bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and commissioning of a hydrogen ion source for the CERN ALPHA experiment
Authors: Johnson M.A. , Bertsche W.A. , Cortázar O.D , Faircloth D. , Kalvas T. , Lawrie S. , Megia Macías A.M. , Tarvainen O. , Barrios Díaz E.
Published: January 2024

The CERN ALPHA experiment makes precision measurements of antihydrogen atoms held in a
superconducting magnetic minimum trap. Recent studies of the antihydrogen spectrum have provided
unique tests of fundamental physics, and to improve on these studies ALPHA is now proposing
upgrades to directly compare hydrogen and antihydrogen within their existing atom trap. One route
towards producing cold, neutral hydrogen atoms is the integration of a hydrogen ion source into
the experiment. Ideally, this should provide both positive (H+, H2
+,
H3
+) and negative (H-) ions to facilitate different schemes for
producing and trapping hydrogen atoms. For compatibility with ALPHA's existing beamlines, the
source must produce modest (∼ 10 μA) beam currents at very low final energies
(<100 eV). PELLIS, previously developed at JYFL, is a filament-driven ion source that
generates 5–10 keV H- beams with small emittances and tens of
microamps of beam current. Here, we present a modified PELLIS design to provide both positive and
negative hydrogen ions for ALPHA. The use of an electromagnet filter field in PELLIS allows for
the optimisation of H- volume production, and also tuning of the positive ion species
fraction. We present simulations of H- (and similarly H+) transport through
the initial extraction optics, which have been configured for a lower beam energy of 5 keV
and designed to match a proposed beamline to interface with ALPHA. We present the results of
detailed vacuum simulations that were used to guide the optics design, allowing the source (at
10-2 mbar) to interface with a transport beamline ∼ 0.5 m downstream
that has strict vacuum requirements of < 10-9 mbar. We present experimental results
from commissioning of the source, and show that it broadly performs as designed for both positive
and negative hydrogen ions.
Atlantic Niño induced sea surface salinity variability as observed from the satellite
Authors: Chen Yihao
Published: January 2024

The Atlantic Niño exerts great impact on surrounding weather and climate anomalies, leading to anomalous wind, temperature, precipitation, etc. However, the impact of Atlantic Niño on ocean salinity in the tropical Atlantic has not been well disclosed. The present study examines the Atlantic Niño induced sea surface salinity (SSS) distribution in both boreal summer and winter seasons by using the satellite data as well as various reanalysis and objective analysis data sets. It concludes that the summer Atlantic Niño leads to large fresh SSS anomalies in the eastern equatorial basin, while the winter Atlantic Niño leads to a meridional dipole structure of SSS anomalies. The former is mostly controlled by the dynamical processes of ocean, while the latter is largely controlled by the atmospheric processes. Accordingly, two SSS indices are developed to describe the relationships in the two seasons. The present study advances our understanding of the Atlantic Niño and its associated SSS variability and reveals the possible deficiencies of current reanalysis and objective analysis data sets in the tropical Atlantic Ocean.
Exploring the Environmental Health Implications of Invisible, Unnoticeable, and Overlooked Mistakes in Hospital Design: A Study in Egypt
Authors: Hussain Adel , Rabie Mohamed , Abdlaty Ramy , Mahdy Mohamed M
Published: January 2024

Hospital Planning and design can have a significant impact on environmental health, and even seemingly minor mistakes or oversights can contribute to negative health outcomes for patients and hospital staff. This paper examines the impact of invisible, unnoticeable, and overlooked mistakes in hospital design on environmental health in Egypt, with a focus on identifying the risks associated with these mistakes and exploring strategies for mitigating negative outcomes. Through a review of the literature, this paper identifies several key environmental factors that can contribute to negative health outcomes in hospitals, including poor air quality, inadequate ventilation, noise pollution, infection, poor materials quality, inadequate lighting and any other factors could harm the hospital occupants. Additionally, this paper examines the impact of these factors on patient outcomes, including length of stay, recovery time, and overall health and well-being. Finally, this paper explores and studies these mistakes which are considered a frequent phenomenon in a large number of hospitals in Egypt to determine these environmental health risks. Overall, this paper highlights the importance of considering even the smallest details in hospital design, and offers recommendations for promoting healthy and safe hospital environments in Egypt.
The Effect of Using Horizontal Shading Elements on the Energy Efficiency of Multistory Residential Buildings
Authors: Alothman R A T , Abdin A R , Mahmoud A H
Published: January 2024

Shading elements have been considered to be an important element in controlling the amount of heat and sunlight entering the spaces, the most common kinds of horizontal shading devices include architectural components including balconies, louvres, and roof overhangs. Residential buildings consume high energy by household appliances from air conditioning, which makes it the most energy consuming building. Therefore, the aim of this research is determine the effect of using horizontal shading elements on the energy efficiency of multi-storey residential buildings. DesignBuilder is a tool used in this research to evaluate the energy efficiency by comparing the typical room without shading elements and with typical room with shading elements with different depths under two district climatic conditions cold semi-arid climate and hot arid climate. The research found that energy saving between 0.5% to 30.8% when using horizontal shading elements depending on the orientation and location of the case study beside the depth of shading elements.
Guidelines for Egyptian Cities Towards Achieving Sustainable Creative Cities (Aswan as a Case Study)
Authors: Atalah E Z , Hussien R G , Qutb S M
Published: January 2024

