bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging clinic and wildlife care with AI-powered pan-species computational pathology
Authors: AbdulJabbar Khalid , Castillo Simon P. , Hughes Katherine , Davidson Hannah , Boddy Amy M. , Abegglen Lisa M. , Minoli Lucia , Iussich Selina , Murchison Elizabeth P. , Graham Trevor A. , Spiro Simon , Maley Carlo C. , Aresu Luca , Palmieri Chiara , Yuan Yinyin 
Published: April 2023

AbstractCancers occur across species. Understanding what is consistent and varies across species can provide new insights into cancer initiation and evolution, with significant implications for animal welfare and wildlife conservation. We build a pan-species cancer digital pathology atlas (panspecies.ai) and conduct a pan-species study of computational comparative pathology using a supervised convolutional neural network algorithm trained on human samples. The artificial intelligence algorithm achieves high accuracy in measuring immune response through single-cell classification for two transmissible cancers (canine transmissible venereal tumour, 0.94; Tasmanian devil facial tumour disease, 0.88). In 18 other vertebrate species (mammalia = 11, reptilia = 4, aves = 2, and amphibia = 1), accuracy (range 0.57–0.94) is influenced by cell morphological similarity preserved across different taxonomic groups, tumour sites, and variations in the immune compartment. Furthermore, a spatial immune score based on artificial intelligence and spatial statistics is associated with prognosis in canine melanoma and prostate tumours. A metric, named morphospace overlap, is developed to guide veterinary pathologists towards rational deployment of this technology on new samples. This study provides the foundation and guidelines for transferring artificial intelligence technologies to veterinary pathology based on understanding of morphological conservation, which could vastly accelerate developments in veterinary medicine and comparative oncology.
Modulation of antibiotic effects on microbial communities by resource competition
Authors: Newton Daniel P. , Ho Po-Yi , Huang Kerwyn Casey 
Published: April 2023

AbstractAntibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such as bacteriophages. Our analyses highlight the complex dependence of species coexistence that can arise from the interplay of resource competition and antibiotic activity, independent of other biological mechanisms. In particular, we identify resource competition structures that cause richness to depend on the order of sequential application of antibiotics (non-transitivity), and the emergence of synergistic and antagonistic effects under simultaneous application of multiple antibiotics (non-additivity). These complex behaviors can be prevalent, especially when generalist consumers are targeted. Communities can be prone to either synergism or antagonism, but typically not both, and antagonism is more common. Furthermore, we identify a striking overlap in competition structures that lead to non-transitivity during antibiotic sequences and those that lead to non-additivity during antibiotic combination. In sum, our results establish a broadly applicable framework for predicting microbial community dynamics under deleterious perturbations.
Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene
Authors: Díez-Mérida J. , Díez-Carlón A. , Yang S. Y. , Xie Y.-M. , Gao X.-J. , Senior J. , Watanabe K. , Taniguchi T. , Lu X. , Higginbotham A. P. , Law K. T. , Efetov Dmitri K. 
Published: April 2023

AbstractThe coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices.
Mini-PCDH15 gene therapy rescues hearing in a mouse model of Usher syndrome type 1F
Authors: Ivanchenko Maryna V. , Hathaway Daniel M. , Klein Alex J. , Pan Bifeng , Strelkova Olga , De-la-Torre Pedro , Wu Xudong , Peters Cole W. , Mulhall Eric M. , Booth Kevin T. , Goldstein Corey , Brower Joseph , Sotomayor Marcos , Indzhykulian Artur A. , Corey David P. 
Published: April 2023

AbstractUsher syndrome type 1 F (USH1F), caused by mutations in the protocadherin-15 gene (PCDH15), is characterized by congenital deafness, lack of balance, and progressive blindness. In hair cells, the receptor cells of the inner ear, PCDH15 is a component of tip links, fine filaments which pull open mechanosensory transduction channels. A simple gene addition therapy for USH1F is challenging because the PCDH15 coding sequence is too large for adeno-associated virus (AAV) vectors. We use rational, structure-based design to engineer mini-PCDH15s in which 3–5 of the 11 extracellular cadherin repeats are deleted, but which still bind a partner protein. Some mini-PCDH15s can fit in an AAV. An AAV encoding one of these, injected into the inner ears of mouse models of USH1F, produces a mini-PCDH15 which properly forms tip links, prevents the degeneration of hair cell bundles, and rescues hearing. Mini-PCDH15s may be a useful therapy for the deafness of USH1F.
Electron-phonon coupling and spin fluctuations in the Ising superconductor NbSe2
Authors: Das S. , Paudyal H. , Margine E. R. , Agterberg D. F. , Mazin I. I. 
Published: April 2023

