bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous multi-segment (SMSeg) EPI over multiple focal regions
Authors: Sun Kaibao , Zhong Zheng , Dan Guangyu , Wang Kezhou , Karaman M Muge , Luo Qingfei , Zhou Xiaohong Joe
Published: January 2023

Objective. This study aimed at developing a simultaneous multi-segment (SMSeg) imaging technique using a two-dimensional (2D) RF pulse in conjunction with echo planar imaging (EPI) to image multiple focal regions. Approach. The SMSeg technique leveraged periodic replicates of the excitation profile of a 2D RF pulse to simultaneously excite multiple focal regions at different locations. These locations were controlled by rotating and scaling transmit k-space trajectories. The resulting multiple isolated focal regions were projected into a composite ‘slice’ for display. GRAPPA-based parallel imaging was incorporated into SMSeg by taking advantage of coil sensitivity variations in both the phase-encoded and slice-selection directions. The SMSeg technique was implemented at 3 T in a single-shot gradient-echo EPI sequence and demonstrated in a phantom and human brains for both anatomic imaging and functional imaging. Main results. In both the phantom and the human brain, SMSeg images from three focal regions were simultaneously acquired. SMSeg imaging enabled up to a six-fold acceleration in parallel imaging without causing appreciable residual aliasing artifacts when compared with a conventional gradient-echo EPI sequence with the same acceleration factor. In the functional imaging experiment, BOLD activations associated with a visuomotor task were simultaneously detected in two non-coplanar segments (each with a size of 240 × 30 mm2), corresponding to visual and motor cortices, respectively. Significance. Our study has demonstrated that SMSeg imaging can be a viable method for studying multiple focal regions simultaneously.
A practical and robust method for beam blocker-based cone beam CT scatter correction
Authors: Cui Hehe , Jiang Xiao , Tang Wei , Lu Hsiao-Ming , Yang Yidong
Published: January 2023

Objective. In the traditional beam-blocker based cone beam CT (CBCT) scatter correction, the scatter measured in the region shaded by lead strips was multiplied by a correction factor to directly represent the scatter in the unblocked region. The correction factor optimization is a tedious process and lacks an objective stop criterion. To skip the optimization process, an indirect scatter estimation method was developed and validated in phantom imaging. Approach. A beam-blocker made of lead strips was mounted between the x-ray source and object for scatter estimation. The primary signal between lead strips in the blocked region was first calculated by subtracting the measured scatter, and then used to calculate the scatter signal in the unblocked region corresponding to the same attenuation path. The calculated scatter signal was smoothed via local filtration and used to correct the measured projection in the unblocked region. Finally, the CBCT was reconstructed via Feldkamp–Davis–Kress algorithm. A Catphan and a head phantom were used to verify the performance of the proposed method in both full- and half-blocker scenarios, and with and without a bow-tie filter. Main Results. For scans without the bow-tie filter, the CT number error was reduced to 3.97

±

2.27 and 5.51

±

3.90 HU in the full- and half-blocker scenarios, respectively, for the Catphan, and to 4.01

±

2.18 and 7.97 ± 4.05 HU for the head phantom. When the bow-tie filter was applied, the CT number error was reduced to 2.29

±

1.42 and 6.72

±

0.77 HU in the full- and half-blocker scenarios, respectively, for the Catphan, and 2.35

±

1.25 and 4.96 ± 1.89 HU for the head phantom. Significance. The proposed method effectively avoids the influence of the inserted beam blocker itself on the scatter intensity estimation, and proves a more practical and robust way for the beam-blocker based scatter correction in CBCT scanning.
The effect of crystal composition and environment on the color Doppler ultrasound twinkling artifact
Authors: Rokni Eric , Simon Julianna C
Published: January 2023

Objective. Pathological mineralizations form throughout the body and can be difficult to detect using conventional imaging methods. Color Doppler ultrasound twinkling highlights ∼60% of kidney stones with a rapid color shift and is theorized to arise from crevice microbubbles as twinkling disappears on kidney stones at elevated pressures and scratched acrylic balls in ethanol. Twinkling also sometimes appears on other pathological mineralizations; however, it is unclear whether the etiology of twinkling is the same as for kidney stones. Approach. In this study, five cholesterol, calcium phosphate, and uric acid crystals were grown in vitro and imaged in Doppler mode with a research ultrasound system and L7-4 transducer in water. To evaluate the influence of pressure on twinkling, the same crystals were imaged in a high-pressure chamber. Then, the effect of surface tension on twinkling was evaluated by imaging crystals in different concentrations of surfactant (1%, 2%, 3%, 4%) and ethanol (10%, 30%, 50%, 70%), artificial urine, bovine blood, and a tissue-mimicking phantom. Main results. Results showed that all crystals twinkled in water, with cholesterol twinkling significantly more than calcium phosphate and uric acid. When the ambient pressure was increased, twinkling disappeared for all tested crystals when pressures reached 7 MPa (absolute) and reappeared when returned to ambient pressure (0.1 MPa). Similarly, twinkling across all crystals decreased with surface tension when imaged in the surfactant and ethanol (statistically significant when surface tension <22 mN m−1) and decreased in blood (surface tension = 52.7 mN m−1) but was unaffected by artificial urine (similar surface tension to water). In the tissue-mimicking phantom, twinkling increased for cholesterol and calcium phosphate crystals with no change observed in uric acid crystals. Significance. Overall, these results support the theory that bubbles are present on crystals and cause twinkling, which could be leveraged to improve twinkling for the detection of other pathological mineralizations.
ResNet-integrated very early bolt looseness monitoring based on intrinsic feature extraction of percussion sounds
Authors: Yuan Rui , Lv Yong , Xu Shijie , Li Li , Kong Qingzhao , Song Gangbing
Published: January 2023

