bluuebunny/crossref_metadata_2025 huggingface dataset:
The Manna Effect – a review of factors influencing hair lichen abundance for Canada's endangered Deep-Snow Mountain Caribou (Rangifer arcticus montanus)
Authors: Goward Trevor , Coxson Darwyn , Gauslaa Yngvar
Published: September 2024

Canada's endangered Deep-Snow Mountain Caribou (DSC) are endemic to mountainous southern inland British Columbia, where they subsist in winter on an almost exclusive diet of epiphytic hair lichens, especially Bryoria fremontii and B. pseudofuscescens (the high-biomass Bryoria spp.) and Alectoria sarmentosa. Importantly, stand-level hair lichen loadings adequate for the dietary needs of DSC rarely occur in forests younger than c. 120–150 years, an unusual form of old-growth dependence hypothetically linked to certain structural features of old forest ecosystems. Not only does this hypothesis accord well with recent insights into hair lichen ecophysiology, it also allows the formulation of a conceptual ‘hyperabundance’ model for the high-biomass Bryoria spp. and lays the foundation for a similar model for A. sarmentosa. In both cases the models point to a massive standing crop of hair lichens in the overstories of old-growth forests; it is this reservoir that, partly by releasing a constant manna-like rain of thallus fragments into the lower canopy, sustains DSC during the winter half year. The outcome is a sustained-yield system resistant to degradation from overbrowsing, yet vulnerable to fragmentation of old-growth forests by industrial forestry, a process of progressive forage reduction that must ultimately place DSC at risk of winter malnutrition. We conclude that stand-level hair lichen hyperabundance is necessarily an attribute of advanced forest age and, at least in the case of Bryoria, cannot be silviculturally induced in stands younger than c. 120–150 years.
Rings of Power: evidence of mud ring feeding performed by Guiana dolphins
Authors: Pierry Julia C. , Novelli Mariane B. S. , Louzada Caio N. , Monteiro-Filho Emygdio L. A.
Published: September 2024

To capture prey more efficiently, cetaceans can display a wide range of foraging tactics to separate individual prey. Barrier feeding tactics are performed to restrict prey movements, using natural and non-natural barriers and some species can even create barriers with their own bodies. Mud ring feeding has been observed in bottlenose dolphins in Florida Bay and in Chetumal-Corozal Bay, where ring-maker dolphins create ring-shaped mud plumes to encircle fish schools. Here, we document for the first time Guiana dolphins performing the mud ring feeding behaviour in the Cananéia estuarine system, in the southern portion of the state of São Paulo, Brazil. A total of 11 dolphins were recorded in four expeditions through aerial footage engaging in the behaviour. These findings expand our knowledge about the behavioural plasticity of the species and builds upon existing records of mud ring feeding behaviour in cetaceans.
Does perceptual high variability phonetic training improve L2 speech production? A meta-analysis of perception-production connection
Authors: Uchihara Takumi , Karas Michael , Thomson Ron I.
Published: September 2024

This meta-analysis of 31 studies aimed to determine the effectiveness of perception-based high variability phonetic training (HVPT) for second language (L2) production learning and to identify learner-related and methodological variables that influence production gains. Based on independent effect sizes for 43 within-participant and 17 between-participant designs, small-to-medium effects of post-training improvement were found. The average production gains for trained items and untrained items were 10.50% and 4.50%, respectively. Neither strong support for long-term retention of production learning nor generalization to untrained stimuli was observed, however. Moderator analyses showed that post-training production gains were influenced by a number of factors related to learner profiles (age and learning context), training features (provision of phonetic information, training duration, and training time per session), and features of production tests (elicitation tasks, prompt modality, and outcome measures). The relationship between perception and production gains was negligible at the participant level, but was significant and moderate at the level of individual studies for post-training and retention data. These findings provide partial support for a perception-production link. This study makes several recommendations for future studies investigating the effects of HVPT on L2 speech production learning.
A scoping review of empirical studies on informal music learning
Authors: Weatherly Katy Ieong Cheng Ho , Weatherly Christopher Alan , Chen Yun , Lau PuiKei
Published: September 2024

Informal music learning, pioneered by Green (2002, 2006, 2017), presents an alternative approach that integrates students’ interests in popular music, bridging the informal and traditional styles of Western music education in schools. We conducted a scoping review adhering to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to investigate informal music learning. Our scoping review encompasses 28 empirical, peer-reviewed articles published from 2006 to 2023. First, we analyse the diverse contexts, methodologies and geographic locations in which informal music learning has been investigated. Second, we explore how different stakeholders perceive and engage with informal music learning in various educational settings. Lastly, we summarise the implications derived from the analysed studies on informal music learning. Our findings reveal that across various educational contexts, informal music learning has consistently demonstrated its positive impact in motivating students. We also find that researchers have extended their investigations from programme reform to exploring pupil and teacher’s musical identities. Recommendations for future research include exploring informal music learning in ensembles and elementary music classrooms and employing quantitative or mixed methods to assess its effectiveness and impact.
Synaptotagmin-9 in mouse retina
Authors: Mesnard Chris S. , Hays Cassandra L. , Townsend Lou E. , Barta Cody L. , Gurumurthy Channabasavaiah B. , Thoreson Wallace B.
Published: September 2024