AbstractIsing superconductivity, observed in NbSe2 and similar materials, has generated tremendous interest. Recently, attention was called to the possible role that spin fluctuations (SF) play in this phenomenon, in addition to the dominant electron–phonon coupling (EPC); the possibility of a predominantly triplet state was discussed and led to a conjecture of viable singlet–triplet Leggett oscillations. However, these hypotheses have not been put to a quantitative test. In this paper, we report first principle calculations of the EPC and also estimate coupling with SF, including full momentum dependence. We find that: (1) EPC is strongly anisotropic, largely coming from the $$K-{K}^{{\prime} }$$

K
−

K

′

scattering, and therefore excludes triplet symmetry even as an excited state; (2) superconductivity is substantially weakened by SF, but anisotropy remains as above; and, (3) we do find the possibility of a Leggett mode, not in a singlet–triplet but in an s++ – s± channel.
Long-range inhibition synchronizes and updates prefrontal task activity
Authors: Cho Kathleen K. A. , Shi Jingcheng , Phensy Aarron J. , Turner Marc L. , Sohal Vikaas S. 
Published: April 2023

AbstractChanges in patterns of activity within the medial prefrontal cortex enable rodents, non-human primates and humans to update their behaviour to adapt to changes in the environment—for example, during cognitive tasks1–5. Parvalbumin-expressing inhibitory neurons in the medial prefrontal cortex are important for learning new strategies during a rule-shift task6–8, but the circuit interactions that switch prefrontal network dynamics from maintaining to updating task-related patterns of activity remain unknown. Here we describe a mechanism that links parvalbumin-expressing neurons, a new callosal inhibitory connection, and changes in task representations. Whereas nonspecifically inhibiting all callosal projections does not prevent mice from learning rule shifts or disrupt the evolution of activity patterns, selectively inhibiting only callosal projections of parvalbumin-expressing neurons impairs rule-shift learning, desynchronizes the gamma-frequency activity that is necessary for learning8 and suppresses the reorganization of prefrontal activity patterns that normally accompanies rule-shift learning. This dissociation reveals how callosal parvalbumin-expressing projections switch the operating mode of prefrontal circuits from maintenance to updating by transmitting gamma synchrony and gating the ability of other callosal inputs to maintain previously established neural representations. Thus, callosal projections originating from parvalbumin-expressing neurons represent a key circuit locus for understanding and correcting the deficits in behavioural flexibility and gamma synchrony that have been implicated in schizophrenia and related conditions9,10.
Multisensory learning binds neurons into a cross-modal memory engram
Authors: Okray Zeynep , Jacob Pedro F. , Stern Ciara , Desmond Kieran , Otto Nils , Talbot Clifford B. , Vargas-Gutierrez Paola , Waddell Scott 
Published: April 2023

AbstractAssociating multiple sensory cues with objects and experience is a fundamental brain process that improves object recognition and memory performance. However, neural mechanisms that bind sensory features during learning and augment memory expression are unknown. Here we demonstrate multisensory appetitive and aversive memory in Drosophila. Combining colours and odours improved memory performance, even when each sensory modality was tested alone. Temporal control of neuronal function revealed visually selective mushroom body Kenyon cells (KCs) to be required for enhancement of both visual and olfactory memory after multisensory training. Voltage imaging in head-fixed flies showed that multisensory learning binds activity between streams of modality-specific KCs so that unimodal sensory input generates a multimodal neuronal response. Binding occurs between regions of the olfactory and visual KC axons, which receive valence-relevant dopaminergic reinforcement, and is propagated downstream. Dopamine locally releases GABAergic inhibition to permit specific microcircuits within KC-spanning serotonergic neurons to function as an excitatory bridge between the previously ‘modality-selective’ KC streams. Cross-modal binding thereby expands the KCs representing the memory engram for each modality into those representing the other. This broadening of the engram improves memory performance after multisensory learning and permits a single sensory feature to retrieve the memory of the multimodal experience.
Isolating sensory artifacts in the suprathreshold TMS-EEG signal over DLPFC
Authors: Poorganji Mohsen , Zomorrodi Reza , Hawco Colin , Hill Aron T. , Hadas Itay , Zrenner Christoph , Rajji Tarek K. , Chen Robert , Voineskos Daphne , Blumberger Daniel M. , Daskalakis Zafiris J. 
Published: April 2023

