bluuebunny/crossref_metadata_2025 huggingface dataset:
Design optimization of one-dimensional aberration-free x-ray gradually focusing lenses
Authors: Xu Yuanze , Lin He , Yi Futing , Liu Jing
Published: January 2023

In our previous work, we proposed a new design method for an aberration-free x-ray refractive focusing lens based on an ideal Cartesian oval shape to solve the aberration problem in x-ray compound refractive focusing. In this paper, we propose an optimization method for this new lens. By reducing the aperture of each lens, we achieve the objective of increasing the effective aperture and improving the focusing performance of the lens. The simulation of the beam propagation method shows that the focusing performance of the optimized lenses is better in compound refractive lens shape but worse in the kinoform shape. This is different from the results obtained with the conventional kinoform lens. After further comparison, we found that this is because the step height of the kinoform lens is small when the lens aperture is very small, resulting in a strong diffraction effect that weakens the focusing performance of the lens. Further modifications to the structure of the kinoform lens are needed to improve this phenomenon.
Experimental analysis on dynamic/morphological quality of cavitation induced by different air injection rates and sites
Authors: H. Malekshah Emad , Wróblewski Włodzimierz , Bochon Krzysztof , Majkut Mirosław
Published: January 2023

Ventilated cavitating flow features resulting from the air injection at the hydrofoil surface are characterized based on experimental investigation. The experiments have been conducted in the cavitation tunnel at the Silesian University of Technology. The main focus of this work is to investigate how both the location of the injection hole at the surface of the hydrofoil (so-called injection site) and the injection rate have an impact on the cavitating flow in various flow conditions (i.e., different cavitation numbers). The Clark Y hydrofoil is fixed at an 8° angle of attack. In addition, three cavitation numbers, σ = 1.1, 1.25, and 1.6; five air injection rates, Q = 0, 0.25, 0.5, 0.75, and 1 l/min; and two injection sites at the surface of hydrofoil (Tap1-injection and Tap5-injection) are selected for the case studies. Furthermore, the level of dissolved air in water is kept constant at 11.7 mg/l. The unsteady measurements and high-speed imagining declare that, regardless of the injection rate, the injection site has a significant effect on the cavitation dynamic features and morphology. Moreover, it is shown that the effectiveness of air injection depends on the flow conditions.
Curious thing, an artificial intelligence (AI)-based conversational agent for COVID-19 patient management
Authors: Chow Josephine Sau Fan , Blight Victoria , Brown Marian , Glynn Vanessa , Lane Brian , Larkin Amanda , Marshall Sonia , Matthews Prue , Rowles Mick , Warner Bradley
Published: January 2023

There are no clear guidelines or validated models for artificial intelligence (AI)-based approaches in the monitoring of coronavirus disease 2019 (COVID-19) patients who were isolated in the community, in order to identify early deterioration of their health symptoms. Developed in partnership with Curious Thing (CT), a Sydney-based AI conversational technology, a new care robot technology was introduced in South Western Sydney (SWS) in September 2021 to manage the large numbers of low-to-medium risk patients with a COVID-19 diagnosis and who were isolating at home. The CT interface made contact with patients via their mobile phone, following a locally produced script to obtain information recording physical condition, wellness and support. The care robot has engaged over 6323 patients between 2 September to 14 December 2021. The AI-assisted phone calls effectively identified the patients requiring further support, saved clinician time by monitoring less ailing patients remotely, and enabled them to spend more time on critically ill patients, thus ensuring that service and supply resources could be directed to those at greatest need. Engagement strategies had ensured stakeholders support of this technology to meet clinical and welfare needs of the identified patient group. Feedback from both the patients and healthcare staff was positive and had informed the ongoing formulation of a more patient-centred model of virtual care.
Cytosolic galectin-4 enchains bacteria, restricts their motility, and promotes inflammasome activation in intestinal epithelial cells
Authors: Li Chi-Shan , Lo Tzu-Han , Tu Ting-Jui , Chueh Di-Yen , Yao Cheng-I , Lin Chun-Hung , Chen Peilin , Liu Fu-Tong
Published: January 2023

Galectin-4, a member of the galectin family of animal glycan-binding proteins (GBPs), is specifically expressed in gastrointestinal epithelial cells and is known to be able to bind microbes. However, its function in host-gut microbe interactions remains unknown. Here, we show that intracellular galectin-4 in intestinal epithelial cells (IECs) coats cytosolic
Salmonella enterica
serovar Worthington and induces the formation of bacterial chains and aggregates. Galectin-4 enchains bacteria during their growth by binding to the O-antigen of lipopolysaccharides. Furthermore, the binding of galectin-4 to bacterial surfaces restricts intracellular bacterial motility. Galectin-4 enhances caspase-1 activation and mature IL-18 production in infected IECs especially when autophagy is inhibited. Finally, orally administered
S. enterica
serovar Worthington, which is recognized by human galectin-4 but not mouse galectin-4, translocated from the intestines to mesenteric lymph nodes less effectively in human galectin-4-transgenic mice than in littermate controls. Our results suggest that galectin-4 plays an important role in host-gut microbe interactions and prevents the dissemination of pathogens. The results of the study revealed a novel mechanism of host–microbe interactions that involves the direct binding of cytosolic lectins to glycans on intracellular microbes.
PCIF1-mediated deposition of 5′-cap
N
6
,2′-
O
-dimethyladenosine in ACE2 and TMPRSS2 mRNA regulates susceptibility to SARS-CoV-2 infection
Authors: Wang Lingling , Wang Shaobo , Wu Lujing , Li Wanyu , Bray William , Clark Alex E. , Gonzalez Gwendolyn Michelle , Wang Yinsheng , Carlin Aaron F. , Rana Tariq M.
Published: January 2023

