bluuebunny/crossref_metadata_2025 huggingface dataset:
Serum Titanium Levels Remain Elevated But Urine Titanium is Undetectable in Children With Early Onset Scoliosis Undergoing Growth-Friendly Surgical Treatment: A Prospective Study
Authors: Shams Kameron , Jha Sahil , Swallow Jennylee , Caird Michelle S. , Farley Frances A. , Stepanovich Matthew , Li Ying
Published: November 2023

Background:

Elevated serum titanium levels have been found in patients with early onset scoliosis (EOS) treated with traditional growing rods (TGR), magnetically controlled growing rods (MCGR), and vertical expandable prosthetic titanium rib (VEPTR). No studies have investigated whether serum titanium remains persistently elevated and if titanium is excreted. Our purpose was to compare serum titanium levels in patients with EOS with growth-friendly instrumentation to age-matched controls and evaluate urine titanium and serial serum titanium levels in patients with EOS.

Methods:

This was a prospective case-control study. Patients with EOS with TGR, MCGR, or VEPTR underwent urine titanium and serial serum titanium collection at a minimum 6-month interval. Control patients did not have a history of metal implant insertion and underwent serum titanium collection before fracture fixation.

Results:

Twenty patients with EOS (6 TGR, 8 MCGR, and 6 VEPTR) and 12 controls were analyzed. The control group had no detectable serum titanium (0 ng/mL), whereas the patients with EOS had a median serum titanium of 4.0 ng/mL (P < 0.001). Analysis of variance showed significantly higher median serum titanium levels in the MCGR and VEPTR groups than the TGR group at time point 1 (5.5 vs 6.0 vs 2.0 ng/mL, P = 0.01) and time point 2 (6.5 vs 7.5 vs 2.0 ng/mL, P < 0.001). Binary comparisons showed a significant difference in serum titanium level between TGR and MCGR (time point 1: P = 0.026, time point 2: P = 0.011) and TGR and VEPTR (time point 1: P = 0.035, time point 2: P = 0.003). However, there was no difference between MCGR and VEPTR (time point 1: P = 0.399, time point 2: P = 0.492) even though the VEPTR group had a longer duration of follow-up (P = 0.001) and a greater number of lengthenings per patient at the first serum collection (P = 0.016). No patients with EOS had detectable urine titanium.

Conclusions:

Patients with EOS treated with titanium alloy growth-friendly instrumentation had elevated serum titanium levels compared with age-matched controls that persisted over time with no evidence of renal excretion. Additional studies are necessary to assess for local and systemic accumulation of titanium and the significance of long-term exposure to titanium in growing children.

Level of Evidence:

Level III, therapeutic.
Self-care Problems and Management Strategies Experienced by Rural Patient/Caregiver Dyads Living With Heart Failure
Authors: Graven Lucinda J. , Durante Angela , Abbott Laurie , Bassi Erika , Howren M. Bryant , Grant Joan S.
Published: November 2023

Background

Rural patients with heart failure (HF) have higher mortality and hospitalization rates compared with their urban counterparts. Although research supports the inclusion of informal caregivers in daily self-care activities, data are limited regarding the problems encountered by rural patient/caregiver dyads living with HF in managing HF in the home and how these problems are managed.

Objective

The aim of this study was to identify and describe HF self-care problems experienced by rural dyads in the home and how these problems are managed.

Methods

Using a descriptive qualitative design, data were collected from rural patient/caregiver dyads living with HF via individual, semistructured, telephone interviews and analyzed using schematic content analysis. Interviews and data analysis occurred concurrently until data saturation was reached.

Results

Thematic data saturation was obtained with 11 dyads. On average, patients were 65.3 (±13.9) years old, and caregivers were 62 (±12.37) years old. Four themes illustrating dyadic HF self-care problems and management strategies emerged: (1) HF self-care components, namely, maintenance, symptom monitoring, and management (diet, exercise, activities, strategies); (2) environment (rural barriers, COVID-19); (3) caregiver contributors (confidence, role); and (4) dyadic contributors (dyadic relationship). Dyads described various self-care problems, with the type of relationship and presence of mutuality influencing the problem-solving process and development of management strategies.

