bluuebunny/crossref_metadata_2025_split huggingface dataset:
DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts
Authors: Kuś Krzysztof , Carrique Loic , Kecman Tea , Fournier Marjorie , Hassanein Sarah Sayed , Aydin Ebru , Kilchert Cornelia , Grimes Jonathan M. , Vasiljeva Lidia 
Published: January 2025

AbstractPrecursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is established, the underlying mechanisms are not fully understood. We show that the key transcription termination factor, RNA exonuclease Xrn2 engages with Pol II forming a stable complex. Xrn2 activity is stimulated by Spt5 to ensure efficient degradation of nascent RNA leading to Pol II dislodgement from DNA. Our results support a model where Xrn2 first forms a stable complex with the elongating Pol II to achieve its full activity in degrading nascent RNA revising the current ‘torpedo’ model of termination, which posits that RNA degradation precedes Xrn2 engagement with Pol II. Spt5 is also a key factor that attenuates the expression of non-coding transcripts, coordinates pre-mRNA splicing and 3’-end processing. Our findings indicate that engagement with the transcribing Pol II is an essential regulatory step modulating the activity of RNA enzymes such as Xrn2, thus advancing our understanding of how RNA maturation is controlled during transcription.
A flexible catheter-based sensor array for upper airway soft tissues pressure monitoring
Authors: Shang Jiang , Ma Xiaoxiao , Zou Peikai , Huang Chenxiao , Lao Zhechen , Wang Junhan , Jiang Tingshu , Fu Yanzhe , Li Jiebo , Zhang Shaoxing , Li Ruya , Fan Yubo 
Published: January 2025

AbstractObstructive sleep apnea is a globally prevalent concern with significant health impacts, especially when coupled with comorbidities. Accurate detection and localization of airway obstructions are crucial for effective diagnosis and treatment, which remains a challenge for traditional sleep monitoring methods. Here, we report a catheter-based flexible pressure sensor array that continuously monitors soft tissue pressure in the upper airway and facilitates at the millimeter level. The sensor’s design and versatile 3D femtosecond laser fabrication process enable adaptation to diverse materials and applications. In vitro testing demonstrates high sensitivity (38.1 Ω/mmHg) and excellent stability. The sensor array effectively monitors distributed airway pressure and accurately identifies obstructions in an obstructive sleep apnea animal model. In this work, we highlight the potential of this catheter-based sensor array for long-term, continuous upper airway pressure monitoring and its prospective applications in other medical devices for pressure measurement in human body cavities.
Asynchronicity of deglacial permafrost thawing controlled by millennial-scale climate variability
Authors: Yan Xinwei , Zhang Xu , Liu Bo , Mithan Huw T. , Hellstrom John , Nuber Sophie , Drysdale Russell , Wu Junjie , Lin Fangyuan , Zhao Ning , Zhang Yuao , Kang Wengang , Liu Jianbao 
Published: January 2025

AbstractPermafrost is a potentially important source of deglacial carbon release alongside deep-sea carbon outgassing. However, limited proxies have restricted our understanding in circumarctic regions and the last deglaciation. Tibetan Plateau (TP), the Earth’s largest low-latitude and alpine permafrost region, remains underexplored. Using speleothem growth phases, we reconstruct TP permafrost thawing history over the last 500,000 years, standardizing chronology to investigate Northern Hemisphere permafrost thawing patterns. We find that, unlike circumarctic permafrost, TP permafrost generally initiates thawing at the onset of deglaciations, coinciding with Weak Monsoon Intervals and sluggish Atlantic Meridional Overturning Circulation (AMOC) during Terminal Stadials. Modeling elaborates that the associated Asian monsoon weakening induces anomalous TP warming through local cloud–precipitation–soil moisture feedback. This, combined with high-latitude cooling, results in asynchronous boreal permafrost thawing. During the last deglaciation, however, anomalous AMOC variability delayed TP and advanced circumarctic permafrost thawing. Our results indicate that permafrost carbon release, influenced by millennial-scale AMOC variability, may have been a non-trivial contributor to deglacial CO2 rise.
Dynamics of specialization in neural modules under resource constraints
Authors: Béna Gabriel , Goodman Dan F. M. 
Published: January 2025

