bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing machine learning techniques for predicting glassy dynamics
Authors: Alkemade Rinske M. , Boattini Emanuele , Filion Laura , Smallenburg Frank
Published: May 2022

In the quest to understand how structure and dynamics are connected in glasses, a number of machine learning based methods have been developed that predict dynamics in supercooled liquids. These methods include both increasingly complex machine learning techniques and increasingly sophisticated descriptors used to describe the environment around particles. In many cases, both the chosen machine learning technique and choice of structural descriptors are varied simultaneously, making it hard to quantitatively compare the performance of different machine learning approaches. Here, we use three different machine learning algorithms—linear regression, neural networks, and graph neural networks—to predict the dynamic propensity of a glassy binary hard-sphere mixture using as structural input a recursive set of order parameters recently introduced by Boattini et al. [Phys. Rev. Lett. 127, 088007 (2021)]. As we show, when these advanced descriptors are used, all three methods predict the dynamics with nearly equal accuracy. However, the linear regression is orders of magnitude faster to train, making it by far the method of choice.
New asymptotically flat static vacuum metrics with near Euclidean boundary data
Authors: An Zhongshan , Huang Lan-Hsuan
Published: May 2022

In our prior work toward Bartnik’s static vacuum extension conjecture for near Euclidean boundary data, we establish a sufficient condition, called static regular, and confirm that large classes of boundary hypersurfaces are static regular. In this paper, we further improve some of those prior results. Specifically, we show that any hypersurface in an open and dense subfamily of a certain general smooth one-sided family of hypersurfaces (not necessarily a foliation) is static regular. The proof uses some of our new arguments motivated from studying the conjecture for boundary data near an arbitrary static vacuum metric.
A microfabricated fiber-integrated diamond magnetometer with ensemble nitrogen-vacancy centers
Authors: Xie Fei , Hu Yuqiang , Li Lingyun , Wang Cao , Liu Qihui , Wang Nan , Wang Lihao , Wang Shuna , Cheng Jiangong , Chen Hao , Wu Zhenyu
Published: May 2022

Miniaturization is a trend of development toward practical applications for diamond nitrogen-vacancy centers-based sensors. We demonstrate a compact diamond magnetic field sensor device using a standard microfabrication process. A single-crystal-diamond plate is embedded in a cavity formed with stacking of three silicon chips. Thermal compression bonding is implemented at silicon–silicon and diamond–silicon interfaces ensuring mechanical robustness. The specific construction volume for the essential sensor component is about 10 × 10 × 1.5 mm3. By integrating a gradient index lens pigtailed fiber to the sensor device, 532-nm laser light and emitted fluorescence share a common path for excitation and detection. An omega-shaped transmission line for applied microwave power is fabricated directly on the surface of diamond. The integrated sensor device exhibits an optimized sensitivity of 2.03 nT·Hz−1/2 and over twofold enhancement of fluorescence collection efficiency compared to bare diamond. Such a sensor is utilized to measure a magnetic field change caused by switching a household electrical appliance.
Sublethal effects of parasitism on ruminants can have cascading consequences for ecosystems
Authors: Koltz Amanda M. , Civitello David J. , Becker Daniel J. , Deem Sharon L. , Classen Aimée T. , Barton Brandon , Brenn-White Maris , Johnson Zoë E. , Kutz Susan , Malishev Matthew , Preston Daniel L. , Vannatta J. Trevor , Penczykowski Rachel M. , Ezenwa Vanessa O.
Published: May 2022

Significance

We found that pervasive parasitic infections reduce herbivory rates and can trigger trophic cascades. Lethal parasites clearly have cascading impacts on ecosystems, but whether common sublethal infections have similar effects is largely unknown. Using a mathematical model, we probed how parasites that reduce host survival, fecundity, or feeding rates can indirectly alter producer biomass in a helminth–ruminant system. We found that both lethal and sublethal infections triggered trophic cascades by altering the biomass of ruminant herbivore hosts and their resources. However, a global meta-analysis revealed that helminths tend to have pervasive sublethal effects on free-living ruminants, including by reducing host feeding rates. Our findings suggest there are widespread, but overlooked, ecological consequences of sublethal infections in natural ecosystems.
Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark
Authors: Womersley Freya C. , Humphries Nicolas E. , Queiroz Nuno , Vedor Marisa , da Costa Ivo , Furtado Miguel , Tyminski John P. , Abrantes Katya , Araujo Gonzalo , Bach Steffen S. , Barnett Adam , Berumen Michael L. , Bessudo Lion Sandra , Braun Camrin D. , Clingham Elizabeth , Cochran Jesse E. M. , de la Parra Rafael , Diamant Stella , Dove Alistair D. M. , Dudgeon Christine L. , Erdmann Mark V. , Espinoza Eduardo , Fitzpatrick Richard , Cano Jaime González , Green Jonathan R. , Guzman Hector M. , Hardenstine Royale , Hasan Abdi , Hazin Fábio H. V. , Hearn Alex R. , Hueter Robert E. , Jaidah Mohammed Y. , Labaja Jessica , Ladino Felipe , Macena Bruno C. L. , Morris John J. , Norman Bradley M. , Peñaherrera-Palma Cesar , Pierce Simon J. , Quintero Lina M. , Ramírez-Macías Dení , Reynolds Samantha D. , Richardson Anthony J. , Robinson David P. , Rohner Christoph A. , Rowat David R. L. , Sheaves Marcus , Shivji Mahmood S. , Sianipar Abraham B. , Skomal Gregory B. , Soler German , Syakurachman Ismail , Thorrold Simon R. , Webb D. Harry , Wetherbee Bradley M. , White Timothy D. , Clavelle Tyler , Kroodsma David A. , Thums Michele , Ferreira Luciana C. , Meekan Mark G. , Arrowsmith Lucy M. , Lester Emily K. , Meyers Megan M. , Peel Lauren R. , Sequeira Ana M. M. , Eguíluz Victor M. , Duarte Carlos M. , Sims David W.
Published: May 2022

