bluuebunny/crossref_metadata_2025 huggingface dataset:
Warming of the Kuroshio Current Over the Last Four Decades has Intensified the Meiyu‐Baiu Rainband
Authors: Qiao Yu‐Xiang , Nakamura Hirohiko , Tomita Tomohiko
Published: January 2024

In recent decades, rise of sea surface temperature (SST) in the Kuroshio region of the East China Sea (ECS), which is associated with global warming, has attracted considerable attention. Despite its relevance to air‐sea interaction phenomena, the atmospheric consequences of this SST increase remain largely unexplored. Using the ERA5 reanalysis data set in conjunction with a moisture budget analysis, we found that during 1979–2022, warming in the ECS‐Kuroshio has contributed to the intensification of the East Asian Meiyu‐Baiu rainband in June. This intensification is attributed to augmented wind convergence in the low‐level free troposphere (950–700 hPa). Importantly, the atmospheric responses to ECS‐Kuroshio warming penetrated the deep troposphere (to approximately 300 hPa), suggesting an enhancement of deep convection. Furthermore, ECS‐Kuroshio warming likely strengthened the overlying atmospheric low pressure, resulting in wind convergence enhancement. The findings clarified the important role of the ECS‐Kuroshio in driving East Asian climate change amid global warming.
Projected Emergence Seasons of Year‐Maximum Near‐Surface Wind Speed
Authors: Yu Yue , Li Zhibo , Yan Zixiang , Yuan Huishuang , Shen Cheng
Published: January 2024

Global warming is expected to have far‐reaching impacts on the frequency and intensity of extreme events, but the effects of anthropogenic warming on the emergence seasons of year‐maximum near‐surface wind speed (NSWS) remain poorly understood. We provide a comprehensive map of the changing emergence seasons of year‐maximum NSWS using Coupled Model Intercomparison Project Phase 6 projections. Our analysis reveals a rapid response of synoptic‐scale extreme NSWS to global warming, with consistent spatial patterns observed across various periods and warming scenarios. The most significant increase (∼16%) in the emergence season is projected to occur in December‐January‐February (DJF) over Mid‐high‐latitude Asia by the end of the 21st century. The study also anticipates changes in the emergence seasons of year‐maximum NSWS at a regional scale. These results deepen our understanding of the complex and interconnected nature of global climate change and underscore the need for concerted efforts in addressing this pressing challenge.
Statistical Characteristics of Multi‐Scale Auroral Arc Width Based on Machine Learning
Authors: Yang Qiuju , Xie Minghao , Su Hang , Han Desheng , He Qiqi
Published: January 2024

Arc width is important for understanding the generation mechanism of auroral arcs. However, the continuity or discreteness of the distribution of small and meso‐large scale auroral arc widths has not been determined in previous studies. This study employs machine learning techniques to investigate the distribution of arc widths across multiple scales using multi‐field‐of‐view (multi‐FOV) auroral observations. Based on the 180°, 47°, and 19° auroral observations at the Antarctic Zhongshan Station from February to October 2012, the statistical results demonstrate that the auroral arc width spectrum is continuously distributed across small, meso, and large scales, suggesting that the mechanisms responsible for their generation are capable of producing arcs at all scales. Furthermore, the arc width distribution at each FOV can be well fitted with a log‐normal function. We also find that the main widths observed at different FOVs depend on the spatial resolution of the instruments. Our work provides new observational evidence for the generation mechanism of auroral arcs.
Trans‐Lithospheric Ascent Processes of the Deep‐Rooted Magma Plumbing System Underneath the Ultraslow‐Spreading SW Indian Ridge
Authors: Ma Ben , Liu Ping‐Ping , Dick Henry J. B. , Zhou Mei‐Fu , Chen Qiong , Liu Chuan‐Zhou
Published: January 2024