AbstractThe brain is structurally and functionally modular, although recent evidence has raised questions about the extent of both types of modularity. Using a simple, toy artificial neural network setup that allows for precise control, we find that structural modularity does not in general guarantee functional specialization (across multiple measures of specialization). Further, in this setup (1) specialization only emerges when features of the environment are meaningfully separable, (2) specialization preferentially emerges when the network is strongly resource-constrained, and (3) these findings are qualitatively similar across several different variations of network architectures. Finally, we show that functional specialization varies dynamically across time, and these dynamics depend on both the timing and bandwidth of information flow in the network. We conclude that a static notion of specialization is likely too simple a framework for understanding intelligence in situations of real-world complexity, from biology to brain-inspired neuromorphic systems.
Cu- or Ag-containing Bi-Sb-Te for in-line roll-to-roll patterned thin-film thermoelectrics
Authors: Tao Xudong , Zheng Qianfang , Zeng Chongyang , Potter Harry , Zhang Zheng , Ellingford Joshua , Bonilla Ruy S. , Bilotti Emiliano , Grant Patrick S. , Assender Hazel E. 
Published: January 2025

AbstractThe Selective Metallization Technique shows promise for roll-to-roll in-line patterning of flexible electronics using evaporated metals, but challenges arise when applied to sputtering functional materials. This study overcomes these challenges with simultaneous sputtering of Bi-Sb-Te and evaporation of metal (Ag or Cu) for thermoelectric layers when using Selective Metallization Technique. Large-scale manufacturing is demonstrated through roll-to-roll processing of a 0.8 m wide polymer web at 25 m/min, achieving high-throughput production of functional thin-film patterns with nanometer thickness. The room-temperature-deposited material system exhibits significantly enhanced thermoelectric performance and facilitates an n-type-to-p-type transition in the Cu- or Ag-containing Bi-Sb-Te-based composite film. Here, we show that while applying Selective Metallization Technique, the evaporation of metal modifies the impact of residual oil on Bi-Sb-Te, which can be effectively removed with a few seconds of plasma exposure, and the fabricated thermoelectric devices are validated in wearable applications utilizing a coiled-up wristband design.
Deeper response predicts better outcomes in high-risk-smoldering-myeloma: results of the I-PRISM phase II clinical trial
Authors: Nadeem Omar , Aranha Michelle P. , Redd Robert , Timonian Michael , Magidson Sophie , Lightbody Elizabeth D. , Alberge Jean-Baptiste , Bertamini Luca , Dutta Ankit K. , El-Khoury Habib , Bustoros Mark , Laubach Jacob P. , Bianchi Giada , O’Donnell Elizabeth , Wu Ting , Tsuji Junko , Anderson Kenneth C. , Getz Gad , Trippa Lorenzo , Richardson Paul G. , Sklavenitis-Pistofidis Romanos , Ghobrial Irene M. 
Published: January 2025

AbstractEarly therapeutic intervention in high-risk smoldering multiple myeloma (HR-SMM) has shown benefits, however, no studies have assessed whether biochemical progression or response depth predicts long-term outcomes. The single-arm I-PRISM phase II trial (NCT02916771) evaluated ixazomib, lenalidomide, and dexamethasone in 55 patients with HR-SMM. The primary endpoint, median progression-free survival (PFS), was not reached (NR) (95% CI: 57.7–NR, median follow-up 50 months). The secondary endpoint, biochemical PFS, was 48.6 months (95% CI: 39.9–NR) and coincided with or preceded SLiM-CRAB in eight patients. For additional secondary objectives, the overall response rate was 93% with 31% achieving complete response (CR) and 45% very good partial response (VGPR) or better. CR correlated strongly with the absence of SLiM-CRAB and biochemical progression. MRD-negativity (10-5 sensitivity) predicted a 5-year biochemical PFS of 100% versus 40% in MRD-positive patients (p = 0.051), demonstrating that deep responses significantly improve time to progression. Exploratory single-cell RNA sequencing linked tumor MHC class I expression to proteasome inhibitor response, and a lower proportion of GZMB+ T cells within clonally expanded CD8+ T cells associated with suboptimal outcomes.
TOPS-speed complex-valued convolutional accelerator for feature extraction and inference
Authors: Bai Yunping , Xu Yifu , Chen Shifan , Zhu Xiaotian , Wang Shuai , Huang Sirui , Song Yuhang , Zheng Yixuan , Liu Zhihui , Tan Sim , Morandotti Roberto , Chu Sai T. , Little Brent E. , Moss David J. , Xu Xingyuan , Xu Kun 
Published: January 2025