Conclusions

The identified themes emphasize the self-care problems experienced by rural dyads living with HF and the contributions of both dyad members to effectively manage these challenges. Findings support the need for culturally sensitive, tailored interventions targeting self-care in rural dyads living with HF.
Respiratory Muscle Strength and Quality of Life in Patients With Heart Failure and Their Main Correlated Factors
Authors: de Noronha Isis Marinho , Almeida Larisse Xavier , de Souza Silva Andrade Nina Vitória , de França Eduardo Eriko Tenório , de Morais Lima José Heriston , Pedrosa Rafaela , Siqueira Fernanda , Onofre Tatiana
Published: November 2023

Background

Heart failure may cause peripheral and respiratory muscle alterations, dyspnea, fatigue, and exercise intolerance, worsening the quality of life of patients.

Objectives

The aims of this study were to analyze respiratory muscle strength and quality of life of patients with heart failure and correlate them with clinical variables and functional classification.

Methods

This cross-sectional study involved patients with heart failure. A manovacuometer assessed maximum inspiratory and expiratory pressures, and quality of life was assessed using the Minnesota Living with Heart Failure Questionnaire. Functional classification was categorized according to the New York Heart Association (NYHA) class in I, II, III, or IV.

Results

We included 60 patients (66.7% male) with a mean age of 62.0 years and mean left ventricular ejection fraction of 42.0%. Maximum inspiratory pressure and maximum expiratory pressure were close to normal (>70% of predicted) in most patients; however, a subgroup composed mostly of patients with dilated heart failure and NYHA class III (n = 21) presented low maximum inspiratory pressure values (59.2%; 95% confidence interval, 55.7%–62.8%). The mean total score of the Minnesota Living with Heart Failure Questionnaire was 44.4 points, being negatively correlated with left ventricular ejection fraction (r = −0.29, P = .02). Patients with NYHA class III and disease duration longer than 120 months presented higher total (P < .01) and physical dimension scores.

Conclusions

Most patients had respiratory muscle strength close to normal; however, those with dilated heart failure and NYHA class III presented low maximum inspiratory pressure values. Quality of life was moderately compromised, mainly because of long disease duration, NYHA class III, and low left ventricular ejection fraction.
Incidence of Ventriculomegaly in Patients With Craniosynostosis
Authors: Liu Baihui , Li Jun , Zhang Songchunyuan , Wang Yueqing , Dong Chenbin
Published: November 2023

Hydrocephalus is variously associated with syndromic craniosynostosis (CS), while it is randomly encountered in nonsyndromic CS. But actually, the ventriculomegaly in CS is less described. In this study, the authors aim to establish whether ventriculomegaly is common in patients with CS, in both syndromic and nonsyndromic. Retrospective measurements of Evans index (EI) were taken from thin-section computed tomography scans of 169 preoperative CS patients to assess cerebral ventricular volume. EI >0.3 indicates ventricular enlargement. A total of 169 CS patients who underwent computed tomography scan from February 2018 to December 2021 were retrospectively evaluated, including 114 males and 55 females. The average age at diagnosis was 16 months (range: 1–103 mo). Among them, 37 with syndromic CS, including 17 ventricular megaly patients, had an EI >0.3 (46.0%), and 4 of them had intracranial hypertension and needed ventriculoperitoneal shunt treatment before cranial vault remolding. One hundred and thirty-two had nonsyndromic CS (100 single-suture CS, 32 multisuture CS), and 26 of them had an EI of 0.3 or greater (19.7%). Ventrocular megaly is common among patients with CS. Early craniotomy may stabilize ventricular dilation.
Spread of the cycles: a feedback perspective on the Anthropocene
Authors: Lenton Timothy M. , Scheffer Marten
Published: November 2023

What propelled the human ‘revolutions' that started the Anthropocene? and what could speed humanity out of trouble? Here, we focus on the role of reinforcing feedback cycles, often comprised of diverse, unrelated elements (e.g. fire, grass, humans), in propelling abrupt and/or irreversible, revolutionary changes. We suggest that differential ‘spread of the cycles' has been critical to the past human revolutions of fire use, agriculture, rise of complex states and industrialization. For each revolution, we review and map out proposed reinforcing feedback cycles, and describe how new systems built on previous ones, propelling us into the Anthropocene. We argue that to escape a bleak Anthropocene will require abruptly shifting from existing unsustainable ‘vicious cycles’, to alternative sustainable ‘virtuous cycles' that can outspread and outpersist them. This will need to be complemented by a revolutionary cultural shift from maximizing growth to maximizing persistence (sustainability). To achieve that we suggest that non-human elements need to be brought back into the feedback cycles underlying human cultures and associated measures of progress.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
The Anthropocene condition: evolving through social–ecological transformations
Authors: Ellis Erle C.
Published: November 2023