Significance

Global vessel traffic is increasing alongside world economic growth. The potential for rising lethal ship strikes on endangered species of marine megafauna, such as the plankton-feeding whale shark, remains poorly understood since areas of highest overlap are seldom determined across an entire species range. Here we show how satellite tracking whale sharks and large vessel movements globally provides a means to localize high-overlap areas and to determine how collision risk changes in time. Our results point to potential high levels of undetected or unreported ship strikes, which may explain why whale shark populations continue to decline despite protection and low fishing-induced mortality. Collision mitigations in high-collision-risk areas appear necessary to help conserve this iconic species.
Tactile suppression stems from specific sensorimotor predictions
Authors: Fuehrer Elena , Voudouris Dimitris , Lezkan Alexandra , Drewing Knut , Fiehler Katja
Published: May 2022

Significance

Tactile sensations on a moving hand are perceived weaker than when presented on the same but stationary hand. There is an ongoing debate about whether this weaker perception is based on sensorimotor predictions or is due to a blanket reduction in sensitivity. Here, we show greater suppression of sensations matching predicted sensory feedback. This reinforces the idea of precise estimations of future body sensory states suppressing the predicted sensory feedback. Our results shine light on the mechanisms of human sensorimotor control and are relevant for understanding clinical phenomena related to predictive processes.
Precipitation behaviour of single and duplex aged metastable β-Ti alloy, Ti–5Al–5Mo–5V–3Cr
Authors: Sharma Deepak , Parfitt David , Roebuck Bryan , Kada Sitarama Raju , Fabijanic Daniel , Fitzpatrick Michael E.
Published: May 2022

This work presents the influence of single-aging and duplex-aging treatments on microstructure evolution and the associated properties of Ti-5553 β-Ti alloy. We found that single-aged samples with a slow heating rate and duplex-aged samples produced approximately the same microstructures and microhardness at all aging conditions. This can be attributed to the same precipitation mechanism in both cases as observed via in situ electrical resistivity measurements. The slowly heated and duplex-aged samples generally produced higher microhardness in comparison to fast-heated samples; however, the difference in the microhardness tended to decrease with aging time at higher temperatures. A correlation ([Formula: see text] ) between the microhardness values and the width of α-phase ( d) was established for all the aged samples.

Highlights Duplex aging and slow heating yield similar microstructure and microhardness. Duplex aging and slow heating showed similar precipitation mechanism. Duplex aging and slow heating generally produced higher hardness than fast heating. The gap in hardness for different aged conditions decreased at higher temperatures. The microhardness values showed a good correlation with the width of α-phase.

GRAPHICAL ABSTRACT
Enhanced Smith–Purcell radiation from bound states in the continuum of metallic gratings
Authors: Chen Zhaofu , Mao Leilei , Jin Mengmeng , Shi Xin , Bai Ningfeng , Sun Xiaohan
Published: May 2022

The enhancement of Smith–Purcell radiation (SPR) produced by electrons moving closely to a grating is a longstanding topic of interest. Here, we systematically investigate the resonant enhancement of SPR for planar metallic gratings. Using an analytic solution for the amplitude of SPR, we show that metallic gratings with a small dutycycle support two type of bound states in the continuum (BICs), i.e. symmetry-protected BICs and accidental BICs, both of which enable the SPR to be enhanced by orders of magnitude at the resonant frequency. The required electron energy for the excitation of BICs can be reduced by employing a higher-order diffraction wave for SPR. Our results present a mechanism for enhancing the SPR produced by metallic gratings, and may find applications in free-electron lasers.
Novel rotation scheme for dual-axis rotational inertial navigation system based on body diagonal rotation of inertial measurement unit
Authors: Wei Qiushuo , Zha Feng , Chang Lubin
Published: May 2022

