bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction by caterpillars of stored and emitted volatiles in terpene chemotypes from populations of wild cotton (Gossypium hirsutum)
Authors: Mamin Marine , Clancy Mary V , Flückiger Galien , Quijano-Medina Teresa , Pérez-Niño Biiniza , Abdala-Roberts Luis , Turlings Ted C.J. , Bustos-Segura Carlos 
Published: April 2024

AbstractBackgroundUpland cotton (Gossypium hirsutum) plants constitutively store volatile terpenes in their leaves, which are steadily emitted at low levels. Herbivory leads to a greater release of these stored volatiles. Additionally, damaged plants increase the accumulation of volatile terpenes in their leaves and begin to emit other terpenes and additional compounds. This has been well characterised for cultivatedG. hirsutum, but little is known about volatile production in response to herbivory in wild populations. We investigated how damage by the beet armyworm (Spodoptera exigua) affects leaf-stored and emitted volatiles in wildG. hirsutumplants. These plants were grown in a greenhouse using seeds collected from populations found along the Yucatan coast, from where this cotton species originates. We assessed whether the differences in leaf terpene profiles between two known chemotypes persisted upon herbivory, in leaves and in head-space emissions, and whether these chemotypes also differed in the production and release of herbivory-induced volatiles. In addition to chemotypic variation, we further investigated intraspecific variation in the volatile response to herbivory among genotypes, populations, and four geographic regions.ResultsThe difference between the two chemotypes persisted after herbivory in the stored volatile profile of induced leaves, as well in the emissions from damaged plants. Therefore, wild cotton chemotypes may differ in their airborne interactions with their environment. The specific terpenes distinguishing these chemotypes showed a weak inducibility, raising questions about their functions. Herbivory triggered changes in stored and emitted volatiles similar to what is known for cultivated varieties ofG. hirsutum.However, we report for the first time on the emission of volatile aldoximes by cotton plants, which were only detected in the headspace upon herbivory, and displayed chemotypic and interpopulation variation. Intraspecific variation was also observed in the induced emissions of nitriles and certain terpenes. Moreover, chemotypes differed in their induction of (E)-β-ocimene stored in the leaves.ConclusionsThis comprehensive insight into herbivore-induced volatiles of wild cotton reveals variation in production and emission among populations. A full understanding of their ecological role may help in the development of future pest-management strategies for cotton crops.
Factors affecting the juvenile departure inOrientobdelloides siamensis(Oka, 1917)
Authors: Trivalairat Poramad , Trivalairat Krittiya , Raquib Tashfia , Purivirojkul Watchariya 
Published: April 2024

AbstractThe departure of juveniles from parental care is an important period influenced by various factors. In the laboratory, 3-5 days after copulation, ten parent individuals ofOrientobdelloides siamensisdeposited approximately 361.6±37.79 eggs on the substrate and covered them until departure. The parents incubated their single-egg cocoons for around 7-9 days until the juveniles hatched. Subsequently, the newborns turned to attach to the ventral annuli of the parent using their caudal sucker. Between seven to eleven days after hatching, when the caudal sucker of juveniles expanded over the parent’s annuli, signaling their readiness to depart, they detached from beneath the parent vent to the substrate but continued to live beneath it. Finally, to determine the timing of juvenile departure, the insufficient space availability beneath the parental vent and yolk depletion around 14-21 days after hatching were analyzed. Through these morphological characteristics and behavior, this study indicated the interactions among these factors contributing to the mechanisms influencing juvenile departure inO. siamensis.
Branched chain amino acids modulate the proteomic profile of Pro-induced differentiation for the infective stages ofTrypanosoma cruzi
Authors: de Freitas Nascimento Janaina , Damasceno Flávia Silva , Marsicobettre Sabrina , Vitorino Francisca Natália de Luna , Achijan Renan Weege , da Cunha Julia Pinheiro Chagas , Silber Ariel Mariano 
Published: April 2024