Anthropogenic planetary disruptions, from climate change to biodiversity loss, are unprecedented challenges for human societies. Some societies, social groups, cultural practices, technologies and institutions are already disintegrating or disappearing as a result. However, this coupling of socially produced environmental challenges with disruptive social changes—the Anthropocene condition—is not new. From food-producing hunter–gatherers, to farmers, to urban industrial food systems, the current planetary entanglement has its roots in millennia of evolving and accumulating sociocultural capabilities for shaping the cultured environments that our societies have always lived in (sociocultural niche construction). When these transformative capabilities to shape environments are coupled with sociocultural adaptations enabling societies to more effectively shape and live in transformed environments, the social–ecological scales and intensities of these transformations can accelerate through a positive feedback loop of ‘runaway sociocultural niche construction’. Efforts to achieve a better future for both people and planet will depend on guiding this runaway evolutionary process towards better outcomes by redirecting Earth's most disruptive force of nature: the power of human aspirations. To guide this unprecedented planetary force, cultural narratives that appeal to human aspirations for a better future will be more effective than narratives of environmental crisis and overstepping natural boundaries.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Positive feedbacks in deep-time transitions of human populations
Authors: Lima Mauricio , Gayo Eugenia M. , Estay Sergio A. , Gurruchaga Andone , Robinson Erick , Freeman Jacob , Latorre Claudio , Bird Darcy
Published: November 2023

Abrupt and rapid changes in human societies are among the most exciting population phenomena. Human populations tend to show rapid expansions from low to high population density along with increased social complexity in just a few generations. Such demographic transitions appear as a remarkable feature of
Homo sapiens
population dynamics, most likely fuelled by the ability to accumulate cultural/technological innovations that actively modify their environment. We are especially interested in establishing if the demographic transitions of pre-historic populations show the same dynamic signature of the Industrial Revolution transition (a positive relationship between population growth rates and size). Our results show that population growth patterns across different pre-historic societies were similar to those observed during the Industrial Revolution in developed western societies. These features, which appear to have been operating during most of our recent demographic history from hunter–gatherers to modern industrial societies, imply that the dynamics of cooperation underlay sudden population transitions in human societies.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Our fragile future under the cumulative cultural evolution of two technologies
Authors: Efferson Charles , Richerson Peter J. , Weinberger Vanessa P.
Published: November 2023

We derive and analyse a model with unusual features characterizing human activities over the long-run. First, human population dynamics draw heavily on consumer–resource modelling in ecology in that humans must consume biological resources to produce new humans. Second, the model also draws heavily from economic growth theory in that humans do not simply consume biological resources; they also produce the resources they consume. Finally, humans use two types of technology. Consumption technology affects the rate at which humans can extract resources. Production technology controls how effectively humans convert labour into new resources. The dynamics of both types of technology are subject to cumulative cultural evolutionary processes that allow both technological progress and regress. The resulting model exhibits a wide range of dynamical regimes. That said, the system is routinely sensitive to initial conditions, with wildly different outcomes given the same parameter values. Moreover, the system exhibits a basic fragility in the sense that human activities often lead to the endogenous extinction of the human species. This can happen gently, or it can follow periods of explosive human activity with super-exponential growth that ends in collapse.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Cities of the Anthropocene: urban sustainability in an eco-evolutionary perspective
Authors: Alberti Marina
Published: November 2023

Cities across the globe are driving systemic change in social and ecological systems by accelerating the rates of interactions and intensifying the links between human activities and Earth's ecosystems, thereby expanding the scale and influence of human activities on fundamental processes that sustain life. Increasing evidence shows that cities not only alter biodiversity, they change the genetic makeup of many populations, including animals, plants, fungi and microorganisms. Urban-driven rapid evolution in species traits might have significant effects on socially relevant ecosystem functions such as nutrient cycling, pollination, water and air purification and food production. Despite increasing evidence that cities are causing rapid evolutionary change, current urban sustainability strategies often overlook these dynamics. The dominant perspectives that guide these strategies are essentially static, focusing on preserving biodiversity in its present state or restoring it to pre-urban conditions. This paper provides a systemic overview of the socio-eco-evolutionary transition associated with global urbanization. Using examples of observed changes in species traits that play a significant role in maintaining ecosystem function and resilience, I propose that these evolutionary changes significantly impact urban sustainability. Incorporating an eco-evolutionary perspective into urban sustainability science and planning is crucial for effectively reimagining the cities of the Anthropocene.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Reducing global inequality increases local cooperation: a simple model of group selection with a global externality
Authors: Safarzynska Karolina , Smaldino Paul E.
Published: November 2023

