bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic regulation of human brain proteome reveals proteins implicated in psychiatric disorders
Authors: Luo Jie , Li Ling , Niu Mingming , Kong Dehui , Jiang Yi , Poudel Suresh , Shieh Annie W. , Cheng Lijun , Giase Gina , Grennan Kay , White Kevin P. , Chen Chao , Wang Sidney H. , Pinto Dalila , Wang Yue , Liu Chunyu , Peng Junmin , Wang Xusheng 
Published: May 2024

AbstractPsychiatric disorders are highly heritable yet polygenic, potentially involving hundreds of risk genes. Genome-wide association studies have identified hundreds of genomic susceptibility loci with susceptibility to psychiatric disorders; however, the contribution of these loci to the underlying psychopathology and etiology remains elusive. Here we generated deep human brain proteomics data by quantifying 11,608 proteins across 268 subjects using 11-plex tandem mass tag coupled with two-dimensional liquid chromatography-tandem mass spectrometry. Our analysis revealed 788 cis-acting protein quantitative trait loci associated with the expression of 883 proteins at a genome-wide false discovery rate <5%. In contrast to expression at the transcript level and complex diseases that are found to be mainly influenced by noncoding variants, we found protein expression level tends to be regulated by non-synonymous variants. We also provided evidence of 76 shared regulatory signals between gene expression and protein abundance. Mediation analysis revealed that for most (88%) of the colocalized genes, the expression levels of their corresponding proteins are regulated by cis-pQTLs via gene transcription. Using summary data-based Mendelian randomization analysis, we identified 4 proteins and 19 genes that are causally associated with schizophrenia. We further integrated multiple omics data with network analysis to prioritize candidate genes for schizophrenia risk loci. Collectively, our findings underscore the potential of proteome-wide linkage analysis in gaining mechanistic insights into the pathogenesis of psychiatric disorders.
Relationship between macular perfusion and lesion distribution in diabetic retinopathy
Authors: Manafi Navid , Oncel Deniz , Verma Aditya , Corradetti Giulia , Kadomoto Shin , Mahmoudi Alireza , Alagorie Ahmed Roshdy , Yadav Naresh Kumar , Pappuru Rajeev R. , Tufail Adnan , Esmaeilkhanian Houri , Nittala Muneeswar G. , Raman Rajiv , Sadda Srinivas 
Published: May 2024

Abstract
Background/objectives
To assess the relationship between macular vessel density metrics and foveal avascular zone (FAZ) characteristics on optical coherence tomography angiography (OCTA) and lesion distribution in eyes with diabetic retinopathy (DR).

Subjects/methods
Patients with DR who underwent both Optos ultrawidefield (UWF) pseudocolor imaging and macular OCTA (Cirrus Angioplex, 6 × 6 mm) were included in this cross-sectional observational study. The distribution of DR lesions was assessed by comparing each of the peripheral ETDRS extended fields (3–7) against their corresponding ETDRS field, hence eyes were defined as either having predominantly peripheral lesions (PPL) or predominantly central lesions (PCL). En face OCTA images from the superficial and deep capillary plexuses (SCP and DCP) were then analysed using Image J software. Perfusion density (PD), vessel length density (VLD), and fractal dimensions (FD) were calculated following binarization and skeletonization of the images.

Results
Out of 344 eyes, 116 (33.72%) eyes had PPL and 228 (66.28%) eyes had PCL. For all DRSS levels, VLD, PD, and FD were not significantly different between eyes with PPL and PCL. The FAZ in eyes with PPL, however, was found to be more circular in shape compared to eyes with PCL (p = 0.037).

Conclusion
Although the presence of PPL has been associated with a higher risk for diabetic retinopathy progression, the macular perfusion is similar in eyes with PPL and PCL. The FAZ is more circular in eyes with PPL, but the clinical relevance of this difference remains to be defined.
Levitation and dynamics of bodies in supersaturated fluids
Authors: Spagnolie Saverio E. , Christianson Samuel , Grote Carsen 
Published: May 2024

