bluuebunny/crossref_metadata_2025 huggingface dataset:
On the public provision of positional goods
Authors: Christofzik Désirée I , Kessing Sebastian G
Published: August 2023

We investigate whether the public provision of positional goods can be a sensible instrument to address inefficiencies arising from relative-standing externalities associated with the excessive consumption of such goods. In situations where consumers face a discrete choice between a private and a public alternative, providing the latter for free or at a subsidized rate generates incentives to opt for the public alternative. This allows to reduce excessive consumption. We show that such policies can increase welfare and characterize situations where they can even implement efficiency. Efficiency can typically be achieved if the non-positional utility component is sufficiently important. Moreover, we investigate how the public provision of positional goods may be a useful policy instrument in second-best situations, where either the government is constrained to rely on distortionary taxes, or where it redistributes facing information constraints.
Health Expenditure Decentralization and Health Outcomes: The Importance of Governance
Authors: Nakatani Ryota , Zhang Qianqian , Garcia Valdes Isaura
Published: August 2023

Does health expenditure decentralization improve a nation’s health? Should countries care about governance quality when they decentralize healthcare spending to local governments? We answer these questions using cross-country data comprising fifty countries from 1996 to 2018. We find that health spending decentralization worsens health outcomes, which are offset by better governance of government. We calibrate the maximum feasible degree of health expenditure decentralization to have positive effects on health outcomes for a given percentile distribution of governance quality. Countries should be mindful of this negative consequence of health spending decentralization and should ensure that the quality of their governance exceeds a certain threshold to offset this negative externality. We also find that vertical fiscal imbalance is negatively associated with health outcomes, underscoring the role of revenue decentralization in improving the fiscal discipline of local governments by avoiding moral hazard caused by soft budget constraints and the common pool problem.
Calibration and simulation of a silicon dosemeter for ambient dose equivalent in low-earth orbit space
Authors: Youn Sukwon , Nam Uk-won , Kim Sunghwan , Kim Hongjoo , Park Won-Kee , Sohn Jongdae , Moon Bongkon , Jun Insoo , Ye Sung-Joon
Published: August 2023

A particle dosemeter (PD) is a payload of NEXTSat-2 in the low-earth orbit (LEO). The absorbed dose in LEO needs to be converted into the ambient dose equivalent (H*(10)). Due to a mixed field in LEO, the calibration factors (klow and khigh) should be determined for the low-and high-linear energy transfers (LET) (below and above 1.5 keV/μm), respectively. The PD was irradiated with a 137Cs source at the Korea Radiation Solution facility to obtain H*(10) and absorbed doses. However due to the lack of sources for the high-LET calibration, H*(10) and an absorbed dose were calculated by simulating PD for the high-energy neutron field at CERN-EU high-energy Reference Field. The measured klow of PD had a difference of 5.1% and 9.5% from the calculated value of PD and the measured value of Liulin detectors, respectively. However, a difference in khigh between PD and Liulin was explained by the contribution of non-neutron components to Liulin in the measurements.
Natural radionuclides in thermal mineral springs in Edipsos Greece
Authors: Kehagia Konstantina , Xarchoulakos Dimitrios C , Bratakos Sotirios M , Potiriadis Constantinos
Published: August 2023

Natural thermal and mineral therapeutic springs exist all over Greece. A radiological survey has been carried out in the municipality of Edipsos to study the naturally occurring alpha emitter radionuclides, 226Ra and the uranium isotopes. Thirteen thermal spring water samples and six tap water samples which were collected from five locations in the municipality of Edipsos, were analysed and measured by a-spectrometry. The obtained results show that 238U activity varies between 2.8 ± 0.3 and 65.0 ± 5.3 mBq/L in hot springs and between 2.70 ± 0.35 and 10.6 ± 0.9 mBq/L in tap water samples. The 234U/238U activity ratio lying between 1.12 ± 0.17 and 2.12 ± 0.30 indicates enrichment in the 234U concentration that can be explained through its ability to be easily leached from mineral surfaces. The 226Ra activity concentration varies between 3.5 ± 0.4 and 1470 ± 127 mBq/L in hot springs and between 6.5 ± 0.9 and 28.2 ± 2.8 mBq/L in tap water samples. Based on these results the estimated doses in this study are below the recommended dose of 1 mSv/y.

Highlights A radiological survey was carried out in the thermal springs of Edipsos, one of the most popular spa towns in Greece. Determination of uranium isotopes and 226Ra via a-spectrometry was performed. Low uranium content was a common characteristic for all the samples.
“You Look Young! Are You a Doctor?” A Qualitative Content Analysis of Anesthesiology Resident Responses to Ageism in Clinical Encounters
Authors: Stosic Morgan D. , Blanch-Hartigan Danielle , Ruben Mollie A. , Meyer Elaine C. , Henig Ariel , Waisel David B. , Blum Richard H.
Published: August 2023

Background

Healthcare trainees frequently report facing comments from their patients pertaining to their age. Exposure to ageist comments from patients may be related to greater stress and/or burnout in residents and may impact the quality of the resident-patient relationship. However, little empirical work has examined ageism expressed toward anesthesiology residents in clinical care, and therefore not much is known about how residents respond to these comments in practice. This research sought to determine how anesthesiology residents responded to ageist comments.