Traditional rotational inertial navigation systems are based on rotation around one or two sensitive axes of inertial sensors. However, as the rotation and sensitive axes of inertial sensors lie along the same direction, it is difficult to modulate the relative error of the inertial sensor in the axial direction. This paper proposes a dual-axis rotation scheme based on the diagonal rotation of the inertial measurement unit (IMU) body. The scheme selects the body diagonal of the three orthogonal inertial sensors of the IMU as the horizontal rotation axis, and sets the vertical rotation axis orthogonal to this axis. As the rotation axis and the inertial sensor are oriented in different directions, at any moment of rotation, the errors of the inertial sensor in the three axial directions can all be modulated, especially the installation error. First, a mathematical model based on the diagonal rotation of the IMU body is established. On this basis, the coordinate transformation relationship and the error equations are derived, and the error propagation characteristics are obtained. Finally, the comprehensive error of the system is tested. Under the same error conditions, the system latitude error is reduced from 0.1089 nautical miles/72 h in the traditional scheme to 0.0368 nautical miles/72 h, and the longitude error is reduced from 0.3587 nautical miles/72 h to 0.1332 nautical miles/72 h. These results verify the effectiveness of the proposed scheme. This method of rotating around the body diagonal of the IMU also exhibits certain advantages when applied to other rotational inertial navigation schemes.
Wearable sectorial electrical impedance tomography and k-means clustering for measurement of gastric processes
Authors: Wicaksono Ridwan , Darma Panji Nursetia , Inoue Atsuo , Tsuji Hideyuki , Takei Masahiro
Published: May 2022

A low-power and handy gastric data acquisition (g-DAQ) system has been proposed to identify the gastric processes in the epigastric region with sectorial electrical impedance tomography (s-EIT) and K-means sectorial clustering algorithm. The g-DAQ with a wearable abdominal sensor investigates gastric retention levels in the epigastric region during the emptying process. A C-runtime engine with Secure Shell protocol optimized an ARM microprocessor and field programmable gate array-based system with bidirectional channels to perform real-time data acquisition. The s-EIT algorithm projects the gastric conductivity distribution in the epigastric region into a cross-sectional image. K-means clustering method quantitatively identifies the gastric content images on the epigastric region to monitor the different clustered conductivity

α
k

. The phantom experiments evaluated the s-EIT using liver-shaped, bone-shaped, and gastric-shaped phantoms in an abdominal-shaped vessel to distinguish gastric phantom conductivity. In human experiments, the proposed method was applied to measure 15 samples of the emptying process to evaluate the retention level of liquid gastric content. As a result, the proposed g-DAQ successfully performed a rapid acquisition at least 50 times faster than the conventional method in terms of the data acquisition rate. The developed g-DAQ with 110 mm × 66 mm × 51 mm of dimensions and 0.16 kg of weight took 0.32 sec to measure 208 points per frame and consumed 3.67 Watt of average power operation. By drinking 500 ml of rehydration water with 0.69 S m−1 of conductivity, In subjects 1–4 and phantoms, the maximum R(t) was identified on t
1 as the gastric volume is fully bloated. During 30 min, the emptying liquid content was well-indicated because the minimum R(t) was identified on t
15 as an empty state. The mean of the measurement results is −0.0387 with the linear equation R(t) = −0.0387t + 0.8105. In conclusion, the body mass index did not significantly affect the trendline.
Development of a virtual teaching environment with Algodoo: ‘eye’ and ‘cactus type light source’ models
Authors: Özdemir Erdoğan , Coramik Mustafa
Published: May 2022

It is often necessary to enrich the teaching environment in order for students to learn optics in depth and to interpret the real optical situations with the information they have learned. In this study, a virtual teaching environment was developed using by Algodoo, a 2D simulation software. An eye model was created in order to explain the formation of the image in the eye in the teaching environment. Also, a cactus type light source model has also been developed to demonstrate that the image can be created in optics by using rays other than special rays. In order to show the success of the virtual teaching environment in modelling, previously known situations that the students had difficulty in understanding were simulated. Finally, some suggestions were made about the use of the virtual teaching environment.
Reply to Comment on ‘On the nuclear explosion fireball’
Authors: Khan F A
Published: May 2022

The comment, on my recent article, regarding its contemporaneous publishing nature and visibility of nuclear explosion fireball is replied.
Motion of a plucked string or spring
Authors: Cross Rod
Published: May 2022

The initial motion of stretched spring, plucked in the middle, was captured with a high speed video camera. The motion is surprising, but the behaviour is similar to that when a guitar string is plucked or when a slinky is held vertically and the top end is released.
Archimedes, the puck, and the turntable
Authors: Binder P-M , Lyons Keith M , Herman Ian K
Published: May 2022

A standard problem in mechanics asks us to look at a frictionless puck sliding over and across a turntable (a rotating platform with constant angular velocity) from the rotating reference frame S′ of the turntable. Here we analyse in some detail the kinematics and dynamics of such a puck, where a type of spiral discovered by Archimedes plays a central role.
Overall survival time prediction for glioblastoma using multimodal deep KNN
Authors: Tang Zhenyu , Cao Hongda , Xu Yuyun , Yang Qing , Wang Jinda , Zhang Han
Published: May 2022