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a major health problem worldwide. Due to the fast emergence of SARS-CoV-2 variants, understanding the molecular mechanisms of viral pathogenesis and developing novel inhibitors are essential and urgent. Here, we investigated the potential roles of
N
6
,2′-
O
-dimethyladenosine (m
6
A
m
), one of the most abundant modifications of eukaryotic messenger ribonucleic acid (mRNAs), in SARS-CoV-2 infection of human cells. Using genome-wide m
6
A
m
-exo-seq, RNA sequencing analysis, and Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing, we demonstrate that phosphorylated C-terminal domain (CTD)-interacting factor 1 (PCIF1), a cap-specific adenine

N
6

-methyltransferase, plays a major role in facilitating infection of primary human lung epithelial cells and cell lines by SARS-CoV-2, variants of concern, and other coronaviruses. We show that PCIF1 promotes infection by sustaining expression of the coronavirus receptors angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) via m
6
A
m
-dependent mRNA stabilization. In PCIF1-depleted cells, both ACE2/TMPRSS2 expression and viral infection are rescued by re-expression of wild-type, but not catalytically inactive, PCIF1. These findings suggest a role for PCIF1 and cap m
6
A
m
in regulating SARS-CoV-2 susceptibility and identify a potential therapeutic target for prevention of infection.
Insect-scale jumping robots enabled by a dynamic buckling cascade
Authors: Wang Yuzhe , Wang Qiong , Liu Mingchao , Qin Yimeng , Cheng Liuyang , Bolmin Ophelia , Alleyne Marianne , Wissa Aimy , Baughman Ray H. , Vella Dominic , Tawfick Sameh
Published: January 2023

Millions of years of evolution have allowed animals to develop unusual locomotion capabilities. A striking example is the legless-jumping of click beetles and trap-jaw ants, which jump more than 10 times their body length. Their delicate musculoskeletal system amplifies their muscles’ power. It is challenging to engineer insect-scale jumpers that use onboard actuators for both elastic energy storage and power amplification. Typical jumpers require a combination of at least two actuator mechanisms for elastic energy storage and jump triggering, leading to complex designs having many parts. Here, we report the new concept of dynamic buckling cascading, in which a single unidirectional actuation stroke drives an elastic beam through a sequence of energy-storing buckling modes automatically followed by spontaneous impulsive snapping at a critical triggering threshold. Integrating this cascade in a robot enables jumping with unidirectional muscles and power amplification (JUMPA). These JUMPA systems use a single lightweight mechanism for energy storage and release with a mass of 1.6 g and 2 cm length and jump up to 0.9 m, 40 times their body length. They jump repeatedly by reengaging the latch and using coiled artificial muscles to restore elastic energy. The robots reach their performance limits guided by theoretical analysis of snap-through and momentum exchange during ground collision. These jumpers reach the energy densities typical of the best macroscale jumping robots, while also matching the rapid escape times of jumping insects, thus demonstrating the path toward future applications including proximity sensing, inspection, and search and rescue.
Non-equilibrium early-warning signals for critical transitions in ecological systems
Authors: Xu Li , Patterson Denis , Levin Simon Asher , Wang Jin
Published: January 2023

Complex systems can exhibit sudden transitions or regime shifts from one stable state to another, typically referred to as critical transitions. It becomes a great challenge to identify a robust warning sufficiently early that action can be taken to avert a regime shift. We employ landscape-flux theory from nonequilibrium statistical mechanics as a general framework to quantify the global stability of ecological systems and provide warning signals for critical transitions. We quantify the average flux as the nonequilibrium driving force and the dynamical origin of the nonequilibrium transition while the entropy production rate as the nonequilibrium thermodynamic cost and thermodynamic origin of the nonequilibrium transition. Average flux, entropy production, nonequilibrium free energy, and time irreversibility quantified by the difference in cross-correlation functions forward and backward in time can serve as early warning signals for critical transitions much earlier than other conventional predictors. We utilize a classical shallow lake model as an exemplar for our early warning prediction. Our proposed method is general and can be readily applied to assess the resilience of many other ecological systems. The early warning signals proposed here can potentially predict critical transitions earlier than established methods and perhaps even sufficiently early to avert catastrophic shifts.
The deformation analysis of friction stir welding with different clamping distances for large thin-walled joints
Authors: Gao Chang , Yu Haidong , Gu Bin , Lin Yujin
Published: January 2023