Synaptotagmin-9 (Syt9) is a Ca2+ sensor mediating fast synaptic release expressed in various parts of the brain. The presence and role of Syt9 in retina is unknown. We found evidence for Syt9 expression throughout the retina and created mice to conditionally eliminate Syt9 in a cre-dependent manner. We crossed Syt9fl/fl mice with Rho-iCre, HRGP-Cre, and CMV-Cre mice to generate mice in which Syt9 was eliminated from rods (rodSyt9CKO), cones (coneSyt9CKO), or whole animals (CMVSyt9). CMVSyt9 mice showed an increase in scotopic electroretinogram (ERG) b-waves evoked by bright flashes with no change in a-waves. Cone-driven photopic ERG b-waves were not significantly different in CMVSyt9 knockout mice and selective elimination of Syt9 from cones had no effect on ERGs. However, selective elimination from rods decreased scotopic and photopic b-waves as well as oscillatory potentials. These changes occurred only with bright flashes where cone responses contribute. Synaptic release was measured in individual rods by recording anion currents activated by glutamate binding to presynaptic glutamate transporters. Loss of Syt9 from rods had no effect on spontaneous or depolarization-evoked release. Our data show that Syt9 acts at multiple sites in the retina and suggest that it may play a role in regulating transmission of cone signals by rods.
Dialect change and language attitudes in Albania
Authors: Riverin-Coutlée Josiane , Kapia Enkeleida , Gubian Michele
Published: September 2024

This study is concerned with attitudes of Albanian listeners toward the two main dialects spoken in Albania: Gheg and Tosk. The study seeks to establish a connection between attitudes and speech features which have been shown to be changing in Gheg, and other features found to be stable. Ratings of four speech features on visual analog scales (VASs) pertaining to dialect identification, status, and solidarity were collected from 125 Albanian listeners and modeled with Bayesian regressions. The results revealed lower status for variants of features found to be changing in Gheg, contrary to stable variants, suggesting a connection between attitudes and dialect change, and highlighting the relevance of both language-external and internal factors in understanding change. All stimuli were also rated as more friendly than unfriendly, which could be related to sociocultural specificities of Albania. The study finally identifies methodological challenges to do with modeling responses from VASs.
Stabilization in a chemotaxis system modelling T-cell dynamics with simultaneous production and consumption of signals
Authors: Tao Youshan , Winkler Michael
Published: September 2024

In a smoothly bounded domain

$\Omega \subset \mathbb{R}^n$

,

$n\ge 1$

, this manuscript considers the homogeneous Neumann boundary problem for the chemotaxis system

\begin{eqnarray*} \left \{ \begin{array}{l} u_t = \Delta u - \nabla \cdot (u\nabla v), \\[5pt] v_t = \Delta v + u - \alpha uv, \end{array} \right . \end{eqnarray*}

with parameter

$\alpha \gt 0$

and with coincident production and uptake of attractants, as recently emphasized by Dallaston et al. as relevant for the understanding of T-cell dynamics.

It is shown that there exists

$\delta _\star =\delta _\star (n)\gt 0$

such that for any given

$\alpha \ge \frac{1}{\delta _\star }$

and for any suitably regular initial data satisfying

$v(\cdot, 0)\le \delta _\star$

, this problem admits a unique classical solution that stabilizes to the constant equilibrium

$(\frac{1}{|\Omega |}\int _\Omega u(\cdot, 0), \, \frac{1}{\alpha })$

in the large time limit.
Comparative analysis of calcium-sensing receptor (CaSR) expression and function in normal and abnormal human sperm and spermatogenic cells
Authors: Qian Zhengli , Luo Keyan , Zhang Mingzhe , Yao Guanping
Published: September 2024

The calcium-sensing receptor (CaSR) is a critical mediator of calcium homeostasis in various tissues. Its role in human reproduction, especially in sperm function and male fertility, remains not fully elucidated. This study investigates the expression patterns of CaSR in normal and abnormal sperm and spermatogenic cells and evaluates its potential effect on sperm motility and morphology. Using immunohistochemistry (IHC), quantitative PCR (qPCR), we assessed the expression levels of CaSR in normal sperm, spermatogonia, and cases of asthenozoospermia, oligozoospermia, and teratozoospermia. In vitro functional assays were performed to analyze the effects of CaSR modulation on sperm motility under varying conditions, including the presence of specific CaSR agonists and antagonists. Our study revealed distinct patterns of CaSR expression in normal sperm and spermatogonia compared with those in abnormal sperm samples, particularly in cases of asthenozoospermia, oligozoospermia, and teratozoospermia. A marked decrease in CaSR expression was evident in these abnormal samples, highlighting its significance in normal sperm functionality. Functional assays further elucidated the role of CaSR in sperm motility. Activation of CaSR through specific agonists enhanced sperm motility, while inhibition by antagonists led to reduced motility. Our findings suggest that CaSR plays a significant role in maintaining sperm functionality and that changes in its expression may be associated with male infertility. These insights into the molecular underpinnings of sperm physiology highlight CaSR as a potential therapeutic target for treating certain forms of male infertility.
Comparison of CellRox green fluorescence upon thawing on in vitro Bos taurus and Bos indicus embryos cryopreserved by slow freezing or vitrification
Authors: Osornio David , Contreras David Alejandro , Jimenez-Diaz Edgar , Fiordelisio Tatiana , López-Damian Patricia , Martínez José Francisco , Galina Carlos Salvador
Published: September 2024