AbstractCombined transcranial magnetic stimulation and electroencephalography (TMS-EEG) is an effective way to evaluate neurophysiological processes at the level of the cortex. To further characterize the TMS-evoked potential (TEP) generated with TMS-EEG, beyond the motor cortex, we aimed to distinguish between cortical reactivity to TMS versus non-specific somatosensory and auditory co-activations using both single-pulse and paired-pulse protocols at suprathreshold stimulation intensities over the left dorsolateral prefrontal cortex (DLPFC). Fifteen right-handed healthy participants received six blocks of stimulation including single and paired TMS delivered as active-masked (i.e., TMS-EEG with auditory masking and foam spacing), active-unmasked (TMS-EEG without auditory masking and foam spacing) and sham (sham TMS coil). We evaluated cortical excitability following single-pulse TMS, and cortical inhibition following a paired-pulse paradigm (long-interval cortical inhibition (LICI)). Repeated measure ANOVAs revealed significant differences in mean cortical evoked activity (CEA) of active-masked, active-unmasked, and sham conditions for both the single-pulse (F(1.76, 24.63) = 21.88,p < 0.001, η2 = 0.61) and LICI (F(1.68, 23.49) = 10.09,p < 0.001, η2 = 0.42) protocols. Furthermore, global mean field amplitude (GMFA) differed significantly across the three conditions for both single-pulse (F(1.85, 25.89) = 24.68,p < 0.001, η2 = 0.64) and LICI (F(1.8, 25.16) = 14.29,p < 0.001, η2 = 0.5). Finally, only active LICI protocols but not sham stimulation ([active-masked (0.78 ± 0.16,P < 0.0001)], [active-unmasked (0.83 ± 0.25,P < 0.01)]) resulted in significant signal inhibition. While previous findings of a significant somatosensory and auditory contribution to the evoked EEG signal are replicated by our study, an artifact attenuated cortical reactivity can reliably be measured in the TMS-EEG signal with suprathreshold stimulation of DLPFC. Artifact attenuation can be accomplished using standard procedures, and even when masked, the level of cortical reactivity is still far above what is produced by sham stimulation. Our study illustrates that TMS-EEG of DLPFC remains a valid investigational tool.
Patterns of multiple brain network activation in dot perspective task
Authors: Montandon Marie-Louise , Rodriguez Cristelle , Herrmann François R. , Eytan Ariel , Pegna Alan J. , Haller Sven , Giannakopoulos Panteleimon 
Published: April 2023

AbstractIn this functional MRI (fMRI) study on 82 healthy adults using the dot perspective task, inconsistency of perspectives was associated with a significant increase of the mean reaction time and number of errors both in Self and Other conditions. Unlike the Arrow (non-mentalizing), the Avatar (mentalizing) paradigm was characterized by the recruitment of parts of the mentalizing and salience networks. These data provide experimental evidence supporting the fMRI distinction between mentalizing and non-mentalizing stimuli. A widespread activation of classical theory of mind (ToM) areas but also of salience network and decision making areas was observed in the Other compared to Self-conditions. Compared to Self-Consistent, Self-Inconsistent trials were related to increased activation in the lateral occipital cortex, right supramarginal and angular gyrus as well as inferior, superior and middle frontal gyri. Compared to the Other-Consistent, Other-Inconsistent trials yielded strong activation in the lateral occipital cortex, precuneus and superior parietal lobule, middle and superior precentral gyri and left frontal pole. These findings reveal that altercentric interference relies on areas involved in self-other distinction, self-updating and central executive functions. In contrast, egocentric interference needs the activation of the mirror neuron system and deductive reasoning, much less related to pure ToM abilities.
Achieving effective interlayer bonding of PLA parts during the material extrusion process with enhanced mechanical properties
Authors: Kumar M. Saravana , Farooq Muhammad Umar , Ross Nimel Sworna , Yang Che-Hua , Kavimani V. , Adediran Adeolu A. 
Published: April 2023