Clamping scheme may change the local stiffness and affect the welding deformation which is very important for the large thin-walled joints connected by friction stir welding with heavy load and heat production. In this paper, the welding experiments of large thin-walled joints were conducted and the numerical simulation model is established based on three-dimensional stress mapping method. The accuracy of the numerical model is verified and welding deformation with various clamping distances is discussed. The restraint intensity index is employed to describe the influence of clamping distance on the stiffness of welding seam and welding deformation. The mechanism of welding deformation with the effect of clamping distance is well revealed by the analysis of welding stress and restraint intensity.
Monitoring melt pool asymmetry in gas metal arc-directed energy deposition
Authors: Chaurasia Prashant Kumar , Goecke Sven-F. , De Amitava
Published: January 2023

Cross-sectional asymmetry of melt pools along adjacent tracks results in an uneven build surface in gas metal arc-directed energy deposition. We present here a novel attempt on real-time monitoring of melt pool cross-sectional asymmetry in terms of its lateral and angular deviations from the track centreline using a two-colour quotient thermal camera. The melt pool lateral and angular deviations are found to be 2–3 mm, and 8–12°, respectively, for the range of process conditions. A unique analytical methodology is proposed that shows a hatch spacing of around 72–76% of the width of a deposited track can reduce melt pool asymmetry and layer height variations along adjacent tracks, which is also observed experimentally.
Moderate continuous‐ and high‐intensity interval training elicit comparable cardiovascular effect among middle‐aged men regardless of recovery mode
Authors: Collins Blake E. G. , Donges Cheyne , Robergs Robert , Cooper Joshua , Sweeney Kristie , Kingsley Michael
Published: January 2023

To assess the effect of active and passive intra‐interval recovery modes in time‐efficient high‐intensity interval training (HIT) on cardiorespiratory fitness, autonomic function, and endothelial function in sedentary middle‐aged men.

Participants (n = 62; age: 49.5 ± 5.8 y; BMI: 29.7 ± 3.7 kg·m−2) completed the assessments of cardiorespiratory fitness, flow‐mediated dilation (FMD) and heart rate variability before being randomly allocated to control (CON; n = 14), moderate intensity continuous training (MICT; n = 15), HIT with passive (P‐HIT; n‐15), or active recovery (A‐HIT; n = 15). Participants performed thrice weekly exercise sessions for 12 weeks. MICT completed 50–60 min of continuous cycling at 60–70% heart rate (HR) maximum. HIT completed 30‐s work intervals (∼85% HR) interspaced with 2.5 min of active or passive recovery.

All exercise modalities increased oxygen uptake (V̇O2) (MD: ≥ 3.1 ml·kg−1·min−1, 95%CI: 1.5–4.7 ml·kg−1·min−1; P < 0.001), power output (MD: ≥ 26 W, 95%CI: 15–37 W; P < 0.001) and cycle duration (MD: ≥ 62 s, 95%CI: 36–88 s; P < 0.001) at 85% HRM. Significant pre‐to‐post differences were observed among all exercise groups for FMD (MD: ≥ 3.4%, 95%CI: 0.3–6.5%; P < 0.05), while MICT and P‐HIT significantly increased the standard deviation of all NN intervals (SDNN) pre‐to‐post intervention (MD: ≥ 7 ms, 2–13 ms; P ≤ 0.05).

Time‐efficient HIT elicits significant improvements in cardiorespiratory fitness, FMD and autonomic modulation following a thrice weekly 12‐week exercise intervention among sedentary middle‐aged men. Active recovery between successive high‐intensity intervals provided no additional benefit among this deconditioned cohort.
Tunable dielectric BIC metasurface for high resolution optical filters
Authors: Tian Fanglin , Zhou Junxiao , Abraham Elizabeth , Liu Zhaowei
Published: January 2023

The dielectric metasurface has become a powerful tool for compact optical components with various wavefront controlling functionalities accompanied by negligible losses at the corresponding working frequencies. In this work, we propose a tunable all-dielectric metasurface as an optical filter with high resolution covering different optical communication bands, where tunability is realized by a combination of changing the incident angle and modulating the refractive index of an optical phase changing material (OPCM). When the incident angle varies, our optical filter based on a two-dimensional bound state in continuums (BIC) metasurface can achieve sequential, extremely sharp resonances. In addition, the resonance peaks could be further shifted to a different frequency band by the refractive index change of OPCM via pulsed laser heating. The proposed scheme can offer optical filters with high spectral resolution and large tunable working wavelength range, which greatly benefits from the topological property of BIC and large modulation depth of OPCM.
Molecular-level uniform graphene/polyaniline composite film for flexible supercapacitors with high-areal capacitance
Authors: Wang Peiyao , Shao Feng , Li Bin , Su Yanjie , Yang Zhi , Hu Nantao , Zhang Yafei
Published: January 2023