Group-structured models often explain the evolution of prosocial activities in terms of selection acting at both individual and group levels. Such models do not typically consider how individuals' behaviours may have consequences beyond the boundaries of their groups. However, many behaviours affect global environmental variables, including climate change and ecosystem fragility. Against this background, we propose a simple model of multi-level selection in the presence of global externalities. In our model, group members can cooperate in a social dilemma with the potential for group-level benefits. The actions of cooperators also have global consequences, which can be positive (a global good) or negative (a global bad). We use simulations to consider scenarios in which the effects of the global externality either are evenly distributed, or have stronger influences on either the rich or the poor. We find that the global externality promotes the evolution of cooperation only if it either disproportionately benefits the poor or disproportionately reduces the payoffs of the rich. If the global externality primarily harms the poor, it undermines the evolution of prosocial behaviour. Understanding this effect is important given concerns that poorer households are more vulnerable to climate change impacts.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Innovation for sustainability: how actors are myopically caught in processes of co-evolution
Authors: Kemp René , van Lente Harro
Published: November 2023

In this paper, we argue that the development, uptake and adoption of innovations resembles an evolutionary process of variation, selection and retention (within broader processes of co-evolution) in which actors are myopically caught. We do so in four steps. First, we review in what ways socio-technical evolution resembles biological evolution. Second, we argue that in socio-technical evolution so-called ‘configurations that work’ can be viewed as evolutionary units, which are subject to selection pressures, variation and human-made couplings between variation and selection. This explains why innovation is often cumulative, based on variation and recombination. Third, we discuss how producers, consumers, governments and scientists are myopically caught in processes of co-evolution. While humans are capable of imagining the need for system change and details of desired systems, they are less capable of accepting the concomitant higher costs and inconveniences and adopt new interpretive schemes. Fourth, in a pluralist world, steering is done by all kind of actors, including those who actively resist transformative change. Because of this, steering by government and coalitions of change can achieve little more than a modulation of ongoing dynamics, despite disturbing evidence of a run-away climate, mass extinction, pervasive ecological degradation and steady depletion of resources. A new consciousness of the Anthropocene can evoke fundamental changes in science and the economy if—and only if—they are sufficiently carried by institutional changes and new practices.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Social-ecological niche construction for sustainability: understanding destructive processes and exploring regenerative potentials
Authors: Dorninger Christian , Menéndez Lumila Paula , Caniglia Guido
Published: November 2023

Through the exponential expansion of human activities, humanity has become the driving force of global environmental change. The consequent global sustainability crisis has been described as a result of a uniquely human form of adaptability and niche construction. In this paper, we introduce the concept of
social-ecological niche construction
focusing on biophysical interactions and outcomes. We use it to address destructive processes and to discuss potential regenerative ones as ways to overcome them. From a niche construction point of view, the increasing disconnections between human activities and environmental feedbacks appear as a success story in the history of human–nature coevolution because they enable humans to expand activities virtually without being limited by environmental constraints. However, it is still poorly understood how suppressed environmental feedbacks affect future generations and other species, or which lock-ins and self-destructive dynamics may unfold in the long-term. This is crucial as the observed escape from natural selection requires growing energy input and represents a temporal deferral rather than an actual liberation from material limitations. Relying on our proposal, we conclude that, instead of further taming nature, there is need to explore the potential of how to tame socio-metabolic growth and impact in niche construction processes.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Competition and co-association, but not phosphorous availability, shape the benefits of phosphate solubilising root bacteria for maize (Zea mays).
Authors: Williamson Joseph , Matthews Andrew Charles , Raymond Ben
Published: November 2023

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilising rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. Maize-associated rhizobacteria with varying phosphate solubilisation ability were used in experiments in soil, sterilised soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: beneficial effects of one Serratia isolate were detectable only when plants were inoculated with a single strain and beneficial effects of a competition sensitive Rhizobium was only detectable in sterilised soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilisation may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.
Comparison of color and water extracts of Caragana
sinica flowers dried at different air
temperatures
Authors: Choi Hye-Jung , Youn Kwang-Sup , Chung Hun-Sik
Published: November 2023

