bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land use change drives major loss of Southeast Asian biodiversity
Authors: Botterill-James Thomas , Yates Luke A. , Buettel Jessie C. , Aandahl Zach , Brook Barry W. 
Published: August 2023

AbstractSoutheast Asia is highly biodiverse and currently experiences among the highest rates of tropical deforestation globally, but impacts on biodiversity are not well synthesized. We use Bayesian multi-level modeling to meta-analyse 831 pairwise comparisons of biodiversity in sites subject to human land use change and anthropogenic forest disturbance (for example in plantations or logged forest) versus undisturbed sites. After controlling for hierarchical dependences, we show that biodiversity is a fifth lower in sites with these land-use changes (95% credible interval= 16-28%, mean = 22%). This reduction was greater when land use change/anthropogenic forest disturbances were high-intensity (34% reduction in biodiversity) compared to low-intensity (18% reduction), and effects were consistent across biogeographic regions and taxa. Oil-palm plantations lead to the greatest reduction in biodiversity (39%, CI 27-48%), and agroforests the least (24%, CI 10-37%). We also find that biodiversity is reduced in young secondary forest by 26% (CI 4-42%) compared to undisturbed forest, but there is no reduction in biodiversity for intermediate or mature-aged secondary forest (although species composition is potentially altered). Overall, our study provides the clearest evidence yet of the substantial detrimental impact of land-use change and anthropogenic forest disturbance on the biodiversity of Southeast Asia.
Effects of shoe heel height on ankle dynamics in running
Authors: Yawar Ali , Lieberman Daniel E. 
Published: August 2023

AbstractShoes alter the evolved biomechanics of the foot, potentially affecting running kinematics and kinetics that can in turn influence injury and performance. An important feature of conventional running shoes is heel height, whose effects on foot and ankle biomechanics remain understudied. Here, we investigate the effects of 6 – 26 mm increases in heel height on ankle dynamics in 8 rearfoot strike runners who ran barefoot and in minimal shoes with added heels. We predicted higher heels would lead to greater frontal plane ankle torques due to the increased vertical moment arm of the mediolateral ground reaction force. Surprisingly, the torque increased in minimal shoes with no heel elevation, but then decreased with further increases in heel height due to changes in foot posture that are probably a strategy to compensate for potentially injurious ankle torques. We also found that increasing heel heights caused a large increase in the ankle plantarflexion velocity at heel strike, which we explain using a passive collision model. Our results highlight how running in minimal shoes may be significantly different from barefoot running due to complex interactions between proprioception and biomechanics that also permit runners to compensate for modifications to shoe design, more in the frontal than sagittal planes.
Transcutaneous cervical vagus nerve stimulation improves sensory performance in humans
Authors: Jigo Michael , Carmel Jason B. , Wang Qi , Rodenkirch Charles 
Published: August 2023

AbstractAccurate senses depend on high-fidelity encoding by sensory receptors and error-free processing in the brain. Progress has been made towards restoring damaged sensory receptors. However, methods for on-demand treatment of impaired central sensory processing are scarce. Prior invasive studies demonstrated that continuous vagus nerve stimulation (VNS) in rodents can activate the locus coeruleus-norepinephrine system to rapidly improve central sensory processing. Here, we investigated whether transcutaneous VNS improves sensory performance in humans. We conducted three sham-controlled experiments, each with 12 neurotypical adults, that measured the effects of transcutaneous VNS on metrics of auditory and visual performance, and heart rate variability (HRV). Continuous stimulation was delivered to cervical (tcVNS) or auricular (taVNS) branches of the vagus nerve while participants performed psychophysics tasks or passively viewed a display. Relative to sham stimulation, tcVNS improved auditory performance by 37% (p=0.00052) and visual performance by 23% (p=0.038). Participants with lower performance during sham conditions experienced larger tcVNS-evoked improvements (p=0.0040). Lastly, tcVNS increased HRV during passive viewing, corroborating vagal engagement. No evidence for an effect of taVNS was observed. These findings validate the effectiveness of tcVNS in humans and position it as a method for on-demand interventions of impairments associated with central sensory processing dysfunction.
Serotonergic amplification of odor-evoked neural responses maps onto flexible behavioral outcomes
Authors: Bessonova Yelyzaveta , Raman Barani 
Published: August 2023