To increase the specific capacitance of supercapacitors, polyaniline (PANI) has been chosen as additive electrode material for the pseudocapacitive performance. Here, we synthesize a molecular-level uniform reduced graphene oxide/PANI (rGO/PANI) composite film with high flexibility and conductivity via self-assembly and specific thermal reduction, which performs great potential in flexible supercapacitors with high areal capacitance. Particularly, the electrode of rGO/PANI-42.9% exhibits a high specific areal capacitance (1826 mF cm−2 at 0.2 mA cm−2), and it also presents a good cycling stability (it remains 76% of its initial capacitance after 10 500 cycles). Moreover, the specific gravimetric capacitance of rGO/PANI-33.3% reaches up to 256.4 F g−1 at 0.2 A g−1, showing greatly enhanced performance compared with the pure rGO electrode (183 F g−1). The results of various characteristic analysis demonstrate that electrochemical performance of the as-prepared rGO/PANI film is closely associated with the uniform distribution of PANI in rGO/PANI composite. Overall, our reported method is convenient and environmental-friendly, and could be beneficial for the development of high-performance capacitive energy storage materials.
Robustness analysis of magnetorheological elastomer-based vibration isolation system with optimal fuzzy controller
Authors: Fu Jie , Liu Jing , Lai Junjie , Zhong Can , Dai Zhenyu , Yu Miao
Published: January 2023

Due to adjustable stuffiness with applied magnetic fields, magnetorheological elastomer (MRE)-based vibration isolation method has attracted more attention in vibration engineering fields, such as precision-fabrication or precision-measurement platform for high-tech facilities, civil structure. However, there exists parameter uncertainty in dynamic model of control system, such as variation load mass in different working conditions, increasing or decreasing stiffness due to the rubber aging induced by the temperature and humidity of the environment. So it is necessary to investigate and evaluate quantitatively the robustness of MRE-based vibration isolation control system. This paper addresses that. Firstly, the dynamic model of MRE vibration isolation system with consideration of uncertain stiffness of the isolator and load mass is established. Then, a fuzzy controller (FC) is designed under the certain amplitude and frequency excitation, the parameters of FC are optimized by genetic algorithm. On this basis, RI (robustness index) is proposed to divide the robustness of the system under variation of parameters (stiffness of MRE isolator and load mass) as ‘good’, ‘fair’ and ‘poor’ level. Lastly, simulation and experiments are carried out to evaluate quantitatively the robustness performance of MRE vibration control system with designed optimal FC, respectively. The results show that the designed optimal FC has greater RI than experienced-based FC for different variation range stiffness of MRE isolator and load mass, and demonstrates outstanding robustness.
Cosmology with the EFTofLSS and BOSS: dark energy constraints and a note on priors
Authors: Carrilho Pedro , Moretti Chiara , Pourtsidou Alkistis
Published: January 2023

We analyse the BOSS DR12 multipoles of the galaxy power spectrum jointly with measurements of the BAO scale for three different models of dark energy. We use recent measurements performed with a windowless estimator, and an independent and fast pipeline based on EFTofLSS modelling implemented via the FAST-PT algorithm to compute the integrals of the redshift-space loop corrections. We accelerate
our analysis further by using the bacco linear power spectrum emulator instead of a Boltzmann solver. We perform two sets of analyses: one including 3σ Planck priors on As
and ns
, and another that is fully CMB-free, i.e., letting the primordial parameters vary freely. The first model we study is ΛCDM, within which we reproduce previous results obtained with the same estimator. We find a low value of the scalar amplitude in the CMB-free case, in agreement with many previous EFT-based full-shape analyses of the BOSS data. We then study wCDM, finding a lower value of the amplitude in the CMB-free run, coupled with a preference for phantom dark energy with w = -1.17+0.12
-0.11, again in broad agreement with previous results. Finally, we investigate the dark scattering model of interacting dark energy, which we label wACDM. In the CMB-free analysis, we find a large degeneracy between the interaction strength A and the amplitude As
, hampering measurements of those parameters. On the contrary, in our run with a CMB prior, we are able to constrain the dark energy parameters to be w = -0.972+0.036
-0.029 and A = 3.9+3.2
-3.7, which show a 1σ hint of interacting dark energy. This is the first measurement of this parameter and demonstrates the ability of this model to alleviate the σ
8 tension. Our analysis can be used as a guide for the analysis of any model with scale-independent growth. Finally, we study the dependence of the results on the priors imposed on the nuisance parameters and find these priors to be informative, with their broadening generating shifts in the contours. We argue for an in depth study of this issue, which can affect current and forthcoming analyses of LSS data.
Ultraviolet unitarity violations in non-minimally coupled scalar-Starobinsky inflation
Authors: Panda Sukanta , Tinwala Abbas Altafhussain , Vidyarthi Archit
Published: January 2023

We perform the calculation for tree-level ultraviolet unitarity violation scales for scalar-R
2 inflation models by including an additional R
2|Φ|2-type term. Due to certain constraints, we resort to the Einstein frame for our calculations, where we separate our analysis between metric and Palatini formulations. We follow recent works in this line that debunk the naive predictions for unitarity violations in Higgs' inflation models to determine how to accurately estimate the behaviour of scattering amplitudes in the UV limit. Later, we work out different cases by assuming potentials corresponding to known inflation scenarios so we could predict the range of coupling parameters for which the theories would remain unitary up to the Planckian regime. We also try to find the behaviour of the scattering amplitudes for these theories during the transition from inflationary to reheating epoch.
Characterization of XIA UltraLo-1800 response to measuring charged samples
Authors: Ange Joshua , Calkins Robert , Posada Andrew
Published: January 2023

