bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects and acceptability of virtual reality to facilitate mindfulness practice in university students
Authors: Modrego-Alarcón Marta , Morillo Héctor , Campos Daniel , Navarro-Gil María Teresa , Montero-Marín Jesús , Monreal-Bartolomé Alicia , García-Campayo Javier , López-Del-Hoyo Yolanda
Published: December 2023

Mindfulness practices have proven to be effective for improving the mental health of many populations, including university students. However, these practices can be challenging for naive meditators. Virtual reality (VR) can create virtual scenarios that facilitate the practice of mindfulness. This study presents secondary data from a randomized controlled trial on the effects and acceptability of mindfulness-based VR environments conducted with a sample of university students. Specifically, it involved a single condition (n = 93) receiving an intervention that comprised six short mindfulness sessions in VR. Measurements were taken of participants’ state mindfulness and emotional state immediately before and after the implementation of each VR environment. Sense of presence was measured subsequent to each VR environment. Furthermore, participants were asked to rate their expectations for at baseline and satisfaction with the experience after the intervention. Participants significantly improved both state mindfulness and emotional states, and they reported a moderate-to-strong sense of presence in each of the VR environments. Moreover, participants reported high expectation and satisfaction scores for the intervention. This study shows the potential of VR in mindfulness, although there is a need for more research in this area and, in particular, more sophisticated trial designs.
Comparing the Effectiveness of a Mindfulness-Based Intervention and Progressive Muscle Relaxation in a Military Context
Authors: Krick Annika , Felfe Jörg
Published: December 2023

Objectives

While stressors of military deployment are known to have profound effects on health, less is known about effective methods for promoting health. A few studies have examined the effectiveness of mindfulness-based interventions (MBIs) in this context; however, fewer have used an active control group and objective health indicators. Therefore, this study examined the effects of an MBI in comparison to a similarly structured traditional stress management intervention (progressive muscle relaxation, PMR) on health indicators among military personnel.

Method

Using a 2 (pre vs. post) × 3 (group: MBI, PMR vs. inactive control group, ICG) experimental mixed design, participants (MBI, n = 118; PMR, n = 55; ICG, n = 156) answered baseline and post-intervention self-reported measures. Physiological parameters were assessed before and after each session.

Results

Results showed that MBI is superior to PMR and ICG, leading to higher increases in mindfulness, positive affect, and self-care, and greater decreases in physical complaints. This is also confirmed by objective data. Participants in the MBI demonstrated improved heart rate variability and reduced heart rate, while no change was evident for PMR and ICG. However, both MBI and PMR were equally effective in reducing strain.

Conclusions

This study provides further evidence for the effectiveness of MBIs in this specific professional group based on rigorous methodology (comparing to a competing intervention, self-reported and objective measures). MBI is even more effective than PMR as a traditional health intervention in terms of promoting mindfulness, positive affect, and health behavior, as well as reducing complaints.

Preregistration

This study is not preregistered.
A New Approach to Measure Absorptive Capacity and Appropriability: a Case of Study in Emerging Markets
Authors: Cuéllar Sergio , Fernandez-Bajón Maria Teresa , de Moya Anegón Felix
Published: December 2023

Absorptive capacity (AC) and appropriability (KA) are crucial elements in generating competitive advantages and improving innovation performance in different countries and organizations. Moreover, the relationship between AC and KA has not been sufficiently studied, and there is still not a clear understanding of the impact they have on in the generation of rents and value. This research proposes a methodology to analyze AC and KA at a country level using the scientific capabilities of a country as base. We identified the Colombian scientific literature SKL (1680 record) from the Patents Lens database, which have been cited at least once or more per patent (3066 records), and we identified the papers that were cited by this SKL (50,697) in order identify the flows between forward citations (FC) and backward citations (BC) at a country level. We associated BC to the AC acquisition stage, SKL to assimilation, and FC to transformation and exploitation AC phases. The patents were also associated with KA. In addition, we focused on the KA process, analyzing the organizations involved in the SKL and KA process by studying when KA was done by local organizations, by international organizations in the SKL development, or when knowledge was leaked -knowledge spillovers- KS. Finally, we identified when the SKL organization was the corresponding author to analyze whether KA changes in these situations. Our main conclusion was that KA and the last stages of AC of native scientific development rarely happen in Colombia. The primary outcome of this absorption is a KS.
Committing to reproducibility and explainability: using Git as a research journal
Authors: Huskey Samuel J.
Published: December 2023

Traditional critical editions in print offer a model for creating a culture of reproducible and explainable research in Digital Humanities. In addition to explaining their editorial methods and practices in a preface, editors provide a critical apparatus to allow readers to evaluate the evidence and decide for themselves whether the editor’s judgment is sound. This paper will argue for viewing distributed, version-controlled data repositories (e.g., Git) in the same way, to empower users to follow the choices and methods of DH researchers and to reproduce their work. Using examples from a current project, this paper will propose some guidelines for using Git to promote reproducibility and explainability in the publication of DH research of all kinds.
Do air pollution levels influence enforcement by regulators? Evidence from China
Authors: Li Chaofan , Zhou Pin
Published: December 2023