AbstractThe additive manufacturing technique of material extrusion has challenge of excessive process defects and not achieving the desired mechanical properties. The industry is trying to develop certification to better control variations in mechanical attributes. The current study is a progress towards understanding the evolution of processing defects and the correlation of mechanical behavior with the process parameters. Modeling of the 3D printing process parameters such as layer thickness, printing speed, and printing temperature is carried out through L27 orthogonal array using Taguchi approach. In addition, CRITIC embedded WASPAS is adopted to optimize the parts' mechanical attributes and overcome the defects. Flexural and tensile poly-lactic acid specimens are printed according to ASTM standards D790 and D638, respectively, and thoroughly analyzed based on the surface morphological analysis to characterize defects. The parametric significance analysis is carried out to explore process science where the layer thickness, print speed, and temperature significantly control the quality and strength of the parts. Mathematical optimization results based on composite desirability show that layer thickness of 0.1 mm, printing speed of 60 mm/s, and printing temperature of 200 °C produce significantly desirable results. The validation experiments yielded the maximum flexural strength of 78.52 MPa, the maximum ultimate tensile strength of 45.52 MPa, and maximum impact strength of 6.21 kJ/m2. It is established that multiple fused layers restricted the propagation of cracks with minimum thickness due to enhanced diffusion between the layers.
Water discharge variations control fluvial stratigraphic architecture in the Middle Eocene Escanilla formation, Spain
Authors: Sharma Nikhil , Whittaker Alexander C. , Watkins Stephen E. , Valero Luis , Vérité Jean , Puigdefabregas Cai , Adatte Thierry , Garcés Miguel , Guillocheau François , Castelltort Sébastien 
Published: April 2023

AbstractAncient fluvial deposits typically display repetitive changes in their depositional architecture such as alternating intervals of coarse-grained highly amalgamated (HA), laterally-stacked, channel bodies, and finer-grained less amalgamated (LA), vertically-stacked, channels encased in floodplain deposits. Such patterns are usually ascribed to slower, respectively higher, rates of base level rise (accommodation). However, “upstream” factors such as water discharge and sediment flux also play a potential role in determining stratigraphic architecture, yet this possibility has never been tested despite the recent advances in the field of palaeohydraulic reconstructions from fluvial accumulations. Here, we chronicle riverbed gradient evolution within three Middle Eocene (~ 40 Ma) fluvial HA-LA sequences in the Escanilla Formation in the south-Pyrenean foreland basin. This work documents, for the first time in a fossil fluvial system, how the ancient riverbed systematically evolved from lower slopes in coarser-grained HA intervals, and higher slopes in finer-grained LA intervals, suggesting that bed slope changes were determined primarily by climate-controlled water discharge variations rather than base level changes as often hypothesized. This highlights the important connection between climate and landscape evolution and has fundamental implications for our ability to reconstruct ancient hydroclimates from the interpretation of fluvial sedimentary sequences.
Automatic evaluation-feedback system for automated social skills training
Authors: Saga Takeshi , Tanaka Hiroki , Matsuda Yasuhiro , Morimoto Tsubasa , Uratani Mitsuhiro , Okazaki Kosuke , Fujimoto Yuichiro , Nakamura Satoshi 
Published: April 2023

AbstractSocial skills training (SST), which is a rehabilitation program for improving daily interpersonal communication, has been used for more than 40 years. Although such training’s demand is increasing, its accessibility is limited due to the lack of experienced trainers. To tackle this issue, automated SST systems have been studied for years. An evaluation-feedback pipeline of social skills is a crucial component of an SST system. Unfortunately, research that considers both the evaluation and feedback parts of automation remains insufficient. In this paper, we collected and analyzed the characteristics of a human–human SST dataset that consisted of 19 healthy controls, 15 schizophreniacs, 16 autism spectrum disorder (ASD) participants, and 276 sessions with score labels of six clinical measures. From our analysis of this dataset, we developed an automated SST evaluation-feedback system under the supervision of professional, experienced SST trainers. We identified their preferred or most acceptable feedback methods by running a user-study on the following conditions: with/without recorded video of the role-plays of users and different amounts of positive and corrective feedback. We confirmed a reasonable performance of our social-skill-score estimation models as our system’s evaluation part with a maximum Spearman’s correlation coefficient of 0.68. For the feedback part, our user-study concluded that people understood more about what aspects they need to improve by watching recorded videos of their own performance. In terms of the amount of feedback, participants most preferred a 2-positive/1-corrective format. Since the average amount of feedback preferred by the participants nearly equaled that from experienced trainers in human–human SSTs, our result suggests the practical future possibilities of an automated evaluation-feedback system that complements SSTs done by professional trainers.
The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon
Authors: Stocco Alice , Pranovi Fabio 
Published: April 2023

AbstractThe Venice lagoon—the largest Mediterranean coastal lagoon—is characterized by the presence at its edges of 31 “valli da pesca”, types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the “open’ lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of “side effects” on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.