Very early bolt looseness monitoring has been a challenge in the field of structural health monitoring. The authors have conducted a further study of the previous researches, with the aim of detecting very early bolt looseness conditions. The intrinsic features of vibro-acoustic signals contain the underlying dynamic characteristics denoting full range bolt looseness conditions. Correspondingly, this paper proposes a novel ResNet-integrated very early bolt looseness monitoring approach based on intrinsic feature extraction of percussion sounds. The intrinsic features of percussion-caused sound signals were extracted by variational mode decomposition (VMD), where the parameters of VMD were determined by grey wolf optimization algorithm. The optimal band-limited intrinsic mode functions were converted into two-dimensional time–frequency maps by continuous wavelet transform. The (red green blue) RGB images were adopted as the input of residual network (ResNet) to monitor very early bolt looseness conditions. The results and analysis illustrate the validity and superiority of the novel ResNet-integrated very early bolt looseness monitoring approach. The proposed approach in our researches provides a novel solution for very early bolt looseness monitoring in the field of structural health monitoring. The strategy can also be extended to other nonlinear signal processing-involved fields.
Deformation of an electron bunch caused by free-electron lasers
Authors: Sei Norihiro , Zen Heishun , Ohgaki Hideaki
Published: January 2023

This study reported the longitudinal compression and extension of an electron bunch by free electron laser (FEL) interaction. By observing coherent edge radiation generated by an FEL facility at Kyoto University, which has the highest extraction efficiency of an FEL oscillation, we found that an electron bunch interacting with a cavity-type linac FEL elongated when a detuning length of an optical cavity was positive. The transition from compression to extension of the electron bunch was bounded by a perfect synchronism condition between the electron bunch and the FEL pulse, and the change rate of the root-mean-square bunch length was as high as 14%. Therefore, it was experimentally demonstrated that a slight temporal difference between the electron bunch and the optical pulse dramatically changed not only the FEL power but also the outline of electron distribution in the bunch.
Probing reaction mechanisms through residual cross section measurement for 7Li+Zn system
Authors: Singh Ankur , Maiti Moumita , Nag T N , Sodaye S
Published: January 2023

Though the picture remains incoherent to draw a concrete conclusion, especially with weakly bound particles, prolific efforts have been devoted to unfolding the reaction mechanisms at energies below 10 MeV/u. The dearth of extensive data and ambiguous findings in the light to medium mass region galvanizes the exploration of the entire mass domain. In the course of discerning the underlying reaction mechanisms in 7Li fusion with natural Zn, the excitation function (EF) analysis has been reported within the energy range of 21–43 MeV. Residual cross sections have been measured employing the stacked foil activation technique followed by offline γ-spectroscopy. Subsequently, the measured EFs have been compared with theoretical predictions from statistical model codes PACE4 and EMPIRE3.2.2. EF analysis affirms the dominance of the complete fusion (CF) mechanism as revealed through the gross satisfaction of measured data from the n-emitting channels by both the model codes. The observed enhancement in subsequent channels relative to theory has been implicitly interpreted as the role of other mechanisms like breakup fusion and/or direct cluster transfer in populating residues owing to the low breakup threshold of weakly bound 7Li. A critical piece of experimental evidence concerning the discrepancy in the branching intensity of 93.31 keV γ-peak from the decay of 67Ga residue reported in various nuclear databases has been witnessed. Thus, the revised estimated intensity value has been reported, along with a discussion on the optimized production of Ga isotopes for medicinal applications.
Neon lasing (λ = 540.1 nm) in a dense optical cavity pumped by a pulsed inductive cylindrical discharge
Authors: Razhev A M , Churkin D S , Tkachenko R A
Published: January 2023

The experimental results of the lasing characteristics dependence of the inductive neon laser (λ = 540.1 nm) on the optical cavity quality factor are presented. In the described experiments, the laser was operated in the amplified spontaneous emission mode. A frontal-substrate resonator (made according to the type of an open Fabry–Perot interferometer) was used, as well as a dense resonator with a reflection coefficient of the front mirror of 82%. Replacing the front substrate with an output mirror resulted in an increase in the lasing energy and optical pulse duration from 8.5 μJ to 41 μJ and from 10.0 ± 0.1 ns to 14.8 ± 0.1 ns, respectively. It is shown that the use of a dense resonator allows us to change the shape of the laser beam in the far field from annular to circular and to obtain intensity distribution close to uniform.
Characterization of micro pore optics for full-field X-ray fluorescence imaging
Authors: An S. , Krapohl D. , Thörnberg B. , Roudot R. , Schyns E. , Norlin B.
Published: January 2023