This paper examines the relationship between air pollution levels and regulators’ enforcement levels and observes that air pollution levels in firms’ locations reduce enforcement from regulators. Moreover, regulators are more likely to suffer from type II errors when air pollution levels in firms’ locations are higher, verifying the effect of regulators’ unwillingness to travel due to air pollution. The cross-sectional analysis suggests that enforcement from regulatory authorities in areas with lower air pollution levels than in firms’ locations, positioned at great distances from firms’ locations, and with greater workloads is less strict when air pollution levels in firms’ locations are higher. We further test whether air pollution levels reduce the efficiency of regulators and find that firms with lower earnings quality and weaker corporate governance are less likely to be subjected to enforcement by regulators when air pollution levels in the firms’ locations are higher.
Abortion education: teaching the next generation of clinicians
Authors: Ishii Megan , Albrecht Sarah , Raidoo Shandhini , Stowers Paris
Published: December 2023

Abortion is a safe and common part of essential healthcare. To ensure patients have access to comprehensive reproductive care, clinical educators are tasked with training the next generation of clinicians in abortion care in the setting of growing restrictions. Medical schools and residency program programs must adopt purposeful strategies to optimize abortion education and increase educational efficacy. Abortion training should ideally combine hands-on clinical skills such as ultrasound imaging and procedural abortion techniques, as well as discussions of medical ethics, advocacy, and strategies to emotionally support patients.
Playwriting, Dramaturgy and Space
Authors: Freeman Sara
Published: December 2023

Theatre has come back to text, but with perspectives shifted by the experimental practices of the twentieth century across performance forms. Contemporary playwriting brings its scenographic engagement to the foreground of the text, reflecting the spatial turn in theory and practice. In production, this spatiality has renewed and enlivened the status and impact of text-based theatre. Theatre studies needs to better describe the artfulness of contemporary text-based theatre, bringing to it the same sophisticated lenses scholars and critics have used for performance-based theatre and other experimental theatre practices. This Element does that by presenting the work of Caryl Churchill, Naomi Iizuka, and Sarah Ruhl as exemplary of the way text-based theatre, both its scripts and productions, now creates and expects a spatialized imaginary and demonstrates the potentials of text-based theatre in an increasingly visual and spatial field of cultural production.
The Life and Music of Elizabeth Maconchy
Authors: Siegel Erica
Published: December 2023

The first full-length biographical study of Elizabeth Maconchy (1907-1994).
Malmesbury Abbey 670-1539
Authors: McAleavy Tony
Published: December 2023

The book tells the story of Malmesbury Abbey in Wiltshire, a major centre of cultural and royal patronage, from the time of Aldhelm in the late seventh century to the Dissolution in 1539.
National Medievalism in the Twenty-First Century
Authors: Berger Matthias D.
Published: December 2023

How ideas and ideals of an imagined, protean, national Middle Ages have once again become a convergence point for anxieties about politics, history and cultural identity in our time - and why.
Performing Arts and Gender in Postcolonial Western Uganda
Authors: Cimardi Linda
Published: December 2023

Focusing on 'runyege', the main traditional performance genre of the Banyoro and Batooro people, this book explores the entanglement of traditional music, dance, and theater with gender and postcolonialism in Western Uganda.
Music and Religion in the Writings of Ian McEwan
Authors: Quinn Iain
Published: December 2023

This book examines Ian McEwan's ability to discern in his writing sentiments that easily resonate with musicians, explores the value of music in exhibiting McEwan's views on the world, and presents his perspective on religion's role within society.
A data-driven method for modelling dissipation rates in stratified turbulence
Authors: Lewin Samuel F. , de Bruyn Kops Stephen M. , Caulfield Colm-cille P. , Portwood Gavin D.
Published: December 2023

We present a deep probabilistic convolutional neural network (PCNN) model for predicting local values of small-scale mixing properties in stratified turbulent flows, namely the dissipation rates of turbulent kinetic energy and density variance,

$\varepsilon$

and

$\chi$

. Inputs to the PCNN are vertical columns of velocity and density gradients, motivated by data typically available from microstructure profilers in the ocean. The architecture is designed to enable the model to capture several characteristic features of stratified turbulence, in particular the dependence of small-scale isotropy on the buoyancy Reynolds number

$Re_b:=\varepsilon /(\nu N^2)$

, where

$\nu$

is the kinematic viscosity and

$N$

is the background buoyancy frequency, the correlation between suitably locally averaged density gradients and turbulence intensity and the importance of capturing the tails of the probability distribution functions of values of dissipation. Empirically modified versions of commonly used isotropic models for

$\varepsilon$

and

$\chi$

that depend only on vertical derivatives of density and velocity are proposed based on the asymptotic regimes

$Re_b\ll 1$

and

$Re_b\gg 1$

, and serve as an instructive benchmark for comparison with the data-driven approach. When trained and tested on a simulation of stratified decaying turbulence which accesses a range of turbulent regimes (associated with differing values of