This study aimed to investigate the drying characteristics of Caragana
sinica Rehder flowers, which are basic data necessary for
increasing utilization. The flowers were harvested in mid-April and dried at
different hot-air temperatures (50-90°C), and the physicochemical
properties of the dried flowers were analyzed. It was found that the drying rate
was proportional to the air temperature. The visual color of dried flowers was
relatively strong in green when dried at 50°C, while browning was
relatively severe when dried at 90°C. The greenness (−a*
value) of the mechanical color of the powder decreased with increasing
temperature, and the yellowness (b* value) decreased with increasing
temperature above 70°C. The soluble solids of the hot water extract were
maintained at a certain level after increasing up to 70°C, and the pH
decreased with increasing temperature. The total polyphenol contents tended to
increase with increasing temperature, and DPPH radical scavenging activity did
not show a significant change after increasing up to 70°C. These results
suggest that the hot-air drying temperature had a significant effect on the
physicochemical characteristics of the C. sinica flower. The
appropriate hot-air drying temperature was judged to be less than 50°C
for maintaining the unique color, and approximately 70°C considering the
high hot-water extraction yield and antioxidant capacity.
Effects of soy defatting on texturization of texturized vegetable
proteins
Authors: Park Chan Soon , Seo Mi Sook , Jung Sun Young , Park Boram , Park Shin Young
Published: November 2023

In this study, the quality characteristics of texturized vegetable proteins (TVP)
produced from defatted soy flour (DSF) were analytically compared with those of
texturized vegetable proteins produced with isolated soy protein (ISP) and
non-defatted soy flour (SF). The base raw material formulation consisted of
50% soy proteins, 30% gluten, and 20% corn starch. A
cooling die-equipped extruder was used with a barrel temperature set at
190°C and screw rotation speed of 250 rpm. With respect to the hardness
of isolate soy proteins, that of soy flour and defatted soy flour was
22.4% and 68.8%, respectively, and gumminess was 17.6% and
44.3%, respectively. Defatting increased chewiness, shear strength, and
springiness. Moisture content was higher in soy flour than in defatted soy
flour, while there were no significant differences in terms of water absorption
and turbidity. The pH was higher with soy flour than with defatted soy flour.
Concerning color, the L and b values were higher with soy flour, while the a
value was higher with defatted soy flour. These results suggest that defatting
soybeans can improve the quality of plant-based proteins. Further research is
needed to address the quality differences from those of isolated soy
proteins.
Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types
Authors: Miller Austin D.C. , Chowdhury Soham P. , Hanson Hadley W. , Linderman Sarah K. , Ghasemi Hannah I. , Miller Wyatt D. , Morrissey Meghan A. , Richardson Chris D. , Gardner Brooke M. , Mukherjee Arnab
Published: November 2023

Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
Socioeconomic resources in youth are linked to divergent patterns of network integration and segregation across the brain’s transmodal axis
Authors: Michael Cleanthis , Taxali Aman , Angstadt Mike , Kardan Omid , Weigard Alexander , Molloy M. Fiona , McCurry Katherine L. , Hyde Luke W. , Heitzeg Mary M. , Sripada Chandra
Published: November 2023

Socioeconomic resources (SER) calibrate the developing brain to the current context, which can confer or attenuate risk for psychopathology across the lifespan. Recent multivariate work indicates that SER levels powerfully influence intrinsic functional connectivity patterns across the entire brain. Nevertheless, the neurobiological meaning of these widespread alterations remains poorly understood, despite its translational promise for early risk identification, targeted intervention, and policy reform. In the present study, we leverage the resources of graph theory to precisely characterize multivariate and univariate associations between household SER and the functional integration and segregation (i.e., participation coefficient, within-module degree) of brain regions across major cognitive, affective, and sensorimotor systems during the resting state in 5,821 youth (ages 9-10 years) from the Adolescent Brain Cognitive Development (ABCD) Study. First, we establish that decomposing the brain into profiles of integration and segregation captures more than half of the multivariate association between SER and functional connectivity with greater parsimony (100-fold reduction in number of features) and interpretability. Second, we show that the topological effects of SER are not uniform across the brain; rather, higher SER levels are related to greater integration of somatomotor and subcortical systems, but greater segregation of default mode, orbitofrontal, and cerebellar systems. Finally, we demonstrate that the effects of SER are spatially patterned along the unimodal-transmodal gradient of brain organization. These findings provide critical interpretive context for the established and widespread effects of SER on brain organization, indicating that SER levels differentially configure the intrinsic functional architecture of developing unimodal and transmodal systems. This study highlights both sensorimotor and higher-order networks that may serve as neural markers of environmental stress and opportunity, and which may guide efforts to scaffold healthy neurobehavioral development among disadvantaged communities of youth.
Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy
Authors: Sarkar Soumyadev , Kazarina Anna , Hansen Paige M. , Ward Kaitlyn , Hargreaves Christopher , Reese Nicholas , Ran Qinghong , Kessler Willow , de Souza Ligia F.T. , Loecke Terry D. , Sarto Marcos V. M. , Rice Charles W. , Zeglin Lydia H. , Sikes Benjamin A. , Lee Sonny T.M.
Published: November 2023