Elemental mapping images can be achieved through step scanning imaging using pinhole optics or micro pore optics (MPO), or alternatively by full-field X-ray fluorescence imaging (FF-XRF). X-ray optics for FF-XRF can be manufactured with different micro-channel geometries such as square, hexagonal or circular channels. Each optic geometry creates different imaging artefacts. Square-channel MPOs generate a high intensity central spot due to two reflections via orthogonal channel walls inside a single channel, which is the desirable part for image formation, and two perpendicular lines forming a cross due to reflections in one plane only. Thus, we have studied the performance of a square-channel MPO in an FF-XRF imaging system. The setup consists of a commercially available MPO provided by Photonis and a Timepix3 readout chip with a silicon detector. Imaging of fluorescence from small metal particles has been used to obtain the point spread function (PSF) characteristics. The transmission through MPO channels and variation of the critical reflection angle are characterized by measurements of fluorescence from copper and titanium metal fragments. Since the critical angle of reflection is energy dependent, the cross-arm artefacts will affect the resolution differently for different fluorescence energies. It is possible to identify metal fragments due to the form of the PSF function. The PSF function can be further characterized using a Fourier transform to suppress diffuse background signals in the image.
Development of a heavy ion beam probe diagnostic for HL-2A tokamak
Authors: Fan H.R. , Gao L.T. , Liu A.D. , Zhuang G. , Ido T. , Xu M. , Huang J.C. , Zhang J. , Feng C.Q. , Zhou C. , Liu H. , Nie L. , Liu Y.X. , Fu B.Z. , Li J.Q. , Liu W.D.
Published: January 2023

A heavy ion beam probe (HIBP) is being developed and tested on the
HL-2A tokamak.
To focus on the turbulence measurement in high beta scenarios with the toroidal
magnetic field of 1.35 T, a 500 kV thallium beam is chosen and optimized.
The locations of the injection and detection system are determined based on the
probing beam trajectory calculations.
The status of the accelerator, sweep system, analyzer, and control
system is described.
Four pairs of sweep plates are positioned in both primary and secondary
beamlines to actively control the beam trajectory, where the
poloidal sweepers require a maximum of 15 kV voltages to be applied.
A parallel-plate energy analyzer with multi-slits is supplied by 100 kV
high voltage for the electric potential measurement.
The signal intensity is also evaluated to be hundreds of nA levels,
5 × 107 V/A amplifiers are therefore designed.
Software is also developed to include the data acquisition as well as the
control and monitoring of HIBP subsystems.
Synergistic contributions of climate and management intensifications to maize yield trends from 1961 to 2017
Authors: Medina Hanoi , Tian Di
Published: January 2023

Understanding contributions of climate and management intensifications to crop yield trends is essential to better adapt to climate changes and gauge future food security. Here we quantified the synergistic contributions of climate and management intensifications to maize yield trends from 1961 to 2017 in Iowa (United States) using a process-based modeling approach with a detailed climatic and agronomic observation database. We found that climate (management intensifications) contributes to approximately 10% (90%), 26% (74%), and 31% (69%) of the yield trends during 1961–2017, 1984–2013, and 1982–1998, respectively. However, the climate contributions show substantial decadal or multi-decadal variations, with the maximum decadal yield trends induced by temperature or radiation changes close to management intensifications induced trends while considerably larger than precipitation induced trends. Management intensifications can produce more yield gains with increased precipitation but greater losses of yields with increased temperature, with extreme drought conditions diminishing the yield gains, while radiation changes have little effect on yield gains from management intensifications. Under the management condition of recent years, the average trend at the higher warming level was about twice lower than that at the lower warming level, and the sensitivity of yield to warming temperature increased with management intensifications from 1961 to 2017. Due to such synergistic effects, management intensifications must account for global warming and incorporate climate adaptation strategies to secure future crop productions. Additional research is needed to understand how plausible adaptation strategies can mitigate synergistic effects from climate and management intensifications.
Integrable boundary conditions for staggered vertex models
Authors: Frahm Holger , Gehrmann Sascha
Published: January 2023

Yang–Baxter integrable vertex models with a generic

Z

2

-staggering can be expressed in terms of composite

R

-matrices given in terms of the elementary R-matrices. Similarly, integrable open boundary conditions can be constructed through generalized reflection algebras based on these objects and their representations in terms of composite boundary matrices

