bluuebunny/crossref_metadata_2025 huggingface dataset:
Microgravity Accelerates Skeletal Muscle Degeneration: Functional and Transcriptomic Insights from a Muscle Lab-on-Chip Model Onboard the ISS.
Authors: Parafati Maddalena , Thwin Zon , Malany Legrand K , Coen Paul M. , Malany Siobhan
Published: January 2025

Microgravity accelerates skeletal muscle degeneration, mimicking aging, yet its effects on human muscle cell function and signaling remain underexplored. Using a muscle lab-on-chip model onboard the International Space Station, we examined how microgravity and electrically stimulated contractions influence muscle biology and age-related muscle changes. Our 3D bioengineered muscle model, cultured for 21 days (12 days in microgravity), included myobundles from young, active and older, sedentary individuals, with and without electrically stimulated contraction. Real-time data collected within an autonomous Space Tango CubeLabTM showed reduced contraction magnitude in microgravity. Global transcriptomic analysis revealed increased gene expression and particularly mitochondrial-related gene expression in microgravity for the electrically stimulated younger myobundles, while the older myobundles were less responsive. Moreover, a comparative analysis using a skeletal muscle aging gene expression database revealed that certain age-induced genes showed changes in expression in myobundles from the younger cohort when exposed to microgravity, whereas these genes remained unchanged in myobundles from the older cohort. Younger, electrically stimulated myobundles in microgravity exhibited higher expression of 45 aging genes involved in key aging pathways related to inflammation and immune function, mitochondrial dysfunction, and cellular stress; and decreased expression of 41 aging genes associated with inflammation, and cell growth. This study highlights a unique age-related molecular signature in muscle cells exposed to microgravity and underscores electrical stimulation as a potential countermeasure. These insights advance understanding of skeletal muscle aging and microgravity-induced degeneration, informing strategies for mitigating age-related muscle atrophy in space and on Earth.
Evaluation of the role of whiB6 and kdpDE in the dominant multidrug resistant clone Mycobacterium tuberculosis B0/W148
Authors: Bonnet Isabelle , Orgeur Mickael , Brossier Florence , Sayes Fadel , Frigui Wafa , Madacki Jan , Varet Hugo , Chauffour Aurélie , Aubry Alexandra , Veziris Nicolas , Sougakoff Wladimir , Brosch Roland , Tournebize Regis
Published: January 2025

Multidrug resistant (MDR) strains of Mycobacterium tuberculosis represent an obstacle to eradicating tuberculosis (TB) due to the low treatment success rate of MDR TB. Among them, the MDR B0/W148 clone has recently evolved from the M. tuberculosis Beijing lineage 2 and widely disseminated in Russia and Europe. To get more insights into the genetic factors underlying the evolutionary success of the MDR M. tuberculosis B0/W148 clone in addition to environmental and patient-related features, we focused on two mutations specific from this clone that are found in the transcriptional regulators WhiB6 and KdpDE and investigated in a H37Rv strain background the transcriptional profile associated with these mutations and their impact on the in vitro and in vivo growth characteristics. Through the construction and use of H37Rv∆whiB6, H37Rv∆kdpDE, and complemented strains, we found that both mutations did not impair the in vitro growth of M. tuberculosis in standard mycobacterial growth media. The mutation T51P in whiB6 prevented the upregulation of 9 genes in the esx-1 core region and 44 genes elsewhere in the genome, while the deletion of two nucleotides in kdpD leads to a fusion protein of KdpD with KdpE that inhibits the transcriptional activity of KdpE. Both mutations did not lead to hypervirulence in a mouse infection model. These results point to the role of other MDR B0/W148 specific mutations in the wide geographic diffusion of this clone, and/or put in question a hypothesized hypervirulence as driving factor for this large dissemination.
Psychromonas aestuariisp. nov., a novel bacterial species isolated from estuarine surface sediment
Authors: Nita Iuliana , Kart Yaren , Strube Mikael Lenz , Bentzon-Tilia Mikkel
Published: January 2025

Using an isolation chip (iChip), two bacterial strains, MME1Tand MME2, exhibiting ovoid to curved rod cell morphologies and white-cream colony pigmentation were isolated from the surface of estuarine sediment at Nivå Bugt Strandenge Bird Sanctuary, Denmark (55°55’42.6’N 12°31’23.6’E). Analysis of the 16S rRNA gene sequence of these isolates suggested them to be members of the genusPsychromonas, as both had above 97.5 % 16S rRNA gene similarity withPsychromonas aquimarina strainJAMM 0404T. Further genomic comparisons suggested MME strains to be representatives of a novel species, having an average nucleotide identity (ANI) < 85 % relative to all other genome sequenced species of thePsychromonasgenus. The G+C content was 39.5 mol %. The species was facultative anaerobic, growing optimally at 15 – 20 °C and pH 7.0. The optimal salinity was lower than for other described species of the genus with 1 – 2 % NaCl, reflecting the estuarine source of isolation. GC-MS analyses identified C16:0, C16:1ω7c/C16:1ω7t/and C14:03OHas the predominant cellular fatty acids. Based on molecular, phenotypic, and chemotaxonomic analyses, we propose that MME1 and MME2 represent a novel species of the genusPsychromonaswith the namePsychromonas aestuariisp. nov. with the MME1T(= DSM 118464T=LMG 33722T) as the type strain.
Symmetries and Continuous Attractors in Disordered Neural Circuits
Authors: Clark David G. , Abbott L.F. , Sompolinsky Haim
Published: January 2025