AbstractBehavioral responses to many odorants are not fixed but are flexible, varying based on organismal needs. How such variations arise and the role of various neuromodulators in achieving flexible neural-to-behavioral mapping is not fully understood. In this study, we examined how serotonin modulates the neural and behavioral responses to odorants in locusts (Schistocerca americana). Our results indicated that serotonin can increase or decrease appetitive behavior in an odor-specific manner. On the other hand, in the antennal lobe, serotonergic modulation enhanced odor-evoked response strength but left the temporal features or the combinatorial response profiles unperturbed. This result suggests that serotonin allows for sensitive and robust recognition of odorants. Nevertheless, the uniform neural response amplification appeared to be at odds with the observed stimulus-specific behavioral modulation. We show that a simple linear model with neural ensembles segregated based on behavioral relevance is sufficient to explain the serotonin-mediated flexible mapping between neural and behavioral responses.
Culture substrate stiffness impacts human myoblast contractility-dependent proliferation and nuclear envelope wrinkling
Authors: Nguyen Jo , Wang Lu , Lei Wen , Hu Yechen , Gulati Nitya , Chavez-Madero Carolina , Ahn Henry , Ginsberg Howard J. , Krawetz Roman , Brandt Matthias , Betz Timo , Gilbert Penney M. 
Published: August 2023

AbstractThe remarkable self-repair ability of skeletal muscle tissues is driven by muscle stem cells, whose activities are orchestrated by a variety of transient cues present in their microenvironment. Understanding how the cross-interactions of these biophysical and biochemical microenvironmental cues influences muscle stem cells and their progeny is crucial in strategizing remedies for pathological dysregulation of these cues in aging and disease. In this study, we investigated the cell-level influences of extracellular matrix ligands in the context of mechanically tuned culture substrates on primary human myoblast contractility and proliferation within 16 hours of plating. We found that fibronectin led to stronger stiffness-dependent responses in myoblasts compared to laminin and collagen as revealed by cell spreading area, focal adhesion morphology, traction stresses, and proliferation. While we did not observe stiffness-dependent changes in cell fate signatures at this early time-point, an analysis of the stiffness-sensitive myoblast proteome uncovered an enrichment for differentiation associated signatures on 17 kPa culture substrates, in addition to distinct profiles with relation to metabolism, cytoskeletal regulation, ECM interactions, and nuclear component enrichment. Interestingly, we found that softer substrates increased the incidence of myoblasts with a wrinkled nucleus, and that the extent of wrinkling could predict Ki67 expression. While nuclear wrinkling and Ki67 expression could be controlled by pharmacological manipulation of cellular contractility, cellular traction stresses did not correlate with nuclear envelope wrinkling level. These results provide new insights into the regulation of human myoblast stiffness-dependent contractility response by ECM ligands and also highlight a link between myoblast contractility and proliferation.
Experimentally quantifying impact of herbivory on duckweed communities in natural pond ecosystems
Authors: Subramanian Swapna K. , Turcotte Martin M. 
Published: August 2023

AbstractPlant herbivory structures communities, impacts energy and nutrient flow in ecosystems, and drives speciation. Yet, our knowledge of plant-herbivore interactions remains limited in freshwater ecosystems compared to terrestrial ones. We still lack robust experimental data on the impact of herbivores in nature on whole families of important macrophytes such as the globally distributed duckweed family (Lemnaceae). We conducted a replicated manipulative field experiment, using exclosures, across multiple bodies of water quantifying both ambient herbivory as well as herbivory caused by the addition of two different weevil and aphid herbivores. We found that invertebrate herbivores can strongly impact duckweed multi-generational population growth (e.g., reducing daily relative growth rate by up to 82% compared to controls) and differentially impact duckweed species composition. These impacts, however, vary greatly across sites and with the identity of the herbivores. Our results suggest that insect herbivores can severely slow the growth of the of the world’s fastest growing plant family. It also provides crucial information as duckweed continue to be developed for various applied purposes such a biofuel production and bioremediation.
Island biogeography theory and the gut: why taller people tend to harbor more diverse gut microbiomes
Authors: Sarmiento Katherine Ramos , Carr Alex , Diener Christian , Locey Kenneth J. , Gibbons Sean M. 
Published: August 2023

AbstractPrior work has shown a positive scaling relationship between vertebrate body size and gut microbiome alpha-diversity. This observation mirrors commonly observed species area relationships (SAR) in many other ecosystems. Here, we show a similar scaling relationship between human height and gut microbiome alpha-diversity across two large, independent cohorts, controlling for a wide range of relevant covariates, such as body mass index, age, sex, and bowel movement frequency. Island Biogeography Theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for these positive SARs. Using an individual-based model of IBT adapted to the gut, we demonstrate that increasing the length of a flow-through ecosystem is associated with increased species diversity. We delve into the possible clinical implications of these SARs in the American Gut Cohort. Consistent with prior observations that lower alpha-diversity is a risk factor forClostridioides difficileinfection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship appeared to be mediated by alpha-diversity. We also observed that vegetable consumption mitigated this risk increase, also by mediation through alpha-diversity. In summary, we find that body size and gut microbiome diversity show a robust positive association, that this macroecological scaling relationship is related to CDI risk, and that greater vegetable intake can mitigate this effect.
Quantitative evaluation of internal clustering validation indices using binary datasets
Authors: Pakgohar Naghmeh , Lengyel Attila , Botta-Dukát Zoltán 
Published: August 2023