Methods

Anesthesiology residents (N = 60) engaged in a preoperative interaction with a standardized patient who was instructed to make an ageist comment to the resident. Resident responses were transcribed and coded using qualitative inductive content analysis to identify response themes.

Results

The most common resident response to the ageist comment, across gender and resident year, was to state their own experience. Some also described how they were still in training or that they were under supervision. Residents rarely reassured the patient that they would receive good care or identified the patient’s anxiety as a cause of the ageist remark.

Conclusions

These results provide a first step in understanding how ageism may be navigated by residents in clinical encounters. The authors discuss potential avenues for future research and education for responding to ageist remarks for both patients and clinicians.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Magnetic Resonance Imaging Manifestations of Annular Ligament Injuries in Children With Monteggia Fractures
Authors: Yue Junyi , Mu Weidong , Sun Zhenzhong , Tang Wei , Jiang Chuanqiang , Mu Mingzhang
Published: August 2023

Background:

Magnetic resonance imaging (MRI) is commonly performed in children with elbow injuries to visualize soft tissues such as the annular ligament. Herein, we investigated the MRI manifestations of annular ligament injuries in children with Monteggia fractures following attempted closed reduction.

Methods:

The clinical and imaging data of 88 children with acute Monteggia fractures treated at our hospital between 2015 and 2019 were analyzed. Clinically and radiographically, 67 patients achieved radiologic reduction of the radial head at the time of MRI, whereas 21 patients had a failed closed reduction. Annular ligament injury and superior radioulnar joint congruency were analyzed qualitatively, and the maximum superior radioulnar joint gap distance was measured.

Results:

MRI manifestations of annular ligament injury were primarily characterized as varying degrees of annular ligament displacement, as follows: I degree (10 patients), the annular ligament encircled the radial head without displacement; II degree (5 patients), the annular ligament was partially displaced but visibly encircled the radial head at the level of the radial notch; and III degree (73 patients), the annular ligament was completely displaced. In 15 patients with I and II degrees annular ligament injuries, the annular ligament encircled the radial head (maximum superior radioulnar joint gap distance, 1.2±0.3 mm), showing good congruency of the superior radioulnar joint. In 73 patients with III degree annular ligament injury, the annular ligament was displaced and did not encircle the radial head (maximum superior radioulnar joint gap distance, 3.3±2.7 mm; P<0.05), showing good congruency of the superior radioulnar joint in 25 of 73 patients, and significantly poor congruency in 48 of 73 patients (P<0.05).

Conclusions:

Annular ligament injuries in children with Monteggia fractures exhibit different degrees of displacement of the annular ligament. In I and II degree annular ligament injuries, the annular ligament still encircles the radial head. In III degree annular ligament injuries, the annular ligament is displaced away and is no longer around the radial head. Without the annular ligament restraining the radial head, the superior radioulnar joint is more likely to exhibit poor congruency and increased gap distance.

Level of Evidence:

Level II.
Outcomes of Adolescent T-condylar Fractures: Kids Do Not Always Make You Look Good
Authors: Young Jason , Hendrick Claudia , Miller Patricia E. , Vuillermin Carley B. , Yen Yi-Meng , Bauer Andrea S.
Published: August 2023

Background:

Optimal treatment for pediatric and adolescent T-condylar fractures remains poorly understood. We sought to assess how functional outcomes and range of motion (ROM) after surgical fixation of T-condylar fractures are affected by patient and surgical factors.

Methods:

This is a retrospective cohort study of 52 patients with operatively treated T-condylar fractures at a single tertiary pediatric referral center between 2003 and 2021. All patients younger than 18 at the time of injury with a radiographically confirmed diagnosis were included.

Results:

Fifty-two T-condylar fractures were included, with a mean patient age of 12.9 years (SD, 2.8). The cohort was 65% male. Nine (19%) fractures were open, 46% (24/52) were AO type C2, and 33% (17/52) occurred in skeletally mature individuals. The surgical approach was through olecranon osteotomy in 29% (15/52) of patients, and fixation included anatomically specific plates and screws in 42% (22/52) of patients. In our cohort, 46% (24/52) achieved good outcomes based on Jarvis ROM criteria and 42% (22/52) achieved good to excellent results based on Roberts functional criteria. The median loss of ROM was 58 degrees at 6 weeks, 20 degrees at 3 and 6 months, and 8 degrees at 1 year postoperatively. We observed a complication rate of 54% (28/52). Patients undergoing adult-type plate fixation had better postoperative range of motion at 6 weeks (ROM loss 52 vs. 80 degrees, P=0.03) and 3 months (10 vs. 35 degrees P=0.004) compared with pediatric-type fixation and trended towards better functional outcomes. We did not identify significant differences in functional outcome scores or complication rates with respect to surgical approach or skeletal maturity.