A major challenge in neuroscience is reconciling idealized theoretical models with complex, heterogeneous experimental data. We address this challenge through the lens of continuous-attractor networks, which model how neural circuits may represent continuous variables, such as head direction or spatial location, through collective dynamics. In classical continuous-attractor models, a continuous symmetry of the connectivity generates a manifold of stable states, resulting in tuning curves that are identical up to shifts. However, mouse head-direction cells show substantial heterogeneity in their responses that appears incompatible with this classical picture. To understand the mechanistic origin of these data, we use an optimization principle to construct recurrent-network models that match the observed responses while exhibiting quasi-continuous-attractor dynamics. To study how such systems scale with increasing numbers of neuronsN, we develop a statistical generative process that produces artificial tuning curves that match many features of the experimental data quantitatively. Due to a continuous symmetry in the generative process, the connectivity matrix exhibits doublet degeneracy in its spectrum at largeN, reflecting an underlying circular geometry. Unlike classical models, where the ring structure is embedded in the neuronal space through a structured Fourier embedding, our model uses a random, disordered embedding. Analysis of the network dynamics in the large-Nlimit through dynamical mean-field theory reveals that the system becomes equivalent to a classical ring-attractor model. We extend this approach to higher-dimensional symmetries, applying it to grid cells in the medial entorhinal cortex and showing that the mean-field description recovers classical continuous-attractor models. Our work implies that large mammalian neural circuits could represent continuous variables using continuous-attractor dynamics, complete with continuous symmetry, in a way that is fully compatible with their heterogeneity and disorder.
The modification of DNA with indole-linked nucleotides alters its sensitivity to enzymatic cleavage
Authors: Lingala Suresh , Fisiuk Anastasiia , Stephen Michelle , Mohanrao Raja , Klingsberg Judah , Vecchioni Simon , Volvovitz Ealonah S , Rozhkov Sergei , Mallikaratchy Prabodhika
Published: January 2025

We describe the synthesis of C-5 indole-tagged pyrimidine and C-8 indole-tagged purine nucleoside phosphoramidites and their incorporation into double-stranded DNA 15 base pairs in length. Of the 23 sequence modifications tested, two induced the DNA duplex to adopt a Z-like left-handed conformation under physiological salt conditions, bypassing the specific sequences typically required for a left-handed Z-DNA structure. The impact of these modifications varied with the linker type: flexible propyl linkers exhibited distinct effects compared to rigid propargyl linkers. Notably, modifications positioned directly on or near a restriction site emphasized the pivotal role of linker rigidity in controlling DNA conformation. Specifically, the conformational change induced by the flexible linker impacted nuclease and restriction endonuclease cleavage, reducing sequence specificity. In contrast, the rigid linker suppressed this effect. Furthermore, our findings indicate that nucleic acid duplexes modified with indole-linked nucleotides using a flexible propyl linker have a pronounced tendency to form BZ or Z-like regions in longer DNA sequences. A higher density of modifications may even induce a full Z-like conformation throughout the duplex. These modified nucleotides hold potential for the development of novel antisense therapeutics and introducing valuable tools for in vitro screening of small molecules targeting distorted B-DNA, BZ-DNA, and Z-DNA structures.
From Local Interactions to Global Patterns: An Analysis of Silk Density in Spider Webs
Authors: Lin Fangyuan , Nagel Kathryn M. , Lee Seewoo , Jiang Jason , Yang Grant , Chang Patrtick , Li Samuel , Sheu Norman
Published: January 2025

This study explores the structural complexity of spider webs through information-theoretic and harmonicity-based frameworks to quantify spatial patterns in silk density across different web regions and reveal the underlying resource allocation strategies. By analyzing the entropy of silk density distributions across different species, we observed that the entropy values follow a normal distribution with a mean of 1.24 bits and a standard deviation of 0.22 bits when using 10 quantization levels. In the second part of the paper, by measuring the harmonicity of the silk density, we reveal that the silk density at a given point can be inferred from its neighbors, with an average harmonicity value of 0.0039 (fraction of total points in point cloud data). The harmonic behavior is notable for its maximum principle, suggesting that the strongest parts of the web appear at the boundaries, aligning with existing knowledge of spider web construction. These findings provide a new technique for quantifying web-building strategies and offer new insights into spider behavior and evolution.
Neuronal Activity-Dependent Gene Dysregulation inC9orf72i3Neuronal Models of ALS/FTD Pathogenesis
Authors: Ghaffari Layla T. , Welebob Emily , Boehringer Ashley , Cyliax Kelly , Pasinelli Piera , Trotti Davide , Haeusler Aaron R.
Published: January 2025