Commercial alpha counters are used in science and industry applications to screen
materials for surface radon progeny contamination. In this paper, we characterize an XIA
UltraLo-1800, an ionization drift alpha counter, and study the response to embedded charge in
polyethylene sample measurements. We show that modeling such effects is possible in a Geant4-based
simulation framework and attempt to derive corrections. This paper also demonstrates the
effectiveness of the use of an anti-static fan to eliminate the embedded charge and recover a
97.73% alpha detection efficiency in the alpha counter.
The lambda extensions of the Ising correlation functions
C(M,N)
Authors: Boukraa S , Maillard J-M
Published: January 2023

We revisit, with a pedagogical heuristic motivation, the lambda extension of the low-temperature row correlation functions

C
(
M
,
N
)

of the two-dimensional Ising model. In particular, using these one-parameter series to understand the deformation theory around selected values of

 
λ

, namely

λ
=
cos
(
π
m
/
n
)

with m and n integers, we show that these series yield perturbation coefficients, generalizing form factors, that are D-finite functions. As a by-product these exact results provide an infinite number of highly non-trivial identities on the complete elliptic integrals of the first and second kind. These results underline the fundamental role of Jacobi theta functions and Jacobi forms, the previous D-finite functions being (relatively simple) rational functions of Jacobi theta functions, when rewritten in terms of the nome of elliptic functions.
Cylindrical ionization chamber response in static and dynamic 6 and 15 MV photon beams
Authors: Andersson P , Swanpalmer J , Palm Å , Båth M , Chakarova R
Published: January 2023

Purpose. To investigate the response of the CC13 ionization chamber under non-reference photon beam conditions, focusing on penumbra and build-up regions of static fields and on dynamic intensity-modulated beams. Methods. Measurements were performed in 6 MV 100 × 100, 20 × 100, and 20 × 20 mm2 static fields. Monte Carlo calculations were performed for the static fields and for 6 and 15 MV dynamic beam sequences using a Varian multi-leaf collimator. The chamber was modelled using EGSnrc egs_chamber software. Conversion factors were calculated by relating the absorbed dose to air in the chamber air cavity to the absorbed dose to water. Correction and point-dose correction factors were calculated to quantify the conversion factor variations. Results. The correction factors for positions on the beam central axis and at the penumbra centre were 0.98–1.02 for all static fields and depths investigated. The largest corrections were obtained for chamber positions beyond penumbra centre in the off-axis direction. Point-dose correction factors were 0.54–0.71 at 100 mm depth and their magnitude increased with decreasing field size and measurement depth. Factors of 0.99–1.03 were obtained inside and near the integrated penumbra of the dynamic field at 100 mm depth, and of 0.92–0.94 beyond the integrated penumbra centre. The variations in the ionization chamber response across the integrated dynamic penumbra qualitatively followed the behaviour across penumbra of static fields. Conclusions. Without corrections, the CC13 chamber was of limited usefulness for profile measurements in 20-mm-wide fields. However, measurements in dynamic small irregular beam openings resembling the conditions of pre-treatment patient quality assurance were feasible. Uncorrected ionization chamber response could be applied for dose verification at 100 mm depth inside and close to large gradients of dynamically accumulating high- and low-dose regions assuming 3% tolerance between measured and calculated doses.
Coherent rotation of a single spin via adiabatic half passage in the presence of a ferromagnetic vortex
Authors: Badea R , Wolf M S , Berezovsky J
Published: January 2023

We experimentally and numerically study possible implementations for

π

/

2

rotations of a single nitrogen-vacancy defect spin state in proximity to a magnetic vortex core. Dynamically controlled magnetic vortex cores have been suggested as a means to provide nanoscale, rapidly-tunable magnetic fields for spin qubit addressability and control. However, driven and thermal non-equilibrium dynamics of the vortex core complicate prospects for high-fidelity gate operations. We find that the complicated profile of the driven vortex core fringe field leads to significant, but unpredictable enhancement of both Zeeman splitting and Rabi frequency. Furthermore, the gyrotropic dynamics of the vortex core lead to a complicated evolution of the spin state. We demonstrate that the fidelity of

π

/

2

rotations can be improved using an adiabatic passage protocol in which the vortex provides an enhancement of spin splitting and Rabi frequency while unwanted vortex dynamics are suppressed.
Lawvere-Tierney topologies for computability theorists
Authors: Kihara Takayuki
Published: January 2023

In this article, we study the lattice of Lawvere-Tierney topologies on Hyland’s effective topos. For this purpose, we introduce a new computability-theoretic reducibility notion, which is a common extension of the notions of Turing reducibility and generalized Weihrauch reducibility. Based on the work by Lee and van Oosten [Ann. Pure Appl. Logic 164 (2013), pp. 866-883], we utilize this reducibility notion for providing a concrete description of the lattice of the Lawvere-Tierney topologies on the effective topos. As an application, we solve several open problems proposed by Lee and van Oosten. For instance, we show that there exists no minimal Lawvere-Tierney topology which is strictly above the identity topology on the effective topos.
Charitable Trusts of Cemeteries and Places of Worship in Thailand: A Historical Anomaly
Authors: Reekie Surutchada
Published: January 2023