The concept of the creative city is considered one of the most important contemporary trends for achieving development plans, although it arose from the beginning of the formation of human settlements since the beginning of human civilization, but the creative discourse has been developed since the end of the last century. UNESCO established the Creative Cities Network in 2005, and the classification included two Egyptian cities In the scope of crafts and folk arts - Aswan in 2005 and Cairo in 2017 - then the United Nations organization put forward the goals of sustainable development, which created a research question about the ability of cities to be sustainable. The research tended to formulate a guide to study the creative capacity of the city based on its components to achieve sustainability, and the axes and criterias of the guide were put forward and discussed with specialists and the community, Aswan was chosen because it is the city with the most momentum in the heritage components, and the guide, axes, and criteria were applied, and the results were analysed. The study concluded that Aswan has the elements that distinguish it to achieve sustainability, and it is possible to focus on positive points that help achieve the goals towards society, the economy and the environment.
Study on immobilisation process on lateral flow assay test strip for detection of Enrofloxacin antibiotic by inkjet printing
Authors: Dinh Duc Minh Trinh , Le Anh Van Thi , Lam Phuong Hong , Le Mai Thi , Dang Dung My Thi , Dang Chien Mau , Le Ngan Nguyen
Published: January 2024

Enrofloxacin has been widely and increasingly used in veterinary medicine to treat infection on animals which could lead to antibiotic resistance for the consumer. Among the available detection techniques for Enrofloxacin, immunoassay lateral flow test strip is realised to be a rapid and accurate detection method for on-site analysis of Enrofloxacin antibiotic. The current study aims to analyse the application of inkjet printing technology on the immobilisation of biological substances at the test line and control line position of the test strip. With the printing parameters value at 35 °C, 35 °C, 7 layers and 15 μm for cartridge temperature, substrate temperature, printing layers and drop spacing, respectively, the fabricated test strips show correlation coefficient R
2 at 0.993 for the test with Enrofloxacin samples in the concentration range from 0 to 100 ppb. Compared to conventional fabrication method, the immobilisation process utilising inkjet printing technology is considered to be superior in printing patterns with a simple and material-saving process, which holds a potential of innovative and financially beneficial approach for on-site detection of Enrofloxacin antibiotic.
Microstructure and magnetic properties of MnBi powders prepared by various ball milling processes
Authors: Li Chengyu , Yang Yang , Lu Shunda , Xiang Zhen , Chen Linfeng , Truong Nguyen Xuan , Xu Huiyu , Lu Wei
Published: January 2024

The MnBi intermetallic compound with high purity of low-temperature phase MnBi (LTP-MnBi) and high maximum energy product (BH)max were successfully prepared using various ball milling processes. The effects of ball milling speed and duration on the microstructures, phase compositions, and magnetic properties of MnBi alloys were systematically investigated. The particle size of MnBi and the purity of LTP-MnBi gradually decreased with increasing ball milling speed. An optimized ball milling speed of 175 rpm resulted in MnBi powder with the (BH)max of 9.22 MGOe and a squareness (M
r/M
s) of 93.7%. Furthermore, the ball milling duration was optimized to observe its impact on the MnBi alloy. As the duration increased, the average particle size of MnBi decreased from 27 μm at 0 h to 1.84 μm at 10 h. Simultaneously, the coercivity (H
c) increased from 0.7 T at 0 h to 1.7 T at 10 h. Ultimately, the powder ball milled at 175 rpm for 5 h exhibited the highest (BH)max of 11.3 MGOe.
High temperature oxidation behaviors of Al/Cr composite coating on Ti2AlNb alloy
Authors: Yang Zhengang , Liang Wenping , Hu Linquan , Zhang Zhengwen , Wang He , Chen Bowen
Published: January 2024

The Al/Cr coatings were deposited on Ti2AlNb alloy by magnetron sputtering and double glow plasma alloying technology to improve the oxidation resistance. The morphology of the protective coating was investigated by scanning electron microcopy and the phase composition of the coating was analyzed using x-ray diffraction. The results suggested that the protective coating with multilayer structure was dense and homogeneous. The formation of Cr inner diffusion layer was beneficial to the bonding strength between the coating and substrate, which was attributable to the double glow technology. The oxidation behaviors of Al/Cr coating were investigated by the isothermal oxidation tests for 100 h at 700 °C, 800 °C and 900 °C, respectively. The results indicated that the protective coating showed a lower oxidation rate. At 700 °C, the Al2O3 oxidation products were formed on the surface of coating at high temperature, which were dense and homogeneous against oxygen diffusion. With the increase of oxidation temperature, the external diffusion of Cr element reacted with oxygen to form Cr2O3, which provided the further protection. As for 900 °C, the volatile CrO3 was formed by the reaction of the external diffusion of Cr and Cr2O3, and the oxidation products Al2O3 and Cr2O3 continued to provide protection for Ti2AlNb alloy.
The effect of MoAlB substitutions on the oxidation behavior of ZrB2-SiC Composites at 1600 °C
Authors: Xu Yashuang , Liu Ling , Liu Yanbo , Ma Zhuang , Yang Shirui
Published: January 2024