The GGGGCC nucleotide repeat expansion (NRE) mutation in theC9orf72(C9) gene is the most common cause of ALS and FTD. Neuronal activity plays an essential role in shaping biological processes within both healthy and neurodegenerative disease scenarios. Here, we show that at baseline conditions, C9-NRE iPSC-cortical neurons display aberrations in several pathways, including synaptic signaling and transcriptional machinery, potentially priming diseased neurons for an altered response to neuronal stimulation. Indeed, exposure to two pathophysiologically relevant stimulation modes, prolonged membrane depolarization, or a blockade of K+channels, followed by RNA sequencing, induces a temporally divergent activity-dependent transcriptome of C9-NRE cortical neurons compared to healthy controls. This study provides new insights into how neuronal activity influences the ALS/FTD-associated transcriptome, offering a dataset that enables further exploration of pathways necessary for conferring neuronal resilience or degeneration.
Flickering white light stimulation at 60 Hz induces strong, widespread neural entrainment and synchrony in healthy subjects
Authors: Alamalhoda MohammadAmin , Leesch Friederike , Giovanetti Francesca , Dunne Eoghan , Pilloni Giuseppina , Caffrey Mark , O’Keeffe Jack , Venturino Alessandro , Ferretti Maria Teresa
Published: January 2025

Background

While the effects of 40 Hz externally-induced neural entrainment have been extensively described, little is known about 60 Hz entrainment in humans. Given the role of 60 Hz in cognition, neuroplasticity and neuropsychiatric disorders, this warrants further investigation.

Objectives

This pilot study characterizes, for the first time, the neural and somatic response to 60 Hz light entrainment in healthy volunteers, over a 3 week-period.

Methods

Fourteen volunteers were randomized to receive either 60 Hz flickering white light or constant light as sham (30-min sessions, for 3 weeks, 5 days a week). Neural entrainment was assessed with EEG on days 1, 5 and 19. Salivary cortisol and C-reactive protein (CRP) levels, measured with ELISA, assessed the somatic response to stimulation. Side effects and well-being were monitored via questionnaires.

Results

60 Hz flickering light induced a strong neural entrainment across visual, parietal, temporal and frontal cortex. The signal was highly synchronous but declined significantly by day 19 compared to day 1, indicating neural habituation. Cortisol and CRP salivary levels were unchanged and the stimulation was well tolerated.

Conclusions

To the best of our knowledge this is the first study to characterize both the neural and the somatic response to flickering light over 3 weeks. The observed neural habituation suggests that neuroplasticity could be induced with repeated stimulations over 3 weeks. 60 Hz stimulation for modulating brain activity and induce neuroplasticity has implications for our basic understanding of brain physiology as well as treatment of psychiatric disorders.
Neural sensitivity to radial frequency patterns in the visual cortex of developing macaques
Authors: Rodríguez Deliz C. L. , Lee Gerick M. , Bushnell Brittany N. , Majaj Najib J. , Movshon J. Anthony , Kiorpes Lynne
Published: January 2025

Visual resolution, contrast sensitivity and form perception improve gradually with age. In nonhuman primates, the sensitivity and resolution of cells in the retina, lateral geniculate nucleus and primary visual cortex (V1) also improve, but not enough to account for the perceptual changes. So, what aspects of visual system development limit visual sensitivity in infants? Improvements in behavioral sensitivity might arise from maturation of regions downstream of V1 such as V2, V4 and IT, which are thought to support increasingly complex perceptual abilities. We recorded the responses of populations of neurons in areas V1, V2, V4, and IT to radial frequency patterns - a type of global form stimulus. Subjects were three young monkeys between the ages of 19 and 54 weeks, and a single adult animal. We found that neurons and neural populations in V4 reliably encoded global form in radial frequency stimuli at the earliest ages we studied, while V1 neurons do not. V2 and IT populations also showed some degree of selectivity for these patterns at early ages, especially at higher radial frequency values. We did not find significant, systematic changes in neural decoding performance that could account for the improvement in behavioral performance over the same age range in an overlapping group of animals (Rodriguez Deliz et al., 2024). Finally, consistent with our prior behavioral results, neural populations in V4 show highest sensitivity for the higher radial frequency values which contain the highest concentration of curvature and orientation cues.

SIGNIFICANCE STATEMENT

Infants have remarkably limited ability to discriminate shapes. These limitations cannot be fully explained by postnatal changes in their eyes, visual thalamus, or primary visual cortex. The perception of shape requires integration of local cues across space to create global form information. We therefore examined populations of neurons in extrastriate visual cortex to learn whether information represented in these regions might limit infants’ abilities to process global forms. We found instead that extrastriate areas involved in global form processing function maturely early in life, by the age of 4-6 months, suggesting that infants’ perceptual limits are set by other aspects of brain development.
Computational modelling of the suppression of optic nerve fibre
Authors: Pratiwi Ariastity , Kekesi Orsolya , Barriga-Rivera Alejandro , Suaning Gregg
Published: January 2025