Conclusions:

Surgical fixation of pediatric and adolescent T-condylar fractures achieved a good to excellent functional outcome in only a minority of patients (46% Jarvis / 42% Roberts) with a high rate of postoperative complications (54%). Future work is needed to elucidate optimal treatment to minimize complications and achieve the best functional outcomes in these challenging fractures.

Level of Evidence:

Level—IV
Systematic review and meta-analysis Literature-based Clinical Retrospective Analysis of Acquired Reactive Perforating Collagenosis
Authors: Hu Qing-Jie , Chen Jing-Jing , Yao Xu
Published: August 2023

Objective:

Acquired reactive perforating collagenosis(ARPC) is a rare dermatosis that usually associated with systemic disease. The associations, characteristics and treatment rigemen of ARPC are not well understood.This study was performed to retrospectively evaluate the diagnosis and treatment statuses of acquired reactive perforating collagenosis (ARPC).

Methods:

A systematic review of the PubMed, Embase, and Scopus databases was independently performed by two reviewers. Data were extracted and qualitatively analyzed. The quality of the articles was assessed by using the Newcastle–Ottawa scale. The data are described in the manuscript. The study was registered with PROSPERO, CRD 42023448576.

Results:

In total, 189 patients (98 women, 91 men) in 124 studies were analyzed. Their mean age was 57.31 ± 15.21 years. A total of 88.89% (n = 168) of the patients had one or more systemic diseases, of which 57.67% (n = 109) had diabetes mellitus, 29.10% (n = 55) had chronic renal failure, 25.93% (n = 49) had hypertension, and 13.76% had malignancy (n = 26). The most frequently affected area was the lower extremities (72.49%, n = 137), followed by the trunk (70.37%, n = 133) and the upper extremities (63.49%, n = 120). One hundred sixty (84.66%) patients had pruritus, and 32.80% (n = 62) of them were positive for the Koebner phenomenon. Oral antihistamines and topical steroids were the most common treatments in this study, followed by narrow-band ultraviolet B therapy and allopurinol. Management of concomitant systemic diseases also resulted in improvement of ARPC.

Conclusion:

In this review, ARPC was frequently associated with systemic diseases, especially diabetes mellitus, renal failure, hypertension, and malignancy. The lower extremities and trunk were the most frequently affected areas, and pruritus usually appeared. Antihistamines and topical steroids were the most commonly used treatments, and we recommend narrow-band ultraviolet B therapy as the first-line treatment. Management of systemic diseases and relief of pruritus should be considered simultaneously.
Solitary Fibrous Tumor of the Pancreas
Authors: Yavas Aslihan , Tan Jianyou , Sahin Ozkan Hulya , Yilmaz Funda , Reid Michelle D. , Bagci Pelin , Shi Jiaqi , Shia Jinru , Adsay Volkan , Klimstra David S. , Basturk Olca
Published: August 2023

Solitary fibrous tumor (SFT) has been increasingly reported in various anatomic sites. However, it is still extremely rare in the pancreas. Herein, we present the first series of primary pancreatic SFTs. Nine cases of primary pancreatic SFTs were analyzed. The mean age was 60 years (36 to 76 y) with no sex predilection. Six tumors were in the head, 3 were in the tail. On imaging studies, tumors were described as a hypervascular mass, 2 revealed cystic areas, and 3 were favored to be neuroendocrine tumors. On biopsy, 2 cases were diagnosed as atypical spindle cell tumor; one was misdiagnosed as suspicious for sarcoma, and another case as metastatic renal cell carcinoma. Two were diagnosed as low-grade sarcoma and low-grade stromal tumor on frozen sections. Grossly, tumors were well-demarcated with a median size of 4 cm (0.9 to 15 cm). Microscopically, they were composed of ovoid to spindle tumor cells with no significant mitotic activity and were arranged in alternating hypercellular and hypocellular areas. Staghorn-like vessels and entrapped pancreatic parenchyma were also detected within all tumors. Tumor cells revealed diffuse/strong nuclear STAT6 expression in 7 of 8, CD34 in 7 of 9, and bcl-2 in 4 of 4 tested cases. One tested tumor harbored NAB2-STAT6 fusion. Eight patients with available follow-up data were free of disease at a mean follow-up of 76 months (3 to 189 mo). SFT should be considered in the differential diagnoses of mesenchymal neoplasms of the pancreas. Immunohistochemical nuclear STAT6 expression is a characteristic feature of SFT. Primary pancreatic SFTs seem to have favorable biological behavior in our series.
Conservation tools: the next generation of engineering–biology collaborations
Authors: Schulz Andrew K. , Shriver Cassie , Stathatos Suzanne , Seleb Benjamin , Weigel Emily G. , Chang Young-Hui , Saad Bhamla M. , Hu David L. , Mendelson Joseph R.
Published: August 2023