ZrB2-SiC ceramics are potential candidates for thermal protection materials for re-entry and hypersonic vehicles. Phases are typically added to ZrB2-SiC to enhance the oxidation resistance of the material. MoAlB is an attractive nanolaminated ternary boride compound. Due to its damage tolerance, crack healing ability, and good oxidation resistance, MoAlB is a promising material for high-temperature applications. Therefore, the effect of MoAlB substitution on the oxidation of ZrB2-SiC at 1600 °C for 10 h was evaluated. Five samples with different MoAlB contents (0 vol%, 4 vol%, 8 vol%, 12 vol%, 16 vol%) were prepared. The results indicate that ZrB2-SiC-8vol%MoAlB exhibits improved oxidation resistance compared to ZrB2-SiC. After being oxidized at 1600 °C for 10 h, the thickness of the oxide layer on ZrB2-SiC-8vol%MoAlB was significantly smaller than that on ZrB2-SiC. The thickness of the oxide layer in ZrB2-SiC was 250 μm, while the thickness of the oxide layer in ZrB2-SiC-8vol%MoAlB was 108 μm. The formation of dendritic crystals on the surface of ZrB2-SiC-4vol%MoAlB destroys the oxide layer, leading to a decrease in the oxidation resistance of material. The mass gain of ZrB2-SiC-12vol%MoAlB and ZrB2-SiC-16vol%MoAlB is greater, and the oxidation layer is thicker, indicating a lower oxidation resistance.
Influence of silica rich HNT/MoS2 hybrid reinforcements on mechanical, wear and corrosion characteristics of magnesium AZ31 alloy
Authors: Aliasker K T , Gopal P M , S Rajesh , Sadasivam Sasivaradhan
Published: January 2024

This article examines the effects of combining silica-rich Halloysite Nano Tube (HNT) and Molybdenum di Sulphide (MoS2) as hybrid reinforcements, dispersed at volumes of 2, 4, and 6%, on the surface of AZ31 alloy through the application of the friction stir process (FSP). The prepared composites were analysed to evaluate their microstructure, mechanical properties, wear resistance, and corrosion characteristics. Microstructural observations indicate the occurrence of rapid recrystallization, resulting in reduced grain size and uniform dispersion. The surface composite demonstrates an increasing trend in hardness with the addition of HNT, while hardness decreases with the inclusion of MoS2. The micro tensile test results exhibits that the composite exhibits an increasing trend in strength, while the micrograph of the fractured surface of the micro tensile specimens reveals reduced ductility. The composite displays enhanced wear behaviour with the increasing volume percentages of HNT and MoS2 particles. Solid lubricant nature of the secondary reinforcement and enhanced hardness due to HNT addition and FSP leads to higher wear resistance of the developed hybrid composite. Additionally, the corrosion rate decreases with the addition of HNT, whereas higher concentrations of MoS2 lead to increased corrosion.
A physiological model of phrenic nerve excitation by electrical stimulation
Authors: Lohse Arnhold , Deininger Matthias Manfred , Loeser Johannes , Roehren Felix , Ziles Dmitrij , Breuer Thomas , Leonhardt Steffen , Walter Marian
Published: January 2024

Mechanical ventilation is essential in intensive care treatment but leads to diaphragmatic atrophy, which in turn contributes to prolonged weaning and increased mortality. One approach to prevent diaphragmatic atrophy while achieving pulmonary ventilation is electrical stimulation of the phrenic nerve. To automize phrenic nerve stimulation resulting in lung protective tidal volumes with lowest possible currents, mathematical models are required. Nerve stimulation models are often complex, so many parameters have to be identified prior to implementation. This paper presents a novel, simplified approach to model phrenic nerve excitation to obtain an individualized patient model using a few data points. The latter is based on the idea that nerve fibers are excited when the electric field exceeds a threshold. The effect of the geometry parameter on the model output was analyzed, and the model was validated with measurement data from a pig trial (RMSE in between 0.44 × 10−2 and 1.64 × 10−2 for parameterized models). The modeled phrenic nerve excitation behaved similarly to the measured tidal volumes, and thus could be used to develop automated phrenic nerve stimulation systems for lung protective ventilation.
Information bottleneck in peptide conformation determination by x-ray absorption spectroscopy
Authors: Eronen Eemeli A , Vladyka Anton , Gerbon Florent , Sahle Christoph J , Niskanen Johannes
Published: January 2024