$Re_b$

), the PCNN outperforms assumptions of isotropy significantly as

$Re_b$

decreases, and additionally demonstrates improvements over the fitted empirical models. A differential sensitivity analysis of the PCNN facilitates a comparison with the theoretical models and provides a physical interpretation of the features enabling it to make improved predictions.
Do human capital and institutional quality contribute to Brazil's long term real convergence/divergence process? A Markov regime-switching autoregressive approach
Authors: Doré Natalia Izelli , Teixeira Aurora A. C.
Published: December 2023

This paper assesses Brazil's real convergence (1822–2019) through unit root tests and Markov Regime-Switching (MS) models in three different scenarios: towards (i) other six Latin American countries (LA6); (ii) Portugal; and (iii) the technological frontier country, the US. The extended unit root test results favour Brazil's very long-run real convergence towards LA6 and Portugal, but not the US. The estimated MS models, involving two different regimes, real convergence and real non-convergence/divergence, capture institutional quality's positive effect in promoting Brazil's real convergence.
Der Fall Hildegard Hetzer (1899 – 1991) und der Anteil weiterer Psychologinnen an der Eindeutschung polnischer Kinder während des Zweiten Weltkriegs
Authors: Stock Armin , Amend Anna-Lena , Koza Miłosz
Published: December 2023

Zusammenfassung: In dieser Arbeit wird der Fall von Prof. Dr. Hildegard Hetzer und ihre Beteiligung an der zwangsweisen Germanisierung polnischer Kinder während des Zweiten Weltkriegs erneut betrachtet. Wir haben dazu über mehrere Jahre und umfangreich in polnischen und anderen Archiven recherchiert und bislang unbekannte neue Dokumente gefunden. Diese erlauben es uns, den Anteil von Frau Prof. Hetzer an dem ihr vorgeworfenen Verbrechen gegen die Menschlichkeit genauer als bisher zu bestimmen und darüber hinaus deutlich mehr belastete und bislang unbekannte Mittäterinnen von Seiten der Psychologie zu identifizieren.
Grassland Greening and Water Resource Availability May Coexist in a Warming Climate in Northern China and the Tibetan Plateau
Authors: Zhang Caijin , Long Di , Liu Tingxi , Slater Louise J. , Wang Guoqiang , Zuo Depeng , Duan Limin , Cui Yanhong , Cui Yingjie
Published: December 2023

Greening of Northern China and the Tibetan Plateau (NCTP) has been observed by increases in the remotely sensed leaf area index (LAI), driven primarily by CO2 fertilization effects, anthropogenic warming, and the implementation of ecological restoration programs. Continued growth of LAI throughout the 21st century is also projected by the Coupled Model Intercomparison Project Phase 6 (CMIP6) scenarios. However, the question of whether local water resources can sustain ongoing grassland greening has not been adequately investigated. Here we assessed the sustainability of water resources under grassland greening across NCTP under various climate scenarios using water yield (WY, defined as precipitation minus actual evapotranspiration) as the key metric. Unexpectedly, we observe the coexistence of increases in LAI and WY in most of NCTP. In a warming climate with increasing precipitation and CO2, we find that grasses maintain high water use efficiency to sustain their growth, contributing to continued local water resource availability. Thus, livestock production may also continue to increase under the simultaneous growth of LAI and WY in the future.
A Statistics‐Based Analytical Framework for Intratidal and Tidally Averaged Salinity Distribution in Estuaries
Authors: Laurel‐Castillo Jorge Armando , Valle‐Levinson Arnoldo
Published: December 2023

Near year‐long time series of salinity at five stations were used to depict the intratidal and subtidal salinity structure along an estuary: the Suwannee River in West Florida. The salinity field was described with statistical and analytical methods. Along‐estuary salinity distributions were first characterized with Hilbert Empirical Orthogonal Functions (HEOFs). Then, an analytical function, based on advection‐diffusion processes, was fitted to the amplitude and phase of the HEOFs to understand the direction of salinity transport due to riverine and oceanic pulses. The statistical and analytical approach proposed here, showed how the salinity distribution varied throughout the year depending on the subtidal water level and the river discharge. Also, the approach identified the dominance of oceanic or riverine pulses in molding the salinity field.
A Lagrangian Perspective on the Atlantic and Pacific Precipitation‐Evaporation Asymmetry
Authors: Craig P. M. , Ferreira D. , Methven J.
Published: December 2023

Total precipitation minus evaporation (P − E) for the Atlantic is negative while it is approximately neutral for the Pacific. This has frequently been attributed to westward Atlantic‐to‐Pacific moisture flux across Central America. However, this Eulerian perspective has limited scope as it does not consider the origins of the water crossing ocean drainage basin boundaries and the possibility that it has remote sources. By using an airmass trajectory model, we take a Lagrangian approach to investigate the origin of the moisture contributing to fluxes, Qn, across these boundaries. Qn is partitioned into contributions from each basin, the stratosphere and trajectories not assigned an origin. The total Qn across each basin boundary are mainly composed of contributions from the two adjacent basins while remote or stratospheric origins make small contributions. Partitioning Qn shows that the atmosphere exports ∼1 Sv water vapor from the Atlantic, Indian and Pacific basins with a similar quantity imported to the Pacific. However, Atlantic and Indian atmospheric imports are ∼0.5–0.6 Sv. Normalizing by drainage basin perimeters reveals that the import to these basins is half as efficient as Pacific import. Partitioning P − E into contributions from other basins shows that Pacific moisture import is dominated by trajectories with Indian basin origin (∼38%, or 0.43 Sv, of total Pacific import). The import is greatest in boreal summer due to the Asian monsoon flow and stronger westward flux across Central America. These anomalies dominate the difference in annual imports between the Pacific, Atlantic and Indian basins.
Summer Extreme Rainfall Over the Middle and Lower Reaches of Yangtze River: Role of Synoptic Patterns in Historical Changes and Future Projections
Authors: Hu Yang , Lin Yanluan , Deng Yi , Bao Jiawei
Published: December 2023

