bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters
Authors: Dueholm Morten Kam Dahl , Andersen Kasper Skytte , Korntved Anne-Kirstine C. , Rudkjøbing Vibeke , Alves Madalena , Bajón-Fernández Yadira , Batstone Damien , Butler Caitlyn , Cruz Mercedes Cecilia , Davidsson Åsa , Erijman Leonardo , Holliger Christof , Koch Konrad , Kreuzinger Norbert , Lee Changsoo , Lyberatos Gerasimos , Mutnuri Srikanth , O’Flaherty Vincent , Oleskowicz-Popiel Piotr , Pokorna Dana , Rajal Veronica , Recktenwald Michael , Rodríguez Jorge , Saikaly Pascal E. , Tooker Nick , Vierheilig Julia , De Vrieze Jo , Wurzbacher Christian , Nielsen Per Halkjær 
Published: June 2024

AbstractAnaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84–99% and 18–61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
From bulk effective mass to 2D carrier mobility accurate prediction via adversarial transfer learning
Authors: Chen Xinyu , Lu Shuaihua , Chen Qian , Zhou Qionghua , Wang Jinlan 
Published: June 2024

AbstractData scarcity is one of the critical bottlenecks to utilizing machine learning in material discovery. Transfer learning can use existing big data to assist property prediction on small data sets, but the premise is that there must be a strong correlation between large and small data sets. To extend its applicability in scenarios with different properties and materials, here we develop a hybrid framework combining adversarial transfer learning and expert knowledge, which enables the direct prediction of carrier mobility of two-dimensional (2D) materials using the knowledge learned from bulk effective mass. Specifically, adversarial training ensures that only common knowledge between bulk and 2D materials is extracted while expert knowledge is incorporated to further improve the prediction accuracy and generalizability. Successfully, 2D carrier mobilities are predicted with the accuracy over 90% from only crystal structure, and 21 2D semiconductors with carrier mobilities far exceeding silicon and suitable bandgap are successfully screened out. This work enables transfer learning in simultaneous cross-property and cross-material scenarios, providing an effective tool to predict intricate material properties with limited data.
Overtone photothermal microscopy for high-resolution and high-sensitivity vibrational imaging
Authors: Wang Le , Lin Haonan , Zhu Yifan , Ge Xiaowei , Li Mingsheng , Liu Jianing , Chen Fukai , Zhang Meng , Cheng Ji-Xin 
Published: June 2024

AbstractPhotothermal microscopy is a highly sensitive pump-probe method for mapping nanostructures and molecules through the detection of local thermal gradients. While visible photothermal microscopy and mid-infrared photothermal microscopy techniques have been developed, they possess inherent limitations. These techniques either lack chemical specificity or encounter significant light attenuation caused by water absorption. Here, we present an overtone photothermal (OPT) microscopy technique that offers high chemical specificity, detection sensitivity, and spatial resolution by employing a visible probe for local heat detection in the C-H overtone region. We demonstrate its capability for high-fidelity chemical imaging of polymer nanostructures, depth-resolved intracellular chemical mapping of cancer cells, and imaging of multicellular C. elegans organisms and highly scattering brain tissues. By bridging the gap between visible and mid-infrared photothermal microscopy, OPT establishes a new modality for high-resolution and high-sensitivity chemical imaging. This advancement complements large-scale shortwave infrared imaging approaches, facilitating multiscale structural and chemical investigations of materials and biological metabolism.
Development of a genetically encoded sensor for probing endogenous nociceptin opioid peptide release
Authors: Zhou Xuehan , Stine Carrie , Prada Patricia Oliveira , Fusca Debora , Assoumou Kevin , Dernic Jan , Bhat Musadiq A. , Achanta Ananya S. , Johnson Joseph C. , Pasqualini Amanda Loren , Jadhav Sanjana , Bauder Corinna A. , Steuernagel Lukas , Ravotto Luca , Benke Dietmar , Weber Bruno , Suko Azra , Palmiter Richard D. , Stoeber Miriam , Kloppenburg Peter , Brüning Jens C. , Bruchas Michael R. , Patriarchi Tommaso 
Published: June 2024