Processes of magma generation and transportation in global mid‐ocean ridges are key to understanding lithospheric architecture at divergent plate boundaries. These magma dynamics are dependent on spreading rate and melt flux, where the SW Indian Ridge represents an end‐member. The vertical extent of ridge magmatic systems and the depth of axial magma chambers (AMCs) are greatly debated, in particular at ultraslow‐spreading ridges. Here we present detailed mineralogical studies of high‐Mg and low‐Mg basalts from a single dredge on Southwest Indian Ridge (SWIR) at 45°E. High‐Mg basalts (MgO = ∼7.1 wt.%) contain high Mg# olivine (Ol, Fo = 85–89) and high‐An plagioclase (Pl, An = 66–83) as phenocrysts, whereas low‐Mg basalts contain low‐Mg# Ol and low‐An Pl (Fo = 75–78, An = 50–62) as phenocrysts or glomerocrysts. One low‐Mg basalt also contains normally zoned Ol and Pl, the core and rim of which are compositionally similar to those in high‐Mg and low‐Mg basalts, respectively. Mineral barometers and MELTS simulation indicate that the high‐Mg melts started to crystallize at ∼32 ± 7.8 km, close to the base of the lithosphere. The low‐Mg melts may have evolved from the high‐Mg melts in an AMC at a depth of ∼13 ± 7.8 km. Such great depths of magma crystallization and the AMC are likely the result of enhanced conductive cooling at ultraslow‐spreading ridges. Combined with diffusion chronometers, the basaltic melts could have ascended from the AMC to seafloor within 2 weeks to 3 months at average rates of ∼0.002–0.01 m/s, which are the slowest reported to date among global ridge systems and may characterize mantle melt transport at the slow end of the ridge spreading spectrum.
Thermal and Structural History of Impact Ejecta Deposits, Ries Impact Structure, Germany
Authors: Sleptsova Iuliia V. , Gilder Stuart A. , Dellefant Fabian , Trepmann Claudia A. , Ahanin Nastaran , Pohl Jean
Published: January 2024

The Ries impact structure (Germany) contains well‐preserved ejecta deposits consisting of melt‐free lithic breccia (Bunte Breccia) overlain by suevite. To test their emplacement conditions, we investigated the magnetic properties and microstructures of 26 polymict breccia clasts and a stratigraphic profile from the clasts into the suevite at the Aumühle quarry. Remanent magnetization directions of the Bunte Breccia clasts fall into two groups: those whose directions mostly lie parallel to the reversed field during impact carried mostly by magnetite, and those whose directions vary widely among each clast carried by titanohematite. Basement clasts containing titanohematite acquired a chemical remanent magnetization (CRM) during the ejection process and then rotated during turbulent deposition. Clasts of sedimentary rocks grew magnetite after turbulent deposition, with CRM directions lying parallel to the paleofield. Suevite holds a thermal remanent magnetization carried by magnetite, except for ∼12 cm from the contact with the Bunte Breccia, where hematite concentrations increase due to hydrothermal alteration. These observations lead us to propose a three‐stage model of (a) turbulent deposition of the melt‐free breccia with clast rotation <580°C, (b) deposition of the overlying suevite, which acted as a semi‐permeable barrier that confined hot (<300°C) oxidizing fluids to the permeable breccia zone, and (c) prolonged hydrothermal activity producing further alteration which ended before the next geomagnetic reversal. Basement outcrops have significantly different magnetic properties than the Bunte Breccia basement clasts with similar lithology. Two basement blocks situated near the inner ring may have been thermally overprinted up to 550°C.
Tracer Stirring and Variability in the Antarctic Circumpolar Current Near the Southwest Indian Ridge
Authors: Balwada Dhruv , Gray Alison R. , Dove Lilian A. , Thompson Andrew F.
Published: January 2024

Oceanic macroturbulence is efficient at stirring and transporting tracers. The dynamical properties of this stirring can be characterized by statistically quantifying tracer structures. Here, we characterize the macroscale (1–100 km) tracer structures observed by two Seagliders downstream of the Southwest Indian Ridge in the Antarctic Circumpolar Current (ACC). These are some of the first glider observations in an energetic standing meander of the ACC, a region associated with enhanced ventilation. The small‐scale density variance in the mixed layer (ML) was relatively enhanced near the surface and base of the ML, while being muted at mid‐depth in the ML, suggesting the formation mechanism to be associated with ML instabilities and eddies. In addition, ML density fronts were formed by comparable contributions from temperature and salinity gradients. In the interior, along‐isopycnal spectra and structure functions of spice indicated that there is relatively lower variance at smaller scales than would be expected based on non‐local stirring, suggesting that flows smaller than the deformation radius play a role in the cascade of tracers to small scales. These interior spice anomalies spanned across isopycnals, and were found to be about 3–5 times flatter than the aspect ratio that would be expected for O(1) Burger number flows like interior QG dynamics, suggesting the ratio of vertical shear to horizontal strain is greater than N/f. This further supports that small‐scale flows, with high‐mode vertical structures, impact tracer distributions.
Global Estimates of Mesoscale Vertical Velocity Near 1,000 m From Argo Observations
Authors: Christensen Katy M. , Gray Alison R. , Riser Stephen C.
Published: January 2024