K

±

. We show that only two types of staggering yield a local Hamiltonian with integrable open boundary conditions in this approach. The staggering in the underlying model allows for a second hierarchy of commuting integrals of motion (in addition to the one including the Hamiltonian obtained from the usual transfer matrix), starting with the so-called quasi momentum operator. In this paper, we show that this quasi momentum operator can be obtained together with the Hamiltonian for both periodic and open models in a unified way from enlarged Yang–Baxter or reflection algebras in the composite picture. For the special case of the staggered six-vertex model, this allows constructing an integrable spectral flow between the two local cases.
The effect of microstructural and texture evolutions during thermomechanical treatment on corrosion resistance of 310s austenitic stainless steel
Authors: Heidari R B , Eskandari M , Yeganeh M
Published: January 2023

In this study, the evolution of the microstructure and texture during thermomechanical treatment and its effect on corrosion properties of 310s austenitic stainless steel were investigated. This stainless steel was cryo-rolled at 50 and 90% thickness reductions, and then the 90% cryo-rolled sample was annealed at 750 °C for 5 and 30 min. SEM and optical microscope images were used to examine the microstructure of the samples. Fritoscopy test was also used to calculate the volume fraction of the martensite phase. Electrochemical impedance spectroscopy (EIS), potentiodynamic polarization and cyclic potentiodynamic polarization tests were performed in the 3.5 wt.% NaCl solution to investigate the corrosion behavior of the studied steel. The results showed that the cryo-rolling process caused the reduction of grain size, texture strengthening and transformation of austenite to strain-inducedαʹ-martensite phase. Decreasing grain size and increasing texture components containing dense planes are beneficial factors and the formation of theαʹ-martensite phase is a harmful factor for corrosion resistance. It was observed that annealing at 750 °C for 30 min caused the grain growth and texture weakening, while a favorable condition is developed in the annealed sample for 5 min. After 90% cryo-rolling and subsequent annealing at 750 °C for 5 min, the corrosion resistance was significantly improved compared to the as-received sample and reached 37 kΩ.cm2. Formation of the sub-micron microstructure along with the high volume fraction of Brass and Goss texture components were the main reasons for improving corrosion resistance at 750 °C–5 min.
Plasma diagnosis of tetrahedral amorphous carbon films by filtered cathodic vacuum arc deposition
Authors: WANG Minglei , ZHANG Lin , LU Wenqi , LIN Guoqiang
Published: January 2023

Filtered cathodic vacuum arc (FCVA) deposition is regarded as an important technique for the synthesis of tetrahedral amorphous carbon (ta-C) films due to its high ionization rate, high deposition rate and effective filtration of macroparticles. Probing the plasma characteristics of arc discharge contributes to understanding the deposition mechanism of ta-C films on a microscopic level. This work focuses on the plasma diagnosis of an FCVA discharge using a Langmuir dual-probe system with a discrete Fourier transform smoothing method. During the ta-C film deposition, the arc current of graphite cathodes and deposition pressure vary from 30 to 90 A and from 0.3 to 0.9 Pa, respectively. The plasma density increases with arc current but decreases with pressure. The carbon plasma density generated by the arc discharge is around the order of 1010 cm−3. The electron temperature varies in the range of 2‒3.5 eV. As the number of cathodic arc sources and the current of the focused magnetic coil increase, the plasma density increases. The ratio of the intensity of the D-Raman peak and G-Raman peak (I
D/I
G) of the ta-C films increases with increasing plasma density, resulting in a decrease in film hardness. It is indicated that the mechanical properties of ta-C films depend not only on the ion energy but also on the carbon plasma density.
Thoughts on complex systems: an interview with Giorgio Parisi
Authors: Parisi Giorgio
Published: January 2023

The Nobel Laureate Giorgio Parisi is interviewed by JPhys Complexity Editor-in-Chief, Ginestra Bianconi, on themes related to the 2021 Nobel Prize in Physics awarded to him for research on complex systems.
A general criterion for the Pólya-Carlson dichotomy and application
Authors: Bell Jason , Gunn Keira , Nguyen Khoa , Saunders J.
Published: January 2023

We prove a general criterion for an irrational power series

f
(
z
)
=

∑

n
=
0

∞

a
n

z
n

f(z)=\sum _{n=0}^{\infty }a_nz^n

with coefficients in a number field

K
K

to admit the unit circle as a natural boundary. As an application, let

F
F

be a finite field, let

d
d

be a positive integer, let

A
∈

M
d

(
F
[
t
]
)

A\in M_d(F[t])

be a

d
×
d

d\times d

-matrix with entries in

F
[
t
]

F[t]

, and let

ζ
A

(
z
)

\zeta _A(z)

be the Artin-Mazur zeta function associated to the multiplication-by-

A
A

map on the compact abelian group

F
(
(
1

/

t
)

)
d

/

F
[
t

]
d

F((1/t))^d/F[t]^d

. We provide a complete characterization of when

ζ
A

(
z
)

\zeta _A(z)

is algebraic and prove that it admits the circle of convergence as a natural boundary in the transcendence case. This is in stark contrast to the case of linear endomorphisms on