AbstractNociceptin/orphanin-FQ (N/OFQ) is a recently appreciated critical opioid peptide with key regulatory functions in several central behavioral processes including motivation, stress, feeding, and sleep. The functional relevance of N/OFQ action in the mammalian brain remains unclear due to a lack of high-resolution approaches to detect this neuropeptide with appropriate spatial and temporal resolution. Here we develop and characterize NOPLight, a genetically encoded sensor that sensitively reports changes in endogenous N/OFQ release. We characterized the affinity, pharmacological profile, spectral properties, kinetics, ligand selectivity, and potential interaction with intracellular signal transducers of NOPLight in vitro. Its functionality was established in acute brain slices by exogeneous N/OFQ application and chemogenetic induction of endogenous N/OFQ release from PNOC neurons. In vivo studies with fibre photometry enabled direct recording of NOPLight binding to exogenous N/OFQ receptor ligands, as well as detection of endogenous N/OFQ release within the paranigral ventral tegmental area (pnVTA) during natural behaviors and chemogenetic activation of PNOC neurons. In summary, we show here that NOPLight can be used to detect N/OFQ opioid peptide signal dynamics in tissue and freely behaving animals.
An in-situ polymerization strategy for gel polymer electrolyte Si||Ni-rich lithium-ion batteries
Authors: Bai Miao , Tang Xiaoyu , Zhang Min , Wang Helin , Wang Zhiqiao , Shao Ahu , Ma Yue 
Published: June 2024

AbstractCoupling the Si-based anodes with nickel-rich LiNixMnyCo1−x−yO2 cathodes (x ≥ 0.8) in the energy-dense cell prototype suffers from the mechanical instability of the Li-Si alloys, cathode collapse upon the high-voltage cycling, as well as the severe leakage current at elevated temperatures. More seriously, the cathode-to-anode cross-talk effect of transitional metal aggravates the depletion of the active Li reservoir. To reconcile the cation utilization degree, stress dissipation, and extreme temperature tolerance of the Si-based anode||NMC prototype, we propose a gel polymer electrolyte to reinforce the mechanical integrity of Si anode and chelate with the transitional cations towards the stabilized interfacial property. As coupling the conformal gel polymer electrolyte encapsulation with the spatial arranged Si anode and NMC811 cathode, the 2.7 Ah pouch-format cell could achieve the high energy density of 325.9 Wh kg−1 (based on the whole pouch cell), 88.7% capacity retention for 2000 cycles, self-extinguish property as well as a wide temperature tolerance. Therefore, this proposed polymerization strategy provides a leap toward the secured Li batteries.
Plasmons in the Kagome metal CsV3Sb5
Authors: Shiravi H. , Gupta A. , Ortiz B. R. , Cui S. , Yu B. , Uykur E. , Tsirlin A. A. , Wilson S. D. , Sun Z. , Ni G. X. 
Published: June 2024

AbstractPlasmon polaritons, or plasmons, are coupled oscillations of electrons and electromagnetic fields that can confine the latter into deeply subwavelength scales, enabling novel polaritonic devices. While plasmons have been extensively studied in normal metals or semimetals, they remain largely unexplored in correlated materials. In this paper, we report infrared (IR) nano-imaging of thin flakes of CsV3Sb5, a prototypical layered Kagome metal. We observe propagating plasmon waves in real-space with wavelengths tunable by the flake thickness. From their frequency-momentum dispersion, we infer the out-of-plane dielectric function $${{{{{{\boldsymbol{\epsilon }}}}}}}_{{{{{{\boldsymbol{c}}}}}}}$$

ϵ

c

that is generally difficult to obtain in conventional far-field optics, and elucidate signatures of electronic correlations when compared to density functional theory (DFT). We propose correlation effects might have switched the real part of $${{{{{{\boldsymbol{\epsilon }}}}}}}_{{{{{{\boldsymbol{c}}}}}}}$$

ϵ

c

from negative to positive values over a wide range of middle-IR frequencies, transforming the surface plasmons into hyperbolic bulk plasmons, and have dramatically suppressed their dissipation.
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
Authors: Salari Hossein , Fourel Geneviève , Jost Daniel 
Published: June 2024

AbstractAlthough our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
Dual polarization-enabled ultrafast bulk photovoltaic response in van der Waals heterostructures
Authors: Zeng Zhouxiaosong , Tian Zhiqiang , Wang Yufan , Ge Cuihuan , Strauß Fabian , Braun Kai , Michel Patrick , Huang Lanyu , Liu Guixian , Li Dong , Scheele Marcus , Chen Mingxing , Pan Anlian , Wang Xiao 
Published: June 2024