We apply a recently developed technique utilizing machine learning for statistical analysis of computational nitrogen K-edge spectra of aqueous triglycine. This method, the emulator-based component analysis, identifies spectrally relevant structural degrees of freedom from a data set filtering irrelevant ones out. Thus tremendous reduction in the dimensionality of the ill-posed nonlinear inverse problem of spectrum interpretation is achieved. Structural and spectral variation across the sampled phase space is notable. Using these data, we train a neural network to predict the intensities of spectral regions of interest from the structure. These regions are defined by the temperature-difference profile of the simulated spectra, and the analysis yields a structural interpretation for their behavior. Even though the utilized local many-body tensor representation implicitly encodes the secondary structure of the peptide, our approach proves that this information is irrecoverable from the spectra. A hard x-ray Raman scattering experiment confirms the overall sensibility of the simulated spectra, but the predicted temperature-dependent effects therein remain beyond the achieved statistical confidence level.
Bound on the distance between controlled quantum state and target state under decoherence
Authors: Kobayashi Kohei
Published: January 2024

To implement quantum information technologies, carefully designed control for preparing a desired state plays a key role. However, in realistic situation, the actual performance of those methodologies is severely limited by decoherence. Therefore, it is important to evaluate how close we can steer the controlled state to a desired target state under decoherence. In this paper, we provide an upper bound of the distance between the two controlled quantum systems in the presence and absence of decoherence. The bound quantifies the degree of achievement of the control for a given target state under decoherence, and can be straightforwardly calculated without solving any equation. Moreover, the upper bound is applied to derive a theoretical limit of the probability for obtaining the target state under decoherence.
Study on the performance of reciprocating seals under the coupling effect of elastohydrodynamic lubrication and rubber wear
Authors: Zhang Yi , Wei Fu , Lin Shuai , Sun Xuebin , Liu Ling
Published: January 2024

Due to the lack of research on the sealing performance of reciprocating combined seals under the coupling of elastohydrodynamic lubrication and rubber wear, this paper uses the UMESHMOTION user subroutine and the improved Archard model to realize the dynamic wear process of the combined seals and the adaptive meshing of the local area to simulate the wear of the seals. At the same time, combined with the elastohydrodynamic lubrication model of the toothed slip ring combined seal ring, the sealing performance of the reciprocating combination under mixed lubrication conditions is studied. Finally, the accuracy of the model is verified by building a two-cylinder reciprocating seal test bench with more accurate measurement. The results show that the influence of the change of fluid pressure on the wear of the seal lip is greater in the fast wear stage than in the stable wear stage. The influence of the change of interference on the wear of the sealing lip is small at different wear stages. The wear of the sealing lip has a significant effect on the sealing performance of the instroke, but has little effect on the sealing performance of the outstroke.
Design of lateral β-Ga2O3 MOSFET with PFOM of 769.42 MW cm–2
Authors: Zhang Yunfei , Luan Suzhen
Published: January 2024

The Power figure of Merit (PFOM = Vbr
2/Ron,sp) is used to evaluate the performance of Gallium Oxide (β-Ga2O3) power devices. In this study, a lateral β-Ga2O3 MOSFET device is designed. The effects of different gate lengths, gate-drain distances, and epitaxial layer doping concentrations on the device performance are investigated. It is found that when the gate length is 3 μm, the breakdown voltage of the device is 3099 V, which is approximately twice that of devices with other gate lengths. The PFOM of the device reaches 769.14MW cm–2. Furthermore, the breakdownvoltage exhibits a trend of initially decreasing and then increasing with the increase of the gate-drain distance. When the gate-drain distance is 37 μm, the breakdown voltage of the device reaches 4367 V. Additionally, it is observed that the device performance is optimal when the epitaxial layer doping concentration is 2 × 1017 cm−3. This study provides a new approach for the design of Gallium Oxide power devices.
Variance extrapolation method for neural-network variational Monte Carlo
Authors: Fu Weizhong , Ren Weiluo , Chen Ji
Published: January 2024

Constructing more expressive ansatz has been a primary focus for quantum Monte Carlo, aimed at more accurate ab initio calculations. However, with more powerful ansatz, e.g. various recent developed models based on neural-network architectures, the training becomes more difficult and expensive, which may have a counterproductive effect on the accuracy of calculation. In this work, we propose to make use of the training data to perform empirical variance extrapolation when using neural-network ansatz in variational Monte Carlo. We show that this approach can speed up the convergence and surpass the ansatz limitation to obtain an improved estimation of the energy. Moreover, variance extrapolation greatly enhances the error cancellation capability, resulting in significantly improved relative energy outcomes, which are the keys to chemistry and physics problems.
CoRe optimizer: an all-in-one solution for machine learning
Authors: Eckhoff Marco , Reiher Markus
Published: January 2024