It is one of the major challenges in climate science to project future changes in extreme rainfall. To overcome this challenge, in this study, four typical synoptic patterns (SPs) triggering summer extreme rainfall over the middle and lower reaches of Yangtze River (MLYR) are identified through hierarchical clustering. These typical SPs share common characteristics of intensified Mei‐yu trough and Western Pacific Subtropical High but differ in terms of mid‐latitudes disturbances, such as an intensified ridge (Cluster 1, Cluster 2) or trough (Cluster 3, Cluster 4) near Lake Baikal (Cluster 1, Cluster 3) or Northeast China (Cluster 2, Cluster 4). The linkage between extreme rainfall and typical SPs is verified at various time scales. The typical SPs associated with extreme rainfall are substantially different from the circulation patterns found on ordinary days, and their frequency is significantly correlated with that of extreme rainfall across the interannual scales. Furthermore, the distinct changes in different typical SPs serve as a “bridge” for understanding the long‐term impact of circulation changes on local extreme rainfall, even though the two do not appear to be connected at first sight. Specifically, the circulation changes imply more (less) frequent SP‐Cluster 1 (SP‐Cluster 3), which tends to produce more extreme rainfall to the south (north) of the Yangtze River within MLYR. To project future changes in extreme rainfall, we utilize a weighting method for the multi‐model ensemble based on each model's capability to capture the observed typical SPs. This method effectively narrows the inter‐model spread.
The human neuropsychiatric risk gene Drd2 is necessary for social functioning across evolutionary distant species
Authors: Ike Kevin G. O. , Lamers Sanne J. C. , Kaim Soumya , de Boer Sietse F. , Buwalda Bauke , Billeter Jean-Christophe , Kas Martien J. H.
Published: December 2023

The Drd2 gene, encoding the dopamine D2 receptor (D2R), was recently indicated as a potential target in the etiology of lowered sociability (i.e., social withdrawal), a symptom of several neuropsychiatric disorders such as Schizophrenia and Major Depression. Many animal species show social withdrawal in response to stimuli, including the vinegar fly Drosophila melanogaster and mice, which also share most human disease-related genes. Here we will test for causality between Drd2 and sociability and for its evolutionary conserved function in these two distant species, as well as assess its mechanism as a potential therapeutic target. During behavioral observations in groups of freely interacting D. melanogaster, Drd2 homologue mutant showed decreased social interactions and locomotor activity. After confirming Drd2’s social effects in flies, conditional transgenic mice lacking Drd2 in dopaminergic cells (autoreceptor KO) or in serotonergic cells (heteroreceptor KO) were studied in semi-natural environments, where they could freely interact. Autoreceptor KOs showed increased sociability, but reduced activity, while no overall effect of Drd2 deletion was observed in heteroreceptor KOs. To determine acute effects of D2R signaling on sociability, we also showed that a direct intervention with the D2R agonist Sumanirole decreased sociability in wild type mice, while the antagonist showed no effects. Using a computational ethological approach, this study demonstrates that Drd2 regulates sociability across evolutionary distant species, and that activation of the mammalian D2R autoreceptor, in particular, is necessary for social functioning.
Generalization of beneficial exposure effects to untreated stimuli from another fear category
Authors: Kodzaga Iris , Dere Ekrem , Zlomuzica Armin
Published: December 2023

Previous research has shown that fear associated with one stimulus often spreads to other stimuli with similar perceptual features as well as across different stimulus categories. Exposure is considered as the most effective intervention to attenuate exaggerated fear. The extent to which exposure treatment effects can generalize to fears not targeted during treatment remains elusive. Previous studies on possible generalization of beneficial effects of exposure used stimuli sharing the same stimulus category and/or stimuli having high perceptual similarity. The current study examined whether exposure treatment generalization can be achieved for untreated stimuli which do not share any perceptual resemblance and belong to a different fear category. An analogue sample of fifty participants with fear of spiders (animal-related fears) and heights (natural environment-related fears) was tested. Participants have been randomly assigned to either an exposure treatment (n = 24) or a control condition (n = 26). Exposure treatment was designed to only target participants’ fear of spiders, leaving their fear of heights untreated. Results demonstrated that the effects of exposure treatment generalized to fear of heights, as indicated by a reduction in behavioral avoidance, as well as self-reported acrophobia symptoms. The present study confutes the assumption that generalization of exposure effects to untreated fears is based on perceptual similarity. Clearly, further research is required to determine the decisive factors, in order to expand the generalization effect permanently to any given type of fear.
Mutual communication between radiosensitive and radioresistant esophageal cancer cells modulates their radiosensitivity
Authors: Xie Congying , Chen Xiao , Chen Yueming , Wang Xingyue , Zuo Jiwei , Zheng Anqi , Luo Zhicheng , Cheng Xiaoxiao , Zhong Shouhui , Jiang Jiayu , Du Jizao , Zhao Yuemei , Jiang Peipei , Zhang Wei , Chen Didi , Pan Huanle , Shen Lanxiao , Zhu Baoling , Zhou Qingyu , Xu Yunsheng , Tang Kai-Fu
Published: December 2023