Background

Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.

Results

We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.

Conclusions

The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA– and AOB-driven nitrogen transformations in soil.
Unveiling the neural dynamics of conscious perception in rapid object recognition
Authors: Motlagh Saba Charmi , Joanisse Marc , Wang Boyu , Mohsenzadeh Yalda
Published: November 2023

Our brain excels at recognizing objects, even when they flash by in a rapid sequence. However, the neural processes determining whether a target image in a rapid sequence can be recognized or not remained elusive. We used electroencephalography (EEG) to investigate the temporal dynamics of brain processes that shape perceptual outcomes in these challenging viewing conditions. Using naturalistic images and advanced multivariate pattern analysis (MVPA) techniques, we probed the brain dynamics governing conscious object recognition. Our results show that although initially similar, the processes for when an object can or cannot be recognized diverge around 180ms post-appearance, coinciding with feedback neural processes. Decoding analyses indicate that object categorization can occur at ∼120ms through feedforward mechanisms. In contrast, object identification is resolved at ∼190ms after target onset, suggesting involvement of recurrent processing. These findings underscore the importance of recurrent neural connections in object recognition and awareness in rapid visual presentations.
MoveR: an R package for easy processing and analysis of animal video-tracking data
Authors: Petitjean Quentin , Lartigue Silène , Cointe Mélina , Ris Nicolas , Calcagno Vincent
Published: November 2023

Animal movement and behavior are critical to understanding ecological and evolutionary processes. Recent years have witnessed an increase in methodological and technological innovations in video-tracking solutions for phenotyping animal behavior. Although these advances enable the collection of high-resolution data describing the movement of multiple individuals, analyzing and interpreting them remains challenging due to their complexity, heterogeneity, and noisiness. Here, we introduce MoveR, an R package for importing, filtering, visualizing, and analyzing data from common video-tracking solutions. MoveR includes flexible tools for polishing data, removing tracking artifacts, subsetting and plotting individual paths, and computing different movement and behavior metrics.

Metadata
Investigating egocentric tuning in hippocampal CA1 neurons using simulated data
Authors: Carpenter Jordan , Blackstad Jan Sigurd , Tingley David , Normand Valentin A. , Moser Edvard I. , Moser May-Britt , Dunn Benjamin A.
Published: November 2023

Navigation requires integrating sensory information with a stable schema to create a dynamic map of an animal’s position using egocentric and allocentric coordinate systems. In the hippocampus, place cells encode allocentric space, but their firing rates may also exhibit directional tuning within egocentric or allocentric reference frames. We compared experimental and simulated data to assess the prevalence of tuning to egocentric bearing (EB) among hippocampal cells in rats foraging in an open field. Using established procedures, we confirmed egocentric modulation of place cell activity in recorded data; however, simulated data revealed a high false positive rate. When we accounted for false positives by comparing with shuffled data that retain correlations between the animal’s direction and position, only a very low number of hippocampal neurons appeared modulated by EB. Our study highlights biases affecting false positive rates and provides insights into the challenges of identifying egocentric modulation in hippocampal neurons.
In vivo and in silicoexperiment onMitragyna speciosaoffers new insight of antidiabetic potentials
Authors: Hossain Mohammad Uzzal , Hossain Md. Shahadat , Dey Shajib , Naimur Rahman A.B.Z. , Chowdhury Zeshan Mahmud , Bhattacharjee Arittra , Ahammad Ishtiaque , Islam Md. Nazrul , Moniruzzaman Md. , Hosen Md. Billal , Ahmed Istiak , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md.
Published: November 2023