AbstractThe bulk photovoltaic effect (BPVE) originating from spontaneous charge polarizations can reach high conversion efficiency exceeding the Shockley-Queisser limit. Emerging van der Waals (vdW) heterostructures provide the ideal platform for BPVE due to interfacial interactions naturally breaking the crystal symmetries of the individual constituents and thus inducing charge polarizations. Here, we show an approach to obtain ultrafast BPVE by taking advantage of dual interfacial polarizations in vdW heterostructures. While the in-plane polarization gives rise to the BPVE in the overlayer, the charge carrier transfer assisted by the out-of-plane polarization further accelerates the interlayer electronic transport and enhances the BPVE. We illustrate the concept in MoS2/black phosphorus heterostructures, where the experimentally observed intrinsic BPVE response time achieves 26 ps, orders of magnitude faster than that of conventional non-centrosymmetric materials. Moreover, the heterostructure device possesses an extrinsic response time of approximately 2.2 ns and a bulk photovoltaic coefficient of 0.6 V−1, which is among the highest values for vdW BPV devices reported so far. Our study thus points to an effective way of designing ultrafast BPVE for high-speed photodetection.
Ag–thiolate interactions to enable an ultrasensitive and stretchable MXene strain sensor with high temporospatial resolution
Authors: Liu Yang , Xu Zijun , Ji Xinyi , Xu Xin , Chen Fei , Pan Xiaosen , Fu Zhiqiang , Chen Yunzhi , Zhang Zhengjian , Liu Hongbin , Cheng Bowen , Liang Jiajie 
Published: June 2024

AbstractHigh-sensitivity strain sensing elements with a wide strain range, fast response, high stability, and small sensing areas are desirable for constructing strain sensor arrays with high temporospatial resolution. However, current strain sensors rely on crack-based conductive materials having an inherent tradeoff between their sensing area and performance. Here, we present a molecular-level crack modulation strategy in which we use layer-by-layer assembly to introduce strong, dynamic, and reversible coordination bonds in an MXene and silver nanowire-matrixed conductive film. We use this approach to fabricate a crack-based stretchable strain sensor with a very small sensing area (0.25 mm2). It also exhibits an ultrawide working strain range (0.001–37%), high sensitivity (gauge factor ~500 at 0.001% and >150,000 at 35%), fast response time, low hysteresis, and excellent long-term stability. Based on this high-performance sensing element and facile assembly process, a stretchable strain sensor array with a device density of 100 sensors per cm2 is realized. We demonstrate the practical use of the high-density strain sensor array as a multichannel pulse sensing system for monitoring pulses in terms of their spatiotemporal resolution.
Interpretable video-based tracking and quantification of parkinsonism clinical motor states
Authors: Deng Daniel , Ostrem Jill L. , Nguyen Vy , Cummins Daniel D. , Sun Julia , Pathak Anupam , Little Simon , Abbasi-Asl Reza 
Published: June 2024

AbstractQuantification of motor symptom progression in Parkinson’s disease (PD) patients is crucial for assessing disease progression and for optimizing therapeutic interventions, such as dopaminergic medications and deep brain stimulation. Cumulative and heuristic clinical experience has identified various clinical signs associated with PD severity, but these are neither objectively quantifiable nor robustly validated. Video-based objective symptom quantification enabled by machine learning (ML) introduces a potential solution. However, video-based diagnostic tools often have implementation challenges due to expensive and inaccessible technology, and typical “black-box” ML implementations are not tailored to be clinically interpretable. Here, we address these needs by releasing a comprehensive kinematic dataset and developing an interpretable video-based framework that predicts high versus low PD motor symptom severity according to MDS-UPDRS Part III metrics. This data driven approach validated and robustly quantified canonical movement features and identified new clinical insights, not previously appreciated as related to clinical severity, including pinkie finger movements and lower limb and axial features of gait. Our framework is enabled by retrospective, single-view, seconds-long videos recorded on consumer-grade devices such as smartphones, tablets, and digital cameras, thereby eliminating the requirement for specialized equipment. Following interpretable ML principles, our framework enforces robustness and interpretability by integrating (1) automatic, data-driven kinematic metric evaluation guided by pre-defined digital features of movement, (2) combination of bi-domain (body and hand) kinematic features, and (3) sparsity-inducing and stability-driven ML analysis with simple-to-interpret models. These elements ensure that the proposed framework quantifies clinically meaningful motor features useful for both ML predictions and clinical analysis.
Tipping point in ice-sheet grounding-zone melting due to ocean water intrusion
Authors: Bradley Alexander T. , Hewitt Ian J. 
Published: June 2024