Retinal neuroprostheses aim to restore vision in degenerated retina but face challenges with low selectivity, where electric current activates both intended and neighbouring neurons. It was hypothesized that optic nerve suppression could improve selectivity using frequency-induced neuromodulation (FIN) with sinusoidal waveforms to selectively block transmission based on optic nerve fibre diameter. To explore the electrical parameters for diameter-based selective suppression, computational models of retinal ganglion cells (RGCs) and the optic nerve were given sinusoidal currents between 25-10000 Hz. FIN was found to induce complete conduction block, with the highest probability of suppression at frequencies above 500 Hz. Additionally, axon fibre diameter influenced the frequency and amplitude of FIN that inhibited conduction, with the highest selectivity between ON and OFF RGC fibres occurring at a diameter of 0.5 µm. Nodal sodium channels were involved in inhibition at frequencies above 500 Hz, supporting findings from studies of peripheral nerve fibres. Overall, suppressing a subset of optic nerve fibres could potentially enhance the selectivity of a bionic eye system by filtering out confounding visual information. However, practical application may be hindered by variability in RGC morphology and biophysical properties, and the possibility of filtering intended stimuli.

Author summary

Retinal neuroprostheses deliver electrical stimulation to retinal cells to produce perceptions of vision called phosphenes. However, the lack of selectivity associated with electrical currents leads to unnatural cell activations, which in turn limits the usability of many visual prostheses. To improve selectivity, we proposed a novel method that involves suppressing the conduction of action potentials along a subset of axon fibres, which carry the information from the eye to the brain’s visual centre. We believe that this could remove superfluous information caused by electrical stimulations. Our findings demonstrated that sinusoidal electrical currents can be given to the optic nerve fibres to induce suppression, and that the effectiveness of suppression is influenced by axon fibre diameters. This suggests that modulating the response of the optic nerve can lead to selective suppression based on the axon fibre diameters, and consequently improving the performance of a retinal neuroprosthesis.
The Network Basis of Pattern Formation: A Topological Atlas of Multifunctional Turing Networks
Authors: Regueira López de Garayo Laura , Marcon Luciano
Published: January 2025

Understanding how genetic networks can drive different self-organizing spatial behaviors remains a significant challenge. Here, we use an automated algebraic method to systematically screen for Turing networks capable of generating diverse spatial patterns from noise, including periodic static waves, traveling waves and noise-amplifying patterns. We organize these networks into a topological atlas—a higher-level graph where nodes represent Turing networks linked together when they differ by only one regulatory interaction. In this atlas, Turing networks are arranged into distinct clusters showing a remarkable correspondence between network topology and self-organizing behaviors. Using an analytical approach, we identify the specific regulatory feedbacks that characterize each behavior. Moreover, we discover that different clusters are interconnected by multifunctional networks that can transition between behaviors upon feedback modulation. Among these networks, we find a new class of multiphase Turing networks capable of altering the phase of periodic wave patterns depending on the parameters, and networks that can transition between static and oscillatory Turing behaviors. The atlas further highlights the crucial role of feedback on immobile nodes in regulating pattern formation speed and precision by canalizing system noise. Overall, our study provides a novel framework to study the evolution and development of multicellular self-organization through changes in network topology and feedback modulation. This offers insights into how genetic regulatory networks can be tuned to drive pattern formation in developmental biology and in stem cell systems like embryoids and organoids.

Significance Statement

By employing an automated algebraic method, Regueria and Marcon construct a topological atlas that categorizes Turing networks based on their ability to produce periodic patterns, traveling waves, or noise amplifying patterns. The atlas identifies distinct topological clusters linked by multi-functional networks that can transition between behaviors through feedback modulation. Key findings highlight how modulation of regulatory cycle strength in time or space can promote transition between static and oscillatory periodic pattern. The study also reveals the importance of feedback on immobile nodes in managing noise and influencing pattern formation. Overall the topological atlas offers a new framework for examining the evolution and development of multicellular self-organization.
A brainstem map of orofacial rhythms
Authors: Kaku Heet , Liu Liu D. , Gao Runbo , West Steven , Liao Song-Mao , Finkelstein Arseny , Kleinfeld David , Thomas Alyse , Tipparaju Sri Laasya , Svoboda Karel , Li Nuo
Published: January 2025

Rhythmic orofacial movements, such as eating, drinking, or vocalization, are controlled by distinct premotor oscillator networks in the brainstem. Orofacial movements must be coordinated with rhythmic breathing to avoid aspiration and because they share muscles. Understanding how brainstem circuits coordinate rhythmic motor programs requires neurophysiological measurements in behaving animals. We used Neuropixels probe recordings to map brainstem neural activity related to breathing, licking, and swallowing in mice drinking water. Breathing and licking rhythms were tightly coordinated and phase-locked, whereas intermittent swallowing paused breathing and licking. Multiple clusters of neurons, each recruited during different orofacial rhythms, delineated a lingual premotor network in the intermediate nucleus of the reticular formation (IRN). Local optogenetic perturbation experiments identified a region in the IRN where constant stimulation can drive sustained rhythmic licking, consistent with a central pattern generator for licking. Stimulation to artificially induce licking showed that coupled brainstem oscillators autonomously coordinated licking and breathing. The brainstem oscillators were further patterned by descending inputs at moments of licking initiation. Our results reveal the logic governing interactions of orofacial rhythms during behavior and outline their neural circuit dynamics, providing a model for dissecting multi-oscillator systems controlling rhythmic motor programs.
Chemical and structural disorder in the kagome spin
S=12
systems
ZnCu3(OH)6Cl2
and
YCu3(OH)6Br2[Brx(OH)1−x]
Authors: Kremer Reinhard K. , Bette Sebastian , Nuss Jürgen , Puphal Pascal
Published: January 2025