This article examines Thailand’s historic charitable trusts for the purpose of establishing and maintaining cemeteries and places of worship. Whilst existing literature explores the reception of English trusts law in British colonial territories in Southeast Asia over the course of nineteenth century, little is discussed in relation to Thailand, historically known as Siam, during the same period. Based on the author’s archival research, this article explores the route and development of these trusts and argues that, due to the Thai Supreme Court’s recognition of their charitable purpose, these trusts are not subject to a rule against perpetuities. Therefore, they will continue to present an anomalous exception to Thailand’s civil law legal framework and offer a fascinating example of the deep, tenacious roots put down by a rejected legal concept from Thailand’s brush with nineteenth century colonial powers.
Alcohol Biomarker Phosphatidylethanol as a Predictor of the Severity of Alcohol Withdrawal Syndrome
Authors: Novak Lan , Soravia Leila M , Bünter Adina , Stöth Frederike , Wopfner Alexander , Weinmann Wolfgang , Pfeifer Philippe
Published: January 2023

Aims

to investigate the relationship between phosphatidylethanol (PEth) and withdrawal severity in patients with alcohol use disorder (AUD).

Methods

in 34 patients with AUD admitted for treatment of acute alcohol withdrawal, data were available for initial blood PEth concentrations and scores throughout detoxification of symptoms of withdrawal assessed by trained medical staff using the alcohol withdrawal syndrome (AWS)-scale, a validated scale consisting of 11 items in the alcohol withdrawal syndrome (two subscales with seven physiological and five psychological symptoms).

Results

a significant positive correlation between PEth and the severity of alcohol withdrawal was found. When the sample was divided into two groups, according to whether or not AWS score at some point in the treatment reached 6 or more, the median PEth score was higher in those whose peak score had been 6 or more (score of 6 being the suggested cutoff to start medicating the withdrawal syndrome). Although there was a trend for some aspects of the clinical history to be more ‘severe’ in those with higher AWS, no differences reached significance.

Conclusion

blood PEth on admission could have a role in identifying patients at risk of more severe AWS.
Pancancer survival prediction using a deep learning architecture with multimodal representation and integration
Authors: Fan Ziling , Jiang Zhangqi , Liang Hengyu , Han Chao
Published: January 2023

Motivation

Use of multi-omics data carrying comprehensive signals about the disease is strongly desirable for understanding and predicting disease progression, cancer particularly as a serious disease with a high mortality rate. However, recent methods currently fail to effectively utilize the multi-omics data for cancer survival prediction and thus significantly limiting the accuracy of survival prediction using omics data.

Results

In this work, we constructed a deep learning model with multimodal representation and integration to predict the survival of patients using multi-omics data. We first developed an unsupervised learning part to extract high-level feature representations from omics data of different modalities. Then, we used an attention-based method to integrate feature representations, produced by the unsupervised learning part, into a single compact vector and finally we fed the vector into fully connected layers for survival prediction. We used multimodal data to train the model and predict pancancer survival, and the results show that using multimodal data can lead to higher prediction accuracy compared to using single modal data. Furthermore, we used the concordance index and the 5-fold cross-validation method for comparing our proposed method with current state-of-the-art methods and our results show that our model achieves better performance on the majority of cancer types in our testing datasets.

Availability and implementation

https://github.com/ZhangqiJiang07/MultimodalSurvivalPrediction.

Supplementary information

Supplementary data are available at Bioinformatics online.
GOThresher: a program to remove annotation biases from protein function annotation datasets
Authors: Joshi Parnal , Banerjee Sagnik , Hu Xiao , Khade Pranav M , Friedberg Iddo
Published: January 2023

Motivation

Advances in sequencing technologies have led to a surge in genomic data, although the functions of many gene products coded by these genes remain unknown. While in-depth, targeted experiments that determine the functions of these gene products are crucial and routinely performed, they fail to keep up with the inflow of novel genomic data. In an attempt to address this gap, high-throughput experiments are being conducted in which a large number of genes are investigated in a single study. The annotations generated as a result of these experiments are generally biased towards a small subset of less informative Gene Ontology (GO) terms. Identifying and removing biases from protein function annotation databases is important since biases impact our understanding of protein function by providing a poor picture of the annotation landscape. Additionally, as machine learning methods for predicting protein function are becoming increasingly prevalent, it is essential that they are trained on unbiased datasets. Therefore, it is not only crucial to be aware of biases, but also to judiciously remove them from annotation datasets.

Results

We introduce GOThresher, a Python tool that identifies and removes biases in function annotations from protein function annotation databases.

Availability and implementation

GOThresher is written in Python and released via PyPI https://pypi.org/project/gothresher/ and on the Bioconda Anaconda channel https://anaconda.org/bioconda/gothresher. The source code is hosted on GitHub https://github.com/FriedbergLab/GOThresher and distributed under the GPL 3.0 license.

Supplementary information

Supplementary data are available at Bioinformatics online.
CAPLA: improved prediction of protein–ligand binding affinity by a deep learning approach based on a cross-attention mechanism
Authors: Jin Zhi , Wu Tingfang , Chen Taoning , Pan Deng , Wang Xuejiao , Xie Jingxin , Quan Lijun , Lyu Qiang
Published: January 2023

Motivation

Accurate and rapid prediction of protein–ligand binding affinity is a great challenge currently encountered in drug discovery. Recent advances have manifested a promising alternative in applying deep learning-based computational approaches for accurately quantifying binding affinity. The structure complementarity between protein-binding pocket and ligand has a great effect on the binding strength between a protein and a ligand, but most of existing deep learning approaches usually extracted the features of pocket and ligand by these two detached modules.