Glioblastoma (GBM) is a severe malignant brain tumor with bad prognosis, and overall survival (OS) time prediction is of great clinical value for customized treatment. Recently, many deep learning (DL) based methods have been proposed, and most of them build deep networks to directly map pre-operative images of patients to the OS time. However, such end-to-end prediction is sensitive to data inconsistency and noise. In this paper, inspired by the fact that clinicians usually evaluate patient prognosis according to previously encountered similar cases, we propose a novel multimodal deep KNN based OS time prediction method. Specifically, instead of the end-to-end prediction, for each input patient, our method first search its K nearest patients with known OS time in a learned metric space, and the final OS time of the input patient is jointly determined by the K nearest patients, which is robust to data inconsistency and noise. Moreover, to take advantage of multiple imaging modalities, a new inter-modality loss is introduced to encourage learning complementary features from different modalities. The in-house single-center dataset containing multimodal MR brain images of 78 GBM patients is used to evaluate our method. In addition, to demonstrate that our method is not limited to GBM, a public multi-center dataset (BRATS2019) containing 211 patients with low and high grade gliomas is also used in our experiment. As benefiting from the deep KNN and the inter-modality loss, our method outperforms all methods under evaluation in both datasets. To the best of our knowledge, this is the first work, which predicts the OS time of GBM patients in the strategy of KNN under the DL framework.
Control of ion flux-energy distributions by low frequency square-shaped tailored voltage waveforms in capacitively coupled plasmas
Authors: Hartmann P , Korolov I , Escandón-López J , van Gennip W , Buskes K , Schulze J
Published: May 2022

Capacitively coupled plasmas are routinely used in an increasing number of technological applications, where a precise control of the quantity and the shape of the energy distribution of ion fluxes impacting boundary surfaces is required. Oftentimes, narrow peaks at controllable energies are required, e.g. to improve selectivity in plasma etching, which cannot be realized in classical discharges. We combine experimental ion flux-energy distribution measurements and PIC/MCC simulations to provide insights into the operation and ion acceleration mechanisms for discharges driven by square-shaped tailored voltage waveforms composed of low-frequency (100 kHz) pulsed and high-frequency (27.12 MHz) signals. The formation of ion flux-energy distributions with a narrow high energy peak and strongly reduced ion fluxes at intermediate energies is observed. The position of the high energy peak on the energy axis can be controlled by adjusting the low-frequency voltage pulse magnitude and duty cycle. The effects of tailoring the driving voltage waveform by adjusting these control parameters as well as its repetition rate on the plasma operation and the ion flux-energy distribution are analysed in depth. We find, e.g. that the duty cycle regime (

<
40

% or

>
60

%) determines if the high energy ions form at the grounded or the powered electrode and that the duration of the pulse must exceed the ion energy relaxation time, on the order of 0.5 μs.
Decade of bio-inspired soft robots: a review
Authors: Ahmed Faheem , Waqas Muhammad , Jawed Bushra , Soomro Afaque Manzoor , Kumar Suresh , Hina Ashraf , Khan Umair , Kim Kyung Hwan , Choi Kyung Hyun
Published: May 2022

Soft robotics is an emerging field of robotics that focuses on the design of soft machines and devices with effective human-machine interaction, high conformity, and environmental adaptability. The conventional robots made of hard materials have already achieved precision and accuracy, but they lack in reachability, adaptability, degree of freedom, and safe interaction. Moreover, soft robots mimic the behavior of biological creatures by mimicking their locomotive patterns. The actuation or the locomotion of the soft robots is achieved by soft actuators which are a very important part of soft robotic systems. Herein, a comprehensive review based on the evolution of six actuation methodologies is presented. Various approaches used for the design and fabrication of soft robots such as pneumatic, shape memory alloy, dielectric elastomers, chemical-reaction enforced, and pneumatic and magneto-rheological elastomers-based actuation methods reported in the last decade. Furthermore, the advancement of these approaches has been rigorously discussed in chronological order for parameters like efficiency, power requirement, frequency, and possible applications. Future challenges and directions toward the advancement in soft robotics are also discussed for achieving the remarkable performance of soft robots in a real-time environment. Furthermore, we believe, this is a complete review package for the young researchers which can help them to understand, how this field has evolved from a performance, application, and efficiency point of view.
Synergic realization of electrical insulation and mechanical strength in liquid nitrogen for high-temperature superconducting tapes with ultra-thin acrylic resin coating
Authors: Guo Chunjiang , Zhang Zhiwei , Wu Yue , Wang Yawei , Ma Guangtong , Shi Jiangtao , Zhong Zhuoyan , Hong Zhiyong , Jin Zhijian , Zhao Yue
Published: May 2022

Insulation coating is a sought after technique for REBa2Cu3O6+x
(REBCO) based high temperature superconducting tapes in practical applications. In this work, we developed a novel technique for preparing ultra-thin and fully surrounded insulation coatings on REBCO tapes. This technique completely eliminates the risk of critical current degradation in REBCO tapes induced by high temperature curing, without sacrificing the mechanical performance and the engineering current density. We adopted CRC-PLASTICOTE-70 as insulation precursor and verified its performance as insulation coating at 77 K. Thickness effect of the insulation coating in liquid nitrogen was investigated in details. Ultra-thin coating (below 5 μm) on REBCO tapes exhibited excellent strength during thermal shock test, while good adhesion of classification 1 was achieved (according to ISO2409-1992). A charge–discharge test was carried out on a test coil wound from as-coated tapes to assess the turn-to-turn insulation performance. The results show that a high turn-to-turn resistivity of 1060 μΩ cm2 is achieved by the insulation coating, which is about two orders of magnitude higher than that of its un-coated counterpart, indicating excellent insulation properties. This work provides a new idea for the development of novel insulation technology for REBCO tapes in practical applications.
Parametrized post-Newtonian formalism in higher-order Teleparallel Gravity
Authors: Gonzalez-Espinoza Manuel , Otalora Giovanni , Kraiselburd Lucila , Landau Susana
Published: May 2022