AbstractComplex-valued neural networks process both amplitude and phase information, in contrast to conventional artificial neural networks, achieving additive capabilities in recognizing phase-sensitive data inherent in wave-related phenomena. The ever-increasing data capacity and network scale place substantial demands on underlying computing hardware. In parallel with the successes and extensive efforts made in electronics, optical neuromorphic hardware is promising to achieve ultra-high computing performances due to its inherent analog architecture and wide bandwidth. Here, we report a complex-valued optical convolution accelerator operating at over 2 Tera operations per second (TOPS). With appropriately designed phasors we demonstrate its performance in the recognition of synthetic aperture radar (SAR) images captured by the Sentinel-1 satellite, which are inherently complex-valued and more intricate than what optical neural networks have previously processed. Experimental tests with 500 images yield an 83.8% accuracy, close to in-silico results. This approach facilitates feature extraction of phase-sensitive information, and represents a pivotal advance in artificial intelligence towards real-time, high-dimensional data analysis of complex and dynamic environments.
Quantum key distribution implemented with d-level time-bin entangled photons
Authors: Yu Hao , Sciara Stefania , Chemnitz Mario , Montaut Nicola , Crockett Benjamin , Fischer Bennet , Helsten Robin , Wetzel Benjamin , Goebel Thorsten A. , Krämer Ria G. , Little Brent E. , Chu Sai T. , Nolte Stefan , Wang Zhiming , Azaña José , Munro William J. , Moss David J. , Morandotti Roberto 
Published: January 2025

AbstractHigh-dimensional photon states (qudits) are pivotal to enhance the information capacity, noise robustness, and data rates of quantum communications. Time-bin entangled qudits are promising candidates for implementing high-dimensional quantum communications over optical fiber networks with processing rates approaching those of classical telecommunications. However, their use is hindered by phase instability, timing inaccuracy, and low scalability of interferometric schemes needed for time-bin processing. As well, increasing the number of time bins per photon state typically requires decreasing the repetition rate of the system, affecting in turn the effective qudit rates. Here, we demonstrate a fiber-pigtailed, integrated photonic platform enabling the generation and processing of picosecond-spaced time-bin entangled qudits in the telecommunication C band via an on-chip interferometry system. We experimentally demonstrate the Bennett-Brassard-Mermin 1992 quantum key distribution protocol with time-bin entangled qudits and extend it over a 60 km-long optical fiber link, by showing dimensionality scaling without sacrificing the repetition rate. Our approach enables the manipulation of time-bin entangled qudits at processing speeds typical of standard telecommunications (10 s of GHz) with high quantum information capacity per single frequency channel, representing an important step towards an efficient implementation of high-data rate quantum communications in standard, multi-user optical fiber networks.
Intratumor heterogeneity of EGFR expression mediates targeted therapy resistance and formation of drug tolerant microenvironment
Authors: Alsaed Bassel , Lin Linh , Son Jieun , Li Jiaqi , Smolander Johannes , Lopez Timothy , Eser Pinar Ö. , Ogino Atsuko , Ambrogio Chiara , Eum Yoonji , Thai Tran , Wang Haiyun , Sutinen Eva , Mutanen Hilma , Duàn Hanna , Bobik Nina , Borenius Kristian , Feng William W. , Nabet Behnam , Mustjoki Satu , Laaksonen Sanna , Eschle Benjamin K. , Poitras Michael J. , Barbie David , Ilonen Ilkka , Gokhale Prafulla , Jänne Pasi A. , Haikala Heidi M. 
Published: January 2025