By single crystal diffraction we characterize the chemostructural disorder introduced by Zn-Cu site mixing in the kagome spin S=12 systems herbertsmithite ZnCu3(OH)6Cl2 and YCu3(OH)6Br2[Brx(OH)1−x]. For an untwinned single crystal of herbertsmithite of composition Zn0.95(1)Cu2.99(3)O5.9(1)H5.8(1)Cl2 we find substitution by Cu of the Zn atoms in the layers separating the kagome layers as well as substantial Zn substitution for Cu in the kagome layers. In YCu3(OH)6Br2[Brx(OH)1−x] site mixing disorder is present for intermediate x. Analogous to the Cl homologous system in crystals with x=1/3 disorder is absent and a low-temperature structural transition emerges driven by strong magnetophonon coupling as a release of frustration. Apart from this structural anomaly we find the physical properties of these crystals unchanged compared to intermediate x and closely resembling the Cl homologue where long-range magnetic order was observed.

Published by the American Physical Society
2025
String tension and Polyakov loop in a rotating background
Authors: Chen Jun-Xia , Wang Sheng , Hou Defu , Ren Hai-Cang
Published: January 2025

We study the influence of a rotation on the string tension and the temperature of the confinement-deconfinement phase transition of gluodynamics by gauge/gravity duality. We explore two distinct approaches, global transformation and local transformation, to introduce rotation and compare the results. It is shown that the string tension extracted from the free energy in the presence of a heavy quarkonium decreases with increasing angular velocity, while the transition temperature determined by the Polyakov loop increases with increasing angular velocity, which is in line with lattice simulations.

Published by the American Physical Society
2025
Reconfiguration and dynamics of clamped fibers under finite-amplitude surface gravity waves
Authors: Foggi Rota Giulio , Chiarini Alessandro , Rosti Marco Edoardo
Published: January 2025

We investigate the behavior of a flexible stem completely submerged under a surface gravity wave of finite amplitude using fully resolved direct numerical simulations. By varying the rigidity of the stem over ten orders of magnitude, we explore its motion in the drag-dominated regime with realistic air and water properties. Our findings reveal two distinct structural responses of the stem depending on the ratio between its natural frequency (fnat) and the wave frequency (fwave). For fnat/fwave≫1, the stem maintains on average a straight configuration and exhibits streamwise oscillations in phase opposition with the wave, moving symmetrically with respect to the vertical direction. Conversely, for fnat/fwave≪1, the stem reconfigures under the influence of the Stokes drift, bending forward and breaking the symmetry, and exhibits oscillations that are more coherent with the surrounding flow field. Resonance is observed when fnat≈fwave. These results provide insights into the dynamics of slender vegetation and manmade structures in wave fields, offering valuable implications for marine biology and engineering.

Published by the American Physical Society
2025
Quantum volunteer's dilemma
Authors: Koh Dax Enshan , Kumar Kaavya , Goh Siong Thye
Published: January 2025

The volunteer's dilemma is a well-known game in game theory that models the conflict players face when deciding whether to volunteer for a collective benefit, knowing that volunteering incurs a personal cost. In this work we introduce a quantum variant of the classical volunteer's dilemma, generalizing it by allowing players to utilize quantum strategies. Employing the Eisert-Wilkens-Lewenstein quantization framework, we analyze a multiplayer quantum volunteer's dilemma scenario with an arbitrary number of players, where the cost of volunteering is shared equally among the volunteers. We derive analytical expressions for the players' expected payoffs and demonstrate the quantum game's advantage over the classical game. In particular, we prove that the quantum volunteer's dilemma possesses symmetric Nash equilibria with larger expected payoffs compared to the unique symmetric Nash equilibrium of the classical game, wherein players use mixed strategies. Furthermore, we show that the quantum Nash equilibria we identify are Pareto optimal. Our findings reveal distinct dynamics in volunteer's dilemma scenarios when players adhere to quantum rules, underscoring a strategic advantage of decision making in quantum settings.

Published by the American Physical Society
2025
Long-Range Optomechanical Interactions in SiN Membrane Arrays
Authors: Yao Xiong , de Jong Matthijs H. J. , Li Jie , Gröblacher Simon
Published: January 2025

Optomechanical systems using a membrane-in-the-middle configuration can exhibit a long-range type of interaction similar to how atoms show collective motion in an optical potential. Photons bounce back and forth inside a high-finesse Fabry-Pérot cavity and mediate the interaction between multiple membranes over a significant distance compared to the wavelength. Recently, it has been demonstrated that off-resonant coupling between light and the intermembrane cavity can lead to coherent mechanical noise cancellation. On-resonance coupling of light with both the Fabry-Pérot and intermembrane cavities, predicted to enhance the single-photon optomechanical coupling, have to date not been experimentally demonstrated, however. In our experiment, a double-membrane system inside a Fabry-Pérot cavity resonantly enhances the cavity field, resulting in a stronger optomechanical coupling strength from the increased radiation pressure. The resonance condition is first identified by analyzing the slope of the dispersion relation. Then, the optomechanical coupling is determined at various chip positions over one wavelength range. The optimum coupling conditions are obtained and enhancement is demonstrated for double-membrane arrays with three different reflectivites, reaching nearly fourfold enhancement for the collective motion of R=65% double membranes. The cavity losses at the optimum coupling are also characterized and the potential of reaching the single-photon strong coupling regime is discussed.