Global estimates of mesoscale vertical velocity remain poorly constrained due to a historical lack of adequate observations on the spatial and temporal scales needed to measure these small magnitude velocities. However, with the wide‐spread and frequent observations collected by the Argo array of autonomous profiling floats, we can now better quantify mesoscale vertical velocities throughout the global ocean. We use the underutilized trajectory data files from the Argo array to estimate the time evolution of isotherm displacement around a float as it drifts at 1,000 m, allowing us to quantify vertical velocity averaged over approximately 4.5 days for that depth level. The resulting estimates have a non‐normal, high‐peak, and heavy‐tail distribution. The vertical velocity distribution has a mean value of (1.9 ± 0.02) × 10−6 m s−1 and a median value of (1.3 ± 0.2) × 10−7 m s−1, but the high‐magnitude events can be up to the order of 10−4 m s−1. We find that vertical velocity is highly spatially variable and is largely associated with a combination of topographic features and horizontal flow. These are some of the first observational estimates of mesoscale vertical velocity to be taken across such large swaths of the ocean without assumptions of uniformity or reliance on horizontal divergence.
Schizophrenia endothelial cells exhibit higher permeability and altered angiogenesis patterns in patient-derived organoids
Authors: Stankovic Isidora , Notaras Michael , Wolujewicz Paul , Lu Tyler , Lis Raphael , Ross M. Elizabeth , Colak Dilek
Published: January 2024

Schizophrenia (SCZ) is a complex neurodevelopmental disorder characterized by the manifestation of psychiatric symptoms in early adulthood. While many research avenues into the origins of SCZ during brain development have been explored, the contribution of endothelial/vascular dysfunction to the disease remains largely elusive. To model the neuropathology of SCZ during early critical periods of brain development, we utilized patient-derived induced pluripotent stem cells (iPSCs) to generate 3D cerebral organoids and define cell-specific signatures of disease. Single-cell RNA sequencing revealed that while SCZ organoids were similar in their macromolecular diversity to organoids generated from healthy controls (CTRL), SCZ organoids exhibited a higher percentage of endothelial cells when normalized to total cell numbers. Additionally, when compared to CTRL, differential gene expression analysis revealed a significant enrichment in genes that function in vessel formation, vascular regulation, and inflammatory response in SCZ endothelial cells. In line with these findings, data from 23 donors demonstrated that PECAM1+ microvascular vessel-like structures were increased in length and number in SCZ organoids in comparison to CTRL organoids. Furthermore, we report that patient-derived endothelial cells displayed higher paracellular permeability, implicating elevated vascular activity. Collectively, our data identified altered gene expression patterns, vessel-like structural changes, and enhanced permeability of endothelial cells in patient-derived models of SCZ. Hence, brain microvascular cells could play a role in the etiology of SCZ by modulating the permeability of the developing blood brain barrier (BBB).
PICH deficiency limits the progression of MYC-induced B-cell lymphoma
Authors: Castejón-Griñán María , Albers Eliene , Simón-Carrasco Lucía , Aguilera Paula , Sbroggio Mauro , Pladevall-Morera David , Ingham Andreas , Lim Ernest , Guillen-Benitez Alba , Pietrini Elena , Lisby Michael , Hickson Ian D. , Lopez-Contreras Andres J.
Published: January 2024

