bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractCancer-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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractPersistent 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

AbstractThe 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

AbstractThe 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

AbstractUsing 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

AbstractThe 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.
Shell biomechanics suggests an aquatic palaeoecology at the dawn of turtle evolution
Authors: Ferreira Gabriel S. , Hermanson Guilherme , Kyriakouli Christina , Dróżdż Dawid , Szczygielski Tomasz 
Published: September 2024

AbstractThe turtle shell is a remarkable structure that has intrigued not only evolutionary biologists but also engineering and material scientists because of its multi-scale complexity and various functions. Although protection is its most apparent role, the carapace and plastron are also related to many physiological functions and their shape influences hydrodynamics and self-righting ability. As such, analysing the functional morphology of the shell could help understanding the ecology of Triassic stem-turtles, which will contribute to the century-long debate on the evolutionary origins of turtles. Here, we used 3D imaging techniques to digitize the shells of two of the earliest stem-turtle taxa, Proganochelys and Proterochersis, and submitted their models to biomechanical and shape analyses. We analysed the strength performance under five predation scenarios and tested the function of two morphological traits found in stem-turtles, the epiplastral processes and an attached pelvic girdle. The latter, also present in the crown-lineage of side-necked turtles, has been suggested to increase load-bearing capacity of the shell or to improve swimming in pleurodires. Our results do not confirm the shell-strengthening hypothesis and, together with the results of our shape analyses, suggest that at least one of the first stem-turtles (Proterochersis) was an aquatic animal.
Faster ciguatoxin extraction methods for toxicity screening
Authors: Loeffler Christopher R. , Spielmeyer Astrid 
Published: September 2024

AbstractCiguatera poisoning (CP) is a severe global public health problem caused by the consumption of seafood products contaminated with ciguatoxins (CTXs). The growing demand for seafood products requires high-throughput testing for CTX-susceptible seafood, however complex extraction and slow cleanup methods inhibit this goal. Herein, several methods for extracting CTXs from fish tissue were established and compared; these methods are sensitive, specific, and valid while achieving higher sample extraction throughput than currently established protocols. The trial fish material was generated from multiple species, with different physical conditions (wet and freeze-dried tissue), and naturally contaminated with various CTXs (i.e., CTX-1B, CTX-3C, and C-CTX-1), thus ensuring these methods are robust and broadly applicable. The extraction methods used were based on mechanical maceration with acetone or methanol or enzymatic digestion followed by acetone and ethyl acetate extraction. Crude extracts were investigated for CTX-like toxicity using an in vitro mouse neuroblastoma (N2a) cell-based assay (CBA). Among the three methods, there was no significant difference in toxin estimates (p = 0.219, two-way ANOVA), indicating their interchangeability. For speed (> 16 samples/day), accuracy (100%), and CTX analog retention confirmation by liquid chromatography-tandem mass spectrometry (LC‒MS/MS), the preferred extraction methods were both methanol and enzyme-based. All extraction methods post hoc confirmation of CTX analogs successfully met international seafood market-based CTX contaminant guidance. These methods can drastically increase global CTX screening capabilities and subsequently relieve sample processing bottlenecks, inhibiting environmental and human health-based CTX analysis.