Published by the American Physical Society
2025
MYTHEN III: advancements in single photon counting detectors for synchrotron powder diffraction experiments
Authors: Andrä Marie , Bergamaschi Anna , Baruffaldi Filippo , Brückner Martin , Carulla Maria , Casati Nicola , Cervellino Antonio , Dinapoli Roberto , Fröjdh Erik , Greiffenberg Dominic , Hasanaj Shqipe , Heymes Julian , Hinger Viktoria , Kozlowski Pawel , Lopez Cuenca Carlos , Meister Dominik , Mezza Davide , Moustakas Konstantinos , Mozzanica Aldo , Paton Kirsty , Ruder Christian , Scagnoli Valerio , Smolentsev Grigory , Schmitt Bernd , Thattil Dhanya , Xie Xiangyu , Zhang Jiaguo
Published: January 2025

The single photon counting microstrip detector MYTHEN III was developed at the Paul Scherrer Institute to satisfy the increasing demands in detector performance of synchrotron radiation experiments, focusing on time-resolved and on-edge powder diffraction measurements. Similar to MYTHEN II, the detector installed on the Material Science beamline covers 120° in 2θ. It is based on the MYTHEN III.0 readout chip wire-bonded to silicon strip sensors with a pitch of 50 µm, and it provides improved performance and features with respect to the previous version. Taking advantage of the three independent comparators of MYTHEN III, it is possible to obtain an improvement in the maximum count rate capability of the detector at 90% efficiency from 2.9 ± 0.8 Mphotons s−1 strip−1 to 11 ± 2 Mphotons s−1 strip−1 thanks to the detection of pile-up at high photon flux. The readout chip offers additional operation modes such as pump–probe and digital on-chip interpolation. The maximum frame rate is up to 360 kHz in 8-bit mode with dead-time-free readout. The minimum detectable energy of MYTHEN III is 4.3 ± 0.3 keV with a minimum equivalent noise charge (ENC) of 121 ± 8 electrons and a threshold dispersion below 33 ± 10 eV. The energy calibration is affected by temperature by less than 0.5% °C−1. This paper presents a comprehensive overview of the MYTHEN III detector system with performance benchmarks, and highlights the improvements reached in powder diffraction experiments compared with the previous detector generation.
Pump–probe reciprocal-space mapping using energy-resolved XFEL pink beam pulses
Authors: Kwon Ouyoung , Ha Sungsoo , Noh Do Young , Kang Hyonchol , Iqbal Mazhar , Anwar Muhammad Ijaz , Kim Sunam
Published: January 2025

We present a 3D reciprocal-space mapping (RSM) method using a pink self-amplified spontaneous emission (SASE) X-ray free-electron laser beam. The energy of each specific pulse in a SASE beam can be determined using the diffraction pattern of a specimen excited by pumping itself as a spectroscopic reference. A thin slab of RSM, whose thickness corresponds to the energy bandwidth of the pink beam, is successfully reconstructed using the proposed method. By rocking a sample in a few steps, we obtained a 3D RSM covering both the diffuse scattering and the Bragg rod in NiO thin films during a pump–probe X-ray diffraction measurement.
Reforming legal and regulatory structure of public–private partnerships in Sri Lanka
Authors: Fernando Pathirahannahelage Gayan , Kulatunga Udayangani , Thayaparan Menaha , Hadiwattege Chandanie
Published: January 2025

Purpose

This paper aims to investigate the current practices and deficiencies in the legal and regulatory structure of public–private partnerships (PPPs) in Sri Lanka and explore recommended practices by international model laws and guidelines addressing such deficiencies.

Design/methodology/approach

Firstly, a desk study review was conducted to explore the current practices of PPP in Sri Lanka. Secondly, nine expert interviews were conducted to comprehend further current PPP practices and identify the deficiencies of legal and regulatory structure of PPP in Sri Lanka, and content analysis was used to analyse the interviews findings. Finally, international model laws and guidelines were reviewed to explore recommended best practices.

Findings

The research explored non-existence of a national PPP policy, lack of clarity of executing a project’s preliminary affordability, and lack of guidance on risk assessment and feasibility studies as current major deficiencies of PPP legal and regulatory structure in Sri Lanka. Further, findings showed that setting-up two project governance structures, a steering committee and a project team, and develop clear guidelines and standard forms can be adapted to strengthen the PPP legal and regulatory structure.

Research limitations/implications

The findings of this study may be useful to policy makers in tracing essential reforms to PPP legal and regulatory structure. This study is limited to legal and regulatory structure of first three phases of the PPP project life cycle: project identification, project preparation and project procurement.