R

d

/

Z

d

\mathbb {R}^d/\mathbb {Z}^d

in which Baake, Lau, and Paskunas [Monatsh. Math. 161 (2010), pp. 33–42] prove that the zeta function is always rational. Some connections to earlier work of Bell, Byszewski, Cornelissen, Miles, Royals, and Ward are discussed. Our method uses a similar technique in recent work of Bell, Nguyen, and Zannier [Amer. Math. Soc. 373 (2020), pp. 4889–4906] together with certain patching arguments involving linear recurrence sequences.
Degenerate linear parabolic equations in divergence form on the upper half space
Authors: Dong Hongjie , Phan Tuoc , Tran Hung
Published: January 2023

We study a class of second-order degenerate linear parabolic equations in divergence form in

(
−
∞
,
T
)
×

R

+
d

(-\infty , T) \times {\mathbb {R}}^d_+

with homogeneous Dirichlet boundary condition on

(
−
∞
,
T
)
×
∂

R

+
d

(-\infty , T) \times \partial {\mathbb {R}}^d_+

, where

R

+
d

=
{
x
∈

R

d

:

x
d

>
0
}

{\mathbb {R}}^d_+ = \{x \in {\mathbb {R}}^d: x_d>0\}

and

T
∈

(
−
∞
,
∞
]

T\in {(-\infty , \infty ]}

is given. The coefficient matrices of the equations are the product of

μ
(

x
d

)

\mu (x_d)

and bounded uniformly elliptic matrices, where

μ
(

x
d

)

\mu (x_d)

behaves like

x
d
α

x_d^\alpha

for some given

α
∈
(
0
,
2
)

\alpha \in (0,2)

, which are degenerate on the boundary

{

x
d

=
0
}

\{x_d=0\}

of the domain. Our main motivation comes from the analysis of degenerate viscous Hamilton-Jacobi equations. Under a partially VMO assumption on the coefficients, we obtain the well-posedness and regularity of solutions in weighted Sobolev spaces. Our results can be readily extended to systems.
Virtual wards: a rapid evidence synthesis and implications for the care of older people
Authors: Norman Gill , Bennett Paula , Vardy Emma R L C
Published: January 2023

Background

Virtual wards are being rapidly developed within the National Health Service in the UK, and frailty is one of the first clinical pathways. Virtual wards for older people and existing hospital at home services are closely related.

Methods

In March 2022, we searched Medline, CINAHL, the Cochrane Database of Systematic Reviews and medRxiv for evidence syntheses which addressed clinical-effectiveness, cost-effectiveness, barriers and facilitators, or staff, patient or carer experience for virtual wards, hospital at home or remote monitoring alternatives to inpatient care.

Results

We included 28 evidence syntheses mostly relating to hospital at home. There is low to moderate certainty evidence that clinical outcomes including mortality (example pooled RR 0.77, 95% CI 0.60–0.99) were probably equivalent or better for hospital at home. Subsequent residential care admissions are probably reduced (example pooled RR 0.35, 95% CI 0.22–0.57). Cost-effectiveness evidence demonstrated methodological issues which mean the results are uncertain. Evidence is lacking on cost implications for patients and carers. Barriers and facilitators operate at multiple levels (organisational, clinical and patient). Patient satisfaction may be improved by hospital at home relative to inpatient care. Evidence for carer experience is limited.

Conclusions

There is substantial evidence for the clinical effectiveness of hospital at home but less evidence for virtual wards. Guidance for virtual wards is lacking on key aspects including team characteristics, outcome selection and data protection. We recommend that research and evaluation is integrated into development of virtual ward models. The issue of carer strain is particularly relevant.
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings
Authors: Yeung Wayland , Zhou Zhongliang , Li Sheng , Kannan Natarajan
Published: January 2023

Protein language modeling is a fast-emerging deep learning method in bioinformatics with diverse applications such as structure prediction and protein design. However, application toward estimating sequence conservation for functional site prediction has not been systematically explored. Here, we present a method for the alignment-free estimation of sequence conservation using sequence embeddings generated from protein language models. Comprehensive benchmarks across publicly available protein language models reveal that ESM2 models provide the best performance to computational cost ratio for conservation estimation. Applying our method to full-length protein sequences, we demonstrate that embedding-based methods are not sensitive to the order of conserved elements—conservation scores can be calculated for multidomain proteins in a single run, without the need to separate individual domains. Our method can also identify conserved functional sites within fast-evolving sequence regions (such as domain inserts), which we demonstrate through the identification of conserved phosphorylation motifs in variable insert segments in protein kinases. Overall, embedding-based conservation analysis is a broadly applicable method for identifying potential functional sites in any full-length protein sequence and estimating conservation in an alignment-free manner. To run this on your protein sequence of interest, try our scripts at https://github.com/esbgkannan/kibby.
scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network
Authors: Wang Jing , Xia Junfeng , Wang Haiyun , Su Yansen , Zheng Chun-Hou
Published: January 2023