The recent increase in public and academic interest in preserving biodiversity has led to the growth of the field of conservation technology. This field involves designing and constructing tools that use technology to aid in the conservation of wildlife. In this review, we present five case studies and infer a framework for designing conservation tools (CT) based on human–wildlife interaction. Successful CT range in complexity from cat collars to machine learning and game theory methodologies and do not require technological expertise to contribute to conservation tool creation. Our goal is to introduce researchers to the field of conservation technology and provide references for guiding the next generation of conservation technologists. Conservation technology not only has the potential to benefit biodiversity but also has broader impacts on fields such as sustainability and environmental protection. By using innovative technologies to address conservation challenges, we can find more effective and efficient solutions to protect and preserve our planet’s resources.
Systems, variational principles and interconnections in non-equilibrium thermodynamics
Authors: Gay-Balmaz François , Yoshimura Hiroaki
Published: August 2023

The paper investigates a systematic approach to modelling in non-equilibrium thermodynamics by focusing upon the notion of interconnections, where we propose a novel Lagrangian variational formulation of such interconnected systems by extending the variational principle of Hamilton in mechanics. In particular, we show how a non-equilibrium thermodynamic system can be regarded as aninterconnected systemof primitive physical elements or subsystems throughout aninterconnection. While this approach is new in non-equilibrium thermodynamics, this idea has been known as a useful tool for the modelling of complicated systems in networks as well as in mechanics. Hence, the setting developed in this paper yields a promising direction for building a unifying description in various areas of modern science via thermodynamic principles, while being at the same time related to the early developments of variational mechanics.

This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.
Quantum theory only makes sense in Lazare Carnot's participatory engineering thermodynamics, a development of Leibniz's dynamics
Authors: Bristol Terry
Published: August 2023

Feynman insisted ‘no one understands quantum theory’. Yet, experimentalists tell us quantum theory is the most successful theory in history. Quantum theory cannot be understood as a classical mechanical theory since it arose through the ‘interpolation’ of two highly successful but complementary classical mechanics: Newtonian particle mechanics and Maxwellian wave mechanics. The two-slit experiment illustrates that what is experienced depends on choice of experimental set-up. Quantum theory is properly understood within the more general framework of engineering thermodynamics. In Part One, I point to four essential characteristics of quantum theory that cannot be understood in any framework defined by the classical mechanical presuppositions of symmetry and conservation. These four characteristics are the participatory, the complementary, the indeterminate and the new non-commutative geometry. In Part Two, articulating engineering thermodynamics, I note there are two histories and two formulations of thermodynamics: Carnot's engineering thermodynamics and the ‘rational mechanical’ tradition of Clausius-Boltzmann. These four essential characteristics of quantum theory are also characteristics of engineering thermodynamics. In Part Three, I trace the precursors of Lazare Carnot's engineering thermodynamics to earlier insights of Huygens, d'Alembert, Leibniz and the Bernoullis. Leibniz brought these forth in his meta-paradigm shift from Statics to Dynamics.

This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.
Theories of disorder and order, energy and information, in sociological thought
Authors: Martin John Levi
Published: August 2023

There has always been a close relation between thermodynamic theory and sociological theory, although they repeatedly part company and later rejoin. I discuss some of the most important ways in which the two have been in contact, focusing on the potential passage from theories of energy to theories of information and vice versa. I close by discussing how a closer engagement with classic thermodynamics may continue to be fruitful for sociological theorizing.

This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.
Non-additive entropies and statistical mechanics at the edge of chaos: a bridge between natural and social sciences
Authors: Tsallis Constantino
Published: August 2023

The Boltzmann–Gibbs (BG) statistical mechanics constitutes one of the pillars of contemporary theoretical physics. It is constructed upon the other pillars—classical, quantum, relativistic mechanics and Maxwell equations for electromagnetism—and its foundations are grounded on the optimization of the BG (additive) entropic functionalSBG=−k∑ipiln⁡pi. Its use in the realm of classical mechanics is legitimate for vast classes of nonlinear dynamical systems under the assumption that the maximal Lyapunov exponent ispositive(currently referred to asstrong chaos), and its validity has been experimentally verified in countless situations. It fails however when the maximal Lyapunov exponentvanishes(referred to asweak chaos), which is virtually always the case with complex natural, artificial and social systems. To overcome this type of weakness of the BG theory, a generalization was proposed in 1988 grounded on the non-additive entropic functionalSq=k((1−∑ipiq)/(q−1)) (q∈R; S1=SBG). The indexqand related ones are to be calculated, whenever mathematically tractable, from first principles and reflect the specific class of weak chaos. We review here the basics of this generalization and illustrate its validity with selected examples aiming to bridge natural and social sciences.