AbstractDifferent clustering methods often classify the same dataset differently. Selecting the ‘best’ clustering solution out of a multitude of alternatives is possible with cluster validation indices. The behavior of validity indices changes with the structure of the sample and the properties of the clustering algorithm. Unique properties of each index cause increasing or decreasing performance in some conditions. Due to the large variety of cluster validation indices, choosing the most suitable index concerning the dataset and clustering algorithms is challenging. We aim to assess different internal clustering validation indices. In the present paper, the validity indices consist of geometric and non-geometric methods. For this purpose, we applied simulated datasets with different noise levels. Each dataset was repeated 20 times. Three clustering algorithms with Jaccard dissimilarity are used, and 27 clustering validation indices are evaluated. The results provide a reliability guideline for the selection cluster validity indices.
CIRI-hub: an integrated and visual analytics platform for circular RNAs in cancers
Authors: Wu Wanying , Zhang Jinyang , Zhao Fangqing 
Published: August 2023

AbstractRecent studies have demonstrated the emerging functions of circular RNAs (circRNAs) in regulating tumor progression and metastasis, and various databases have been established for exploring the expression patterns and features of circRNAs. However, all these databases only provide simple browsing or searching functions with a limited collection of samples, and none of them provides integrated analytical functions of given circRNAs or in-house RNA-Seq data. Here, we developed CIRI-hub, which provides a user-friendly webserver for integrative analyses of circRNAs and outputting publication-quality figures. CIRI-hub integrates a compendium of 2187 tumor and 680 normal RNA-seq libraries spanning 33 tissue types. The CIRI-hub webserver can accept various formats of input, and perform automated analysis of circRNAs in user input data as well as a variety of tumor and matching normal tissues. All analysis results can be downloaded as vectorized figures, and thresholds and plotting parameters can be interactively customized using the visual interface. We believe that CIRI-Hub will serve as a powerful tool for identifying novel cancer biomarkers and exploring the biological functions of circRNAs in tumorigenesis.Key PointsCIRI-hub integrates a compendium of 2187 tumor and 680 normal RNA-seq libraries spanning 33 tissue types, and provides comprehensive analysis and visualization functions for pan-cancer circRNA analysis.CIRI-hub permits users to specific circRNAs of their interests or upload their dataset and provides interactively customization of analysis algorithms and plotting parameters on the web interface.CIRI-hub can serve as a powerful tool for identifying novel cancer biomarkers and exploring the biological functions of circRNAs in tumorigenesis.
Noninvasive focal transgene delivery with viral neuronal tracers in the marmoset monkey
Authors: Parks T. Vincenza , Szczupak Diego , Choi Sang-Ho , Schaeffer David J. 
Published: August 2023

AbstractAlthough preclinical neuroscientific modeling species permit invasive intracranial delivery of targeted neurotropic agents, direct intracranial injections are not readily translatable to clinical therapeutics. Transcranial focused ultrasound (tFUS) has been identified as a technique to circumvent surgical injections altogether by transiently opening the blood-brain barrier (BBB) with selective focus. We have recently characterized the ability to focally deliver substances across the BBB in the marmoset, a non-human primate model with similar husbandry requirements to rodents but with cortical topologies more similar to humans. Here, we establish a reliable method for selectively delivering adeno-associated viral vectors (AAVs) across the BBB in marmoset frontal cortex with tFUS and demonstrate long-range anterograde neuronal tracing. Using a single-element 1.46 MHz transducer, we focally perturbed the BBB (∼1 x 2 mm) in area 8aD of frontal cortex in four adult marmoset monkeys using low-intensity focused ultrasound aided by microbubbles. We confirmed BBB opening via a gadolinium-enhanced MRI at 9.4 T prior to AAV delivery. Within an hour of opening the BBB, either AAV2 or AAV9 was delivered systemically via tail-vein injection. Four to six weeks later, animals were sacrificed, and microscopy was performed to confirm the presence of neurons transduced as indicated by EGFP or mCherry fluorescence. In all four marmosets, neurons were observed at the site of BBB perturbation, with AAV2 showing an exiguous distribution of transduced neurons when compared to AAV9. The results are compared to direct intracortical injections of anterograde tracers into area 8aD and similar (albeit sparser) long-range connectivity was observed. With evidence of transduced neurons specific to the region of BBB opening as well as long-distance tracing, we establish a framework for focal noninvasive transgene delivery to the marmoset brain. This technique will be of utility for the burgeoning marmoset model, with applications for noninvasive delivery of therapeutics, genetic delivery of precursors for techniques like two-photon imaging, or neuronal tracing across the lifespan.
Fractionating difficulty during sentence comprehension using functional neuroimaging
Authors: Thothathiri Malathi , Basnakova Jana , Lewis Ashley G. , Briand Josephine M. 
Published: August 2023