Originality/value

This paper establishes a novel framework to visualise the current practices and deficiencies in the PPP legal and regulatory framework in Sri Lanka, and the way of incorporating recommended practices by international model laws and guidelines for its future reformations.
Positive feedback between parasite infection and poor host body condition reduces host survival in the wild
Authors: Hasegawa Ryota , Otsuki Yasuhiko , Uemura Yohsuke , Furusawa Chiharu , Naka Masahiro , Kanno Yoichiro , Koizumi Itsuro
Published: January 2025

Host–parasite relationships are ubiquitous on Earth. Although parasites reduce host health, parasite infections also occur due to compromised host health. Both causalities could induce positive feedback, in which infected hosts with poor body conditions may suffer further infection. Such positive feedback could increase host mortality and may finally affect host population dynamics. However, both causalities and how positive feedback affect host population dynamics has rarely been demonstrated in the wild, mainly due to methodological difficulties.

Here, we used a mark‐recapture survey combined with structural equation modelling (SEM) to examine whether both causalities and positive feedback occurred in a host stream salmonid and parasitic copepod system. We also examined the factors affecting the apparent survival of hosts during the mark‐recapture period using a Cormack–Jolly–Seber (CJS) model. Our target parasitic copepod Salmincola markewitschi is relatively large, attaching to the mouth cavity of host white‐spotted charr Salvelinus leucomaenis, which enabled long‐term tracking in natural conditions without sacrificing either host or parasite.

SEM using time‐series snapshot data detected simultaneous occurrence of both causalities, that is the parasitic copepods reduced host body condition and host with poorer body condition were more likely infected by parasites, suggesting the positive feedback. Furthermore, the negative effects of parasites on host body condition were more frequently detected compared to the opposite causal link (high susceptibility to infections in hosts with poor body condition), and the strengths of both causal links fluctuated across seasons and initial infection statuses. The CJS model revealed that both parasite infection and poor host condition reduced apparent survival.

The mouth‐attaching copepods might have reduced host body conditions by altering host foraging behaviour and/or inducing physiological costs such as immunity. High susceptibility in fish with poorer body condition was probably caused by low resource allocations to immunity and behavioural defences against parasites. These direct and indirect processes should incur strong stresses to host fish, finally leading to higher mortality.

Our findings provided the first empirical evidence on how positive feedback between parasite infection and reduced host condition could influence the wild host population via reduction of host survival. Heavily infected hosts created by positive feedback may also play important roles in parasite spreading, for example, as a super spreader. Together, positive feedback would thus be important ecological processes to better understand host and parasite dynamics in the wild populations.

Read the free Plain Language Summary for this article on the Journal blog.
Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors
Authors: Zeng Yan , Zhong Xiaozhong , Chen Yating , Gou Min , Yu Ke , Tang Yue‐Qin
Published: January 2025

Anaerobic digestion (AD) of organic wastes relies on the interaction and cooperation of various microorganisms. Phages are crucial components of the microbial community in AD systems, but their diversity and interactions with the prokaryotic populations are still inadequately comprehended. In this study, 2121 viral operational taxonomic units (vOTUs) were recovered from 12 anaerobic fatty acid–fed reactors. Notably, 63.1% of these vOTUs could not be assigned to any known family, revealing a substantial presence of uncharted phages specifically associated with AD environments. Over half of the vOTUs associated with hosts had the capability to infect multiple hosts, ranging from 2 to 49, with a prevalent tendency to infect 2–5 hosts. In silico predictions of phage‐host linkages uncovered that only a small fraction of vOTUs were shared across different functional groups, including fermentative bacteria, syntrophic fatty acid–oxidising bacteria (SFOB) and methanogens. Phages linked to hosts in all three groups primarily consisted of generalists and temperate species, especially those linked to SFOB. Additionally, metabolic reconstruction identified auxiliary metabolic genes participating in fatty acid degradation, methanogenesis and energy conservation. The present study provides insights into phage characteristics and their in situ interactions with prokaryotic hosts, highlighting their ecological role in AD systems.
Evolutionary Novelties in Bacteria and the Missing Backdrop of the Environment
Authors: Karve Shraddha
Published: January 2025

Evolutionary novelty has been one of the central themes in the field of evolutionary biology for many years. Structural and functional innovations such as scales in the reptiles, fins in the fishes and mammary glands in the mammals have been the focus of the studies. Insights obtained from these studies have shaped the criterion for the identification of novelty as well as provide the framework for studying novelty. In this article, I argue that unicellular organisms present an excellent opportunity for the investigation of evolutionary novelty. Even though bacteria share some fundamental aspects of novelty with higher organisms, there are definite departures. Here, I outline these departures in four different contexts: criterion for the identification of novelty, types of evolutionary novelties, level of biological complexity that bacteria embody and, most importantly, the role of the environment. Identifying the role of the environment allows the categorisation of novelty as probable or improbable and adaptive or latent. This categorisation of novel traits, based on the role of the environment, can facilitate the study of novelty in bacteria. Insights obtained from such studies are crucial for understanding the fundamental aspects of evolutionary novelty.
The Co‐op's Golden Opportunity? Exploring the Prospects of Labour's Sister Party under Keir Starmer's Labour Government
Authors: Kippin Sean
Published: January 2025