This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.
Development of a thermodynamics of human cognition and human culture
Authors: Aerts D. , Aerts Argüelles J. , Beltran L. , Sozzo S.
Published: August 2023

Inspired by foundational studies in classical and quantum physics, and by information retrieval studies in quantum information theory, we prove that the notions of ‘energy’ and ‘entropy’ can be consistently introduced in human language and, more generally, in human culture. More explicitly, if energy is attributed to words according to their frequency of appearance in a text, then the ensuing energy levels are distributed non-classically, namely, they obey Bose–Einstein, rather than Maxwell–Boltzmann, statistics, as a consequence of the genuinely ‘quantum indistinguishability’ of the words that appear in the text. Secondly, the ‘quantum entanglement’ due to the way meaning is carried by a text reduces the (von Neumann) entropy of the words that appear in the text, a behaviour which cannot be explained within classical (thermodynamic or information) entropy. We claim here that this ‘quantum-type behaviour is valid in general in human language’, namely, any text is conceptually more concrete than the words composing it, which entails that the entropy of the overall text decreases. In addition, we provide examples taken from cognition, where quantization of energy appears in categorical perception, and from culture, where entities collaborate, thus ‘entangle’, to decrease overall entropy. We use these findings to propose the development of a new ‘non-classical thermodynamic theory’ for human cognition, which also covers broad parts of human culture and its artefacts and bridges concepts with quantum physics entities.

This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.
BunDLe-Net: Neuronal Manifold Learning Meets Behaviour
Authors: Kumar Akshey , Gilra Aditya , Gonzalez-Soto Mauricio , Meunier Anja , Grosse-Wentrup Moritz
Published: August 2023

Neuronal manifold learning techniques represent high-dimensional neuronal dynamics in low-dimensional embeddings to reveal the intrinsic structure of neuronal manifolds. A common goal of these techniques is to learn embeddings that allow a good reconstruction of the original data. We introduce a novel neuronal manifold learning technique, BunDLe-Net, that learns a low-dimensional Markovian embedding of the neuronal dynamics which pre-serves only those aspects of the neuronal dynamics that are relevant for a given behavioural context. In this way, BunDLe-Net eliminates neuronal dynamics that are irrelevant for decoding behaviour, effectively de-noising the data to reveal better the intricate relationships between neuronal dynamics and behaviour. We show that BunDLe-Net learns highly consistent manifolds across animals that reveal the building blocks of their neuronal manifolds on a variety of data sets, ranging from calcium imaging data recorded in the nematodeC. elegansto spiking data from the rat hippocampus and primate somatosensory cortex.
Eccentricity-Dependent Saccadic Reaction Time: The Roles of Foveal Magnification and Attentional Orienting
Authors: Zhang Yufeng , Fries Pascal
Published: August 2023

A hallmark of primate vision is the emphasis on foveal processing, accompanied by frequent saccades that bring the fovea to salient parts of the scene, or to newly appearing stimuli. A saccade to a new stimulus is one of the most fundamental sensory-motor transformations. In macaque monkeys, we show that foveal magnification is not only the reason for saccades, but it also affects the dynamics of saccade initiation. In a task where the monkeys made saccades to peripheral target onsets, saccadic reaction time (SRT) increased with target eccentricity. Notably, we effectively eliminated this increase by scaling the target size according to the foveal magnification factor in the superior colliculus. We repeated the comparison between non-scaled and scaled targets, while changing the task to a delayed saccade task. In this task, the target was presented long before the saccade, and the saccade was triggered by foveal fixation offset rather than target onset, such that target onset long before fixation offset was essentially irrelevant for SRT. In this task, we found that SRT increased with target eccentricity, with similar rate for both non-scaled and scaled targets. Furthermore, this increase survived the addition of a salient distracting flash resetting attention to the foveal. The results obtained with the delayed saccades task are consistent with an attentional scan from the fovea to the target, a recently hypothesized general mechanism of attention.
IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits
Authors: Kossinna Pathum , Kumarapeli Senitha , Zhang Qingrun
Published: August 2023

