bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactive electrical behaviour in mormyrid weakly electric fish: Jamming avoidance response or social interaction?
Authors: Weimar Nils , Maxeiner Moritz , Wong Emily M , Rick Ingolf P , Hocke Mathis , Landgraf Tim , von der Emde Gerhard 
Published: February 2025

AbstractWeakly electric fish emit electric organ discharges (EODs) for both active electrolocation and electrocommunication. In African mormyrids, pulse-type EODs are produced at highly variable inter-discharge intervals (IDIs), forming sequences that can convey contextual and behavioural information to conspecifics. Neighbouring fish frequently engage in time-locked interactive behaviours, such as fixed-latency echo responses and EOD synchronisation. These behaviours have been proposed to function either as a jamming avoidance response (JAR), preventing simultaneous discharges and interference with electrolocation, or as a form of social signal. To test these hypotheses, we analysed interactions between pairs ofMormyrus rume proboscirostris, quantifying EOD synchronisations, echo events, and instances of jamming. Our results show that jamming is rare in this species. We found no correlation between jamming frequency and echoing behaviour, nor evidence that synchronisation and echo events are direct responses to recent jams. Instead, these interactive behaviours were associated with specific movement patterns and social contexts. Synchronisations were mainly initiated by stationary hovering individuals, while echo responses were more frequent in smaller fish actively following a social partner, suggesting a role in leader-follower dynamics. Pairs with more frequent echoing also exhibited reduced inter-individual distances, indicating that interactive electrical signalling promotes social cohesion. Rather than mitigating jamming, interactive electrical behaviours in mormyrids likely serve as communicative strategies to maintain group coherence or allocate social attention. These findings highlight the role of electrocommunication in structuring social interactions. Investigating the rules of these behaviours could eventually decipher which specific IDI patterns signal social intent and help to understand the underlying mechanisms of electrocommunication.HighlightsMormyrid fish frequently perform interactive signalling during electrocommunication.Interactive electrical signalling is associated with specific locomotor behaviours.Echo responses and signal synchronisations are not linked to jamming.Signal synchronisations may support mutual assessment upon encounters.Interactive signalling promotes social cohesion and leader-follower dynamics.
Transcription Factor Driven Gene Regulation in Autism Spectrum Disorder
Authors: Ghosh Nimisha , Arancio Walter , Al Jabry Tariq , Al-Maskari Raya , Santoni Daniele 
Published: February 2025

AbstractAutism Spectrum Disorders (ASD) encompass a group of neurodevelopmental disorders in which an affected individual faces challenges in social interaction and communication, along with restricted and repetitive stereotypic behavioral patterns and interests. In this work, we have studied the differential gene regulation between patients and controls, mediated by Transcription Factors (TFs), of key genes involved in ASD. Nine and seven TFs have been identified as potential regulators of the set of syndromic and non-syndromic key high confident genes retrieved by the Simons Foundation Autism Research Initiative (SFARI) database. We have also identified significant couples of Transcription Factor - Target Gene potentially associated with an altered regulation in ASD patients. Consistently, many identified couples are involved in processes associated with brain morphogenesis and development. In this regard, this biased regulation could be the target of some experimental design in order to 1) test this hypothesis and 2) try to target this altered regulation pattern in ASD samples. In conclusion, we would like to emphasize that the present work proposes an effective and reliable computational approach that could be applied to any disease with known key genes and available gene expression data.
Metabolic state modulates risky foraging behavior via multiple branches of the insulin/IGF-1-like pathway inC. elegans
Authors: Price Kaiden H. , Braco Jason T. , Sareen Preeti F. , Niesman Peter J. , Nitabach Michael N. 
Published: February 2025