We study the parametrized post-Newtonian (PPN) limit of higher-derivative-torsion Modified Teleparallel Gravity. We start from the covariant formulation of modified Teleparallel Gravity by restoring the spin connection of the theory. Then, we perform the post-Newtonian expansion of the tetrad field around the Minkowski background and find the perturbed field equations. We compute the PPN metric for the higher-order Teleparallel Gravity theories which allows us to show that at the post-Newtonian limit this more general class of theories are fully conservative and indistinguishable from General Relativity . In this way, we extend the results that were already found for F(T) gravity in previous works. Furthermore, our calculations reveal the importance of considering a second post-Newtonian (2PN) order approximation or a parametrized post-Newtonian cosmology (PPNC) framework where additional perturbative modes coming from general modifications of Teleparallel Gravity could lead to new observable imprints.
Shadow thermodynamics of an AdS black hole in regular spacetime *
Authors: Guo Sen , Li Guan-Ru , Li Guo-Ping
Published: May 2022

The dependence of the black hole (BH) shadow and thermodynamics may be structured in regular spacetime. Taking a regular Bardeen-AdS BH as an example, the relationship between the shadow radius and event horizon radius is derived. It is found that these two radii display a positive correlation, implying that the BH temperature can be rewritten as a function of shadow radius in regular spacetime. By analyzing the phase transition curves under the shadow context, we find that the shadow radius can replace the event horizon radius to present the BH phase transition process, and the phase transition grade can also be revealed by the shadow radius, indicating that the shadow radius may serve as a probe for phase structure in regular spacetime. Utilizing the temperature-shadow radius function, the thermal profile of the Bardeen-AdS BH is established. Moreover, the temperature exhibits an N-type change trend in the

situation. These results suggest that the phase transition process of a regular AdS BH can be completely presented in the thermal profile, and the relationship between the BH shadow and thermodynamics can also be established in regular spacetime.
Aeroacoustic source prediction using material surfaces bounding the flow
Authors: McPhail M J , Krane M H
Published: May 2022

This article presents an extension of Liepmann’s characterization of an aeroacoustic source in terms of the motion of a bounding surface containing the source region. Rather than using an arbitrary surface, we express the problem in terms of bounding material surfaces, identified by Lagrangian coherent structures (LCSs), which demarcate flow into regions with distinct dynamics. The sound generation of the flow is written in terms of the motion of these material surfaces using the Kirchhoff integral equation, so that the flow noise problem now appears like that of a deforming body. This approach provides a natural connection between the flow topology, as revealed through LCS analysis, and sound generation mechanisms. As examples, we examine two-dimensional cases of co-rotating vortices and leap-frogging vortex pairs and compare estimated sound sources to vortex sound theory.
Vortex technique to track 3D object displacement in CGH
Authors: Villamizar Amado Astrid Lorena , Velez-Zea Alejandro , Tebaldi Myrian
Published: May 2022

In this work, we introduce and test a technique to track the movement of objects from computer-generated holographic videos, without the need for reconstruction. To achieve this, we first generated holographic videos of moving 3D objects using a random phase layer-based approach. Then, we analyzed the hologram phase to determine the locations of the optical vortices. We used the core properties of each vortex to track its movement over all the frames of the video, and then establish a relationship between the object and the vortex movement. We also tested the vortex tracking over a pseudo-phase obtained by performing the Laguerre–Gauss transform of the hologram, which enables more precise control over the number of optical vortices that can be tracked. Our proposal was tested with holographic videos generated with one and two objects, using two different hologram generation approaches.
The equivalence theory for infinite type hypersurfaces in ℂ²
Authors: Ebenfelt Peter , Kossovskiy Ilya , Lamel Bernhard
Published: May 2022

We develop a classification theory for real-analytic hypersurfaces in

C

2

\mathbb {C}^{2}

in the case when the hypersurface is of infinite type at the reference point. This is the remaining, not yet understood case in

C

2

\mathbb {C}^{2}

in the Problème local, formulated by H. Poincaré in 1907 and asking for a complete biholomorphic classification of real hypersurfaces in complex space. One novel aspect of our results is a notion of smooth normal forms for real-analytic hypersurfaces. We rely fundamentally on the recently developed CR-DS technique in CR-geometry.
On the various notions of Poincaré duality pair
Authors: Klein John , Qin Lizhen , Su Yang
Published: May 2022

We establish a number of foundational results on Poincaré spaces which result in several applications. One application settles an old conjecture of C.T.C. Wall in the affirmative. Another result shows that for any natural number

n
n

, there exists a finite CW pair

(
X
,
Y
)

(X,Y)

satisfying relative Poincaré duality in dimension

n
n

with the property that

Y
Y

fails to satisfy Poincaré duality. We also prove a relative version of a result of Gottlieb about Poincaré duality and fibrations.
Do marginal plant populations enhance the fitness of larger core units under ongoing climate change? Empirical insights from a rare carnation
Authors: Gargano Domenico , Bernardo Liliana , Rovito Simone , Passalacqua Nicodemo G , Abeli Thomas
Published: May 2022