The advances in single-cell ribonucleic acid sequencing (scRNA-seq) allow researchers to explore cellular heterogeneity and human diseases at cell resolution. Cell clustering is a prerequisite in scRNA-seq analysis since it can recognize cell identities. However, the high dimensionality, noises and significant sparsity of scRNA-seq data have made it a big challenge. Although many methods have emerged, they still fail to fully explore the intrinsic properties of cells and the relationship among cells, which seriously affects the downstream clustering performance. Here, we propose a new deep contrastive clustering algorithm called scDCCA. It integrates a denoising auto-encoder and a dual contrastive learning module into a deep clustering framework to extract valuable features and realize cell clustering. Specifically, to better characterize and learn data representations robustly, scDCCA utilizes a denoising Zero-Inflated Negative Binomial model-based auto-encoder to extract low-dimensional features. Meanwhile, scDCCA incorporates a dual contrastive learning module to capture the pairwise proximity of cells. By increasing the similarities between positive pairs and the differences between negative ones, the contrasts at both the instance and the cluster level help the model learn more discriminative features and achieve better cell segregation. Furthermore, scDCCA joins feature learning with clustering, which realizes representation learning and cell clustering in an end-to-end manner. Experimental results of 14 real datasets validate that scDCCA outperforms eight state-of-the-art methods in terms of accuracy, generalizability, scalability and efficiency. Cell visualization and biological analysis demonstrate that scDCCA significantly improves clustering and facilitates downstream analysis for scRNA-seq data. The code is available at https://github.com/WJ319/scDCCA.
Capturing variation in metagenomic assembly graphs with MetaCortex
Authors: Martin Samuel , Ayling Martin , Patrono Livia , Caccamo Mario , Murcia Pablo , Leggett Richard M
Published: January 2023

Motivation

The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example, viral haplotypes, or bacterial strain-level diversity, is even more challenging.

Results

We present MetaCortex, a metagenome assembler that captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain-level diversity and on simulated communities containing simulated strains.

Availability and implementation

Source code is freely available to download from https://github.com/SR-Martin/metacortex, is implemented in C and supported on MacOS and Linux. The version used for the results presented in this article is available at doi.org/10.5281/zenodo.7273627.

Supplementary information

Supplementary data are available at Bioinformatics online.
CAMR: cross-aligned multimodal representation learning for cancer survival prediction
Authors: Wu Xingqi , Shi Yi , Wang Minghui , Li Ao
Published: January 2023

Motivation

Accurately predicting cancer survival is crucial for helping clinicians to plan appropriate treatments, which largely improves the life quality of cancer patients and spares the related medical costs. Recent advances in survival prediction methods suggest that integrating complementary information from different modalities, e.g. histopathological images and genomic data, plays a key role in enhancing predictive performance. Despite promising results obtained by existing multimodal methods, the disparate and heterogeneous characteristics of multimodal data cause the so-called modality gap problem, which brings in dramatically diverse modality representations in feature space. Consequently, detrimental modality gaps make it difficult for comprehensive integration of multimodal information via representation learning and therefore pose a great challenge to further improvements of cancer survival prediction.

Results

To solve the above problems, we propose a novel method called cross-aligned multimodal representation learning (CAMR), which generates both modality-invariant and -specific representations for more accurate cancer survival prediction. Specifically, a cross-modality representation alignment learning network is introduced to reduce modality gaps by effectively learning modality-invariant representations in a common subspace, which is achieved by aligning the distributions of different modality representations through adversarial training. Besides, we adopt a cross-modality fusion module to fuse modality-invariant representations into a unified cross-modality representation for each patient. Meanwhile, CAMR learns modality-specific representations which complement modality-invariant representations and therefore provides a holistic view of the multimodal data for cancer survival prediction. Comprehensive experiment results demonstrate that CAMR can successfully narrow modality gaps and consistently yields better performance than other survival prediction methods using multimodal data.

Availability and implementation

CAMR is freely available at https://github.com/wxq-ustc/CAMR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimation of high-dimensional vector autoregression via sparse precision matrix
Authors: Poignard Benjamin , Asai Manabu
Published: January 2023

We consider the problem of estimating sparse vector autoregression (VAR) via penalized precision matrices. This matrix is the output of the underlying directed acyclic graph of the VAR process, whose zero components correspond to the zero coefficients of the graphical representation of the VAR. The sparsity-based precision matrix estimator is deduced from the D-trace loss with convex and nonconvex penalty functions. We establish the consistency of the penalized estimator and provide the conditions for which all true zero entries of the precision matrix are actually estimated as zero with probability tending to one. The relevance of the method is supported by simulated experiments and a real data application.
Evaluation of coronary flow is useful in patients with left coronary cusp thrombus formation after left ventricular assist device implantation
Authors: Sato Tasuku , Hieda Michinari , Futami Shutaro , Fukata Mitsuhiro , Shiose Akira
Published: January 2023