The contribution of genetic variants to a complex phenotype may be mediated by various forms of complicated interactions. Currently, the discovery of genetic variants underlying interaction is limited, partly due to that the real interaction patterns are diverse and unknown, whereas exhaustively examining all potential combinations confers the risk of overfitting and instability. We propose IBAS, Interaction-Bridged Association Study, a new model using statistical learning techniques to extract representations of interaction patterns in transcriptome data, which act as a mediator for the next genotype-phenotype association test. Using simulated perturbation experiments, it is demonstrated that IBAS is more robust to noise than similar mediation-based protocols replying on single-genes, i.e., transcriptome-wide association studies (TWAS). By applying IBAS to real genotype-phenotype and expression data, we reported additional genes underlying complex traits as well as their biological annotations. IBAS unlocks the power of integrating gene-gene interactions in association mapping without concerning overfitting and instability.
spatiAlign: An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics
Authors: Zhang Chao , Liu Lin , Zhang Ying , Li Mei , Fang Shuangsang , Kang Qiang , Chen Ao , Xu Xun , Zhang Yong , Li Yuxiang
Published: August 2023

Integrative analysis of spatially resolved transcriptomics datasets empowers a deeper understanding of complex biological systems. However, integrating multiple tissue sections presents challenges for batch effect removal, particularly when the sections are measured by various technologies or collected at different times. Here, we propose spatiAlign, an unsupervised contrastive learning model that employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections. It enables the joint downstream analysis of multiple datasets not only in low-dimensional embeddings but also in the reconstructed full expression space. In benchmarking analysis, spatiAlign outperforms state-of-the-art methods in learning joint and discriminative representations for tissue sections, each potentially characterized by complex batch effects or distinct biological characteristics. Furthermore, we demonstrate the benefits of spatiAlign for the integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires a corrected gene expression matrix.
Comparing the advantages and disadvantages of physics-based and neural network-based modelling for predicting cycling power
Authors: Mayerhofer Patrick , Bajić Ivan , Donelan J. Maxwell
Published: August 2023

Models of physical phenomena can be developed using two distinct approaches: using expert knowledge of the underlying physical principles, or using experimental data to train a neural network. Here, our aim was to better understand the advantages and disadvantages of these two approaches. We chose to model cycling power because the physical principles are already well understood. Nine participants followed changes in cycling cadence transmitted through a metronome via earphones and we measured their cadence and power. We then developed and trained a physics-based model and a simple neural network model, where both models had cadence, derivative of cadence, and gear ratio as input, and power as output. We found no significant differences in the prediction performance between the models. The advantages of the neural network model were that, for similar performance, it did not require an understanding of the underlying principles of cycling nor did it require measurements of fixed parameters such as system weight or wheel size. These same features also give the physics-based model the advantage of interpretability, which can be important when scientists want to better understand the process being modelled.
The entropy of resting-state neural dynamics is a marker of general cognitive ability in childhood
Authors: Zdorovtsova Natalia , Young Edward J. , Akarca Danyal , Anwyl-Irvine Alexander ,   The RED Team,   The CALM Team, Astle Duncan E.
Published: August 2023

1

Resting-state network activity has been associated with the emergence of individual differences across childhood development. However, due to the limitations of time-averaged representations of neural activity, little is known about how cognitive and behavioural variability relates to the rapid spatiotemporal dynamics of these networks. Magnetoencephalography (MEG), which records neural activity at a millisecond timescale, can be combined with Hidden Markov Modelling (HMM) to track the spatial and temporal characteristics of transient neural states. We applied HMMs to resting-state MEG data from (n = 46) children aged 8-13, who were also assessed on their cognitive ability and across multiple parent-report measures of behaviour. We found that entropy-related properties of participants’ resting-state time-courses were positively associated with cognitive ability. Additionally, cognitive ability was positively correlated with the probability of transitioning into HMM states involving fronto-parietal and somatomotor activation, and negatively associated with a state distinguished by default-mode network suppression. We discuss how using dynamical measures to characterise rapid, spontaneous patterns of brain activity can shed new light on neurodevelopmental processes implicated in the emergence of cognitive differences in childhood.

Significance Statement

There is increasing evidence that the function of resting-state brain networks contributes to individual differences in cognition and behaviour across development. However, the relationship between dynamic, transient patterns of switching between resting-state networks and neurodevelopmental diversity is largely unknown. Here, we show that cognitive ability in childhood is related to the complexity of resting-state brain dynamics. Additionally, we demonstrate that the probability of transitioning into and remaining in certain ‘states’ of brain network activity predicts individual differences in cognitive ability.
The Dynamic Response of Human Lungs Due to Underwater Shock Wave Exposure
Authors: Bar-Kochba Eyal , Iwaskiw Alexander S. , Dunn Jenna M. , Ott Kyle A. , Harrigan Timothy P. , Demetropoulos Constantine K.
Published: August 2023