Assisted gene flow (AGF) can restore fitness in small plant populations. Due to climate change, current fitness patterns could vary in the future ecological scenario, as highly performant lineages can undergo maladaptation under the new climatic contexts. Peripheral populations have been argued to represent a potential source of species adaptation against climate change, but experimental evidence is poor. This paper considers the consequences of within- and between-population mating between a large core population and the southernmost population, the rare Dianthus guliae, to evaluate optimal AGF design under current and future conditions. We performed experimental self-pollinations and within- and between-population cross-pollinations to generate seed material and test its adaptive value to aridity. Seed germination, seedling growth and survival were measured under current and expected aridity. Effects of population type, pollination treatment and stress treatment on fitness components were analysed by generalized linear models. Relative measures of inbreeding depression and heterosis were taken under different stress treatments. Self-pollination reduced fitness for all the considered traits compared to within- and between-population cross-pollination. Under current aridity regime, the core population expressed higher fitness, and a larger magnitude of inbreeding depression. This indicated the core unit is close to its fitness optimum and could allow for restoring the fitness of the small peripheral population. Contrarily, under increased aridity, the fitness of outbred core lineages decreased, suggesting the rise of maladaptation. In this scenario, AGF from the small peripheral population enhanced the fitness of the core unit, whereas AGF from the core population promoted a fitness loss in the peripheral population. Hence, the small peripheral population could improve fitness of large core units versus climate change, while the contrary could be not true. Integrating reciprocal breeding programmes and fitness analyses under current and predicted ecological conditions can support optimal AGF design in a long-term perspective.
OMEN: network-based driver gene identification using mutual exclusivity
Authors: Van Daele Dries , Weytjens Bram , De Raedt Luc , Marchal Kathleen
Published: May 2022

Motivation

Network-based driver identification methods that can exploit mutual exclusivity typically fail to detect rare drivers because of their statistical rigor. Propagation-based methods in contrast allow recovering rare driver genes, but the interplay between network topology and high-scoring nodes often results in spurious predictions. The specificity of driver gene detection can be improved by taking into account both gene-specific and gene-set properties. Combining these requires a formalism that can adjust gene-set properties depending on the exact network context within which a gene is analyzed.

Results

We developed OMEN: a logic programming framework based on random walk semantics. OMEN presents a number of novel concepts. In particular, its design is unique in that it presents an effective approach to combine both gene-specific driver properties and gene-set properties, and includes a novel method to avoid restrictive, a priori filtering of genes by exploiting the gene-set property of mutual exclusivity, expressed in terms of the functional impact scores of mutations, rather than in terms of simple binary mutation calls. Applying OMEN to a benchmark dataset derived from TCGA illustrates how OMEN is able to robustly identify driver genes and modules of driver genes as proxies of driver pathways.

Availability and implementation

The source code is freely available for download at www.github.com/DriesVanDaele/OMEN. The dataset is archived at https://doi.org/10.5281/zenodo.6419097 and the code at https://doi.org/10.5281/zenodo.6419764.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genomic sequences and RNA-binding proteins predict RNA splicing efficiency in various single-cell contexts
Authors: Hou Ruiyan , Huang Yuanghua
Published: May 2022

Motivation

The RNA splicing efficiency is of high interest for both understanding the regulatory machinery of gene expression and estimating the RNA velocity in single cells. However, its genomic regulation and stochasticity across contexts remain poorly understood.

Results

Here, by leveraging the recent RNA velocity tool, we estimated the relative splicing efficiency across a variety of single-cell RNA-Seq data sets. We further extracted large sets of genomic features and 120 RNA-binding protein features and found they are highly predictive to relative RNA splicing efficiency across multiple tissues and organs on human and mouse. This predictive power brings promise to reveal the complexity of RNA processing and to enhance the analysis of single-cell transcription activities.

Availability and implementation

In order to ensure reproducibility, all preprocessed datasets and scripts used for the prediction and figure generation are publicly available at https://doi.org/10.5281/zenodo.6513669.

Supplementary information

Supplementary data are available at Bioinformatics online.
Public Responsiveness to Declining Crime Rates in the United States and England and Wales
Authors: Enns Peter K , Harris Jacob , Kenny John , Roescu Andra , Jennings Will
Published: May 2022

During much of the second half of the twentieth century, public opinion in both the United States and Britain became more punitive as crime rates rose. These shifting public attitudes had a profound influence on criminal justice policies. What is less understood is how public attitudes in these countries have responded to declining crime rates since the early-1990s. To understand how the public reacts to declining crime rates, we focus on crimes recorded by the police as well as data on actual victimisation. We also draw on more than 4,000 national survey questions to construct measures of public concern about crime and support for punitive criminal justice responses. Our analyses illustrate parallels in the crime drop measured by victimisation surveys in the two countries (with recorded violent crime in England and Wales the exception to this overall trend). The over-time patterns in public concern about crime and punitive sentiment are more complex, with the US public becoming less punitive (in line with declining crime rates) while the British public’s concern with crime appears more in tune with actual crime rates. Given the distinct social, political and institutional settings offered by the two countries, the parallel dynamics of crime and the mixed response of public opinion help illustrate the importance of the comparative analysis of crime and its effects on society as well as the importance of considering multiple measures of public opinion related to crime and punishment.
Crime And Punishment: Public Opinion And Political Law-And-Order Rhetoric In Europe 1996–2019
Authors: Karstedt Susanne , Endtricht Rebecca
Published: May 2022