Radiotherapy is an important treatment modality for patients with esophageal cancer; however, the response to radiation varies among different tumor subpopulations due to tumor heterogeneity. Cancer cells that survive radiotherapy (i.e., radioresistant) may proliferate, ultimately resulting in cancer relapse. However, the interaction between radiosensitive and radioresistant cancer cells remains to be elucidated. In this study, we found that the mutual communication between radiosensitive and radioresistant esophageal cancer cells modulated their radiosensitivity. Radiosensitive cells secreted more exosomal let-7a and less interleukin-6 (IL-6) than radioresistant cells. Exosomal let-7a secreted by radiosensitive cells increased the radiosensitivity of radioresistant cells, whereas IL-6 secreted by radioresistant cells decreased the radiosensitivity of radiosensitive cells. Although the serum levels of let-7a and IL-6 before radiotherapy did not vary significantly between patients with radioresistant and radiosensitive diseases, radiotherapy induced a more pronounced decrease in serum let-7a levels and a greater increase in serum IL-6 levels in patients with radioresistant cancer compared to those with radiosensitive cancer. The percentage decrease in serum let-7a and the percentage increase in serum IL-6 levels at the early stage of radiotherapy were inversely associated with tumor regression after radiotherapy. Our findings suggest that early changes in serum let-7a and IL-6 levels may be used as a biomarker to predict the response to radiotherapy in patients with esophageal cancer and provide new insights into subsequent treatments.
Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer
Authors: Lu Di , Wu Xuanzhen , Wu Wendy , Wu Shuangxiu , Li Hui , Zhang Yuhong , Yan Xuebin , Zhai Jianxue , Dong Xiaoying , Feng Siyang , Zhang Xueying , Sun Fuming , Wang Shaobo , Cai Kaican
Published: December 2023

Esophageal cancer is a highly incidence and deadly disease with a poor prognosis, especially in developing countries. Owing to the lack of specific symptoms and early diagnostic biomarkers, most patients are diagnosed with advanced disease, leading to a 5-year survival rate of less than 15%. Early (n = 50) and middle-advanced (n = 50) esophageal squamous cell carcinoma (ESCC) patients, as well as 71 healthy individuals, underwent 5-hydroxymethylcytosine (5hmC) sequencing on their plasma cell-free DNA (cfDNA). A Northern Chinese cohort of cfDNA 5hmC dataset of 150 ESCC patients and 183 healthy individuals were downloaded for validation. A diagnostic model was developed using cfDNA 5hmC signatures and then improved by low-pass whole genome sequencing (WGS) features of cfDNA. Conserved cfDNA 5hmC modification motifs were observed in the two independent ESCC cohorts. The diagnostic model with 5hmC features achieved an AUC of 0.810 and 0.862 in the Southern and Northern cohorts, respectively, with sensitivities of 69.3–74.3% and specificities of 82.4–90.7%. The performance was well maintained in Stage I to Stage IV, with accuracy of 70–100%, but low in Stage 0, 33.3%. Low-pass WGS of cfDNA improved the AUC to 0.934 with a sensitivity of 82.4%, a specificity of 88.2%, and an accuracy of 84.3%, particularly significantly in Stage 0, with an accuracy up to 80%. 5hmC and WGS could efficiently differentiate very early ESCC from healthy individuals. These findings imply a non-invasive and convenient method for ESCC detection when clinical treatments are available and may eventually prolong survival.
Ultra-wide field and new wide field composite retinal image registration with AI-enabled pipeline and 3D distortion correction algorithm
Authors: Kalaw Fritz Gerald P. , Cavichini Melina , Zhang Junkang , Wen Bo , Lin Andrew C. , Heinke Anna , Nguyen Truong , An Cheolhong , Bartsch Dirk-Uwe G. , Cheng Lingyun , Freeman William R.
Published: December 2023

Purpose

This study aimed to compare a new Artificial Intelligence (AI) method to conventional mathematical warping in accurately overlaying peripheral retinal vessels from two different imaging devices: confocal scanning laser ophthalmoscope (cSLO) wide-field images and SLO ultra-wide field images.