AbstractSentence comprehension is highly practiced and largely automatic, but this belies the complexity of the underlying processes. We used functional neuroimaging (fMRI) to investigate garden-path sentences that cause difficulty during comprehension, in order to unpack the different processes used to support sentence interpretation. By investigating garden-path and other types of sentences within the same individuals, we functionally profiled different regions within the temporal and frontal cortices in the left hemisphere. The results revealed that different aspects of comprehension difficulty are handled by left posterior temporal, left anterior temporal, ventral left frontal, and dorsal left frontal cortices. The functional profiles of these regions likely lie along a spectrum of specificity to generality, including language-specific processing of linguistic representations, more general conflict resolution processes operating over linguistic representations, and processes for handling difficulty in general. These findings suggest that difficulty is not unitary and that there is a role for a variety of linguistic and non-linguistic processes in supporting comprehension.
Uumarrty: Agent Based Simulation Model of Predator Prey Interactions with a Game Theoretical Framework
Authors: Remington Michael , Clark Rulon W. , Hanscom Ryan , Higham Timothy E. , Sukumaran Jeet 
Published: August 2023

ABSTRACTEvolutionary game theory boasts a rich history of application in the study of phenotypic evolution and behavioral strategies. Complementing this, agent-based modeling offers a powerful simulation framework that allows for explicit modeling and parameterization of individual agents within a virtual environment. The agent-based modelling approach empowers ecologists and evolutionary biologists to accurately model highly complex and dynamic systems. Leveraging these methodologies, we developed the agent-based model Uumarrty, which integrates concepts from game theory to investigate the evolution of behavioral phenotypes. Our model embraces essential game theoretical principles, including pay-offs, mixed versus pure strategies, and optimal behavioral strategies, seamlessly within the agent-based framework. Furthermore, we introduced a novel metric called the Nash score, which serves as an analog of the evolutionarily stable strategy within our agent-based environment. With this innovative approach, researchers gain a versatile tool to comprehensively explore optimal behavioral strategies and assess their evolutionary stability. To demonstrate the efficacy of our model, we applied it to a predator-prey system involving kangaroo rats and rattlesnakes. By examining various factors such as differing foraging gains by kangaroo rats, varying strike success of rattlesnakes by microhabitat, and the influence of introducing a second predator, we gained valuable insights into the evolution of microhabitat preferences within this predator-prey system.
Stellate Ganglion Block to Treat Long COVID-19 Syndrome, A 41 patient Retrospective Cohort Study
Authors: Pearson Lisa , Maina Alfred , Thompson Leah , Harden Sherri , Aaroe Abbey , Compratt Taylor 
Published: August 2023

AbstractPost Covid-19 condition (PCC), long COVID-19 syndrome and post-acute sequelae of SARS-CoV-2 (PASC) all refer to a constellation of symptoms that are unresolved long after the acute phase of the viral infection. The severity of symptoms can vary from mild and tolerable to severe and debilitating.1,2Due to the evolving nature of the SARS-CoV-2 pandemic, treatment protocols for the illness are in a constant state of evolution. The early stage of long COVID-19 syndrome contributes to a dearth of treatment protocols based on empirical evidence, while the absence of a conclusive pathophysiological understanding further complicates the development of such protocols. Current treatment regimens include homeopathic medicine, specialist system focused treatments, infusion therapies, hyperbaric oxygenation, and polypharmacy. The physiological, psychological, and societal impact of long COVID-19 cannot be approached casually and must govern the intensity with which the healthcare community approaches treatment of long COVID-19 syndrome.In this 41-patient cohort study from a chronic pain management practice, the use of either unilateral or bilateral stellate ganglion block (SGB) was explored to manage symptoms associated with long COVID-19 syndrome. Results indicated that a substantial proportion of patients (86%) experienced a reduction of their symptoms following SGB treatment.