The optimization algorithm and its hyperparameters can significantly affect the training speed and resulting model accuracy in machine learning (ML) applications. The wish list for an ideal optimizer includes fast and smooth convergence to low error, low computational demand, and general applicability. Our recently introduced continual resilient (CoRe) optimizer has shown superior performance compared to other state-of-the-art first-order gradient-based optimizers for training lifelong ML potentials. In this work we provide an extensive performance comparison of the CoRe optimizer and nine other optimization algorithms including the Adam optimizer and resilient backpropagation (RPROP) for diverse ML tasks. We analyze the influence of different hyperparameters and provide generally applicable values. The CoRe optimizer yields best or competitive performance in every investigated application, while only one hyperparameter needs to be changed depending on mini-batch or batch learning.
Pluricanonical cycles and tropical covers
Authors: Cavalieri Renzo , Markwig Hannah , Ranganathan Dhruv
Published: January 2024

We extract a system of numerical invariants from logarithmic intersection theory on pluricanonical double ramification cycles, and show that these invariants exhibit a number of properties that are enjoyed by double Hurwitz numbers. Among their properties are (i) the numbers can be efficiently calculated by counts of tropical curves with a modified balancing condition, (ii) they are piecewise polynomial in the entries of the ramification vector, and (iii) they are matrix elements of operators on the Fock space. The numbers are extracted from the logarithmic double ramification cycle, which is a lift of the standard double ramification cycle to a blowup of the moduli space of curves. The blowup is determined by tropical geometry. We show that the traditional double Hurwitz numbers are intersections of the refined cycle with the cohomology class of a piecewise polynomial function on the tropical moduli space of curves. This perspective then admits a natural, combinatorially motivated, generalization to the pluricanonical setting. Tropical correspondence results for the new invariants lead immediately to the structural results for these numbers.
Effects of past mating behavior versus past ejaculation on male mate choice and male attractiveness
Authors: Chung Meng-Han Joseph , Head Megan L , Fox Rebecca J , Jennions Michael D
Published: January 2024

Past reproductive effort allows males to assess their ability to acquire mates, but it also consumes resources that can reduce their future competitive ability. Few studies have examined how a male’s reproductive history affects his subsequent mate choice, and, to date, no study has determined the relative contribution of past mating behavior and past ejaculate production because these two forms of investment are naturally highly correlated. Here, we disentangled the relative effects of past mating behavior and past ejaculate production in mosquitofish (Gambusia holbrooki) by experimentally preventing some males from ejaculating when trying to mate. We assessed the effect of mating behavior on mate choice by comparing males that had previously been with or without access to females and male rivals for 8 and 16 weeks and assessed the effect of ejaculation on mate choice by comparing males that either could or could not ejaculate when they had access to females for 16 weeks. Reproductive treatment did not affect male attractiveness, but it did affect male mate choice. Somewhat surprisingly, in five of the six treatment-by-age at testing combinations, males preferred a female in the vicinity of a male rival over a solitary female. This preference was marginally stronger for males that had previously engaged in mating behavior but were unaffected by past ejaculate production. We discuss the potential benefits to males of associating with another male when seeking mates. This is the first study to quantify the relative influence of pre- and post-copulatory reproductive investment on male mate choice.
Population turnover, behavioral conservatism, and rates of cultural evolution
Authors: Dyble Mark , Micheletti Alberto J C
Published: January 2024

Cultural evolution facilitates behavioral adaptation in many species. The pace of cultural evolution can be accelerated by population turnover, where newcomers (immigrants or juvenile recruits) introduce adaptive cultural traits into their new group. However, where newcomers are naïve to the challenges of their new group, population turnover could potentially slow the rate of cultural evolution. Here, we model cultural evolution with population turnover and show that even if turnover results in the replacement of experienced individuals with naïve ones, turnover can still accelerate cultural evolution if (1) the rate of social learning is more than twice as fast as the turnover rate and (b) newcomers are more likely to learn socially than behaviorally conservative existing group members. Although population turnover is a relatively simple factor, it is common to all animal societies, and variation in the turnover rate may potentially play an important role in explaining variation in the occurrence and rates of adaptive cultural evolution across species.
Low sex drive and choosy females: fungal infections are a reproductive downfall for male house flies
Authors: Edwards Sam , Bath Eleanor , De Fine Licht Henrik H
Published: January 2024

Many entomopathogenic fungi cause infections that kill their insect host. Little is understood about changes in the reproductive investment that occurs during an infection by a lethal disease over the waning life of an insect. Life-history theory suggests the host will respond by investing resources into fighting the disease or increasing reproduction. Here, we investigate how the reproductive life of adult house flies, Musca domestica, is impacted by its host-specific fungal pathogen, Entomophthora muscae. Specifically, we test how the week-long infection alters the mating behavior of virgin adult male house flies. We find that the pathogen significantly decreases male libido, an effect which grows stronger over the course of the infection. Furthermore, females were significantly less likely to choose an infected male, reducing male mating success. Additionally, we assessed sperm viability to understand the reproductive costs for monandrous females to mate with infected males. Analyses revealed that sperm quality decreases as early as 3 days post-infection. These results show that E. muscae, which can have a prevalence near 100% in wild populations, causes severe lifetime reproductive costs to male house flies. Understanding how host–pathogen interactions affect host life history is crucial for elucidating all the negative effects pathogen virulence exerts on hosts.
A new trophic specialization buffers a top predator against climate-driven resource instability
Authors: Gangoso Laura , Viana Duarte S , Merchán Marina , Figuerola Jordi
Published: January 2024