Results

In this work, a new deep learning approach based on the cross-attention mechanism named CAPLA was developed for improved prediction of protein–ligand binding affinity by learning features from sequence-level information of both protein and ligand. Specifically, CAPLA employs the cross-attention mechanism to capture the mutual effect of protein-binding pocket and ligand. We evaluated the performance of our proposed CAPLA on comprehensive benchmarking experiments on binding affinity prediction, demonstrating the superior performance of CAPLA over state-of-the-art baseline approaches. Moreover, we provided the interpretability for CAPLA to uncover critical functional residues that contribute most to the binding affinity through the analysis of the attention scores generated by the cross-attention mechanism. Consequently, these results indicate that CAPLA is an effective approach for binding affinity prediction and may contribute to useful help for further consequent applications.

Availability and implementation

The source code of the method along with trained models is freely available at https://github.com/lennylv/CAPLA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Kidney and blood pressure regulation—latest evidence for molecular mechanisms
Authors: Suzumoto Yoko , Zucaro Laura , Iervolino Anna , Capasso Giovambattista
Published: January 2023

Hypertension is one of the major health problems leading to the development of cardiovascular diseases. Despite a rapid expansion in global hypertension prevalence, molecular mechanisms leading to hypertension are not fully understood largely due to the complexity of pathogenesis involving several factors. Salt intake is recognized as a leading determinant of blood pressure, since reduced dietary salt intake is related to lower morbidity and mortality, and hypertension in relation to cardiovascular events. Compared with salt-resistant populations, salt-sensitive individuals exhibit high sensitivity in blood pressure responses according to changes in salt intake. In this setting, the kidney plays a major role in the maintenance of blood pressure under the hormonal control of the renin–angiotensin–aldosterone system. In the present review, we summarize the current overview on the molecular mechanisms for modulation of blood pressure associated with renal ion channels/transporters including sodium–hydrogen exchanger isoform 3 (NHE3), Na+-K+-2Cl– cotransporter (NKCC2), sodium–chloride cotransporter (NCC), epithelial sodium channel (ENaC) and pendrin expressed in different nephron segments. In particular, recent studies on experimental animal models with deletion of renal ion channels led to the identification of several crucial physiological mechanisms and molecules involved in hypertension. These findings could further provide a potential for novel therapeutic approaches applicable on human patients with hypertension.
Extreme tolerance for nocturnal emergence at low body temperatures in a high-latitude lizard: implications for future climate warming
Authors: Chukwuka Christian O , Monks Joanne M , Cree Alison
Published: January 2023

High-latitude lizards live in environments where ambient air temperature at night is frequently below retreat temperatures, which likely has implications for nocturnal emergence and activity. However, patterns of lizard activity at night under current temperate climates are poorly understood, a situation that limits our understanding of potential effects of climate change. We investigated patterns of nocturnal emergence and activity in the cold-adapted, viviparous gecko (Woodworthia ‘Otago/Southland’). We measured operative environmental temperature (Te) available to geckos that emerged at night and simultaneously assessed nighttime emergence activity using time-lapse trail cameras. Also, we assessed field body temperature (Tb) of emerged geckos of various life history groups at night using thermography to understand how current weather conditions affect field Tb of emerged geckos. Our results show that Te, nocturnal emergence activity and field-active Tb increased with nighttime air temperature. Nocturnal emergence was highest in spring and summer but also occurred in autumn and (unexpectedly) in winter. Geckos were active over a broad range of Tb down to 1.4°C (a new record low for lizards) and on rock surfaces typically warmer than air temperature or Tb. We conclude that this nocturnal, high-latitude lizard from the temperate zone is capable of activity at low winter temperatures, but that current climate limits emergence and activity at least in autumn and winter. Activity levels for cool-temperate reptiles will probably increase initially as climates warm, but the consequences of increased nocturnal activity under climate change will probably depend on how climate change affects predator populations as well as the focal species’ biology.
Proteomic profiling identifies novel independent relationships between inflammatory proteins and myocardial infarction
Authors: Valdes-Marquez Elsa , Clarke Robert , Hill Michael , Watkins Hugh , Hopewell Jemma C
Published: January 2023

Background

Inflammation has been implicated in the pathogenesis of coronary heart disease, but the relevance and independence of individual inflammatory proteins is uncertain.

Objective

To examine the relationships between a spectrum of inflammatory proteins and myocardial infarction (MI).

Methods and results

A panel of 92 inflammatory proteins was assessed using an OLINK multiplex immunoassay among 432 MI cases (diagnosed < 66 years) and 323 controls. Logistic regression was used to estimate associations between individual proteins and MI, after adjustment for established cardiovascular risk factors and medication use, and stepwise regression to identify proteins with independent effects. Machine learning techniques (Boruta analysis and LASSO regression) and bioinformatic resources were used to examine the concordance of results with those obtained by conventional methods and explore the underlying biological processes to inform the validity of the associations. Among the 92 proteins studied, 62 (67%) had plasma concentrations above the lower limit of detection in at least 50% of samples. Of these, 15 individual proteins were significantly associated with MI after covariate adjustment and correction for multiple testing. Five of these 15 proteins (CDCP1, CD6, IL1–8R1, IL-6, and CXCL1) were independently associated with MI, with up to three-fold higher risks of MI per doubling in plasma concentrations. Findings were further validated using machine learning techniques and biologically focused analyses.