Diabetes Mellitus (DM) is a serious metabolic disease with several treatments available for managing it, however, they can be expensive and have side effects. Medicinal plants have been used for many years to treat numerous diseases.Mitragyna speciosa (M. speciosa) plant has been shown to have anti-diabetic properties in preclinical studies. Hence, this study aimed to investigate the phytochemical compositions and anti-diabetic effects ofM. speciose,using bothin vivoandin silicoapproaches. In the in vivo study, experimental diabetes was induced in Swiss albino mice using the drug alloxan (150 mg/kg). Four groups of diabetic mice were taken. Two of the groups were given extracts at doses of 200 mg/kg and 400 mg/kg respectively. Diabetic mice treated with the reference drug, glibenclamide (5mg/kg) were chosen as a positive control, and mice with only vehicles were considered as a negative control. The Oral Glucose Tolerance Test (OGTT) and the acute toxicity test were performed. In thein silicostudy, molecular docking and dynamics were performed for the identification of the plant compounds that could effectively bind with the DPP4 receptor. Analysis of the study suggested that the lethal dose (LD50) values were greater than 2000 mg/kg, indicating that a dose below this level can be selected. The OGTT results showed that both doses ofM. specioseextracts significantly reduced blood glucose levels (P<0.0001). However, neither dose exhibited a significantly higher blood glucose reduction compared to glibenclamide (5 mg/kg) (P > 0.05). Phytochemical screening and the ADMET profile analysis suggested four key compounds: Mitragynine, Corynantheidine, Corynoxine, and Speciociliatine inM. speciosa.The molecular docking analysis revealed these four compounds as potential antidiabetic agents considering their high binding affinity to the DPP4 receptor. These compounds were also found to be stable in the DPP4 binding pocket, as evidenced by the molecular dynamics simulation. Lastly, it can be demonstrated that thein silicoexperiments confirmedM. speciosaextracts to be capable of reducing blood glucose levels because of the presence of compounds.
Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes
Authors: Farrell Kurt , Humphrey Jack , Chang Timothy , Zhao Yi , Leung Yuk Yee , Kuksa Pavel P , Patil Vishakha , Lee Wan-Ping , Kuzma Amanda B. , Valladares Otto , Cantwell Laura B. , Wang Hui , Ravi Ashvin , Sanctis Claudia De , Han Natalia , Christie Thomas D. , Whitney Kristen , Krassner Margaret M. , Walsh Hadley , Kim SoongHo , Dangoor Diana , Iida Megan A. , Casella Alicia , Walker Ruth H. , Nirenberg Melissa J. , Renton Alan E. , Babrowicz Bergan , Coppola Giovanni , Raj Towfique , Höglinger Günter U. , Golbe Lawrence I. , Morris Huw R. , Hardy John , Revesz Tamas , Warner Tom T. , Jaunmuktane Zane , Mok Kin Y. , Rademakers Rosa , Dickson Dennis W. , Ross Owen A. , Wang Li-San , Goate Alison , Schellenberg Gerard , Geschwind Daniel H. ,   PSP genetics study group, Crary John F. , Naj Adam
Published: November 2023

Progressive supranuclear palsy (PSP) is a rare Parkinsonian disorder characterized by problems with movement, balance, cognition, and other symptoms. PSP differs from Alzheimer’s disease (AD) and other neurodegenerative diseases displaying abnormal forms of the microtubule-associated protein tau (“tauopathies”) by the presence of pathology not only in neurons, but also in astrocytes and oligodendrocytes. Genetic contributors may mediate these differences, however much of PSP genetics remains unexplained. Here we conducted the largest genome-wide association study (GWAS) of PSP to date including 2,779 cases (2,595 neuropathologically-confirmed) and 5,584 controls and identified six independent PSP susceptibility loci with genome-wide significant (p< 5×10-8) associations including five known (MAPT,MOBP,STX6,RUNX2,SLCO1A2) and one novel locus (C4A). Integration with cell type-specific epigenomic annotations revealed a unique oligodendrocytic signature that distinguishes PSP from AD and Parkinson’s disease. Candidate PSP risk gene prioritization using expression quantitative trait loci (eQTLs) identified oligodendrocyte-specific effects on gene expression in half of the genome-wide significant loci, as well as an association with elevatedC4Aexpression in bulk brain tissue which may be driven by increasedC4Acopy number in PSP cases. Finally, histological studies demonstrated abnormal tau aggregates in oligodendrocytes that colocalize with C4 (complement) deposition. Integrating GWAS with functional studies including epigenomic and eQTL analyses, we identified potential causal roles for variation inMOBP,STX6,RUNX2,SLCO1A2, andC4Ain the pathogenesis of PSP.
Tuning the brakes – Modulatory role of transcranial random noise stimulation on inhibition
Authors: Mandali Alekhya , Torrecillos Flavie , Wiest Christoph , Pogosyan Alek , He Shenghong , Soriano Diogo Coutinho , Tan Huiling , Stagg Charlotte , Cagnan Hayriye
Published: November 2023