The aim of this study was to compare the levels of reactive oxygen species (ROS) in Bos taurus and Bos indicus in vitro embryos cryopreserved using either slow freezing or vitrification. Embryos were divided into four groups based on subspecies and freezing method: Bos indicus slow freezing (BiSF; n = 8), Bos indicus vitrification (BiVT; n = 10), Bos taurus slow freezing (BtSF; n = 9), and Bos taurus vitrification (BtVT; n = 6). After thawing, the embryos were incubated with CellRox Green and images were obtained using a confocal microscope. The fluorescence intensity of each cell was measured and expressed as arbitrary units of fluorescence (auf) and compared using a multiple regression and unpaired t-test with α = 0.05. Results showed that subspecies and the freezing method significantly affected auf (P < 0.001; R2 = 0.1213). Bos indicus embryos had higher auf than Bos taurus embryos, whether frozen by slow freezing (67.05 ± 23.18 vs 51.30 ± 16.84, P < 0.001) or vitrification (64.44 ± 23.32 vs 47.86 ± 17.53, P < 0.001). Slow freezing induced higher auf than vitrification in both Bos taurus (51.30 ± 16.84 vs 47.86 ± 17.53, P < 0.001) and Bos indicus (67.05 ± 23.18 vs 64.44 ± 23.32, P < 0.014). In conclusion, Bos taurus embryos had lower ROS levels when frozen using vitrification, while Bos indicus embryos had consistent ROS patterns regardless of the freezing method. However, Bos indicus embryos frozen by slow freezing tended to have a higher number of cells with elevated ROS levels.
Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility
Authors: Sindhu Pushpa , Magotra Ankit , Sindhu Vikas , Chaudhary Pradeep
Published: September 2024

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring’s epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.
Prehospital Care Under Fire: Strategies for Evacuating Victims from the Mega Terrorist Attack in Israel on October 7, 2023
Authors: Jaffe Eli , Dadon Ziv , Alpert Evan Avraham
Published: September 2024

On October 7, 2023, somewhere around 1,500-3,000 terrorists invaded southern Israel killing 1,200 people, injuring 1,455, and taking 239 as hostages resulting in the largest mass-casualty event (MCE) in the country’s history. Most of the victims were civilians who suffered from complex injuries including high-velocity gunshot wounds, blast injuries from rocket-propelled grenades, and burns. Many would later require complex surgeries by all disciplines including general surgeons, vascular surgeons, orthopedists, neurosurgeons, cardiothoracic surgeons, otolaryngologists, oral maxillofacial surgeons, and plastic surgeons. Magen David Adom (MDA) is Israel’s National Emergency Prehospital Medical Organization and a member of the International Red Cross. While there are also private and non-profit ambulance services in Israel, the Ministry of Health has mandated MDA with the charge of managing an MCE. For this event, MDA incorporated a five-part strategy in this mega MCE: (1) extricating victims from areas under fire by bulletproof ambulances, (2) establishing casualty treatment stations in safe areas, (3) ambulance transport from the casualty treatment stations to hospitals, (4) ambulance transport of casualties from safe areas to hospitals, and (5) helicopter transport of victims to hospitals. This is the first time that MDA has responded to a mega MCE of this magnitude and lessons are continually being learned.
Neuropsychological application of the International Test Commission Guidelines for Translation and Adapting of Tests
Authors: Nguyen Christopher Minh , Rampa Shathani , Staios Mathew , Nielsen T. Rune , Zapparoli Busisiwe , Zhou Xinyi Emily , Mbakile-Mahlanza Lingani , Colon Juliet , Hammond Alexandra , Hendriks Marc , Kgolo Tumelo , Serrano Yesenia , Marquine María J. , Dutt Aparna , Evans Jonathan , Judd Tedd
Published: September 2024

Objective:

The number of test translations and adaptations has risen exponentially over the last two decades, and these processes are now becoming a common practice. The International Test Commission (ITC) Guidelines for Translating and Adapting Tests (Second Edition, 2017) offer principles and practices to ensure the quality of translated and adapted tests. However, they are not specific to the cognitive processes examined with clinical neuropsychological measures. The aim of this publication is to provide a specialized set of recommendations for guiding neuropsychological test translation and adaptation procedures.

Methods:

The International Neuropsychological Society’s Cultural Neuropsychology Special Interest Group established a working group tasked with extending the ITC guidelines to offer specialized recommendations for translating/adapting neuropsychological tests. The neuropsychological application of the ITC guidelines was formulated by authors representing over ten nations, drawing upon literature concerning neuropsychological test translation, adaptation, and development, as well as their own expertise and consulting colleagues experienced in this field.