AbstractTrypanosoma cruzi, the causative agent of Chagas disease, undergoes a complex life cycle involving triatomine insects as vectors and mammals. The differentiation of epimastigote forms into metacyclic trypomastigotes within the insect vector is crucial for the parasite’s life cycle progression. Factors influencing this process, including temperature, pH, and nutritional stress, along with specific metabolite availability, play a pivotal role. Amino acids like Pro, His, and Gln support cell differentiation, while branched-chain amino acids (BCAAs) inhibit it. Interestingly, combining the pro-metacyclogenic amino acid Pro with one of the anti-metacyclogenic BCAAs results in viable metacyclics with significantly reduced infectivity. To explore the characteristics of metacyclic parasites differentiated in the presence of BCAAs, proteomics analyses were conducted. Metacyclics obtained in triatomine artificial urine (TAU) supplemented with Pro alone and in combination with Leu, Ile, or Val were compared. The analyses revealed differential regulation of 40 proteins in TAU-Pro-Leu, 131 in TAU-Pro-Ile, and 179 in TAU-Pro-Val, as compared to metacyclics from TAU-Pro. Among these, 22%, 11%, and 13% of the proteins were associated with metabolic processes, respectively. Notably, enzymes related to glycolysis and the tricarboxylic acid (TCA) cycle were reduced in metacyclics with Pro-BCAAs, while enzymes involved in amino acid and purine metabolic pathways were increased. Furthermore, metacyclics with Pro-Ile and Pro-Val exhibited elevated enzymes linked to lipid and redox metabolism. These findings suggest that the presence of BCAAs can reshape the metabolism of metacyclics, contributing to the observed reduction in infectivity in these parasites.
Implementation of Robson classification for caesarean section using health insurance claims: the experience of Indonesia
Authors: Khoe Levina Chandra , Sari Euis Ratna , Amelia Dwirani , Islamy Tauhid , Megraini Amila , Nadjib Mardiati , Wiweko Budi , Widyahening Indah Suci 
Published: April 2024

AbstractRobson classification has been recommended by the World Health Organization (WHO) as a monitoring tool for caesarean section (CS), however, it has not been implemented in Indonesia. In this study, we hypothesize that the National Health Insurance (NHI) claims data can be used to classify pregnant women into several obstetric groups. This study aims to examine the use of NHI claims database for analyzing CS according to the WHO manual for Robson classification. This study is a cross-sectional analysis using delivery claims from NHI sample set data from 2017 to 2018. We categorized the International Classification of Diseases (ICD) 10 codes in the claims data according to the Robson classification system using the following variables: multiple pregnancy, fetal presentation, previous obstetric record, previous CS record, gestational age, and onset of labor. Data was analyzed using IBM SPSS Statistics. A total of 31,375 deliveries were included in the analysis. Overall, mean age of mothers was 29.2±5.9 years. The CS rate in this population was 37.0% in 2017 and 38.7% in 2018. Highest CS rate was found in nulliparous (group 2: 26.6%) and multiparous women (group 4: 24.8%) if labour induced or had prelabour CS, followed by multiparous women with previous uterine scar (group 5: 22.5%). We found an alarmingly high rate of CS among Indonesian women. Implementation of Robson classification in the National Health Insurance claims data is feasible and should be considered by the policy makers as an audit tool to identify the groups that contributes the most to the CS rate.
Detecting directed motion and confinement in single-particle trajectories using hidden variables
Authors: Simon François , Ramadier Guillaume , Fonquernie Inès , Zsok Janka , Patskovsky Sergiy , Meunier Michel , Boudoux Caroline , Dultz Elisa , Weiss Lucien E. 
Published: April 2024

AbstractSingle-particle tracking is a powerful tool for understanding protein dynamics and characterizing microenvironments. As the motion of unconstrained nanoscale particles is governed by Brownian diffusion, deviations from this behavior are biophysically insightful. However, the stochastic nature of particle movement and the presence of localization error pose a challenge for the robust classification of non-Brownian motion. Here, we presentaTrack, a versatile tool for classifying track behaviors and extracting key parameters for particles undergoing Brownian, confined, or directed motion. Our tool quickly and accurately estimates motion parameters from individual tracks and determines their likely motion state. Further, our tool can analyze populations of tracks and determine the most likely number of motion states. We determine the working range of our approach on simulated tracks and demonstrate its application for characterizing particle motion in cells and for biosensing applications. Our tool is implemented as a stand-alone software package, making it simple to analyze tracking data.
Mice tails function in response to external and self-generated balance perturbation on the roll plane
Authors: Lacava Salvatore Andrea , Isilak Necmettin , Uusisaari Marylka Yoe 
Published: April 2024