Methods

Images were captured using the Heidelberg Spectralis 55-degree field-of-view and Optos ultra-wide field. The conventional mathematical warping was performed using Random Sample Consensus—Sample and Consensus sets (RANSAC-SC). This was compared to an AI alignment algorithm based on a one-way forward registration procedure consisting of full Convolutional Neural Networks (CNNs) with Outlier Rejection (OR CNN), as well as an iterative 3D camera pose optimization process (OR CNN + Distortion Correction [DC]). Images were provided in a checkerboard pattern, and peripheral vessels were graded in four quadrants based on alignment to the adjacent box.

Results

A total of 660 boxes were analysed from 55 eyes. Dice scores were compared between the three methods (RANSAC-SC/OR CNN/OR CNN + DC): 0.3341/0.4665/4784 for fold 1-2 and 0.3315/0.4494/4596 for fold 2-1 in composite images. The images composed using the OR CNN + DC have a median rating of 4 (out of 5) versus 2 using RANSAC-SC. The odds of getting a higher grading level are 4.8 times higher using our OR CNN + DC than RANSAC-SC (p < 0.0001).

Conclusion

Peripheral retinal vessel alignment performed better using our AI algorithm than RANSAC-SC. This may help improve co-localizing retinal anatomy and pathology with our algorithm.
Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves
Authors: Cooke Rob , Sayol Ferran , Andermann Tobias , Blackburn Tim M. , Steinbauer Manuel J. , Antonelli Alexandre , Faurby Søren
Published: December 2023

Birds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the introduction of invasive species) have been recorded, the true number is likely much larger. Here, by combining recorded extinctions with model estimates based on the completeness of the fossil record, we suggest that at least ~1300–1500 bird species (~12% of the total) have gone extinct since the Late Pleistocene, with 55% of these extinctions undiscovered (not yet discovered or left no trace). We estimate that the Pacific accounts for 61% of total bird extinctions. Bird extinction rate varied through time with an intense episode ~1300 CE, which likely represents the largest human-driven vertebrate extinction wave ever, and a rate 80 (60–95) times the background extinction rate. Thus, humans have already driven more than one in nine bird species to extinction, with likely severe, and potentially irreversible, ecological and evolutionary consequences.
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
Authors: Janesick Amanda , Shelansky Robert , Gottscho Andrew D. , Wagner Florian , Williams Stephen R. , Rouault Morgane , Beliakoff Ghezal , Morrison Carolyn A. , Oliveira Michelli F. , Sicherman Jordan T. , Kohlway Andrew , Abousoud Jawad , Drennon Tingsheng Yu , Mohabbat Seayar H. ,   10x Development Teams, Taylor Sarah E. B.
Published: December 2023

Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.
Magmatic immiscibility and the origin of magnetite-(apatite) iron deposits
Authors: Pietruszka Dorota K. , Hanchar John M. , Tornos Fernando , Wirth Richard , Graham Nathan A. , Severin Kenneth P. , Velasco Francisco , Steele-MacInnis Matthew , Bain Wyatt M.
Published: December 2023

The origin of magnetite-(apatite) iron deposits (MtAp) is one of the most contentious issues in ore geology with competing models that range from hydrothermal to magmatic processes. Here we report melt inclusions trapped in plagioclase phenocrysts in andesite hosting the MtAp mineralization at El Laco, Chile. The results of our study reveal that individual melt inclusions preserve evidence of complex processes involved in melt immiscibility, including separation of Si- and Fe-rich melts, the latter hosting Cu sulfide-rich, phosphate-rich, and residual C-O-HFSE-rich melts, with their melting temperature at 1145 °C. This association is consistent with the assemblages observed in the ore, and provides a link between silicate and Fe-P-rich melts that subsequently produced the magnetite-rich magmas that extruded on the flanks of the volcano. These results strongly suggest that the El Laco mineralization was derived from crystallization of Fe-P-rich melts, thus providing insight into the formation of similar deposits elsewhere.
Strongly interacting matter exhibits deconfined behavior in massive neutron stars
Authors: Annala Eemeli , Gorda Tyler , Hirvonen Joonas , Komoltsev Oleg , Kurkela Aleksi , Nättilä Joonas , Vuorinen Aleksi
Published: December 2023

Neutron-star cores contain matter at the highest densities in our Universe. This highly compressed matter may undergo a phase transition where nuclear matter melts into deconfined quark matter, liberating its constituent quarks and gluons. Quark matter exhibits an approximate conformal symmetry, predicting a specific form for its equation of state (EoS), but it is currently unknown whether the transition takes place inside at least some physical neutron stars. Here, we quantify this likelihood by combining information from astrophysical observations and theoretical calculations. Using Bayesian inference, we demonstrate that in the cores of maximally massive stars, the EoS is consistent with quark matter. We do this by establishing approximate conformal symmetry restoration with high credence at the highest densities probed and demonstrating that the number of active degrees of freedom is consistent with deconfined matter. The remaining likelihood is observed to correspond to EoSs exhibiting phase-transition-like behavior, treated as arbitrarily rapid crossovers in our framework.
Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms
Authors: Pennacchietti Francesca , Alvelid Jonatan , Morales Rodrigo A. , Damenti Martina , Ollech Dirk , Oliinyk Olena S. , Shcherbakova Daria M. , Villablanca Eduardo J. , Verkhusha Vladislav V. , Testa Ilaria
Published: December 2023