Results:

A summary of neuropsychological-specific commentary regarding the ITC test translation and adaptation guidelines is presented. Additionally, examples of applying these recommendations across a broad range of criteria are provided to aid test developers in attaining valid and reliable outcomes.

Conclusions:

Establishing specific neuropsychological test translation and adaptation guidelines is critical to ensure that such processes produce reliable and valid psychometric measures. Given the rapid global growth experienced in neuropsychology over the last two decades, the recommendations may assist researchers and practitioners in carrying out such endeavors.
The ruble lever: Soviet development knowledge and the political economy of the UN
Authors: Banks Elizabeth
Published: September 2024

From the early 1950s, the USSR was the second largest contributor to the UN. Following UN rules, it gave much of its contribution in rubles, an infamously unconvertible currency that generally limited Soviet actions overseas. In the hands of UN officials, however, these ‘weak’ rubles became a powerful lever that made UN development projects more Soviet. Seeking to extract value from the ruble, officials increased the amount of UN development training held in the USSR, prioritized the purchase of Soviet equipment, and incentivized agencies to distribute Soviet manuals. Exploring the ruble lever contributes to our knowledge of the Soviet presence at the UN while foregrounding political economy as a key mechanism shaping UN practices more widely. Following the money in forms other than the dollar can reveal how economies of power at the UN intersect with global economic history, as well as the conceptual and contemporary challenges of international cooperation among wildly unequal economies.
Post-SSRI sexual dysfunction: barriers to quantifying incidence and prevalence
Authors: Healy David , Mangin Dee
Published: September 2024

While sexual dysfunction is a well-known side effect of taking selective serotonin reuptake inhibitors (SSRIs), in an undetermined number of patients, sexual function does not return to pre-drug baseline after stopping SSRIs. The condition is known as post-SSRI sexual dysfunction (PSSD) and is characterised most commonly by genital numbness, pleasureless or weak orgasm, loss of libido and erectile dysfunction. This article provides a commentary on the incidence and prevalence of PSSD based on a combination of academic literature as well as clinical and research experience. A number of obstacles to quantifying the occurrence of PSSD are outlined including difficulty in designing a suitable study method. Other contextual obstacles include patient embarrassment at raising sexual concerns, the response of healthcare professionals, inability to stop an antidepressant due to withdrawal issues in a proportion of patients and patient unawareness that their sexual difficulties are linked to prior medication compounded by variability of online information and a lack of information aimed at public education. A definition of PSSD with diagnostic criteria has been published. A MedDRA code for PSSD has also been introduced, but this is yet to be adopted by regulators.
Analysis of Agricultural Water Security Based on Network Invulnerability: A Case Study in China's Virtual Water Trade Networks
Authors: Liang X. , Long A. , Han X. , Lai X. , Meng Y.
Published: September 2024

“Invulnerability” of complex network was firstly introduced to virtual water (VW) research, aiming to broaden the scope of studies on water use and management. Beginning with the construction of China's virtual water trade networks (VWTNs) of major grain crops, Node Degree (K) and Betweenness Centrality (B) are employed to evaluate and rank the importance of China's 31 regions. Regions with high values for both indicators are identified as playing pivotal roles in the VWTNs: Jiangsu (ranking 1st for both K and B), Hubei (2nd for K, 3rd for B), Henan (3rd for K, 6th for B), Hebei (4th for K, 4th for B), Hunan (4th for K, 5th for B). Using this ranking to simulate the invulnerability of VWTNs under random and intentional attacks. The results reveal a rapid decrease in both Network Efficiency (E) and Maximum Connectivity (C) under intentional attack. In comparison to seven random attacks, E falls below 0.1 and C drops below 0.5 after only three intentional attacks, and the network completely collapsed after 10 intentional attacks. This highlights the VWTN's vulnerability in maintaining food supply and agricultural water security when key regions are subjected to man‐made destruction, such as military blockades or occupations. Future work should include integrating climate change models, crops yield models, and water resource allocation models to protect the key areas. Furthermore, interdisciplinary approaches are crucial for overcoming the limitations of VW research and these findings will provide valuable insights to enhance the optimal regulation of VWTNs.
Prevalence and Propagation of Lightning‐Generated Whistlers in Van Allen Probes EFW Burst Data
Authors: Wold Alexandra M. , Marshall Robert A. , Malaspina David M. , Shane Alexander D.
Published: September 2024

We assess the prevalence of ducted and non‐ducted whistler propagation using burst mode data from the Van Allen Probes Electric Field and Waves instrument (EFW). We have identified burst periods containing lightning‐generated whistlers (LGWs), resulting in a data set available for future use. The entire burst data set is filtered through an analysis of the search coil magnetometer (SCM) noise, identifying signals in frequency space that exceed an adaptive noise threshold. We implement DBSCAN (Density‐Based Spatial Clustering of Applications with Noise) to identify individual whistlers and clusters of whistlers. With magnetic spectral analysis, we calculate the mean wave normal angle (WNA) for each LGW group. We use ray tracing to estimate the expected WNA distributions for non‐ducted LGWs to compare to the data and determine methods for identifying potentially ducted LGWs. The ray‐tracing results provide a clear threshold in WNA for ducted whistlers. Using this threshold, we estimate that at least of LGWs in this data set are ducted. We find that the majority of potentially ducted whistlers are below and nearly half of LGWs below and within 9–18 MLT may be ducted.
Hysteresis in Water Content of Ultrafine Glassy Organic Aerosol Particles
Authors: Cheng Manqiu , Li Ying , Kuwata Mikinori
Published: September 2024