AbstractMarine ice sheets are highly sensitive to submarine melting in their grounding zones, where they transition between grounded and floating ice. Recently published studies of the complex hydrography of grounding zones suggest that warm ocean water can intrude large distances beneath the ice sheet, with dramatic consequences for ice dynamics. Here we develop a model to capture the feedback between intruded ocean water, the melting it induces and the resulting changes in ice geometry. We reveal a sensitive dependence of the grounding-zone dynamics on this feedback: as the grounding zone widens in response to melting, both temperature and flow velocity in the region increase, further enhancing melting. We find that increases in ocean temperature can lead to a tipping point being passed, beyond which ocean water intrudes in an unbounded manner beneath the ice sheet, via a process of runaway melting. Additionally, this tipping point may not be easily detected with early warning indicators. Although completely unbounded intrusions are not expected in practice, this suggests a mechanism for dramatic changes in grounding-zone behaviour, which are not currently included in ice-sheet models. We consider the susceptibility of present-day Antarctic grounding zones to this process, finding that both warm and cold water cavity ice shelves may be vulnerable. Our results point towards a stronger sensitivity of ice-sheet melting, and thus higher sea-level-rise contribution in a warming climate, than has been previously understood.
Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes
Authors: Grodner Benjamin , Shi Hao , Farchione Owen , Vill Albert C. , Ntekas Ioannis , Diebold Peter J. , Wu David T. , Chen Chia-Yu , Kim David M. , Zipfel Warren R. , Brito Ilana L. , De Vlaminck Iwijn 
Published: June 2024

AbstractThe exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.
Characterization of an expanded set of assays for immunomodulatory proteins using targeted mass spectrometry
Authors: Whiteaker Jeffrey R. , Zhao Lei , Schoenherr Regine M. , Huang Dongqing , Kennedy Jacob J. , Ivey Richard G. , Lin Chenwei , Lorentzen Travis D. , Colantonio Simona , Caceres Tessa W. , Roberts Rhonda R. , Knotts Joseph G. , Reading Joshua J. , Perry Candice D. , Garcia-Buntley Sandra S. , Bocik William , Hewitt Stephen M. , Paulovich Amanda G. 
Published: June 2024

AbstractImmunotherapies are revolutionizing cancer care, but many patients do not achieve durable responses and immune-related adverse events are difficult to predict. Quantifying the hundreds of proteins involved in cancer immunity has the potential to provide biomarkers to monitor and predict tumor response. We previously developed robust, multiplexed quantitative assays for immunomodulatory proteins using targeted mass spectrometry, providing measurements that can be performed reproducibly and harmonized across laboratories. Here, we expand upon those efforts in presenting data from a multiplexed immuno-oncology (IO)-3 assay panel targeting 43 peptides representing 39 immune- and inflammation-related proteins. A suite of novel monoclonal antibodies was generated as assay reagents, and the fully characterized antibodies are made available as a resource to the community. The publicly available dataset contains complete characterization of the assay performance, as well as the mass spectrometer parameters and reagent information necessary for implementation of the assay. Quantification of the proteins will provide benefit to correlative studies in clinical trials, identification of new biomarkers, and improve understanding of the immune response in cancer.
A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits
Authors: Paës Charlotte , Beaumont Martin , Gidenne Thierry , Bébin Karine , Duperray Joël , Gohier Charly , Guené-Grand Emeline , Rebours Gwénaël , Castinel Adrien , Barilly Céline , Gabinaud Béatrice , Bannelier Carole , Gress Laure , Laperruque François , Aymard Patrick , Debrusse Anne-Marie , Cauquil Laurent , Pascal Géraldine , Combes Sylvie 
Published: June 2024

AbstractThe transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.
The Subnational Corruption Database: Grand and petty corruption in 1,473 regions of 178 countries, 1995–2022
Authors: Crombach Lamar , Smits Jeroen 
Published: June 2024

AbstractThis data descriptor presents the Subnational Corruption Database (SCD), which provides data on corruption in 1,473 subnational areas of 178 countries. The SCD includes a comprehensive overall corruption index, the Subnational Corruption Index (SCI), and its two components: the Subnational Grand Corruption Index (SGCI) and Subnational Petty Corruption Index (SPCI). The SCD is constructed by combining data of 807 surveys held in the period 1995–2022 and includes the corruption experiences and perceptions of 1,326,656 respondents along 19 separate dimensions. The data are available for multiple years, allowing longitudinal analyses. At the national level, the SCI correlates strongly with established corruption indices, like the Transparency International Corruption Perceptions Index (CPI) and the World Bank Control of Corruption Index (CCI). We create subnational estimates of the CPI and CCI by superimposing the subnational variation of the SCI around the national averages of these indices. The presentation of subnational data in the SCD and the separation between grand and petty corruption significantly broaden the global knowledge base in the field of corruption.