The Co‐operative Party is back in power. Forty‐three of its members of Parliament sit on the government benches in the House of Commons, of which four sit in the Cabinet, including the business and trade secretary. Six ‘metro mayors’ also wear the co‐operative badge, along with over 1,600 local councillors and representatives in the Scottish Parliament and Welsh Senedd. With Labour back in government, this under‐explored party may be on the cusp of its peak relevance in British politics. In partnership with Labour since 1927, it pursues a co‐operative agenda in politics and policy making. This article explores the role it may play in a Keir Starmer‐led Labour majority government. It places these observations in the context of Labour and the Co‐operative Party's previous period in power between 1997–2010, considering some opportunities and potential barriers to the party's ability to influence government policy in the UK's post‐Brexit, multilevel polity.
Jerusalem artichoke: A comprehensive review of nutritional composition, health benefits and emerging trends in food applications
Authors: Chauhan Divya Singh , Vashisht Pranav , Bebartta Ram Prasad , Thakur Dhruv , Chaudhary Vandana
Published: January 2025

The Jerusalem artichoke (JA), a plantrelated to sunflowers and native to North America, has long been valued for its versatility, especially during periods of food scarcity. This resilient crop serves multiple purposes, functioning as a vegetable, medicinal herb, grazing crop, and even a biofuel source. In recent years, interest in JA has grown, largely due to its high nutritional profile and associated health benefits. This review explores JA's nutritional composition, the benefits of its consumption, and its botanical and agricultural characteristics. Additionally, the various applications of JA in the food industry are discussed, including its use in dairy products, snacks, baked goods, beverages, and functional foods. This review also examines the processing techniques involved in harvesting JA, extracting its valuable components, and incorporating it into food products. Notably, JA is a rich source of fiber and minerals, and incorporating it into food products not only enhances their nutritional value but also improves fermentation processes, lowers the glycemic index, and enhances sensory properties, all while reducing production costs. However, several challenges remain in JA production. These include optimizing growing conditions, addressing high labor costs, developing suitable machinery, determining the ideal harvesting time, increasing pest resistance, identifying suitable packaging materials, and developing sustainable production strategies. These challenges require further research to fully unlock JA's potential as a valuable crop.
The rarity of mutations and the inflation of bacterial effective population sizes
Authors: Borges Rui
Published: January 2025

Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of their frequency and the timescale over which they occur. A common assumption is that mutations are infrequent, so when a new mutation arises, the previous one has either become fixed or lost. This assumption implies that mutations occur exclusively at fixed sites and is referred to as the boundary mutation model. However, one can alternatively assume a recurrent mutation model, which additionally considers mutations contributing to shifts in allele frequency.

In this study, we compare these two models. By examining mutation rates and effective population sizes across the Tree of Life, we demonstrate that the boundary mutation model remains valid for most species but significantly deviates in bacteria. Our analyses further reveal that the boundary mutation model tends to overestimate the effective population size, particularly in bacteria, where estimated population sizes can be more than five times larger than those expected by the recurrent mutation model. We address these biases by proposing a Bayesian estimator for population size that accounts for recurrent mutations.

To illustrate how mutation models can influence the quantification of forces other than drift, we further present a case study showing that the boundary mutation model exaggerates the intensity of selective constraints acting on the three codon positions of the bacterium Pseudomonas fluorescens.

This study emphasizes the importance of considering recurrent mutations in highly diverse species for accurate population genetics inference.
Effects of a video‐supported Cawthorne–Cooksey exercise program in older adults with balance deficits and dizziness: A preliminary randomised pilot study
Authors: Athanasiadou Olga , Lytras Dimitrios , Iakovidis Paris , Kasimis Konstantinos , Koutras Georgios , Apostolou Thomas
Published: January 2025

Objectives

To determine the safety and efficacy of a video‐supported Cawthorne–Cooksey exercise program (CCEP) in improving balance, dizziness and decreasing fear of falling in older adults with balance deficits and dizziness.

Methods

Thirty‐two older adults were divided into two groups (intervention and control). The intervention group followed a video‐supported CCEP group, while the control group received written instructions to maintain their usual activity and counselling on fall prevention. Balance was assessed using the Berg Balance Scale (BBS), fear of falling with the Fall Efficacy Scale International (FES‐I), and dizziness impact on daily life with the Dizziness Handicap Inventory (DHI) at baseline, the 4th week and at the 1‐month follow‐up. Analysis of variance with repeated measures was applied, and the level of significance was set at p < .05.

Results

Statistically significant differences were found between groups at the 4th week, with the CCEP group showing significant improvement in all outcome measures (BBS, FES‐I, DHI scores) (p < .05). These differences remained statistically significant at the 1‐month follow‐up (p < .05). No adverse effects were detected.

Conclusion

A 4‐week video‐supported CCEP is safe and effective in improving balance, dizziness impact on daily life and fear of falling in older adults with age‐related dizziness and imbalance.