Water content of aerosol particles is atmospherically important. Water content of organic aerosol (OA) particles has been estimated by assuming thermodynamic equilibrium. Here, we discovered that the hysteresis phenomenon occurred to water content of glassy ultrafine OA particles, demonstrating that thermodynamically non‐equilibrium states need to be considered. Hygroscopic growth for monodisperse ultrafine particles (sucrose and glucose) was investigated for the temperature range from 252 to 296 K. Hysteresis was not observable at 296 K, consistent with literature data. However, hysteresis in water content was observed at sub‐273 K. The lowest relative humidity (RH), at which hygroscopic growth of particles did not depend on exposure history to water vapor, was defined as threshold RH. Threshold RH for 100 nm particles was approximately the same as the glass transition points when hysteresis clearly happened, demonstrating that water diffusion in a highly viscous matrix of organic aerosols was the key to the phenomenon. Employment of a kinetic multi‐layer model quantitatively predicted threshold RH as a function of temperature, exposure time, and the particle size. Considering the temperature and RH range of Earth's atmosphere, we hypothesize that hysteresis in water content for organic aerosols ubiquitously occurs in the upper troposphere, impacting chemical aging and cloud formation processes.
Topography Controls Variability in Circumpolar Permafrost Thaw Pond Expansion
Authors: Abolt C. J. , Atchley A. L. , Harp D. R. , Jorgenson M. T. , Witharana C. , Bolton W. R. , Schwenk J. , Rettelbach T. , Grosse G. , Boike J. , Nitze I. , Liljedahl A. K. , Rumpca C. T. , Wilson C. J. , Bennett K. E.
Published: September 2024

One of the most conspicuous signals of climate change in high‐latitude tundra is the expansion of ice wedge thermokarst pools. These small but abundant water features form rapidly in depressions caused by the melting of ice wedges (i.e., meter‐scale bodies of ice embedded within the top of the permafrost). Pool expansion impacts subsequent thaw rates through a series of complex positive and negative feedbacks which play out over timescales of decades and may accelerate carbon release from the underlying sediments. Although many local observations of ice wedge thermokarst pool expansion have been documented, analyses at continental to pan‐Arctic scales have been rare, hindering efforts to project how strongly this process may impact the global carbon cycle. Here we present one of the most geographically extensive and temporally dense records yet compiled of recent pool expansion, in which changes to pool area from 2008 to 2020 were quantified through satellite‐image analysis at 27 survey areas (measuring 10–35 km2 each, or 400 km2 in total) dispersed throughout the circumpolar tundra. The results revealed instances of rapid expansion at 44% (15%) of survey areas. Considered alone, the extent of departures from historical mean air temperatures did not account for between site variation in rates of change to pool area. Pool growth was most clearly associated with upland (i.e., hilly) terrain and elevated silt content at soil depths greater than one meter. These findings suggest that, at short time scales, pedologic and geomorphologic conditions may exert greater control on pool dynamics in the warming Arctic than spatial variability in the rate of air temperature increases.
Circumpolar Transport and Overturning Strength Inferred From Satellite Observables Using Deep Learning in an Eddying Southern Ocean Channel Model
Authors: Meng Shuai , Stewart Andrew L. , Manucharyan Georgy
Published: September 2024

The Southern Ocean connects the ocean's major basins via the Antarctic Circumpolar Current (ACC), and closes the global meridional overturning circulation (MOC). Observing these transports is challenging because three‐dimensional mesoscale‐resolving measurements of currents, temperature, and salinity are required to calculate transport in density coordinates. Previous studies have proposed to circumvent these limitations by inferring subsurface transports from satellite measurements using data‐driven methods. However, it is unclear whether these approaches can identify the signatures of subsurface transport in the Southern Ocean, which exhibits an energetic mesoscale eddy field superposed on a highly heterogeneous mean stratification and circulation. This study employs Deep Learning techniques to link the transports of the ACC and the upper and lower branches of the MOC to sea surface height (SSH) and ocean bottom pressure (OBP), using an idealized channel model of the Southern Ocean as a test bed. A key result is that a convolutional neural network produces skillful predictions of the ACC transport and MOC strength (skill score of 0.74 and 0.44, respectively). The skill of these predictions is similar across timescales ranging from daily to decadal but decreases substantially if SSH or OBP is omitted as a predictor. Using a fully connected or linear neural network yields similarly accurate predictions of the ACC transport but substantially less skillful predictions of the MOC strength. Our results suggest that Deep Learning offers a route to linking the Southern Ocean's zonal transport and overturning circulation to remote measurements, even in the presence of pronounced mesoscale variability.
Basal-to-inflammatory transition and tumor resistance via crosstalk with a pro-inflammatory stromal niche
Authors: Li Nancy Yanzhe , Zhang Weiruo , Haensel Daniel , Jussila Anna R. , Pan Cory , Gaddam Sadhana , Plevritis Sylvia K. , Oro Anthony E.
Published: September 2024