Photolabeling of intracellular molecules is an invaluable approach to studying various dynamic processes in living cells with high spatiotemporal precision. Among fluorescent proteins, photoconvertible mechanisms and their products are in the visible spectrum (400–650 nm), limiting their in vivo and multiplexed applications. Here we report the phenomenon of near-infrared to far-red photoconversion in the miRFP family of near infrared fluorescent proteins engineered from bacterial phytochromes. This photoconversion is induced by near-infrared light through a non-linear process, further allowing optical sectioning. Photoconverted miRFP species emit fluorescence at 650 nm enabling photolabeling entirely performed in the near-infrared range. We use miRFPs as photoconvertible fluorescent probes to track organelles in live cells and in vivo, both with conventional and super-resolution microscopy. The spectral properties of miRFPs complement those of GFP-like photoconvertible proteins, allowing strategies for photoconversion and spectral multiplexed applications.
High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos
Authors: Mukashyaka Patience , Kumar Pooja , Mellert David J. , Nicholas Shadae , Noorbakhsh Javad , Brugiolo Mattia , Courtois Elise T. , Anczukow Olga , Liu Edison T. , Chuang Jeffrey H.
Published: December 2023

Three-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate traditional luminescence-based drug response of cells with complex drug sensitivities, while also quantifying changes in organoid and nuclear morphologies caused by treatment as well as cell-cell spatial relationships that reflect ecological affinity. Cellos provides powerful tools to perform high-throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging.
Antigen recognition reinforces regulatory T cell mediated Leishmania major persistence
Authors: Zayats Romaniya , Mou Zhirong , Yazdanpanah Atta , Gupta Gaurav , Lopez Paul , Nayar Deesha , Koh Wan H. , Uzonna Jude E. , Murooka Thomas T.
Published: December 2023

Cutaneous Leishmania major infection elicits a rapid T cell response that is insufficient to clear residually infected cells, possibly due to the accumulation of regulatory T cells in healed skin. Here, we used Leishmania-specific TCR transgenic mice as a sensitive tool to characterize parasite-specific effector and immunosuppressive responses in vivo using two-photon microscopy. We show that Leishmania-specific Tregs displayed higher suppressive activity compared to polyclonal Tregs, that was mediated through IL-10 and not through disrupting cell-cell contacts or antigen presentation. In vivo expansion of endogenous Leishmania-specific Tregs resulted in disease reactivation that was also IL-10 dependent. Interestingly, lack of Treg expansion that recognized the immunodominant Leishmania peptide PEPCK was sufficient to restore robust effector Th1 responses and resulted in parasite control exclusively in male hosts. Our data suggest a stochastic model of Leishmania major persistence in skin, where cellular factors that control parasite numbers are counterbalanced by Leishmania-specific Tregs that facilitate parasite persistence.
Polycyclic aromatic hydrocarbon (PAH) source identification and a maternal transfer case study in threatened killer whales (Orcinus orca) of British Columbia, Canada
Authors: Lee Kiah , Raverty Stephen , Cottrell Paul , Zoveidadianpour Zeinab , Cottrell Brendan , Price Dana , Alava Juan José
Published: December 2023

The northeastern Pacific (NEP) Ocean spans the coast of British Columbia (Canada) and is impacted by anthropogenic activities including oil pipeline developments, maritime fossil fuel tanker traffic, industrial chemical effluents, agricultural and urban emissions in tandem with stormwater and wastewater discharges, and forest wildfires. Such events may expose surrounding marine environments to toxic polycyclic aromatic hydrocarbons (PAHs) and impact critical habitats of threatened killer whales (Orcinus orca). We analyzed skeletal muscle and liver samples from stranded Bigg’s killer whales and endangered Southern Resident killer whales (SRKWs) for PAH contamination using LRMS. C3-phenanthrenes/anthracenes (mean: 632 ng/g lw), C4-dibenzothiophenes (mean: 334 ng/g lw), and C4-phenanthrenes/anthracenes (mean: 248 ng/g lw) presented the highest concentrations across all tissue samples. Diagnostic ratios indicated petrogenic-sourced contamination for SRKWs and pyrogenic-sourced burdens for Bigg’s killer whales; differences between ecotypes may be attributed to habitat range, prey selection, and metabolism. A mother-fetus skeletal muscle pair provided evidence of PAH maternal transfer; low molecular weight compounds C3-fluorenes, dibenzothiophene, and naphthalene showed efficient and preferential exposure to the fetus. This indicates in-utero exposure of PAH-contamination to the fetus. Our results show that hydrocarbon-related anthropogenic activities are negatively impacting these top predators; preliminary data found here can be used to improve oil spill and other PAH pollution management and regulation efforts, and inform policy to conserve killer whale habitats in the NEP.
Integration of multiomics analysis to reveal the major pathways of vitamin A deficiency aggravates acute respiratory distress syndrome in neonatal rats
Authors: Tang Jia , Yuan Jiaqin , Sun Jinghao , Yan Mi , Li Mengchun , Liu Yanfei , Xu Shaohua , Li Jing , Fu Hong , Li Wanwei , Hu Zhangxue
Published: December 2023