AbstractA body immersed in a supersaturated fluid like carbonated water can accumulate a dynamic field of bubbles upon its surface. If the body is mobile, the attached bubbles can lift it upward against gravity, but a fluid-air interface can clean the surface of these lifting agents and the body may plummet. The process then begins anew, and continues for as long as the concentration of gas in the fluid supports it. In this work, experiments using fixed and free immersed bodies reveal fundamental features of force development and gas escape. A continuum model which incorporates the dynamics of a surface buoyancy field is used to predict the ranges of body mass and size, and fluid properties, for which the system is most dynamic, and those for which body excursions are suppressed. Simulations are then used to probe systems which are dominated by a small number of large bubbles. Body rotations at the surface are critical for driving periodic vertical motions of large bodies, which in turn can produce body wobbling, rolling, and damped surface ’bouncing’ dynamics.
Nonvolatile optical phase shift in ferroelectric hafnium zirconium oxide
Authors: Taki Kazuma , Sekine Naoki , Watanabe Kouhei , Miyatake Yuto , Akazawa Tomohiro , Sakumoto Hiroya , Toprasertpong Kasidit , Takagi Shinichi , Takenaka Mitsuru 
Published: May 2024

AbstractA nonvolatile optical phase shifter is a critical component for enabling the fabrication of programmable photonic integrated circuits on a Si photonics platform, facilitating communication, computing, and sensing. Although ferroelectric materials such as BaTiO3 offer nonvolatile optical phase shift capabilities, their compatibility with complementary metal-oxide-semiconductor fabs is limited. Hf0.5Zr0.5O2 is an emerging ferroelectric material, which exhibits complementary metal-oxide-semiconductor compatibility. Although extensively studied for ferroelectric transistors and memories, its application to photonics remains relatively unexplored. Here, we show the optical phase shift induced by ferroelectric Hf0.5Zr0.5O2. We observed a negative change in refractive index at a 1.55 μm wavelength in a pristine device regardless of the direction of the applied electric field. The nonvolatile phase shift was only observed once in a pristine device. This non-reversible phase shift can be attributed to the spontaneous polarization within the Hf0.5Zr0.5O2 film along the external electric field.
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications
Authors: Acera Mateos P , J Sethi A , Ravindran A , Srivastava A , Woodward K , Mahmud S , Kanchi M , Guarnacci M , Xu J , W S Yuen Z , Zhou Y , Sneddon A , Hamilton W , Gao J , M Starrs L , Hayashi R , Wickramasinghe V , Zarnack K , Preiss T , Burgio G , Dehorter N , E Shirokikh N , Eyras E 
Published: May 2024

AbstractThe epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI’s capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
Ocean internal tides suppress tropical cyclones in the South China Sea
Authors: Guan Shoude , Jin Fei-Fei , Tian Jiwei , Lin I-I , Pun Iam-Fei , Zhao Wei , Huthnance John , Xu Zhao , Cai Wenju , Jing Zhao , Zhou Lei , Liu Ping , Zhang Yihan , Zhang Zhiwei , Zhou Chun , Yang Qingxuan , Huang Xiaodong , Hou Yijun , Song Jinbao 
Published: May 2024

AbstractTropical Cyclones (TCs) are devastating natural disasters. Analyzing four decades of global TC data, here we find that among all global TC-active basins, the South China Sea (SCS) stands out as particularly difficult ocean for TCs to intensify, despite favorable atmosphere and ocean conditions. Over the SCS, TC intensification rate and its probability for a rapid intensification (intensification by ≥ 15.4 m s−1 day−1) are only 1/2 and 1/3, respectively, of those for the rest of the world ocean. Originating from complex interplays between astronomic tides and the SCS topography, gigantic ocean internal tides interact with TC-generated oceanic near-inertial waves and induce a strong ocean cooling effect, suppressing the TC intensification. Inclusion of this interaction between internal tides and TC in operational weather prediction systems is expected to improve forecast of TC intensity in the SCS and in other regions where strong internal tides are present.
Sustainable 3D printing by reversible salting-out effects with aqueous salt solutions
Authors: Ji Donghwan , Liu Joseph , Zhao Jiayu , Li Minghao , Rho Yumi , Shin Hwansoo , Han Tae Hee , Bae Jinhye 
Published: May 2024

AbstractAchieving a simple yet sustainable printing technique with minimal instruments and energy remains challenging. Here, a facile and sustainable 3D printing technique is developed by utilizing a reversible salting-out effect. The salting-out effect induced by aqueous salt solutions lowers the phase transition temperature of poly(N-isopropylacrylamide) (PNIPAM) solutions to below 10 °C. It enables the spontaneous and instant formation of physical crosslinks within PNIPAM chains at room temperature, thus allowing the PNIPAM solution to solidify upon contact with a salt solution. The PNIPAM solutions are extrudable through needles and can immediately solidify by salt ions, preserving printed structures, without rheological modifiers, chemical crosslinkers, and additional post-processing steps/equipment. The reversible physical crosslinking and de-crosslinking of the polymer through the salting-out effect demonstrate the recyclability of the polymeric ink. This printing approach extends to various PNIPAM-based composite solutions incorporating functional materials or other polymers, which offers great potential for developing water-soluble disposable electronic circuits, carriers for delivering small materials, and smart actuators.
East European sedimentary basins long heated by a fading mantle upwelling
Authors: Ismail-Zadeh Alik , Davaille Anne , Besse Jean , Volozh Yuri 
Published: May 2024