Cancer-associated inflammation is a double-edged sword possessing both pro- and anti-tumor properties through ill-defined tumor-immune dynamics. While we previously identified a carcinoma tumor-intrinsic resistance pathway, basal-to-squamous cell carcinoma transition, here, employing a multipronged single-cell and spatial-omics approach, we identify an inflammation and therapy-enriched tumor state we term basal-to-inflammatory transition. Basal-to-inflammatory transition signature correlates with poor overall patient survival in many epithelial tumors. Basal-to-squamous cell carcinoma transition and basal-to-inflammatory transition occur in adjacent but distinct regions of a single tumor: basal-to-squamous cell carcinoma transition arises within the core tumor nodule, while basal-to-inflammatory transition emerges from a specialized inflammatory environment defined by a tumor-associated TREM1 myeloid signature. TREM1 myeloid-derived cytokines IL1 and OSM induce basal-to-inflammatory transition in vitro and in vivo through NF-κB, lowering sensitivity of patient basal cell carcinoma explant tumors to Smoothened inhibitor treatment. This work deepens our knowledge of the heterogeneous local tumor microenvironment and nominates basal-to-inflammatory transition as a drug-resistant but targetable tumor state driven by a specialized inflammatory microenvironment.
Orbital selective commensurate modulations of the local density of states in ScV6Sn6 probed by nuclear spins
Authors: Guehne Robin , Noky Jonathan , Yi Changjiang , Shekhar Chandra , Vergniory Maia G. , Baenitz Michael , Felser Claudia
Published: September 2024

The kagome network is a unique platform that harbors a diversity of special electronic states due to its inherent band structure features comprising Dirac cones, van Hove singularities, and flat bands. Some kagome-based metals have recently been found to exhibit favorable properties, including superconductivity, charge order, and signatures of an anomalous Hall effect. The kagome system ScV6Sn6 is a promising candidate for studying the emergence of an unconventional charge order and accompanying effects. We use 51V nuclear magnetic resonance to explore the local properties of the charge ordered phase in single crystalline ScV6Sn6, aided by density functional theory. We show the local charge symmetry of V to reflect a commensurate modulation with $${{\bf{q}}}=\left(\frac{1}{3},\frac{1}{3},\frac{1}{3}\right)$$
q
=

1

3

,

1

3

,

1

3

, the density of states to drop by about a factor of $$\sqrt{2}$$

2

during the phase transition, and an unusual orientation dependent change in the shift splitting symmetry to reveal orbital selective modulations of the local density of states.
Exploring dynamic solvation kinetics at electrocatalyst surfaces
Authors: Sarabia Francisco , Gomez Rodellar Carlos , Roldan Cuenya Beatriz , Oener Sebastian Z.
Published: September 2024

The interface between electrocatalyst and electrolyte is highly dynamic. Even in absence of major structural changes, the intermediate coverage and interfacial solvent are bias and time dependent. This is not accounted for in current kinetic models. Here, we study the kinetics of the hydrogen evolution, ammonia oxidation and oxygen reduction reactions on polycrystalline Pt with distinct intrinsic rates and intermediates (e.g. *H, *OH, *NH2, *N). Despite these differences, we discover shared relationships between the pre-exponential factor and the activation energy that we link to solvation kinetics in the presence of electronic excess charge and charged intermediates. Further, we study dynamic changes of these kinetic parameters with a millisecond time resolution during electrosorption and double layer charging and dynamic *N and *NO poisoning. Finally, we discover a pH-dependent activation entropy that explains non-Nernstian overpotential shifts with pH. In sum, our results demonstrate the importance of accounting for a bias and time-dependent interfacial solvent and catalyst surface.
Dependency of tensile properties and biodegradation on molecular mass during hydrolysis of poly(butylene succinate)
Authors: Eckel Felix , Van Opdenbosch Daniel , Schandl Katharina Sophie , Zollfrank Cordt
Published: September 2024

The molecular mass of biodegradable polymers often explains the varying biodegradation results in outdoor environments and determines the mechanical properties and embrittlement of polymer samples. Accordingly, we have investigated the relationship between the molecular mass of poly(butylene succinate) (PBS) and its tensile properties and mineralisation. With decreasing molecular mass, we found that Young’s modulus was rising while tensile strength and elongation at break were decreasing. A ductile-brittle transition was found between a Mw of 80,000 g/mol and 110,000 g/mol. The dependency of mechanical properties on molecular mass as determined after hydrolysis differed significantly from a study performed on freshly synthesised PBS. Biodegradation to CO2 by microorganisms in a mixture of field soil and compost soil was found to begin at a Mw between 8060 g/mol and 26,666 g/mol. These results are essential for estimating the service life of products made from PBS.
Vortex-induced anomalies in the superconducting quantum interference patterns of topological insulator Josephson junctions
Authors: Rashidi Arman , Huynh William , Guo Binghao , Ahadi Sina , Stemmer Susanne
Published: September 2024