Since the 19th century, underwater explosions have posed a significant threat to service members. While there have been attempts to establish injury criteria for the most vulnerable organs, namely the lungs, existing criteria are highly variable due to insufficient human data and the corresponding inability to understand the underlying injury mechanisms. This study presents an experimental characterization of isolated human lung dynamics during simulated exposure to underwater shock waves. We found that the large acoustic impedance at the surface of the lung severely attenuated transmission of the shock wave into the lungs. However, the shock wave initiated large bulk pressure-volume cycles that are distinct from the response of the solid organs under similar loading. These pressure-volume cycles are due to compression of the contained gas, which we modeled with the Rayleigh-Plesset equation. The extent of these lung dynamics was dependent on physical confinement, which in real underwater blast conditions is influenced by factors such as rib cage properties and donned equipment. Findings demonstrate a potential causal mechanism for implosion injuries, which has significant implications for the understanding of primary blast lung injury due to underwater blast exposures.
BRAND: A platform for closed-loop experiments with deep network models
Authors: Ali Yahia H. , Bodkin Kevin , Rigotti-Thompson Mattia , Patel Kushant , Card Nicholas S. , Bhaduri Bareesh , Nason-Tomaszewski Samuel R. , Mifsud Domenick M. , Hou Xianda , Nicolas Claire , Allcroft Shane , Hochberg Leigh R. , Yong Nicholas Au , Stavisky Sergey D. , Miller Lee E. , Brandman David M. , Pandarinath Chethan
Published: August 2023

Artificial neural networks (ANNs) are state-of-the-art tools for modeling and decoding neural activity, but deploying them in closed-loop experiments with tight timing constraints is challenging due to their limited support in existing real-time frameworks. Researchers need a platform that fully supports high-level languages for running ANNs (e.g., Python and Julia) while maintaining support for languages that are critical for low-latency data acquisition and processing (e.g., C and C++). To address these needs, we introduce the Backend for Realtime Asynchronous Neural Decoding (BRAND). BRAND comprises Linux processes, termednodes, which communicate with each other in agraphvia streams of data. Its asynchronous design allows for acquisition, control, and analysis to be executed in parallel on streams of data that may operate at different timescales. BRAND uses Redis to send data between nodes, which enables fast inter-process communication and supports 54 different programming languages. Thus, developers can easily deploy existing ANN models in BRAND with minimal implementation changes. In our tests, BRAND achieved <600 microsecond latency between processes when sending large quantities of data (1024 channels of 30 kHz neural data in 1-millisecond chunks). BRAND runs a brain-computer interface with a recurrent neural network (RNN) decoder with less than 8 milliseconds of latency from neural data input to decoder prediction. In a real-world demonstration of the system, participant T11 in the BrainGate2 clinical trial performed a standard cursor control task, in which 30 kHz signal processing, RNN decoding, task control, and graphics were all executed in BRAND. This system also supports real-time inference with complex latent variable models like Latent Factor Analysis via Dynamical Systems. By providing a framework that is fast, modular, and language-agnostic, BRAND lowers the barriers to integrating the latest tools in neuroscience and machine learning into closed-loop experiments.
Graph Theoretical Network Structures Underlie Age-Related Differences in the Functional Connectome During Rest and Music Listening
Authors: Belden Alexander , Loui Psyche
Published: August 2023

Aging is associated with decreased functional connectivity within the default mode network, as well as auditory and reward systems which are involved in music listening. Understanding how music listening affects network organization of the aging brain, both globally and specific to the brain networks, will have implications for designing lifestyle interventions that tap into distinct networks in the brain. Here we apply graph-theory metrics of modularity, global efficiency, clustering coefficients, degrees, and betweenness centrality to compare younger and older adults (YA/OA, N=24 per group) in fMRI connectivity during rest and a music listening task. Results show a less modular but more globally efficient connectome in OAs, especially during music listening, resulting in main effects of group and task, as well as group-by-task interactions. ROI analyses indicated that the posterior cingulate is more centrally located than the medial prefrontal cortex in OAs. Overall, reduced modularity and increased global efficiency with age is in keeping with previously-observed functional reorganizations, and interaction effects show that age-related differences in baseline network organization are reflected in, potentially magnified by, music listening.
Profiling novel lateral gene transfer events in the human microbiome
Authors: Hsu Tiffany Y. , Nzabarushimana Etienne , Wong Dennis , Luo Chengwei , Beiko Robert G. , Langille Morgan , Huttenhower Curtis , Nguyen Long H. , Franzosa Eric A.
Published: August 2023

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (∼2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available athttp://huttenhower.sph.harvard.edu/waafle.
Enhanced generalization and specialization of brain representations of semantic knowledge in healthy aging
Authors: Margolles Pedro , Soto David
Published: August 2023