Intraspecific phenotypic variability is key to respond to environmental changes and anomalies. However, documenting the emergence of behavioral diversification in natural populations has remained elusive due to the difficulty of observing such a phenomenon at the right time and place. Here, we investigated how the emergence of a new trophic strategy in a population subjected to high fluctuations in the availability of its main trophic resource (migrating songbirds) affected the breeding performance, population structure, and population fitness of a specialized color polymorphic predator, the Eleonora’s falcon from the Canary Islands. Using long-term data (2007–2022), we found that the exploitation of an alternative prey (a local petrel species) was associated with the growth of a previously residual falcon colony. Pairs in this colony laid earlier and raised more fledglings than in the other established colonies. The specialization on petrels increased over time, independently of annual fluctuations in prey availability. Importantly, however, the positive effect of petrel consumption on productivity was stronger in years with lower food availability. This trophic diversification was further associated with the genetically determined color morph, with dark individuals preying more frequently on petrels than pale ones, which might promote the long-term maintenance of genotypic and phenotypic diversity. We empirically demonstrate how the emergence of an alternative trophic strategy can buffer populations against harsh environmental fluctuations by stabilizing their productivity.
Accurate identification of structural variations from cancer samples
Authors: Li Le , Hong Chenyang , Xu Jie , Chung Claire Yik-Lok , Leung Alden King-Yung , Boncan Delbert Almerick T , Cheng Lixin , Lo Kwok-Wai , Lai Paul B S , Wong John , Zhou Jingying , Cheng Alfred Sze-Lok , Chan Ting-Fung , Yue Feng , Yip Kevin Y
Published: January 2024

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework
Authors: Loyer Gabriel , Reinharz Vladimir
Published: January 2024

Motivation

The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of noncanonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops.

Results

We previously developed the integer programming framework RNA Motifs over Integer Programming (RNAMoIP) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all nonredundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information, and (iv) noncanonical motifs at kink-turn locations.

Availability and implementation

The source code of the framework is available at https://gitlab.info.uqam.ca/cbe/RNAMoIP and an interactive web server at https://rnamoip.cbe.uqam.ca/.
Prediction of cervical lymph node metastasis in differentiated thyroid cancer based on radiomics models
Authors: Mu Jingshi , Cao Yuan , Zhong Xiao , Diao Wei , Jia Zhiyun
Published: January 2024

Objective

The accurate clinical diagnosis of cervical lymph node metastasis plays an important role in the treatment of differentiated thyroid cancer (DTC). This study aimed to explore and summarize a more objective approach to detect cervical malignant lymph node metastasis of DTC via radiomics models.

Methods

PubMed, Web of Science, MEDLINE, EMBASE, and Cochrane databases were searched for all eligible studies. Articles using radiomics models based on ultrasound, computed tomography, or magnetic resonance imaging to assess cervical lymph node metastasis preoperatively were included. Characteristics and diagnostic accuracy measures were extracted. Bias and applicability judgments were evaluated by the revised QUADAS-2 tool. The estimates were pooled using a random-effects model. Additionally, the leave-one-out method was conducted to assess the heterogeneity.

Results

Twenty-nine radiomics studies with 6160 validation set patients were included in the qualitative analysis, and 11 studies with 3863 validation set patients were included in the meta-analysis. Four of them had an external independent validation set. The studies were heterogeneous, and a significant risk of bias was found in 29 studies. Meta-analysis showed that the pooled sensitivity and specificity for preoperative prediction of lymph node metastasis via US-based radiomics were 0.81 (95% CI, 0.73-0.86) and 0.87 (95% CI, 0.83-0.91), respectively.

Conclusions

Although radiomics-based models for cervical lymphatic metastasis in DTC have been demonstrated to have moderate diagnostic capabilities, broader data, standardized radiomics features, robust feature selection, and model exploitation are still needed in the future.

Advances in knowledge

The radiomics models showed great potential in detecting malignant lymph nodes in thyroid cancer.
Imaging characterization of paediatric tumours with the neurotrophic tyrosine receptor kinase fusion transcript
Authors: Hermann Anne-Laure , Lemelle Lauriane , Pierron Gaëlle , Gauthier Arnaud , Nicolas Nayla , Cardoen Liesbeth , Moalla Salma , Petit Philippe , Morel Baptiste , Ducou Le Pointe Hubert , Hassani Adnan , Fréneaux Paul , Guillemot Delphine , Carton Matthieu , Corradini Nadège , Rome Angélique , Castex Marie-Pierre , Defachelles Anne-Sophie , Schleiermacher Gudrun , Berlanga Pablo , Delattre Olivier , Orbach Daniel , Brisse Hervé J
Published: January 2024

Objectives

The neurotrophic tyrosine receptor kinase (NTRK) fusion transcript (FT) is a major genetic landmark of infantile fibrosarcoma (IFS) and cellular congenital mesoblastic nephroma (cCMN) but is also described in other tumours. The recent availability of NTRK-targeted drugs enhances the need for better identification. We aimed to describe the anatomic locations and imaging features of tumours with NTRK-FT in children.