This article explores in which ways politicians’ law-and-order rhetoric and citizens’ attitudes and concerns about crime engage with each other in European countries. The focus is on the ‘constructionist’ or ‘framing’ model which posits that citizens’ attitudes about crime and punishment are influenced and ‘framed’ by political rhetoric. We capture the overall ‘tone’ of political rhetoric around crime and criminal justice using law-and-order statements in political party manifestos. Our indicators of crime concerns and punitive sentiment among the public are ‘crime salience’ (crime as the most important problem) and punitive preferences. We link law-and-order statements with survey data from the Eurobarometer and European Social Survey to explore the relationship between citizens and political elites for 26 European countries between 1996 and 2019. In line with previous research, we show that political law-and-order rhetoric indeed provides a framing narrative for citizens but limited to their punitive preferences. In contrast, European citizens’ assessment of crime as a problem is shaped by the level of serious violent crime (homicide) in their country during this period. This suggests a risk-based assessment and an ‘objectivist’ model. We discuss these results in the context of differences between the politization of criminal law in Europe and the United States.
Glucagonoma syndrome
Authors: Sonmez Recep Ercin , Serin Kursat
Published: May 2022

Glucagonoma is an extremely rare neuroendocrine tumor taking origin from islet alpha cells of the pancreas. Surgery is the mainstay of treatment for the disease and associated symptoms.
Detection of 94 PDE-5is and Their Analogs Including N-Desmethylthiosildenafil in Various Formulations of Dietary Supplements and Food Samples Using HPLC and LC-Q-TOF/MS
Authors: Lee Ji Hyun , Park Ok Rim , Yang Yoon Ji , Han Ji Hye , Jung Eun Ju , Kim Nam Sook , Baek Sun Young
Published: May 2022

Consumption of foods and dietary supplements (DS) adulterated with unprescribed or non-permitted phosphodiesterase-5 inhibitors (PDE-5i) and their analogs can cause serious risk to human health. This study aims to analyze 93 PDE-5i and their analogs present in adulterated foods and DS using an established and validated method involving high-performance liquid chromatography (HPLC). The method was validated in solid and liquid samples, resulting in a limit of detection and quantitation of 0.03–0.5 and 0.08–1.6 μg/mL, respectively. Using the validated method, a total of 404 samples were screened. It was found that 32% of 404 samples were illegally adulterated with PDE-5i and their analogs; moreover, 16.9% of the adulterated samples were found to contain more than three compounds. HPLC-quadrupole-time-of-flight (TOF)/mass spectrometry (MS) analysis was conducted on all the samples to confirm the detected compounds accurately based on fragmentation ion patterns. In addition, sildenafil and tadalafil were detected from the capsule shells of DS unusually. Subsequently, the detected compounds were identified and quantified using HPLC at concentrations ranging from 0.007 to 370.0 mg/g. NMR analysis was carried out to confirm the accurate chemical structure of a compound found during the TOF/MS analysis, which did not match with the 93 reference standards.; it was identified to be N-desmethylthiosildenafil. In this study, various PDE-5i compounds and their analogs were detected from low to high concentrations in a sample. Therefore, the study sheds light on the misuse of PDE-5i and their analogs in consumable products, which pose a severe threat to public health.
Analysis of Fixed-Dose Combination of Three Antihypertensive Drugs by a Green and Quality by Design Approach
Authors: Mandić-Kovačević Nebojša , Kasagić-Vujanović Irena , Popović Bijelić Ana
Published: May 2022

This paper presents the result of a combined employment of Analytical Quality-by-Design and Green Analytical Chemistry principles for the development of a robust high-performance liquid chromatography method for simultaneous determination of fixed-dose combination of three drugs, perindopril tert-butylamine, amlodipine besylate and indapamide. Optimum conditions were achieved on ZORBAX Eclipse XDB-C18 column (150 mm × 4.6 mm, 5 μm particle size), the mobile phase comprising acetonitrile and phosphate buffer (30 mM, pH 2.7) in the ratio 34:66 (v/v), the flow rate of 1 mL min−1, injection volume of 10 μL and UV detection at 210 nm. By assigning the design space from the overlay plot, the regions within which the robustness of the method is achieved were defined and confirmed by Dong’s algorithm calculations. The proposed method was validated and shown to be applicable for the determination of the three drugs in commercially available tablets. In addition, the impact of the method on the environment was assessed through four different analytical tools: National Environmental Methods Index, Analytical Eco-Scale, Green Analytical Procedure Index and Assessment of Green Profile. The proposed method was determined to be greener, with minimal impact on the environment with regard to waste production, energy consumption and use of hazardous chemicals.
Resilience to stress in bipartite networks: application to the Islamic State recruitment network
Authors: Wang Selena , Edgerton Jared
Published: May 2022