ABSTRACTForaging to acquire nutrients is an essential and sometimes risky behavior displayed by nearly all animals. Appropriately balancing foraging risks with nutrient requirements is pivotal for peak survival and reproduction, and metabolic state (i.e., how urgently the animal requires nutrients) is a strong modulator of risky foraging behavior. In this study, we asked what molecular signal allowsC. elegansto change its foraging behavior in response to changes in its metabolic state. We used an assay of risky foraging behavior, where wild type worms increase risky foraging behavior after food deprivation, to screen for candidate genes. We found that DAF-2, the singular receptor in theC. elegansinsulin/IGF-1 signaling (IIS) pathway, is necessary for worms to modulate risky foraging behavior in response to short-term food deprivation. Worms with mutations in genes upstream and downstream ofdaf-2in the IIS pathway also exhibited a reduction in the effect of food deprivation. While a canonical understanding of the IIS pathway would suggest that the FOXO transcription factor DAF-16 is the primary downstream IIS pathway target, we found that DAF-16 was not required for worms to exhibit food-deprivation-driven changes in foraging behavior. Furthermore, we determined that the calsyntenin ortholog CASY-1, which allows DAF-2c to traffic to axons, is required for food deprivation to modulate risky foraging behavior. These results both validate the IIS receptor as a pivotal regulator of risky foraging behavior and suggest a multi-pronged downstream pathway. Overall, these data enrich our understanding of how organisms transduce metabolic state information to make vital decisions about when to engage in risky foraging behaviors.ARTICLE SUMMARYC. eleganschanges its foraging behavior from a low-risk to a high-risk strategy when it is food deprived. Our paper demonstrates that the DAF-2 insulin/IGF-1-like receptor is an essential modulator for this behavior following food deprivation. Moreover, the regulation of risky foraging behavior is enacted by multiple downstream effectors of the insulin/IGF-1-like pathway, including a canonical pathway involving the FOXO transcription factor DAF-16 and a non-canonical pathway involving CASY-1, which can traffic an isoform of DAF-2 to axons.
Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues
Authors: Murakami Tatsuya C. , Belenko Nick , Dennis Griffin , Wang Cuidong , Siantoputri Maria Esterlita , Maeda Yurie , Pressl Christina , Heintz Nathaniel 
Published: February 2025

ABSTRACTFluorescent imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescent imaging in human tissue has been limited by endogenous pigments that can block the light path or emit an autofluorescence, thereby interfering with the specific imaging of target molecules. Although photobleachers have been developed to quench endogenous pigments, the lack of customizability limits their utility for a broad range of applications. Here, we present a high luminous-intensity photobleacher that is based on rigorous simulations of illumination patterns using the laws of radiation, along with the framework to maximize bleaching efficiency. This open-source project is designed to help researchers customize and scale according to the tissue types and the research goals. The photobleacher is applicable to both thin tissue slices and large-volume cleared tissue samples to enable serial three-dimensional imaging of postmortem human brain using multiplexed antibody or oligonucleotide probes.SIGNIFICANCE STATEMENTPhotobleaching is an effective technique for quenching endogenous pigments, enabling multiplexed fluorescent imaging of pigment-rich tissues, such as postmortem human samples. While many photobleaching strategies have been proposed, there is no standard guidance on how to design and use a photobleacher. This study introduces a general strategy for designing an effective, scalable, and customizable photobleacher, and proposes a workflow for properly treating tissues with the photobleacher. The technique enables high-contrast molecular visualization in tissues of various sizes, including large volumetric cleared tissues. Our framework will accelerate the quantitative understanding of human molecular anatomy and is applicable to diverse biological fields, including medical diagnostics.
High-Precision Lighting for Plants: Laser Diodes Outperform LEDs in Photosynthesis and Plant Growth
Authors: Li Lie , Sugita Ryusei , Yamaguchi Kampei , Togawa Hiroyuki , Terashima Ichiro , Yamori Wataru 
Published: February 2025

AbstractThe optimization of plant productivity in indoor horticulture relies heavily on artificial light systems, which serve as the primary light source for plant growth. Although light-emitting diodes (LEDs) have been extensively studied in recent decades, there is limited research on laser diodes (LDs). LDs offer several advantages such as adjustable light wavebands, remote illumination that minimizes heat accumulation near plants, and enhanced energy efficiency. This study investigated the impact of red LD light on plant photosynthesis and growth, exploring its potential applications in indoor horticulture. The research examined the gas exchange of tobacco plants (Nicotiana tabacumL. cv. Wisconsin-38) under six red LED and LD light sources with varying spectral characteristics. Two specific light sources were selected for further study: LED 664 (emission peak at 664 nm, waveband of 625~678 nm) and LD 660 (emission peak at 660 nm, waveband of 657~664 nm) as they demonstrated the greatest gas exchange efficiency among the tested LED and LD light sources. These two light sources were then evaluated for their effects on photochemical efficiency, carbohydrate accumulation and plant growth. The present study showed that compared with LED 664, LD 660 significantly increased Y(II), qL, and starch accumulation in tobacco leaves. Additionally, after 12 d of continuous irradiation with LD 660, both tobacco and Arabidopsis plants exhibited increased photosynthetic capacity, and all three plant species showed increased shoot dry weights and leaf areas compared with those under LED 664. These findings suggest that LDs present significant advantages over LEDs for indoor plant production.
Study of the exotic three-body
ND*K¯*
system
Authors: Zhai Qing-Yu , Molina Raquel , Oset Eulogio , Geng Li-Sheng 
Published: February 2025