Case series

Imaging characteristics of NTRK-FT tumours of 41 children (median age: 4 months; 63% <1 year old; range: 0-188) managed between 2001 and 2019 were retrospectively analysed. The tumours were located in the soft tissues (n = 24, including 19 IFS), kidneys (n = 9, including 8 cCMN), central nervous system (CNS) (n = 5), lung (n = 2), and bone (n = 1). The tumours were frequently deep-located (93%) and heterogeneous (71%) with necrotic (53%) or haemorrhagic components (29%). Although inconstant, enlarged intratumoural vessels were a recurrent finding (70%) with an irregular distribution (63%) in the most frequent anatomical locations.

Conclusion

Paediatric NTRK-FT tumours mainly occur in infants with very variable histotypes and locations. Rich and irregular intra-tumoural vascularization are recurrent findings.

Advances in knowledge

Apart from IFS of soft tissues and cCMN of the kidneys, others NTRK-FT tumours locations have to be known, as CNS tumours. Better knowledge of the imaging characteristics may help guide the pathological and biological identification.
Incidence and outcomes of surgical pulmonary embolectomy in the UK
Authors: Argyriou Amerikos , Vohra Hunaid , Chan Jeremy , Ahmed Eltayeb Mohamed , Rajakaruna Cha , Angelini Gianni Davide , Fudulu Daniel Paul
Published: January 2024

Background

Surgical pulmonary embolectomy is rarely used for the treatment of massive acute pulmonary embolism. The aim of this study was to assess the incidence and outcomes of this operation by undertaking a retrospective analysis of a large national registry in the UK.

Methods

All acute pulmonary embolectomies performed between 1996 and 2018 were captured in the National Institute of Cardiovascular Outcomes Research central database. Trends in the number of operations performed during this interval and reported in-hospital outcomes were analysed retrospectively. Multivariable logistic regression was used to identify independent risk factors for in-hospital death.

Results

All 256 patients treated surgically for acute pulmonary embolism during the study interval were included in the analysis. Median age at presentation was 54 years, 55.9% of the patients were men, 48.0% had class IV heart failure symptoms, and 37.5% had preoperative cardiogenic shock. The median duration of bypass was 73 min, and median cross-clamp time was 19 min. Cardioplegic arrest was used in 53.1% of patients. The median duration of hospital stay was 11 days. The in-hospital mortality rate was 25%, postoperative stroke occurred in 5.4%, postoperative dialysis was required in 16%, and the reoperation rate for bleeding was 7.5%. Risk-adjusted multivariable analysis revealed cardiogenic shock (OR 2.54, 95% c.i. 1.05 to 6.21; P = 0.038), preoperative ventilation (OR 5.85, 2.22 to 16.35; P < 0.001), and duration of cardiopulmonary bypass exceeding 89 min (OR 7.82, 3.25 to 20.42; P < 0.001) as significant independent risk factors for in-hospital death.

Conclusion

Surgical pulmonary embolectomy is rarely performed in the UK, and is associated with significant mortality and morbidity. Preoperative ventilation, cardiogenic shock, and increased duration of bypass were significant predictors of in-hospital death.
An electronic nose can identify humans by the smell of their ear
Authors: Brener Stephanie , Snitz Kobi , Sobel Noam
Published: January 2024

Terrestrial mammals identify conspecifics by body odor. Dogs can also identify humans by body odor, and in some instances, humans can identify other humans by body odor as well. Despite the potential for a powerful biometric tool, smell has not been systematically used for this purpose. A question arising in the application of smell to biometrics is which bodily odor source should we measure. Breath is an obvious candidate, but the associated humidity can challenge many sensing devices. The armpit is also a candidate source, but it is often doused in cosmetics. Here, we test the hypothesis that the ear may provide an effective source for odor-based biometrics. The inside of the ear has relatively constant humidity, cosmetics are not typically applied inside the ear, and critically, ears contain cerumen, a potent source of volatiles. We used an electronic nose to identify 12 individuals within and across days, using samples from the armpit, lower back, and ear. In an identification setting where chance was 8.33% (1 of 12), we found that we could identify a person by the smell of their ear within a day at up to ~87% accuracy (~10 of 12, binomial P < 10−5), and across days at up to ~22% accuracy (~3 of 12, binomial P < 0.012). We conclude that humans can indeed be identified from the smell of their ear, but the results did not imply a consistent advantage over other bodily odor sources.
Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization
Authors: Deogharia Manisha , Venegas-Zamora Leslye , Agrawal Akanksha , Shi Miusi , Jain Abhinav K , McHugh Kevin J , Altamirano Francisco , Marian Ali J , Gurha Priyatansh
Published: January 2024

Aims

Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.