AbstractEpidermal growth factor receptor (EGFR) tyrosine kinase inhibitors are commonly used to treat non-small cell lung cancers with EGFR mutations, but drug resistance often emerges. Intratumor heterogeneity is a known cause of targeted therapy resistance and is considered a major factor in treatment failure. This study identifies clones of EGFR-mutant non-small cell lung tumors expressing low levels of both wild-type and mutant EGFR protein. These EGFR-low cells are intrinsically more tolerant to EGFR inhibitors, more invasive, and exhibit an epithelial-to-mesenchymal-like phenotype compared to their EGFR-high counterparts. The EGFR-low cells secrete Transforming growth factor beta (TGFβ) family cytokines, leading to increased recruitment of cancer-associated fibroblasts and immune suppression, thus contributing to the drug-tolerant tumor microenvironment. Notably, pharmacological induction of EGFR using epigenetic inhibitors sensitizes the resistant cells to EGFR inhibition. These findings suggest that intrinsic drug resistance can be prevented or reversed using combination therapies.
Functional large-conductance calcium and voltage-gated potassium channels in extracellular vesicles act as gatekeepers of structural and functional integrity
Authors: Sanghvi Shridhar , Sridharan Divya , Evans Parker , Dougherty Julie , Szteyn Kalina , Gabrilovich Denis , Dyta Mayukha , Weist Jessica , Pierre Sandrine V. , Gururaja Rao Shubha , Halm Dan R. , Chen Tingting , Athanasopoulos Panagiotis S. , Dolga Amalia M. , Yu Lianbo , Khan Mahmood , Singh Harpreet 
Published: January 2025

Abstract
Extracellular vesicles (EVs) are associated with intercellular communications, immune responses, viral pathogenicity, cardiovascular diseases, neurological disorders, and cancer progression. EVs deliver proteins, metabolites, and nucleic acids into recipient cells to effectively alter their physiological and biological response. During their transportation from the donor to the recipient cell EVs face differential ionic concentrations, which can be detrimental to their integrity and impact their cargo content. EVs are known to possess ion channels and transporters in their membrane but neither the function nor the role of these channels in EVs is known. In this study, we discover a functional calcium-activated large-conductance potassium channel (BKCa) in the membrane of EVs. Furthermore, we establish that BKCa is essential for the structural and functional integrity of EVs. Together, these findings establish the critical role of ion channels such as BKCa in functioning as gatekeepers and maintaining EV-mediated signaling.
An aperiodic chiral tiling by topological molecular self-assembly
Authors: Voigt Jan , Baljozović Miloš , Martin Kévin , Wäckerlin Christian , Avarvari Narcis , Ernst Karl-Heinz 
Published: January 2025

AbstractStudying the self-assembly of chiral molecules in two dimensions offers insights into the fundamentals of crystallization. Using scanning tunneling microscopy, we examine an uncommon aggregation of polyaromatic chiral molecules on a silver surface. Dense packing is achieved through a chiral triangular tiling of triads, with N and N ± 1 molecules at the edges. The triangles feature a random distribution of mirror-isomers, with a significant excess of one isomer. Chirality at the domain boundaries causes a lateral shift, producing three distinct topological defects where six triangles converge. These defects partially contribute to the formation of supramolecular spirals. The observation of different equal-density arrangements suggests that entropy maximization must play a crucial role. Despite the potential for regular patterns, all observed tiling is aperiodic. Differences from previously reported aperiodic molecular assemblies, such as Penrose tiling, are discussed. Our findings demonstrate that two-dimensional molecular self-assembly can be governed by topological constraints, leading to aperiodic tiling induced by intermolecular forces.
Exact projected entangled pair ground states with topological Euler invariant
Authors: Wahl Thorsten B. , Jankowski Wojciech J. , Bouhon Adrien , Chaudhary Gaurav , Slager Robert-Jan 
Published: January 2025

AbstractWe report on a class of gapped projected entangled pair states (PEPS) with non-trivial Euler topology motivated by recent progress in band geometry. In the non-interacting limit, these systems have optimal conditions relating to saturation of quantum geometrical bounds, allowing for parent Hamiltonians whose lowest bands are completely flat and which have the PEPS as unique ground states. Protected by crystalline symmetries, these states evade restrictions on capturing tenfold-way topological features with gapped PEPS. These PEPS thus form the first tensor network representative of a non-interacting, gapped two-dimensional topological phase, similar to the Kitaev chain in one dimension. Using unitary circuits, we then formulate interacting variants of these PEPS and corresponding gapped parent Hamiltonians. We reveal characteristic entanglement features shared between the free-fermionic and interacting states with Euler topology. Our results hence provide a rich platform of PEPS models that have, unexpectedly, a finite topological invariant, forming the basis for new spin liquids, quantum Hall physics, and quantum information pursuits.
Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming
Authors: Theulot Bertrand , Tourancheau Alan , Simonin Chavignier Emma , Jean Etienne , Arbona Jean-Michel , Audit Benjamin , Hyrien Olivier , Lacroix Laurent , Le Tallec Benoît 
Published: January 2025

