bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational modelling of the suppression of optic nerve fibre
Authors: Pratiwi Ariastity , Kekesi Orsolya , Barriga-Rivera Alejandro , Suaning Gregg 
Published: January 2025

AbstractRetinal 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 summaryRetinal 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 StatementBy 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

AbstractRhythmic 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.
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.
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

PurposeThis 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/approachFirstly, 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.FindingsThe 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/implicationsThe 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/valueThis 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

Abstract

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

ABSTRACTAnaerobic 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

ABSTRACTEvolutionary 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

AbstractThe 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

AbstractThe 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

Abstract

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

AbstractObjectivesTo 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.MethodsThirty‐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.ResultsStatistically 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.ConclusionA 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.