We have studied the ND*K¯* system in the framework of the fixed center approximation to the Faddeev equations, taking the exotic D*K¯* system as the cluster and allowing the N to interact with the components of the cluster. Previous studies have determined the existence of three states of spin 0, 1, 2 for the D*K¯* system, the one of spin 0 associated to the X0(2900) state observed by the LHCb Collaboration. From this perspective, we find five states with total spin 1/2,3/2,5/2, with bindings from 10 to 30 MeV and widths below 60 MeV, which could be well identified. We also discuss the decay channels of these states that should help in future experimental searches for these states.

Published by the American Physical Society
2025
Generalized HMC using Nambu mechanics for lattice QCD
Authors: Lundstrum Erik 
Published: February 2025

We describe a generalization of the hybrid Monte Carlo (HMC) algorithm in which the molecular dynamics steps utilize Nambu generalized Hamiltonian dynamics. Nambu mechanics contains multiple Hamiltonian functions. Using one of these Hamiltonians in the Metropolis accept/reject step is enough to guarantee the correct target distribution. The other Hamiltonians can include arbitrary functions of the gauge field. We examine the simplest case with two Hamiltonians and choose the second to include nonlocal functions of the gauge field. In this way, the links are updated with instantaneous knowledge of far-separated link variables. This represents a promising method for reducing critical slowing down in lattice QCD simulations.

Published by the American Physical Society
2025
Simulated clinical placements in health care education: a scoping review and evidence and gap map protocol
Authors: Pollock Danielle , Marley Charles , McBride Grace , Dias Mafalda , Kanukula Raju , Hasanoff Sabira , Price Carrie , Tieu Matthew , Montagu Adam , Munn Zachary , Davies Ellen 
Published: February 2025

Objective:
This protocol details the methods for a scoping review that will examine the evidence on the design, implementation, delivery, and evaluation of simulated clinical placements.

Introduction:
Clinical placements allow health professions students to apply theoretical knowledge in clinical settings. For various economical, practical, and preferential reasons, some programs and institutions have trialed and established simulated clinical placements.

Inclusion criteria:
The review will include sources that have examined the design, implementation, delivery, and evaluation of simulated clinical placements in tertiary undergraduate and postgraduate education programs for health professions. Primary research studies, evidence syntheses, discussion articles, and commentaries will be included.

Methods:
The review will be conducted according to the JBI guidance for scoping reviews and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The following electronic databases will be searched: PubMed (NCBI), Embase (Elsevier), CINAHL Plus with Full Text (EBSCOhost), and PsycINFO (EBSCOhost). Forward and backward citation searching of the included evidence sources will be conducted using SpiderCite. At least 2 reviewers will assess sources for eligibility at title and abstract, and full-text screening stage, and extract data from included sources. Data will be analyzed using qualitative content analysis and frequencies and will be presented as a narrative summary. Data will also be presented in an evidence and gap map, and as tables and other visual summaries.
Within-host modeling of primaquine-induced hemolysis in hemizygote glucose-6-phosphate dehydrogenase deficient healthy volunteers
Authors: Watson James A. , Mehdipour Parinaz , Moss Robert , Jittamala Podjanee , Zaloumis Sophie , Price David J. , Dini Saber , Hanboonkunupakarn Borimas , Leungsinsiri Pawanrat , Poovorawan Kittiyod , Chotivanich Kesinee , Bancone Germana , Commons Robert J. , Day Nicholas P. J. , Pukrittayakamee Sasithon , Taylor Walter R. J. , White Nicholas J. , Simpson Julie A. 
Published: February 2025