Left ventricular assist device (LVAD) is essential for patients with severe heart failure, but there is a risk of thrombus formation on the aortic root and cusps, leading to coronary artery occlusion. Even with the narrowing of the echo-window due to LVAD, careful observation of coronary flow by transthoracic echocardiography can evaluate the patency of coronary flow non-invasively and immediately.
ESC/EACTS vs. ACC/AHA guidelines for the management of severe aortic stenosis
Authors: Lee Grace , Chikwe Joanna , Milojevic Milan , Wijeysundera Harindra C , Biondi-Zoccai Giuseppe , Flather Marcus , Gaudino Mario F L , Fremes Stephen E , Tam Derrick Y
Published: January 2023

Aortic stenosis (AS) is a serious and complex condition, for which optimal management continues to evolve rapidly. An understanding of current clinical practice guidelines is critical to effective patient care and shared decision-making. This state of the art review of the 2021 European Society of Cardiology/European Association for Cardio-Thoracic Surgery Guidelines and 2020 American College of Cardiology/American Heart Association Guidelines compares their recommendations for AS based on the evidence to date. The European and American guidelines were generally congruent with the exception of three key distinctions. First, the European guidelines recommend intervening at a left ventricular ejection fraction of 55%, compared with 60% over serial imaging by the American guidelines for asymptomatic patients. Second, the European guidelines recommend a threshold of ≥65 years for surgical bioprosthesis, whereas the American guidelines employ multiple age categories, providing latitude for patient factors and preferences. Third, the guidelines endorse different age cut-offs for transcatheter vs. surgical aortic valve replacement, despite limited evidence. This review also discusses trends indicating a decreasing proportion of mechanical valve replacements. Finally, the review identifies gaps in the literature for areas including transcatheter aortic valve implantation in asymptomatic patients, the appropriateness of Ross procedures, concomitant coronary revascularization with aortic valve replacement, and bicuspid AS. To summarize, this state of the art review compares the latest European and American guidelines on the management of AS to highlight three areas of divergence: timing of intervention, valve selection, and surgical vs. transcatheter aortic valve replacement criteria.
Elevated remnant cholesterol, plasma triglycerides, and cardiovascular and non-cardiovascular mortality
Authors: Wadström Benjamin N , Pedersen Kasper M , Wulff Anders B , Nordestgaard Børge G
Published: January 2023

Aims

Cholesterol carried in triglyceride-rich lipoproteins, also called remnant cholesterol, is being increasingly acknowledged as an important causal risk factor for atherosclerosis. Elevated remnant cholesterol, marked by elevated plasma triglycerides, is associated causally with an increased risk of atherosclerotic cardiovascular disease. The association with cause-specific mortality is, however, unclear. The aim of this study was to test the hypothesis that elevated remnant cholesterol and plasma triglycerides are associated with increased mortality from cardiovascular disease, cancer, and other causes.

Methods and results

Using a contemporary population-based cohort, 87 192 individuals from the Copenhagen General Population Study aged 20–69 years at baseline in 2003–2015 were included. During up to 13 years of follow-up, 687 individuals died from cardiovascular disease, 1594 from cancer, and 856 from other causes, according to the National Danish Causes of Death Registry. In individuals with remnant cholesterol ≥1.0 mmol/L (≥39 mg/dL; 22% of the population) compared with those with levels <0.5 mmol/L (<19 mg/dL), multivariable-adjusted mortality hazard ratios were 2.2 (95% confidence interval 1.3–3.5) for cardiovascular disease, 1.0 (0.7–1.3) for cancer, and 2.1 (1.4–3.3) for other causes. Exploratory analysis of the cause of death subcategories showed corresponding hazard ratios of 4.4 (1.6–11) for ischemic heart disease, 8.4 (2.0–34) for infectious diseases, and 9.1 (1.9–43) for endocrinological diseases. Results for plasma triglycerides >2 vs. <1 mmol/L (>177 vs. <89 mg/dL) were similar.

Conclusion

Remnant cholesterol of ≥1 mmol/L (39 mg/dL), present in 22% of the population, and plasma triglycerides of ≥2 mmol/L (177 mg/dL), present in 28% of the population, were associated with two-fold mortality from cardiovascular and other causes, but not from cancer. This novel finding should be confirmed in other cohorts.
Audit and feedback interventions involving pharmacists to influence prescribing behaviour in general practice: a systematic review and meta-analysis
Authors: Carter Mary , Abutheraa Nouf , Ivers Noah , Grimshaw Jeremy , Chapman Sarah , Rogers Philip , Simeoni Michelle , Antony Jesmin , Watson Margaret C
Published: January 2023

Introduction

Pharmacists, as experts in medicines, are increasingly employed in general practices and undertake a range of responsibilities. Audit and feedback (A&F) interventions are effective in achieving behaviour change, including prescribing. The extent of pharmacist involvement in A&F interventions to influence prescribing is unknown. This review aimed to assess the effectiveness of A&F interventions involving pharmacists on prescribing in general practice compared with no A&F/usual care and to describe features of A&F interventions and pharmacist characteristics.