AbstractThe functionality of mouse tails has been unexplored in the scientific literature, to the extent that they might seem to be considered as a passive appendage. Previous research on mouse locomotion has largely omitted tail dynamics, but hints at its potential use in balancing can be seen in the natural habitats and behaviors of these rodents. Here, leveraging high-speed videography, a novel naturalistic locomotory task and a simple biomechanical model analysis, we investigated the behavioral utility of the mouse tail.We observed that mice engage their tails on narrow ridge environments that mimic tree branches with narrow footholds prone to roll-plane perturbations, using different control strategies under two defined conditions: during external perturbations of the ridge where they primarily work to maintain posture and avoid falling, and during non-perturbated locomotion on the ridge, where the challenge is to dynamically control the center of mass while progressing forward.These results not only advance the existing understanding of mouse tail functionality but also open avenues for more nuanced explorations in neurobiology and biomechanics. Furthermore, we call for inclusions of tail dynamics for a holistic understanding of mammalian locomotor strategies.Author summaryWe describe and quantify the rapid mouse tail movements in response to external balance perturbations, possibly constituting a novel balance-compensatory motor program. Furthermore, we bring to light the consistent, context-dependent movements of the tail during increasingly precarious locomotion. The observations highlight the tail as an integral component of the mouse locomotory system, contributing to balancing and putatively movement efficacy, and call for inclusion of the tail in future works examining motor (dys)function.
Amino Acid and Glucose Fermentation Maintain ATP Content in Mouse and Human Malignant Glioma Cells
Authors: Lee Derek C. , Ta Linh , Mukherjee Purna , Duraj Tomas , Domin Marek , Greenwood Bennett , Karmacharya Srada , Narain Niven R. , Kiebish Michael , Chinopoulos Christos , Seyfried Thomas N. 
Published: April 2024

AbstractEnergy is necessary for tumor cell viability and growth. Aerobic glucose-driven lactic acid fermentation is a common metabolic phenotype seen in most cancers including malignant gliomas. This metabolic phenotype is linked to abnormalities in mitochondrial structure and function. A luciferin-luciferase bioluminescence ATP assay was used to measure the influence of amino acids, glucose, and oxygen on ATP content and viability in mouse (VM-M3 and CT-2A) and human (U-87MG) glioma cells that differed in cell biology, genetic background, and species origin. Oxygen consumption was measured using the Resipher system. Extracellular lactate and succinate were measured as end products of the glycolysis and glutaminolysis pathways, respectively. The results showed that: 1) glutamine was a source of ATP content irrespective of oxygen. No other amino acid could replace glutamine in sustaining ATP content and viability; 2) ATP content persisted in the absence of glucose and under hypoxia, ruling out substantial contribution through either glycolysis or oxidative phosphorylation (OxPhos) under these conditions; 3) Mitochondrial complex IV inhibition showed that oxygen consumption was not an accurate measure for ATP production through OxPhos. The glutaminase inhibitor, 6-diazo-5-oxo-L-norleucine (DON), reduced ATP content and succinate export in cells grown in glutamine. The data suggests that mitochondrial substrate level phosphorylation in the glutamine-driven glutaminolysis pathway contributes to ATP content in these glioma cells. A new model is presented highlighting the synergistic interaction between the high-throughput glycolysis and glutaminolysis pathways that drive malignant glioma growth and maintain ATP content through the aerobic fermentation of both glucose and glutamine.Summary statementMalignant gliomas, regardless of cell of origin or species, rely on fermentation mechanisms for ATP production due to OxPhos insufficiency. Glucose and glutamine together are necessary and sufficient for dysregulated tumor cell growth, whereas OxPhos is neither necessary nor sufficient.
Sensorimotor delays constrain robust locomotion in a 3D kinematic model of fly walking
Authors: Karashchuk Lili , Li Jing Shuang Lisa , Chou Grant M. , Walling-Bell Sarah , Brunton Steven L. , Tuthill John C. , Brunton Bingni W. 
Published: April 2024

AbstractWalking animals must maintain stability in the presence of external perturbations, despite significant temporal delays in neural signaling and muscle actuation. Here, we develop a 3D kinematic model with a layered control architecture to investigate how sensorimotor delays constrain robustness of walking behavior in the fruit fly, Drosophila. Motivated by the anatomical architecture of insect locomotor control circuits, our model consists of three component layers: a neural network that generates realistic 3D joint kinematics for each leg, an optimal controller that executes the joint kinematics while accounting for delays, and an inter-leg coordinator. The model generates realistic simulated walking that resembles real fly walking kinematics and sustains walking even when subjected to unexpected perturbations, generalizing beyond its training data. However, we found that the model’s robustness to perturbations deteriorates when sensorimotor delay parameters exceed the physiological range. These results suggest that fly sensorimotor control circuits operate close to the temporal limit at which they can detect and respond to external perturbations. More broadly, we show how a modular, layered model architecture can be used to investigate physiological constraints on animal behavior.
Using muscle-tendon load limits to assess unphysiological musculoskeletal model deformation and Hill-type muscle parameter choice
Authors: Nölle Lennart V. , Wochner Isabell , Hammer Maria , Schmitt Syn 
Published: April 2024