ABSTRACT

Primaquine is the only widely available drug to prevent relapses of
Plasmodium vivax
malaria. Primaquine is underused because of concerns over oxidant hemolysis in glucose-6-phosphate dehydrogenase (G6PD) deficiency. A pharmacometric trial showed that ascending-dose radical cure primaquine regimens causing ‘slow burn’ hemolysis were safe in G6PD-deficient Thai and Burmese male volunteers. We developed and calibrated a within-host model of primaquine hemolysis in G6PD deficiency, using detailed serial hemoglobin and reticulocyte count data from 23 hemizygote deficient volunteers given ascending-dose primaquine (1,523 individual measurements over 656 unique time points). We estimate that primaquine doses of ~0.75 mg base/kg reduce the circulating lifespan of deficient erythrocytes by ~30 days in individuals with common Southeast Asian
G6PD
variants. We predict that 5 mg/kg primaquine total dose can be administered safely to G6PD-deficient individuals over 14 days with expected hemoglobin drops of 18 to 43% (2.7 to 6.5 g/dL drop from a baseline of 15 g/dL).

CLINICAL TRIALS

This study is registered with the Thai Clinical Trials Registry (TCTR) as
TCTR20170830002
a

nd
TCTR20220317004

.
Eco-microbiology: discovering biochemical enhancers of PET biodegradation by
Piscinibacter sakaiensis
Authors: Piedra Felipe-Andrés , Salazar Miguel A. , Abouelniaj Sara , Rahman Raayed , Clark Justin C. , Han Yimo , Wang Zhao , Maresso Anthony 
Published: February 2025

ABSTRACT

The scale of plastic pollution boggles the mind. Nearly 400 megatons of virgin plastics are produced annually, with an environmental release rate of 80%, and plastic waste, including microplastics and nanoplastics, is associated with a plethora of problems. The naturally evolved abilities of plastic-degrading microbes offer a starting point for generating sustainable and eco-centric solutions to plastic pollution—a field of endeavor we term eco-microbiology. Here, we developed an iterative discovery procedure coupling faster polyethylene terephthalate (PET)-dependent bioactivity screens with longer-term PET biodegradation assays to find biochemical boosters of PET consumption by the bacterium
Piscinibacter sakaiensis
. We discovered multiple hits supporting the enhancement of PET biodegradation, with a 0.39% dilution of growth medium #802, a rich medium similar to Luria-Bertani broth, on average more than doubling the rate of PET biodegradation both alone and in combination with 0.125% ethylene glycol. In addition, we identified other chemical species (sodium phosphate, L-serine, GABA) worth further exploring, especially in combination with growth medium #802, for enhanced PET biodegradation by
P. sakaiensis
. This work represents an important step toward the creation of a low-cost PET fermentation process needed to help solve PET plastic pollution.

IMPORTANCE

Plastic pollution is an urgent issue. Adding to the well-known problems of bulk plastic litter, shed microplastics and nanoplastics are globally distributed, found in diverse organisms including human foodstuffs and tissues, and increasingly associated with chronic disease. Solutions are needed and the microbial world offers abundant help via naturally evolved consumers of plastic waste. We are working to accelerate polyethylene terephthalate (PET) plastic biodegradation by
Piscinibacter sakaiensis
, a recently described bacterium that evolved to slowly but completely consume PET, one of the most common types of plastic pollution. We used a combination of PET-dependent bioactivity screens and biodegradation tests to find stimulators of PET biodegradation. Out of hundreds, we found a small number of biochemical conditions that more than double the PET biodegradation rate. Our work provides a foundation for further studies to realize a fermentation process needed to help solve PET plastic pollution.
HilD-regulated chemotaxis proteins contribute to
Salmonella
Typhimurium colonization in the gut
Authors: Cooper Kendal G. , Kari Laszlo , Chong Audrey , Tandon Naman , Doran Kathleen , Gomes Da Silva Lidiane , Cockrell Diane C. , Baylink Arden , Steele-Mortimer Olivia 
Published: February 2025