AbstractA strong negative anomaly of seismic wave velocities at the core-mantle boundary (the Perm Anomaly) beneath the East European platform is attributed to the remnant of a deep mantle upwelling. The interaction between the upwelling and the East European lithosphere in the geological past and its resulting surface manifestations are still poorly understood. Using mantle plume modelling and global plate motion reconstructions, we show here that the East European lithosphere is likely to have been situated over the weakening Perm Anomaly upwelling for about 150–200 million years. As the East European platform moved above the Perm Anomaly in post-Jurassic times, the vertical tectonic movements recorded in sedimentary hydrocarbon-rich basins show either hiatus/uplift or insignificant subsidence. Analytical modelling of heat conduction through the lithosphere demonstrates that the basins have been slowly heated for a long time by the Perm Anomaly upwelling, creating suitable conditions for hydrocarbon maturation. This suggests a profound relationship between mantle plume dynamics, basin evolution, and hydrocarbon generation.
Large transverse thermoelectric effect induced by the mixed-dimensionality of Fermi surfaces
Authors: Manako Hikari , Ohsumi Shoya , Sato Yoshiki J. , Okazaki R. , Aoki D. 
Published: May 2024

AbstractTransverse thermoelectric effect, the conversion of longitudinal heat current into transverse electric current, or vice versa, offers a promising energy harvesting technology. Materials with axis-dependent conduction polarity, known as p × n-type conductors or goniopolar materials, are potential candidate, because the non-zero transverse elements of thermopower tensor appear under rotational operation, though the availability is highly limited. Here, we report that a ternary metal LaPt2B with unique crystal structure exhibits axis-dependent thermopower polarity, which is driven by mixed-dimensional Fermi surfaces consisting of quasi-one-dimensional hole sheet with out-of-plane velocity and quasi-two-dimensional electron sheets with in-plane velocity. The ideal mixed-dimensional conductor LaPt2B exhibits an extremely large transverse Peltier conductivity up to ∣αyx∣ = 130 A K−1 m−1, and its transverse thermoelectric performance surpasses those of topological magnets utilizing the anomalous Nernst effect. These results thus manifest the mixed-dimensionality as a key property for efficient transverse thermoelectric conversion.
Western US intraplate deformation controlled by the complex lithospheric structure
Authors: Cao Zebin , Liu Lijun 
Published: May 2024

AbstractThe western United States is one of Earth’s most tectonically active regions, characterized by extensive crustal deformation through intraplate earthquakes and geodetic motion. Such intracontinental deformation is usually ascribed to plate boundary forces, lithospheric body forces, and/or viscous drag from mantle flow. However, their relative importance in driving crustal deformation remains controversial due to inconsistent assumptions on crustal and mantle structures in prior estimations. Here, we utilize a fully dynamic three-dimensional modeling framework with data assimilation to simultaneously compute lithospheric and convective mantle dynamics within the western United States. This approach allows for quantitative estimations of crustal deformation while accounting for the realistic three-dimensional lithospheric structure. Our results show the critical role of the complex lithospheric structure in governing intraplate deformation. Particularly, the interaction between the asthenospheric flow and lithospheric thickness step along the eastern boundary of the Basin and Range represents a key driving mechanism for localized crustal deformation and seismicity.
Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition
Authors: Linker T. M. , Krishnamoorthy A. , Daemen L. L. , Ramirez-Cuesta A. J. , Nomura K. , Nakano A. , Cheng Y. Q. , Hicks W. R. , Kolesnikov A. I. , Vashishta P. D. 
Published: May 2024

AbstractVibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes. This is achieved by training neural network models using ab-initio path-integral molecular dynamics (PIMD) simulations, thereby encompassing large spatiotemporal trajectories required to resolve low energy dynamics while retaining NQEs. Our results not only establish the role of NQEs in ammonia but also provide general computational frameworks to study complex molecular systems with NQEs.
A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution
Authors: Kaczmarczyk Andreas , van Vliet Simon , Jakob Roman Peter , Teixeira Raphael Dias , Scheidat Inga , Reinders Alberto , Klotz Alexander , Maier Timm , Jenal Urs 
Published: May 2024

AbstractMonitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.
Synthesis of 13C-depleted organic matter from CO in a reducing early Martian atmosphere
Authors: Ueno Yuichiro , Schmidt Johan A. , Johnson Matthew S. , Zang Xiaofeng , Gilbert Alexis , Kurokawa Hiroyuki , Usui Tomohiro , Aoki Shohei 
Published: May 2024

AbstractOrganic matter found in early Martian sediment may yield clues to the planet’s environmental conditions, prebiotic chemistry and habitability, but its origin remains unclear. Strong 13C depletion in sedimentary organic matter at Gale crater was recently detected by the Curiosity rover. Although this enigmatic depletion remains debated, if correct, a mechanism to cause such strong 13C depletion is required. Here we show from CO2 photolysis experiments and theoretical considerations that solar ultraviolet photolysis of CO2 in a reducing atmosphere can yield strongly 13C-depleted CO. We suggest that atmospheric synthesis of organic compounds from photolysis-produced CO is a plausible mechanism to explain the source of isotopically depleted organic matter in early Martian sediments. Furthermore, this mechanism could explain 13C enrichment of early Martian CO2 without requiring long-term carbon escape into space. A mass balance model calculation using our estimated isotopic fractionation factor indicates the conversion of approximately 20% of volcanic CO2 emissions on early Mars into organics via CO, consistent with the available data for carbon isotopes of carbonate. Although alternative pathways for organic compound production have been proposed, our findings suggest that considerable amounts of organic matter may have been synthesized from CO in a reducing early Martian atmosphere and deposited in sediments.
Tracking single-cell evolution using clock-like chromatin accessibility loci
Authors: Xiao Yu , Jin Wan , Ju Lingao , Fu Jie , Wang Gang , Yu Mengxue , Chen Fangjin , Qian Kaiyu , Wang Xinghuan , Zhang Yi 
Published: May 2024

AbstractSingle-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Previous studies showed age-associated DNA methylation (DNAm) changes in specific genomic regions, termed clock-like differential methylation loci (ClockDML). Age-associated DNAm could either result from or result in chromatin accessibility changes at ClockDML. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. In this study, we developed a method, called EpiTrace, that counts the fraction of opened clock-like loci from scATAC-seq data to determine cell age and perform lineage tracing in various cell lineages and animal species. It shows concordance with known developmental hierarchies, correlates well with DNAm-based clocks and is complementary with mutation-based lineage tracing, RNA velocity and stemness predictions. Applying EpiTrace to scATAC-seq data reveals biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification.
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing
Authors: Nanda Arjun S. , Wu Ke , Irkliyenko Iryna , Woo Brian , Ostrowski Megan S. , Clugston Andrew S. , Sayles Leanne C. , Xu Lingru , Satpathy Ansuman T. , Nguyen Hao G. , Alejandro Sweet-Cordero E. , Goodarzi Hani , Kasinathan Sivakanthan , Ramani Vijay 
Published: May 2024

AbstractConcurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
Enhancing the trustworthiness of chaos and synchronization of chaotic satellite model: a practice of discrete fractional-order approaches
Authors: Rashid Saima , Hamidi Sher Zaman , Akram Saima , Alosaimi Moataz , Chu Yu-Ming 
Published: May 2024

AbstractAccurate development of satellite maneuvers necessitates a broad orbital dynamical system and efficient nonlinear control techniques. For achieving the intended formation, a framework of a discrete fractional difference satellite model is constructed by the use of commensurate and non-commensurate orders for the control and synchronization of fractional-order chaotic satellite system. The efficacy of the suggested framework is evaluated employing a numerical simulation of the concerning dynamic systems of motion while taking into account multiple considerations such as Lyapunov exponent research, phase images and bifurcation schematics. With the aid of discrete nabla operators, we monitor the qualitative behavioural patterns of satellite systems in order to provide justification for the structure’s chaos. We acquire the fixed points of the proposed trajectory. At each fixed point, we calculate the eigenvalue of the satellite system’s Jacobian matrix and check for zones of instability. The outcomes exhibit a wide range of multifaceted behaviours resulting from the interaction with various fractional-orders in the offered system. Additionally, the sample entropy evaluation is employed in the research to determine complexities and endorse the existence of chaos. To maintain stability and synchronize the system, nonlinear controllers are additionally provided. The study highlights the technique’s vulnerability to fractional-order factors, resulting in exclusive, changing trends and equilibrium frameworks. Because of its diverse and convoluted behaviour, the satellite chaotic model is an intriguing and crucial subject for research.