Acute respiratory distress syndrome (ARDS) is a major disease that threatens the life and health of neonates. Vitamin A (VA) can participate in early fetal lung development and affect lung immune function. Researches revealed that the serum VA level in premature infants with ARDS was lower than that in premature infants without ARDS of the same gestational age, and premature infants with VA deficiency (VAD) were more likely to develop ARDS. Moreover, the VA levels can be used as a predictor of the development and severity of neonatal ARDS. However, the critical question here is; Does ARDS develop due to VAD in these systemic diseases? Or does ARDS develop because these diseases cause VAD? We hypothesize that VAD may aggravate neonatal ARDS by affecting immunity, metabolism, barriers and other pathways. In this article, we used multiomics analysis to find that VAD may aggravate ARDS mainly through the Fc epsilon RI signaling pathway, the HIF-1 signaling pathway, glutathione metabolism, and valine, leucine and isoleucine degradation signaling pathways, which may provide the molecular pathogenic mechanism behind the pathology of VAD-aggravated ARDS and can also provide potential molecular targets for subsequent research on ARDS.
4D evolutions of cracks, voids, and corrosion products in reinforced concrete materials
Authors: Taheri-Shakib Jaber , Al-Mayah Adil
Published: December 2023

This research paper presents a comprehensive investigation into the corrosion process in reinforced concrete structures using advanced analytical techniques, namely non-destructive X-ray computed tomography (CT) imaging, scanning electron microscopy (SEM) images, energy dispersive x-ray spectrometry (EDS), and Raman spectroscopy. The CT image analysis allowed for the identification and quantification of pore structures, crack propagation, and corrosion progression at different stages of corrosion. CT scanning and data analysis offer valuable 4D (3D spatial + time) insights into corrosion in reinforced concrete, revealing changes in pore sizes, with smaller pores increasing and larger pores decreasing as corrosion progresses. Our investigation reveals dynamic changes in reinforced concrete pores during the accelerated corrosion test leading to new pore formation and cracking. The research identifies two distinct types of cracks: one filled with corrosion products and the other, zipper-like cracks, resulting from the connection of deformed pores without corrosion products. The SEM images and EDS analysis confirmed the absence of corrosion products within these unique zipper cracks, suggesting a different mechanism of crack formation compared to the first type of cracks. The results revealed two distinct categories of corrosion products: iron oxides and iron hydroxides, with their distribution correlated to the duration of accelerated corrosion testing. The integration and verification of results from X-ray CT imaging and Raman spectroscopy established a comprehensive understanding of corrosion-induced damage in the reinforced concrete specimen, shedding light on complex interactions among different corrosion products during the corrosion process. These findings offer crucial insights for better understanding of the corrosion process in reinforced concrete paving the way for future development of effective treatments and strategies to mitigate corrosion impact.
Improved speech intelligibility in the presence of congruent vibrotactile speech input
Authors: Schulte Alina , Marozeau Jeremy , Ruhe Anna , Büchner Andreas , Kral Andrej , Innes-Brown Hamish
Published: December 2023

Vibrotactile stimulation is believed to enhance auditory speech perception, offering potential benefits for cochlear implant (CI) users who may utilize compensatory sensory strategies. Our study advances previous research by directly comparing tactile speech intelligibility enhancements in normal-hearing (NH) and CI participants, using the same paradigm. Moreover, we assessed tactile enhancement considering stimulus non-specific, excitatory effects through an incongruent audio-tactile control condition that did not contain any speech-relevant information. In addition to this incongruent audio-tactile condition, we presented sentences in an auditory only and a congruent audio-tactile condition, with the congruent tactile stimulus providing low-frequency envelope information via a vibrating probe on the index fingertip. The study involved 23 NH listeners and 14 CI users. In both groups, significant tactile enhancements were observed for congruent tactile stimuli (5.3% for NH and 5.4% for CI participants), but not for incongruent tactile stimulation. These findings replicate previously observed tactile enhancement effects. Juxtaposing our study with previous research, the informational content of the tactile stimulus emerges as a modulator of intelligibility: Generally, congruent stimuli enhanced, non-matching tactile stimuli reduced, and neutral stimuli did not change test outcomes. We conclude that the temporal cues provided by congruent vibrotactile stimuli may aid in parsing continuous speech signals into syllables and words, consequently leading to the observed improvements in intelligibility.
A probabilistic early fault detection model for a feedback machining system with multiple types of spares
Authors: El-Hadidy Mohamed Abd Allah , Elshenawy Assem Omar
Published: December 2023

This paper studies corrective and preventive maintenance to provide a quality control policy. The corrective maintenance, depending on the time, of a feedback machining system model with a finite source and standbys is presented. Moreover, the system has a known number of servers to repair the damaged units, and it contains an inspector to ensure the maintenance quality of the repaired units. The exact value of the probability of n units in the system will be obtained by using an efficient algorithm that depends on the Laplace transformation. To promote the concept of preventive maintenance, we use this probability to get the probability of early fault detection as a function of time and in the steady state. The applicability of this model is discussed for different system capacities.