Conclusions

This study, demonstrating independent relationships between five inflammatory proteins and MI, provides important novel insights into the inflammatory hypothesis of MI and the potential utility of proteomic analyses in precision medicine.
Reasons mothers of young children delayed or skipped preventive health care during the first year of the COVID-19 pandemic
Authors: Heersping Grace E , Waring Molly E
Published: January 2023

Background

Preventive health care provides opportunity for preventive screenings and health promotion. Mothers of young children may disproportionately experience barriers to preventive care during the COVID-19 pandemic.

Methods

We examined delaying and skipping preventive health care during the first year of the COVID-19 pandemic among mothers and described reasons for delaying or skipping care. Mothers of children aged 0–12 years from the United States completed an online survey in February/March 2021 and reported receipt of preventive care during the COVID-19 pandemic, reasons for delaying or skipping care, demographics, and experiences with COVID-19.

Results

Participants (N = 306) were on average 35.9 (SD: 6.2) years old, racially/ethnically diverse, and 74.8% had at least a Bachelor’s degree. From March 2020 to March 2021, 16.0% delayed and 20.6% skipped their physical examination, and 20.9% had not planned on receiving a physical examination. The most common reasons for delaying and skipping care were COVID-19 infection concerns, perception that delaying care would not negatively impact health, provider rescheduling, time, and childcare.

Conclusions

Primary care teams may need to re-engage mothers who skipped preventive care during the pandemic, including addressing concerns about COVID-19 infection.
Lissencephaly-1 mutations enhance traumatic brain injury outcomes in Drosophila
Authors: Katzenberger Rebeccah J , Ganetzky Barry , Wassarman David A
Published: January 2023

Traumatic brain injury (TBI) outcomes vary greatly among individuals, but most of the variation remains unexplained. Using a Drosophila melanogaster TBI model and 178 genetically diverse lines from the Drosophila Genetic Reference Panel (DGRP), we investigated the role that genetic variation plays in determining TBI outcomes. Following injury at 20–27 days old, DGRP lines varied considerably in mortality within 24 h (“early mortality”). Additionally, the disparity in early mortality resulting from injury at 20–27 vs 0–7 days old differed among DGRP lines. These data support a polygenic basis for differences in TBI outcomes, where some gene variants elicit their effects by acting on aging-related processes. Our genome-wide association study of DGRP lines identified associations between single nucleotide polymorphisms in Lissencephaly-1 (Lis-1) and Patronin and early mortality following injury at 20–27 days old. Lis-1 regulates dynein, a microtubule motor required for retrograde transport of many cargoes, and Patronin protects microtubule minus ends against depolymerization. While Patronin mutants did not affect early mortality, Lis-1 compound heterozygotes (Lis-1x/Lis-1y) had increased early mortality following injury at 20–27 or 0–7 days old compared with Lis-1 heterozygotes (Lis-1x/+), and flies that survived 24 h after injury had increased neurodegeneration but an unaltered lifespan, indicating that Lis-1 affects TBI outcomes independently of effects on aging. These data suggest that Lis-1 activity is required in the brain to ameliorate TBI outcomes through effects on axonal transport, microtubule stability, and other microtubule proteins, such as tau, implicated in chronic traumatic encephalopathy, a TBI-associated neurodegenerative disease in humans.
Cognitive Frailty and Functional Disability Among Community-Dwelling Older Adults: A Systematic Review
Authors: Tang Kar Foong , Teh Pei-Lee , Lee Shaun Wen Huey
Published: January 2023

Background and Objectives

This review aimed to summarize the association between cognitive frailty (presence of frailty and cognitive impairment) and the risk of disabilities in activities of daily living (ADL), instrumental ADL (IADL), mobility, or other functional disabilities among older adults.

Research Design and Methods

PubMed, Embase, CINAHL Plus, and PsycINFO were searched from January 2001 to May 14, 2022, for observational studies that reported cognitive frailty among community-dwelling individuals aged 60 years and above. Results were narratively synthesized.

Results

Eleven studies encompassing 44 798 participants were included, with a prevalence of cognitive frailty ranging from 1.4% to 39.3%. Individuals with cognitive frailty were more likely to develop disabilities in ADL and IADL compared to robust (absence of frailty and cognitive impairment) individuals. Significant disability burden and elevated risk of combined ADL/IADL disability or physical limitation among participants with cognitive frailty were reported. There was limited evidence on the association between cognitive frailty and mobility disability.

Discussion and Implications

Individuals with cognitive frailty were likely at higher risk of developing functional disability and incurring higher disability burden than robust individuals, but evidence remains limited for those with prefrailty with cognitive impairment. Further research on this gap and standardization of cognitive frailty assessments would facilitate comparisons across populations.

PROSPERO Registration

CRD42021232222