AbstractMusculoskeletal simulations are a useful tool for improving our understanding of the human body. However, the physiological validity of predicted kinematics and forces is highly dependent upon the correct calibration of muscle parameters and the structural integrity of a model’s internal skeletal structure. In this study, we show how ill-tuned muscle parameters and unphysiological deformations of a model’s skeletal structure can be detected by using muscle elements as sensors with which modelling and parameterization inconsistencies can be identified through muscle and tendon strain injury assessment.To illustrate our approach, two modelling issues were recreated. First, a model repositioning simulation using the THUMS AM50 occupant model version 5.03 was performed to show how internal model deformations can occur during a change of model posture. Second, the muscle material parameters of the OpenSim gait2354 model were varied to illustrate how unphysiological muscle forces can arise if material parameters are inadequately calibrated. The simulations were assessed for muscle and tendon strain injuries using previously published injury criteria and a newly developed method to determine tendon strain injury threshold values.Muscle strain injuries in the left and rightmusculus pronator tereswere detected during the model repositioning. This straining was caused by an unphysiologically large gap (12.92 mm) that had formed in the elbow joint. Similarly, muscle and tendon strain injuries were detected in the modified right-handmusculus gastrocnemius medialisof the gait2354 model where an unphysiological reduction of the tendon slack length introduced large pre-strain of the muscle-tendon-unit.The results of this work show that the proposed method can quantify the internal distortion behaviour of musculoskeletal human body models and the validity of Hill-type muscle parameter choice via strain injury assessment. Furthermore, we highlight possible actions to avoid the presented issues and inconsistencies in literature data concerning the material characteristics of human tendons.
The advantage of periodic over constant signalling in microRNA-mediated repression
Authors: Ferro Elsi , Szischik Candela L. , Ventura Alejandra C. , Bosia Carla 
Published: April 2024

AbstractCells have been found out to exploit oscillatory rather than constant gene expression to encode biological information. Temporal features of oscillations such as pulse frequency and amplitude have been shown determinant for the outcome of signaling pathways. However, little effort has been devoted to unveiling the role of pulsatility in the context of post-transcriptional gene regulation, where microRNAs (miRNAs) - repressors of gene expression - act by binding to RNAs. Here we study the effects of periodic against constant miRNA synthesis. We model periodic pulses of miRNA synthesis in a minimal miRNA-target RNA network by ODEs, and we compare the RNA repression to that resulting from constant synthesis of the repressor. We find that a pulsatile synthesis can induce more effective target RNA repression in the same timespan, despite an identical amount of repressor. In particular, a stronger fold repression is induced if the miRNA is synthesized at optimal frequencies, thereby showing a frequency preference behaviour - also known as “band-pass filtering”. Moreover, we show that the preference for specific input frequencies is determined by relative miRNA and target kinetic rates, thereby highlighting a potential mechanism of selective target regulation. Such ability to differentially regulate distinct targets might represent a functional advantage in post-transcriptional repression, where multiple competing targets are regulated by the same miRNA. Thereby analyzing a model with two RNA target species, we show how competition influences the frequency-dependent RNA repression. Eventually, we find that periodic miRNA expression can lead to exclusive frequency-dependent repression on distinct RNA species, and we show how this depends on their relative kinetics of interaction with the repressor. Our findings might have implications for experimental studies aimed at understanding how periodic patterns drive biological responses through miRNA-mediated signalling, and provide suggestions for validation in a synthetic miRNA-target network.
A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot
Authors: Hillsley Alexander , Stein Johannes , Tillberg Paul W. , Stern David L. , Funke Jan 
Published: April 2024

AbstractWe address the problem of inferring the number of independently blinking fluorescent light emitters, when only their combined intensity contributions can be observed at each timepoint. This problem occurs regularly in light microscopy of objects that are smaller than the diffraction limit, where one wishes to count the number of fluorescently labelled subunits. Our proposed solution directly models the photo-physics of the system, as well as the blinking kinetics of the fluorescent emitters as a fully differentiable hidden Markov model. Given a trace of intensity over time, our model jointly estimates the parameters of the intensity distribution per emitter, their blinking rates, as well as a posterior distribution of the total number of fluorescent emitters. We show that our model is consistently more accurate and increases the range of countable subunits by a factor of two compared to current state-of-the-art methods, which count based on autocorrelation and blinking frequency. Furthermore, we demonstrate that our model can be used to investigate the effect of blinking kinetics on counting ability, and therefore can inform experimental conditions that will maximize counting accuracy.
Morphogenesis of bacterial colonies in polymeric environments
Authors: La Corte Sebastian Gonzalez , Stevens Corey A. , Cárcamo-Oyarce Gerardo , Ribbeck Katharina , Wingreen Ned S. , Datta Sujit S. 
Published: April 2024

AbstractMany bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life—how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine “cables” as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.