Methods and results

KDM5A, B, and C proteins were mainly expressed in the early post-natal stages, and their expressions were progressively downregulated in the post-natal CMs and were absent in adult hearts and CMs. In contrast, KDM5 proteins were persistently expressed in the iPSC-CMs up to 60 days after the induction of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor, induced differential expression of 2372 genes, including upregulation of genes involved in fatty acid oxidation (FAO), OXPHOS, and myogenesis in the iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the cleavage under targets and release using nuclease assay showed enriched of the H3K4me3 peaks at the promoter regions of genes encoding FAO, OXPHOS, and sarcomere proteins. Consistent with the chromatin and gene expression data, KDM5 inhibition increased the expression of multiple sarcomere proteins and enhanced myofibrillar organization. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene and increased its RNA and protein levels. Knockdown of ESRRA in KDM5-C70-treated iPSC-CM suppressed expression of a subset of the KDM5 targets. In conjunction with changes in gene expression, KDM5 inhibition increased oxygen consumption rate and contractility in iPSC-CMs.

Conclusion

KDM5 inhibition enhances maturation of iPSC-CMs by epigenetically upregulating the expressions of OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
Asymptotic properties of endogeneity corrections using nonlinear transformations
Authors: Breitung Jörg , Mayer Alexander , Wied Dominik
Published: January 2024

This paper studies the asymptotic properties of endogeneity corrections based on nonlinear transformations without external instruments, which were originally proposed by Park and Gupta (2012) and have become popular in applied research. In contrast to the original copula-based estimator, our approach is based on a nonparametric control function and does not require a conformably specified copula. Moreover, we allow for exogenous regressors, which may be (linearly) correlated with the endogenous regressor(s). We establish consistency, asymptotic normality, and validity of the bootstrap for the unknown model parameters. An empirical application on wage data of the US Current Population Survey demonstrates the usefulness of the method.
Clonal haematopoiesis of indeterminate potential and atrial fibrillation: an east Asian cohort study
Authors: Ahn Hyo-Jeong , An Hong Yul , Ryu Gangpyo , Lim Jiwoo , Sun Choonghyun , Song Han , Choi Su-Yeon , Lee Heesun , Maurer Taylor , Nachun Daniel , Kwon Soonil , Lee So-Ryoung , Lip Gregory Y H , Oh Seil , Jaiswal Siddhartha , Koh Youngil , Choi Eue-Keun
Published: January 2024

Background and Aims

Both clonal haematopoiesis of indeterminate potential (CHIP) and atrial fibrillation (AF) are age-related conditions. This study investigated the potential role of CHIP in the development and progression of AF.

Methods

Deep-targeted sequencing of 24 CHIP mutations (a mean depth of coverage = 1000×) was performed in 1004 patients with AF and 3341 non-AF healthy subjects. Variant allele fraction ≥ 2.0% indicated the presence of CHIP mutations. The association between CHIP and AF was evaluated by the comparison of (i) the prevalence of CHIP mutations between AF and non-AF subjects and (ii) clinical characteristics discriminated by CHIP mutations within AF patients. Furthermore, the risk of clinical outcomes—the composite of heart failure, ischaemic stroke, or death—according to the presence of CHIP mutations in AF was investigated from the UK Biobank cohort.

Results

The mean age was 67.6 ± 6.9 vs. 58.5 ± 6.5 years in AF (paroxysmal, 39.0%; persistent, 61.0%) and non-AF cohorts, respectively. CHIP mutations with a variant allele fraction of ≥2.0% were found in 237 (23.6%) AF patients (DNMT3A, 13.5%; TET2, 6.6%; and ASXL1, 1.5%) and were more prevalent than non-AF subjects [356 (10.7%); P < .001] across the age. After multivariable adjustment (age, sex, smoking, body mass index, diabetes, and hypertension), CHIP mutations were 1.4-fold higher in AF [adjusted odds ratio (OR) 1.38; 95% confidence interval 1.10–1.74, P < .01]. The ORs of CHIP mutations were the highest in the long-standing persistent AF (adjusted OR 1.50; 95% confidence interval 1.14–1.99, P = .004) followed by persistent (adjusted OR 1.44) and paroxysmal (adjusted OR 1.33) AF. In gene-specific analyses, TET2 somatic mutation presented the highest association with AF (adjusted OR 1.65; 95% confidence interval 1.05–2.60, P = .030). AF patients with CHIP mutations were older and had a higher prevalence of diabetes, a longer AF duration, a higher E/E′, and a more severely enlarged left atrium than those without CHIP mutations (all P < .05). In UK Biobank analysis of 21 286 AF subjects (1297 with CHIP and 19 989 without CHIP), the CHIP mutation in AF is associated with a 1.32-fold higher risk of a composite clinical event (heart failure, ischaemic stroke, or death).

Conclusions

CHIP mutations, primarily DNMT3A or TET2, are more prevalent in patients with AF than non-AF subjects whilst their presence is associated with a more progressive nature of AF and unfavourable clinical outcomes.