Networks are resilient to internal failures or external attacks. The resiliency is often beneficial, but there are scenarios where the collapse of a network would benefit society, such as the dismantlement of terrorist, rebel or organized crime groups. In this article, we develop a method to estimate the effect of knockouts and apply our method to the Islamic State recruitment network. Using our novel application, we demonstrate how coordinated attacks against recruiters might reduce the Islamic State’s ability to mobilize new fighters. This analysis has direct implications for research on network resilience and terrorist recruitment.
Detailed behaviour of endothelial wall shear stress across coronary lesions from non-invasive imaging with coronary computed tomography angiography
Authors: van den Hoogen Inge J , Schultz Jussi , Kuneman Jurrien H , de Graaf Michiel A , Kamperidis Vasileios , Broersen Alexander , Jukema J Wouter , Sakellarios Antonis , Nikopoulos Sotirios , Kyriakidis Savvas , Naka Katerina K , Michalis Lampros , Fotiadis Dimitrios I , Maaniitty Teemu , Saraste Antti , Bax Jeroen J , Knuuti Juhani
Published: May 2022

Aims

Evolving evidence suggests that endothelial wall shear stress (ESS) plays a crucial role in the rupture and progression of coronary plaques by triggering biological signalling pathways. We aimed to investigate the patterns of ESS across coronary lesions from non-invasive imaging with coronary computed tomography angiography (CCTA), and to define plaque-associated ESS values in patients with coronary artery disease (CAD).

Methods and results

Symptomatic patients with CAD who underwent a clinically indicated CCTA scan were identified. Separate core laboratories performed blinded analysis of CCTA for anatomical and ESS features of coronary atherosclerosis. ESS was assessed using dedicated software, providing minimal and maximal ESS values for each 3 mm segment. Each coronary lesion was divided into upstream, start, minimal luminal area (MLA), end and downstream segments. Also, ESS ratios were calculated using the upstream segment as a reference. From 122 patients (mean age 64 ± 7 years, 57% men), a total of 237 lesions were analyzed. Minimal and maximal ESS values varied across the lesions with the highest values at the MLA segment [minimal ESS 3.97 Pa (IQR 1.93–8.92 Pa) and maximal ESS 5.64 Pa (IQR 3.13–11.21 Pa), respectively]. Furthermore, minimal and maximal ESS values were positively associated with stenosis severity (P < 0.001), percent atheroma volume (P < 0.001), and lesion length (P ≤ 0.023) at the MLA segment. Using ESS ratios, similar associations were observed for stenosis severity and lesion length.

Conclusions

Detailed behaviour of ESS across coronary lesions can be derived from routine non-invasive CCTA imaging. This may further improve risk stratification.
Peer Effects in Academic Research: Senders and Receivers
Authors: Bosquet Clément , Combes Pierre-Philippe , Henry Emeric , Mayer Thierry
Published: May 2022

Using an instrument based on a national contest in France determining researchers’ location, we find evidence of peer effects in academia, when focusing on precise groups of senders (producing the spillovers) and receivers (benefiting from the spillovers), defined based on field of specialisation, gender and age. These peer effects are present even outside formal co-authorship relationships. Furthermore, the match between the characteristics of senders and receivers plays a critical role. In particular, men benefit a lot from peer effects provided by other men, while all other types of gender combinations produce spillovers twice as small. Part of the peer effects results from researchers switching research fields.
Repair of insufficient aortic valve and single coronary artery with intramural course
Authors: Ikeno Yuki , Motoki Tatsuo , Kurushima Atsushi , Fukumura Yoshiaki
Published: May 2022

We report about a patient with severe bicuspid aortic valve insufficiency and a single coronary artery with an intramural course. Aortic valve repair with double plication and coronary translocation was satisfactory.
How do informal international organizations govern? The G20 and orchestration
Authors: Downie Christian
Published: May 2022

One dimension of the growth in informal global governance has been the rapid rise in the number of informal international organizations (IOs). While some of these organizations, such as the Group of Twenty (G20), are now at the centre of global debates across multiple policy domains we know very little about how they govern. We do not have answers to critical questions, including to what extent do informal IOs rely on indirect forms of governance? On what basis do they select IOs as intermediaries? And why do IOs choose to participate as intermediaries? Drawing on an original database of G20 orchestration between 2008 and 2019, combined with interviews with IO officials and G20 negotiators, this article provides answers to these questions. The data highlight the frequency of G20 orchestration, the importance of capabilities and control in intermediary selection, and IO efforts to solicit G20 orchestration. The findings advance debates on informal IOs to consider how they govern, how intermediaries like the OECD can shape G20 agendas, and why IOs participate in these indirect governance arrangements.
Environmental Cue Integration and Phenology in a Changing World
Authors: Watts Heather E , Robart Ashley R , Hahn Thomas P , Gomulkiewicz Richard
Published: May 2022

Many organisms use environmental cues to time events in their annual cycle, such as reproduction and migration, with the appropriate timing of such events impacting survival and reproduction. As the climate changes, evolved mechanisms of cue use may facilitate or limit the capacity of organisms to adjust phenology accordingly, and organisms often integrate multiple cues to fine-tune the timing of annual events. Yet, our understanding of how suites of cues are integrated to generate observed patterns of seasonal timing remains nascent. We present an overarching framework to describe variation in the process of cue integration in the context of seasonal timing. This framework incorporates both cue dependency and cue interaction. We then summarize how existing empirical findings across a range of vertebrate species and life cycle events fit into this framework. Finally, we use a theoretical model to explore how variation in modes of cue integration may impact the ability of organisms to adjust phenology adaptively in the face of climate change. Such a theoretical approach can facilitate the exploration of complex scenarios that present challenges to study in vivo but capture important complexity of the natural world.