The superconducting quantum interference (SQI) patterns of Josephson junctions fabricated from hybrid structures that interface an s-wave superconductor with a topological insulator can be used to detect signatures of novel quasiparticle states. Here, we compare calculated and experimental SQI patterns obtained from hybrid junctions fabricated on cadmium arsenide, a two-dimensional topological insulator. The calculations account for the effects of Abrikosov (anti-) vortices in the superconducting contacts. They describe the experimentally observed deviations of the SQI from an ideal Fraunhofer pattern, including anomalous phase shifts, node lifting, even/odd modulations of the lobes, irregular lobe spacing, and an asymmetry in the positive/negative magnetic field. We also show that under a current bias, these vortices enter the electrodes even if there is no intentionally applied external magnetic field. The results show that Abrikosov vortices in the electrodes of the junctions can explain many of the observed anomalies in the SQI patterns of topological insulator Josephson junctions.
Advanced CMOS manufacturing of superconducting qubits on 300 mm wafers
Authors: Van Damme J. , Massar S. , Acharya R. , Ivanov Ts. , Perez Lozano D. , Canvel Y. , Demarets M. , Vangoidsenhoven D. , Hermans Y. , Lai J. G. , Vadiraj A. M. , Mongillo M. , Wan D. , De Boeck J. , Potočnik A. , De Greve K.
Published: September 2024

The development of superconducting qubit technology has shown great potential for the construction of practical quantum computers1,2. As the complexity of quantum processors continues to grow, the need for stringent fabrication tolerances becomes increasingly critical3. Utilizing advanced industrial fabrication processes could facilitate the necessary level of fabrication control to support the continued scaling of quantum processors. However, at present, these industrial processes are not optimized to produce high-coherence devices, nor are they a priori compatible with the approaches commonly used to make superconducting qubits. Here we demonstrate superconducting transmon qubits manufactured in a 300 mm complementary metal–oxide–semiconductor (CMOS) pilot line using industrial fabrication methods, with resulting relaxation and coherence times exceeding 100 μs. We show across-wafer, large-scale statistics of coherence, yield, variability and ageing that confirm the validity of our approach. The presented industry-scale fabrication process, which uses only optical lithography and reactive-ion etching, has a performance and yield in line with conventional laboratory-style techniques utilizing metal lift-off, angled evaporation and electron-beam writing4. Moreover, it offers the potential for further upscaling through three-dimensional integration5 and more process optimization. This result marks the advent of an alternative and new, large-scale, truly CMOS-compatible fabrication method for superconducting quantum computing processors.
Commensal consortia decolonize Enterobacteriaceae via ecological control
Authors: Furuichi Munehiro , Kawaguchi Takaaki , Pust Marie-Madlen , Yasuma-Mitobe Keiko , Plichta Damian R. , Hasegawa Naomi , Ohya Takashi , Bhattarai Shakti K. , Sasajima Satoshi , Aoto Yoshimasa , Tuganbaev Timur , Yaginuma Mizuki , Ueda Masahiro , Okahashi Nobuyuki , Amafuji Kimiko , Kiridoshi Yuko , Sugita Kayoko , Stražar Martin , Avila-Pacheco Julian , Pierce Kerry , Clish Clary B. , Skelly Ashwin N. , Hattori Masahira , Nakamoto Nobuhiro , Caballero Silvia , Norman Jason M. , Olle Bernat , Tanoue Takeshi , Suda Wataru , Arita Makoto , Bucci Vanni , Atarashi Koji , Xavier Ramnik J. , Honda Kenya
Published: September 2024

Persistent colonization and outgrowth of potentially pathogenic organisms in the intestine can result from long-term antibiotic use or inflammatory conditions, and may perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, although an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5–7. Here we isolated and down-selected commensal bacterial consortia from stool samples from healthy humans that could strongly and specifically suppress intestinal Enterobacteriaceae. One of the elaborated consortia, comprising 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby re-establishing colonization resistance and alleviating Klebsiella- and Escherichia-driven intestinal inflammation in mice. Harnessing these activities in the form of live bacterial therapies may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant Enterobacteriaceae infection.
Two-factor authentication underpins the precision of the piRNA pathway
Authors: Dias Mirandela Madeleine , Zoch Ansgar , Leismann Jessica , Webb Shaun , Berrens Rebecca V. , Valsakumar Devisree , Kabayama Yuka , Auchynnikava Tania , Schito Martina , Chowdhury Tamoghna , MacLeod David , Xiang Xinyu , Zou Juan , Rappsilber Juri , Allshire Robin C. , Voigt Philipp , Cook Atlanta G. , Barau Joan , O’Carroll Dónal
Published: September 2024