Aging is often associated with a decrease in cognitive capacities. However, semantic memory appears relatively well preserved in healthy aging. Both behavioral and neuroimaging studies support the view that changes in brain networks contribute to this preservation of semantic cognition. However, little is known about the role of healthy aging in the brain representation of semantic categories. Here we used pattern classification analyses and computational models to examine the neural representations of living and non-living word concepts. The results demonstrate that brain representations of animacy in healthy aging exhibit increased similarity across categories, even across different task contexts. This pattern of results aligns with the neural dedifferentiation hypothesis that proposes that aging is associated with decreased specificity in brain activity patterns and less efficient neural resource allocation. However, the loss in neural specificity for different categories was accompanied by increased dissimilarity of item-based conceptual representations within each category. Taken together, the age-related patterns of increased generalization and specialization in the brain representations of semantic knowledge may reflect a compensatory mechanism that enables a more efficient coding scheme characterized by both compression and sparsity, thereby helping to optimize the limited neural resources and maintain semantic processing in the healthy aging brain.
Stimulus invariant aspects of the retinal code drive discriminability of natural scenes
Authors: Hoshal Benjamin D. , Holmes Caroline M. , Bojanek Kyle , Salisbury Jared , Berry Michael J. , Marre Olivier , Palmer Stephanie E.
Published: August 2023

Everything that the brain sees must first be encoded by the retina, which maintains a reliable representation of the visual world in many different, complex natural scenes while also adapting to stimulus changes. This study quantifies whether and how the brain selectively encodes stimulus features about scene identity in complex naturalistic environments. While a wealth of previous work has dug into the static and dynamic features of the population code in retinal ganglion cells, less is known about how populations form both flexible and reliable encoding in natural moving scenes. We record from the larval salamander retina responding to five different natural movies, over many repeats, and use these data to characterize the population code in terms of single-cell fluctuations in rate and pairwise couplings between cells. Decomposing the population code into independent and cell-cell interactions reveals how broad scene structure is encoded in the retinal output. while the single-cell activity adapts to different stimuli, the population structure captured in the sparse, strong couplings is consistent across natural movies as well as synthetic stimuli. We show that these interactions contribute to encoding scene identity. We also demonstrate that this structure likely arises in part from shared bipolar cell input as well as from gap junctions between retinal ganglion cells and amacrine cells.
A taxon-restricted duplicate ofIroquois3is required for patterning the spider waist
Authors: Setton Emily V. W. , Ballesteros Jesús A. , Blaszczyk Pola O. , Klementz Benjamin C. , Sharma Prashant P.
Published: August 2023

The chelicerate body plan is distinguished from other arthropod groups by its division of segments into two tagmata: the anterior prosoma (“cephalothorax”) and the posterior opisthosoma (“abdomen”). Little is understood about the genetic mechanisms that establish the prosomal-opisthosomal (PO) boundary. To discover these mechanisms, we created high-quality genomic resources for the large-bodied spiderAphonopelma hentzi. We sequenced specific territories along the antero-posterior axis of developing embryos and applied differential gene expression analyses to identify putative regulators of regional identity. After bioinformatic screening for candidate genes that were consistently highly expressed in the posterior segments, we validated the function of highly ranked candidates in the tractable spider modelParasteatoda tepidariorum. Here, we show that an arthropod homolog of the Iroquois complex of homeobox genes is required for proper formation of the boundary between arachnid tagmata. The function of this homolog had not been previously characterized, because it was lost in the common ancestor of Pancrustacea, precluding its investigation in well-studied insect model organisms. Knockdown of the spider copy of this gene, which we designate aswaist-less, inP. tepidariorumresulted in embryos with defects in the PO boundary, incurring discontinuous spider germ bands. We show thatwaist-lessis required for proper specification of dorso-ventral identity in the segments that span the prosoma-opisthosoma boundary, which in adult spiders corresponds to the narrowed pedicel. Our results suggest the requirement of an ancient, taxon-restricted paralog for the establishment of the tagmatic boundary that defines Chelicerata.
Tail length in male versus female fox squirrels (Sciurus niger)
Authors: Nichols Hannah K. , Smith Shaylee K. , Eddington Valerie M. , Calistri-Yeh Adrienne , Kloepper Laura N. , Hilliard Young Vanessa K
Published: August 2023

Background

Arboreal mammals rely on their tails to aid in balance while maneuvering complex habitats. Females experience additional challenges to locomotion due to reproductive demands including altered body mass and/or body shape, which leads to shifts in center of mass. Without compensation, this may increase the risk of losing balance and falling out of trees. We tested the hypothesis that female squirrels have longer tails than males to offset shifts in center of mass that may result from pregnancy.

Results

Morphological data were collected from 57 fox squirrels (Sciurus niger) in northern Indiana in summer 2019 and 2021. Although our initial t-test analysis of relative tail length (RTL) showed that female squirrels had longer tails than males (p= 0.02), a subsequent ANCOVA that controlled for effect of body length indicated no significant effect of sex on tail length (p= 0.42).

Conclusions

The results of this study demonstrate the potential impacts of different analysis methods on overall understanding of organismal functional morphology and are an important addition to the literature on tail form and function, which remains poorly understood compared to other appendages.