seen when sampling occurred later than 2 half-lives. Theoretical GFR uncertainty could be lowered 3.2-fold if individually optimized time points for sampling had been used in our 731 clearance measurements. Using Taylor expansions to approximate the moments of transformed random variables, the uncertainty of an individual GFR measurement could be calculated in a simple enough way to be applicable by laboratory software.

Conclusions

We provide a theoretical foundation to select patient-optimal time points that may both limit errors and allow calculation of GFR uncertainty.
An unusual case of stabbing chest pain …literally: a case report
Authors: Santos João , Neto Vanda , Marmelo Bruno , Correia Miguel
Published: July 2022

Background

Cardiac surgery is associated with a significant risk of potential postoperative complications. We describe a case of a patient with an unusual late cardiac perforation caused by a needle used to fix temporary epicardial pacing wires to the skin, which slowly migrated across subcutaneous tissues for 2 years following postoperative period.

Case summary

We report a case of middle-aged woman admitted to the cardiac intensive care unit due to suspected acute myocardial infarction. Multimodality imaging revealed the presence of an unusual intracardiac foreign body, located inside the interventricular septum and perforating towards the left atria, complicated by a small intracardiac fistula between septal coronary branches and the right ventricle. Analysis of previous examinations revealed that a needle used to fix temporary epicardial pacing wires to the skin had been left inside the patient, beneath the level of the diaphragm, after cardiac surgery in 2018. This foreign body slowly migrated across the diaphragm, towards the mediastinum, finally lodging inside the heart, after a period of 3 years. The patient was referred to cardiac surgery for foreign body retrieval.

Discussion

We describe an unusual case of cardiac perforation caused by a needle used to fix these wires to the skin, which migrated across subcutaneous tissues and finally lodged inside the basal interventricular septum and left atria. Full compliance with standardized surgical care bundles, as well as the implementation of a structured incident reporting system, is of upmost importance to prevent postoperative complications and improve surgical care.
Fulminant myocarditis after the first dose of mRNA-1273 vaccination in a patient with previous COVID-19: a case report
Authors: Horiuchi Kohei , Kosugi Shumpei , Abe Haruhiko , Ueda Yasunori
Published: July 2022

Background

COVID-19 vaccines have shown success in protecting people worldwide, although serious adverse effects have been reported in very rare cases.

Case summary

A 32-year-old male with a prior medical history of mild COVID-19 infection developed fulminant myocarditis five days after mRNA-1273 vaccination (first dose), which was confirmed using endomyocardial biopsy. He acutely developed respiratory failure and cardiogenic shock with ventricular tachycardia, but recovered completely with short-term high-dose steroid therapy and mechanical cardiac support, which is the recommended treatment for fulminant lymphocytic myocarditis.

Discussion

COVID-19 vaccine-induced myocarditis varies from mild to severe. In the present case, the patient was treated as for fulminant lymphocytic myocarditis and recovered relatively quickly. The mechanism of COVID-19 vaccine-associated myocarditis needs to be urgently investigated.