The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice1. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1 (refs. 2–5). Transposon methylation requires great precision: every copy needs to be methylated but off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 interacts directly with SPIN1 (SPINDLIN1), a chromatin reader that primarily binds to H3K4me3-K9me3 (ref. 6). The prevailing assumption is that all the molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. We find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1 copies, but not old ones, are marked by H3K4me3, H3K9me3 and SPIN1 before the initiation of piRNA-directed DNA methylation. We generated a Spocd1 separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the interaction between SPOCD1 and SPIN1 is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that piRNA-directed LINE1 DNA methylation requires a developmentally timed two-factor authentication process. The first authentication is the recruitment of SPIN1–SPOCD1 to the young LINE1 promoter, and the second is MIWI2 engagement with the nascent transcript. In summary, independent authentication events underpin the precision of piRNA-directed LINE1 DNA methylation.
On complexity of colloid cellular automata
Authors: Adamatzky Andrew , Roberts Nic , Fortulan Raphael , Kheirabadi Noushin Raeisi , Mougkogiannis Panagiotis , Tsompanas Michail-Antisthenis , Martínez Genaro J. , Sirakoulis Georgios Ch. , Chiolerio Alessandro
Published: September 2024

The colloid cellular automata do not imitate the physical structure of colloids but are governed by logical functions derived from them. We analyze the space-time complexity of Boolean circuits derived from the electrical responses of colloids-specifically ZnO (zinc oxide, an inorganic compound also known as calamine or zinc white, which naturally occurs as the mineral zincite), proteinoids (microspheres and crystals of thermal abiotic proteins), and their combinations in response to electrical stimulation. To extract Boolean circuits from colloids, we send all possible configurations of two-, four-, and eight-bit binary strings, encoded as electrical potential values, to the colloids, record their responses, and infer the Boolean functions they implement. We map the discovered functions onto the cell-state transition rules of cellular automata-arrays of binary state machines that update their states synchronously according to the same rule-creating the colloid cellular automata. We then analyze the phenomenology of the space-time configurations of the automata and evaluate their complexity using measures such as compressibility, Shannon entropy, Simpson diversity, and expressivity. A hierarchy of phenomenological and measurable space-time complexity is constructed.
Monitoring SARS-CoV-2 IgA, IgM and IgG antibodies in dried blood and saliva samples using antibody proximity extension assays (AbPEA)
Authors: Wang Mengqi , Kamali-Moghaddam Masood , Löf Liza , Cortabarría Fernandez Matilde , Díaz Codina Roger , Sterky Fredrik H. , Åberg Mikael , Landegren Ulf , Zhao Hongxing
Published: September 2024

Using a modified proximity extension assay, total and immunoglobulin (Ig) class-specific anti-SARS-CoV-2 antibodies were sensitively and conveniently detected directly from ø1.2 mm discs cut from dried blood and saliva spots (DBS and DSS) without the need for elution. For total Ig detection, antigen probes were prepared by conjugating recombinant spike protein subunit 1 (S1-RBD) to a pair of oligonucleotides. To detect isotype-specific antibody reactivity, one antigen probe was replaced with oligonucleotide-conjugated antibodies specific for antibody isotypes. Binding of pairs of oligonucleotide-conjugated probes to antibodies in patient samples brings oligonucleotides in proximity. An added DNA polymerase uses a transient hybridization between the oligonucleotides to prime synthesis of a DNA strand, which serves as a DNA amplicon that is quantified by real-time PCR. The S1-RBD-specific IgG, IgM, and IgA antibodies in DBS samples collected over the course of a first and second vaccination exhibited kinetics consistent with previous reports. Both DBS and DSS collected from 42 individuals in the autumn of 2023 showed significant level of total S1-RBD antibodies with a correlation of R = 0.70. However, levels in DSS were generally 10 to 100-fold lower than in DBS. Anti-S1-RBD IgG and IgA in DSS demonstrated a correlation of R = 0.6.
The effect of hemicelluloses on biosynthesis, structure and mechanical performance of bacterial cellulose-hemicellulose hydrogels
Authors: Chibrikov Vadym , Pieczywek Piotr Mariusz , Cybulska Justyna , Zdunek Artur
Published: September 2024

The primary plant cell wall (PCW) is a specialized structure composed predominantly of cellulose, hemicelluloses and pectin. While the role of cellulose and hemicelluloses in the formation of the PCW scaffold is undeniable, the mechanisms of how hemicelluloses determine the mechanical properties of PCW remain debatable. Thus, we produced bacterial cellulose–hemicellulose hydrogels as PCW analogues, incorporated with hemicelluloses. Next, we treated samples with hemicellulose degrading enzymes, and explored its structural and mechanical properties. As suggested, difference of hemicelluloses in structure and chemical composition resulted in a variety of the properties studied. By analyzing all the direct and indirect evidences we have found that glucomannan, xyloglucan and arabinoxylan increased the width of cellulose fibers both by hemicellulose surface deposition and fiber entrapment. Arabinoxylan increased stresses and moduli of the hydrogel by its reinforcing effect, while for xylan, increase in mechanical properties was determined by establishment of stiff cellulose–cellulose junctions. In contrast, increasing content of xyloglucan decreased stresses and moduli of hydrogel by its weak interactions with cellulose, while glucomannan altered cellulose network formation via surface deposition, decreasing its strength. The current results provide evidence for structure–dependent mechanisms of cellulose–hemicellulose interactions, suggesting the specific structural role of the latter.