AbstractCurrent temporal studies of DNA replication are either low-resolution or require complex cell synchronisation and/or sorting procedures. Here we introduce Nanotiming, a single-molecule, nanopore sequencing-based method producing high-resolution, telomere-to-telomere replication timing (RT) profiles of eukaryotic genomes by interrogating changes in intracellular dTTP concentration during S phase through competition with its analogue bromodeoxyuridine triphosphate (BrdUTP) for incorporation into replicating DNA. This solely demands the labelling of asynchronously growing cells with an innocuous dose of BrdU during one doubling time followed by BrdU quantification along nanopore reads. We demonstrate in S. cerevisiae model eukaryote that Nanotiming reproduces RT profiles generated by reference methods both in wild-type and mutant cells inactivated for known RT determinants. Nanotiming is simple, accurate, inexpensive, amenable to large-scale analyses, and has the unique ability to access RT of individual telomeres, revealing that Rif1 iconic telomere regulator selectively delays replication of telomeres associated with specific subtelomeric elements.
Deciphering metabolic differentiation during Bacillus subtilis sporulation
Authors: Tibocha-Bonilla Juan D. , Lyda Jelani , Riley Eammon , Pogliano Kit , Zengler Karsten 
Published: January 2025

AbstractThe bacterium Bacillus subtilis undergoes asymmetric cell division during sporulation, producing a mother cell and a smaller forespore connected by the SpoIIQ-SpoIIIA (or Q-A) channel. The two cells differentiate metabolically, and the forespore becomes dependent on the mother cell for essential building blocks. Here, we investigate the metabolic interactions between mother cell and forespore using genome-scale metabolic and expression models as well as experiments. Our results indicate that nucleotides are synthesized in the mother cell and transported in the form of nucleoside di- or tri-phosphates to the forespore via the Q-A channel. However, if the Q-A channel is inactivated later in sporulation, then glycolytic enzymes can form an ATP and NADH shuttle, providing the forespore with energy and reducing power. Our integrated in silico and in vivo approach sheds light into the intricate metabolic interactions underlying cell differentiation in B. subtilis, and provides a foundation for future studies of metabolic differentiation.
Surface molecular engineering to enable processing of sulfide solid electrolytes in humid ambient air
Authors: Liu Mengchen , Hong Jessica J. , Sebti Elias , Zhou Ke , Wang Shen , Feng Shijie , Pennebaker Tyler , Hui Zeyu , Miao Qiushi , Lu Ershuang , Harpak Nimrod , Yu Sicen , Zhou Jianbin , Oh Jeong Woo , Song Min-Sang , Luo Jian , Clément Raphaële J. , Liu Ping 
Published: January 2025

AbstractSulfide solid-state electrolytes (SSEs) are promising candidates to realize all solid-state batteries (ASSBs) due to their superior ionic conductivity and excellent ductility. However, their hypersensitivity to moisture requires processing environments that are not compatible with today’s lithium-ion battery manufacturing infrastructure. Herein, we present a reversible surface modification strategy that enables the processability of sulfide SSEs (e. g., Li6PS5Cl) under humid ambient air. We demonstrate that a long chain alkyl thiol, 1-undecanethiol, is chemically compatible with the electrolyte with negligible impact on its ion conductivity. Importantly, the thiol modification extends the amount of time that the sulfide SSE can be exposed to air with 33% relative humidity (33% RH) with limited degradation of its structure while retaining a conductivity of above 1 mS cm-1 for up to 2 days, a more than 100-fold improvement in protection time over competing approaches. Experimental and computational results reveal that the thiol group anchors to the SSE surface, while the hydrophobic hydrocarbon tail provides protection by repelling water. The modified Li6PS5Cl SSE maintains its function after exposure to ambient humidity when implemented in a Li0.5In | |LiNi0.8Co0.1Mn0.1O2 ASSB. The proposed protection strategy based on surface molecular interactions represents a major step forward towards cost-competitive and energy-efficient sulfide SSE manufacturing for ASSB applications.