ABSTRACT

In the enteric pathogen
Salmonella
Typhimurium, invasion and motility are coordinated by HilD, a master regulator that activates expression of genes encoding the type III secretion system 1 and some motility genes, including the chemotaxis gene
mcpC
. Previously, we have shown that McpC induces smooth swimming, which is important for type III secretion system 1-dependent invasion of epithelial cells. Here, we have studied another
Salmonella
-specific chemotaxis gene,
mcpA
, and demonstrate that it is also HilD regulated. Whereas HilD induction of
mcpC
occurs by direct derepression of H-NS,
mcpA
induction requires neither H-NS derepression nor the flagellar-specific sigma factor
fliA
; instead it occurs through a HilD-SprB regulatory cascade, providing experimental confirmation of previous transcriptional regulatory mapping. McpA and McpC contain methyl-accepting domains characteristic of bacterial chemoreceptors, and McpA also contains a chemoreceptor zinc-binding (CZB) protein domain found in a variety of bacterial proteins, many of which are involved in signaling or regulatory roles. Here, we show that, in a mouse model for acute
Salmonella
colitis, both
mcpA
and
mcpC
deletion mutants are outcompeted by wild-type
Salmonella
Typhimurium in the gut lumen. CZB domains bind Zn
2+
through a conserved cysteine residue and are thought to perform redox-sensing through redox-initiated alterations in zinc homeostasis. We found that the conserved cysteine is required for McpA function in the mouse gut, thus demonstrating a virulence role for the CZB Zn
2+
-binding site during infection.

IMPORTANCE

The gut-adapted bacterium
Salmonella
Typhimurium causes inflammatory diarrhea via a process that involves active invasion of intestinal epithelial cells, secretion of inflammatory molecules, and recruitment of immune cells. Although bacterial motility and invasion of host cells are coordinated, how directed movement facilitates luminal survival and growth or invasion at the mucosal surface is not understood. Chemotaxis is the process by which bacteria control movement toward attractants and away from repellents. Previously, we identified a
Salmonella
-specific chemoreceptor, McpC, that is co-expressed with the invasion machinery and promotes smooth swimming for optimal host cell invasion. Here, we investigated another chemoreceptor, McpA, also regulated with invasion-associated genes and show it contributes to luminal expansion rather than invasion of epithelial cells. McpA activity requires a conserved Zn
2+
-binding domain, thought to be involved in sensing inflammation. This work demonstrates that coordination of invasion and chemotaxis plays a significant role in the gut.
Acinetobacter baumannii
OmpA hinders host autophagy via the CaMKK2-reliant AMPK-pathway
Authors: Woo Kyungho , Kim Dong Ho , Park Ho-Sung , Oh Man Hwan , Lee Je Chul , Choi Chul Hee 
Published: February 2025

ABSTRACT

Outer membrane protein A (OmpA) plays a vital role in the interactions between
Acinetobacter baumannii
and host cells. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria, thereby safeguarding cells against microbial infections. While it has been observed that
A. baumannii
triggers cellular autophagy, the precise role of its virulence protein OmpA in this process remains uncertain. In this study, we investigated the effects of
A. baumannii
OmpA (AbOmpA) on autophagy and explored the underlying molecular mechanisms. We found that AbOmpA exerted its autophagy-suppressive effect through inhibition of CaMKK2 phosphorylation. Compared to the wild-type strain, the
ompA
-deletion mutant strain displayed considerably enhanced autophagy induction,
via
the AMPK-ULK1 pathway. AbOmpA hindered starvation-induced autophagy, while
A. baumannii
-Omp33 (AbOmp33) and
Escherichia coli
-OmpA (EcOmpA) did not. Importantly, we confirmed that exogenous AbOmpA suppressed autophagy through the CaMKK2-AMPK-ULK1 pathway during
A. baumannii
infection. These findings reveal a novel mechanism for AbOmpA-mediated autophagy evasion, providing new insights into the pathogenesis of
A. baumannii
infection.

IMPORTANCE

Acinetobacter baumannii
is a significant clinical pathogen notorious for causing infections in hospitals. Its outer membrane protein A acts as a virulence factor and helps the bacteria evade host defenses. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria. While it has been observed that
A. baumannii
triggers cellular autophagy, the precise role of its AbOmpA in this process remains uncertain. Our studies demonstrate the AbOmpA of
A. baumannii
inhibits the cellular defense process, autophagy, through the CaMKK2-AMPK-ULK1 signaling cascade, thereby enhancing bacterial survival. This insight into how AbOmpA bypasses autophagy sheds light on
A. baumannii
infection's novel virulence strategy and suggests possible treatments.