Methods

Electronic databases (MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, (Social) Science Citation Indexes, ISI Web of Science) were searched (2012, 2019, 2020). Cochrane systematic review methods were applied to trial identification, selection, and risk of bias. Results were summarized descriptively and heterogeneity was assessed. A random-effects meta-analysis was conducted where studies were sufficiently homogenous in design and outcome.

Results

Eleven cluster-randomized studies from 9 countries were included. Risk of bias across most domains was low. Interventions focussed on older patients, specific clinical area(s), or specific medications. Meta-analysis of 6 studies showed improved prescribing outcomes (pooled risk ratio: 0.78, 95% confidence interval: 0.64–0.94). Interventions including both verbal and written feedback or computerized decision support for prescribers were more effective. Pharmacists who received study-specific training, provided ongoing support to prescribers or reviewed prescribing for individual patients, contributed to more effective interventions.

Conclusions

A&F interventions involving pharmacists can lead to small improvements in evidence-based prescribing in general practice settings. Future implementation of A&F within general practice should compare different ways of involving pharmacists to determine how to optimize effectiveness.

PRISMA-compliant abstract included in Supplementary Material 1.
The synthesis, biological activities and applications of protein–polysaccharide conjugates in food system: a review
Authors: Zhang Shixuan , Wang Kai , Qin Yongtao , Zhu Shunyi , Gao Qikuan , Liu Diru
Published: January 2023

Proteins are important ingredients in the food industry for their excellent nutritional, functional and biological properties, while the application is limited by their sensitivity to environmental stresses such as high temperature, pH changes and ionic strength. The Maillard reaction and transglutaminase-catalyzed glycosylation are the two main effective glycosylation ways to improve the stability and biological properties of proteins by mainly attaching monosaccharides or disaccharides to proteins, while protein–polysaccharide conjugates with superior functional properties are rarely discussed. Therefore, the present study reviews current state of the synthesis, biological activities and applications in the food system of protein–polysaccharide conjugates formed via the Maillard reaction and transglutaminase-catalyzed glycosylation. The biological activities including antioxidant, antimicrobial and immunomodulatory activities of proteins are improved after glycosylation, and the formed protein–polysaccharide conjugates can be applied to stabilize emulsions or deliver bioactive compounds in foods. The bioactivities produced under precisely controlled glycosylation conditions would make protein–polysaccharide conjugates a promising application in foods with healthy properties.
Metagenomics Shines Light on the Evolution of “Sunscreen” Pigment Metabolism in theTeloschistales(Lichen-Forming Ascomycota)
Authors: Llewellyn Theo , Nowell Reuben W , Aptroot Andre , Temina Marina , Prescott Thomas A K , Barraclough Timothy G , Gaya Ester
Published: January 2023

Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.
Ethylene oxide emissions and incident breast cancer and non-Hodgkin lymphoma in a US cohort
Authors: Jones Rena R , Fisher Jared A , Medgyesi Danielle N , Buller Ian D , Liao Linda M , Gierach Gretchen , Ward Mary H , Silverman Debra T
Published: January 2023

Background

Ethylene oxide (EtO) is a carcinogenic gas used in chemical production and to sterilize medical equipment that has been linked to risk of breast and lymphohematopoietic cancers in a small number of occupational studies. We investigated the relationship between environmental EtO exposure and risk of these cancers.

Methods

Using the US Environmental Protection Agency’s Toxics Release Inventory, we estimated historical exposures for National Institutes of Health–AARP Diet and Health Study participants enrolled in 1995-1996. We constructed 2 metrics at 3, 5, and 10 km: 1) distance between residences and EtO-emitting facilities, weighted by the proportion of time the home was downwind of each facility, and 2) distance-weighted, wind direction–adjusted average airborne emissions index (AEI=∑[lbs EtO/km2]). We estimated risk (hazard ratio [HR], 95% confidence interval [CI]) of incident breast cancer (in situ and invasive) among postmenopausal women (n = 173 670) overall and by tumor estrogen receptor status and non-Hodgkin lymphoma in the full cohort (n = 451 945).

Results

We observed an increased risk of breast cancer associated with EtO-emitting facilities within 10 km (HR[≤10vs>10] = 1.05, 95% CI = 1.00 to 1.10) that appeared stronger for in situ (HR[≤10vs>10] = 1.13, 95% CI = 1.00 to 1.27) than invasive (HR[≤10vs>10] = 1.03, 95% CI = 0.97 to 1.09) disease. Risk of breast cancer in situ was also increased in the top AEI quartiles, and associations weakened with larger distances (HR[Q4vs0] = 1.60, 95% CI = 0.98 to 2.61; HR[Q4vs0] = 1.28, 95% CI = 0.92 to 1.79; HR[Q4vs0] = 1.25, 95% CI = 1.02 to 1.53 at 3, 5, and 10 km, respectively). No differences in breast cancer risk were observed by estrogen receptor status. We found no clear pattern of increased non-Hodgkin lymphoma risk.

Conclusions

A novel potential association between EtO emissions and risk of in situ, but not invasive, breast cancer warrants additional evaluation.