Background

Everyday decision-making requires the ability to flexibly modify and sometimes terminate our actions, such as avoiding a tempting slice of cake to hitting the brakes in an emergency. Neural oscillations, such as beta-band rhythms observed over the medial prefrontal cortex(mPFC), help regulate these context-dependent behaviours. However, how random noise stimulation would modulate neural rhythms and corresponding inhibitory behaviors remain understudied.

Objectives

To target the mPFC using random noise stimulation and modulate neural activity underlying inhibitory behaviours.

Methods

Using a single-blinded within-subject design, fifteen participants received random noise or sham stimulation in a pseudo-randomized order while performing a Go/Conflict/No-Go task. We measured neural activity and behavior before and after stimulation.

Results

We show that random noise stimulation significantly improved inhibitory behaviors (4.6±4.42percent) by reducing the number of errors in No-Go trials. This improvement was a function of participants’ impulsivity-levels and baseline performance, i.e., impulsive individuals who made more baseline errors improved more after receiving stimulation. At the neural level, we show that random noise stimulation increases low-beta power at stimulation site, mediated by an increase in the duration of intermittent beta-bursts.

Conclusion

We show for the first time that random noise stimulation improves the ability to withhold response to unexpected inhibitory cues as a function of an individual’s impulsivity level. This improvement could be attributed to increased low-beta band power and intermittent-burst duration. These results suggest that random noise stimulation of the mPFC could potentially be used as a neuromodulatory intervention to target maladaptive behaviors in impulse control disorders.
SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes
Authors: Bhogale Shounak , Seward Chris , Stubbs Lisa , Sinha Saurabh
Published: November 2023

A common way to investigate gene regulatory mechanisms is to identify differentially expressed genes using transcriptomics, find their candidate enhancers using epigenomics, and search for over-represented transcription factor (TF) motifs in these enhancers using bioinformatics tools. A related follow-up task is to model gene expression as a function of enhancer sequences and rank TF motifs by their contribution to such models, thus prioritizing among regulators.

We present a new computational tool called SEAMoD that performs the above tasks of motif finding and sequence-to-expression modeling simultaneously. It trains a convolutional neural network model to relate enhancer sequences to differential expression in one or more biological conditions. The model uses TF motifs to interpret the sequences, learning these motifs and their relative importance to each biological condition from data. It also utilizes epigenomic information in the form of activity scores of putative enhancers and automatically searches for the most promising enhancer for each gene. Compared to existing neural network models of non-coding sequences, SEAMoD uses far fewer parameters, requires far less training data, and emphasizes biological interpretability.

We used SEAMoD to understand regulatory mechanisms underlying the differentiation of neural stem cell (NSC) derived from mouse forebrain. We profiled gene expression and histone modifications in NSC and three differentiated cell types and used SEAMoD to model differential expression of nearly 12,000 genes with an accuracy of 81%, in the process identifying the Olig2, E2f family TFs, Foxo3, and Tcf4 as key transcriptional regulators of the differentiation process.
Genetic Insights into Agronomic and Morphological Traits of Drug-Type Cannabis Revealed by Genome-Wide Association Studies
Authors: de Ronne Maxime , Lapierre Éliana , Torkamaneh Davoud
Published: November 2023

Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research and industry growth. However, years of prohibition have left the cannabis research community underdeveloped and lacking knowledge about cannabis genetics and trait inheritance. To bridge this gap, we conducted a comprehensive genome-wide association study (GWAS), using a panel of 176 drug-type cannabis accessions, curated to represent the Canadian legal market. This pioneering GWAS harnessed the power of high-density genotyping-by-sequencing (HD-GBS), resulting in an exhaustive catalog of 800K genetic variants. These variants served as the bedrock for a GWAS designed to dissect the genetic foundations of nine key traits. To identify the most robust markers associated with these traits, two sophisticated statistical methodologies were used (SUPER and BLINK), ultimately identifying 33 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to a rich trove of putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These markers show great promise for revolutionizing cannabis breeding to meet diverse needs. In doing so, they lay the solid foundation for an innovative cannabis industry poised to reshape the future.