Plk1-interacting checkpoint helicase (PICH) is a DNA translocase involved in resolving ultrafine anaphase DNA bridges and, therefore, is important to safeguard chromosome segregation and stability. PICH is overexpressed in various human cancers, particularly in lymphomas such as Burkitt lymphoma, which is caused by MYC translocations. To investigate the relevance of PICH in cancer development and progression, we have combined novel PICH-deficient mouse models with the Eμ-Myc transgenic mouse model, which recapitulates B-cell lymphoma development. We have observed that PICH deficiency delays the onset of MYC-induced lymphomas in Pich heterozygous females. Moreover, using a Pich conditional knockout mouse model, we have found that Pich deletion in adult mice improves the survival of Eμ-Myc transgenic mice. Notably, we show that Pich deletion in healthy adult mice is well tolerated, supporting PICH as a suitable target for anticancer therapies. Finally, we have corroborated these findings in two human Burkitt lymphoma cell lines and we have found that the death of cancer cells was accompanied by chromosomal instability. Based on these findings, we propose PICH as a potential therapeutic target for Burkitt lymphoma and for other cancers where PICH is overexpressed.
Pharmacology of LRRK2 with type I and II kinase inhibitors revealed by cryo-EM
Authors: Zhu Hanwen , Hixson Patricia , Ma Wen , Sun Ji
Published: January 2024

LRRK2 is one of the most promising drug targets for Parkinson’s disease. Though type I kinase inhibitors of LRRK2 are under clinical trials, alternative strategies like type II inhibitors are being actively pursued due to the potential undesired effects of type I inhibitors. Currently, a robust method for LRRK2–inhibitor structure determination to guide structure-based drug discovery is lacking, and inhibition mechanisms of available compounds are also unclear. Here we present near-atomic-resolution structures of LRRK2 with type I (LRRK2-IN-1 and GNE-7915) and type II (rebastinib, ponatinib, and GZD-824) inhibitors, uncovering the structural basis of LRRK2 inhibition and conformational plasticity of the kinase domain with molecular dynamics (MD) simulations. Type I and II inhibitors bind to LRRK2 in active-like and inactive conformations, so LRRK2–inhibitor complexes further reveal general structural features associated with LRRK2 activation. Our study provides atomic details of LRRK2–inhibitor interactions and a framework for understanding LRRK2 activation and for rational drug design.
Novel frameshift variant of WNT10A in a Japanese patient with hypodontia
Authors: Ando Michiyo , Aoki Yoshihiko , Sano Yasuto , Adachi Junya , Sana Masatoshi , Miyabe Satoru , Watanabe Satoshi , Hasegawa Shogo , Miyachi Hitoshi , Machida Junichiro , Goto Mitsuo , Tokita Yoshihito
Published: January 2024

Congenital tooth agenesis is caused by the impairment of crucial genes related to tooth development, such as Wnt signaling pathway genes. Here, we investigated the genetic causes of sporadic congenital tooth agenesis. Exome sequencing, followed by Sanger sequencing, identified a novel single-nucleotide deletion in WNT10A (NC_000002.12(NM_025216.3):c.802del), which was not found in the healthy parents of the patient. Thus, we concluded that the variant was the genetic cause of the patient’s agenesis.
An IL-10/DEL-1 axis supports granulopoiesis and survival from sepsis in early life
Authors: Vergadi Eleni , Kolliniati Ourania , Lapi Ioanna , Ieronymaki Eleftheria , Lyroni Konstantina , Alexaki Vasileia Ismini , Diamantaki Eleni , Vaporidi Katerina , Hatzidaki Eleftheria , Papadaki Helen A. , Galanakis Emmanouil , Hajishengallis George , Chavakis Triantafyllos , Tsatsanis Christos
Published: January 2024

The limited reserves of neutrophils are implicated in the susceptibility to infection in neonates, however the regulation of neutrophil kinetics in infections in early life remains poorly understood. Here we show that the developmental endothelial locus (DEL-1) is elevated in neonates and is critical for survival from neonatal polymicrobial sepsis, by supporting emergency granulopoiesis. Septic DEL-1 deficient neonate mice display low numbers of myeloid-biased multipotent and granulocyte-macrophage progenitors in the bone marrow, resulting in neutropenia, exaggerated bacteremia, and increased mortality; defects that are rescued by DEL-1 administration. A high IL-10/IL-17A ratio, observed in newborn sepsis, sustains tissue DEL-1 expression, as IL-10 upregulates while IL-17 downregulates DEL-1. Consistently, serum DEL-1 and blood neutrophils are elevated in septic adult and neonate patients with high serum IL-10/IL-17A ratio, and mortality is lower in septic patients with high serum DEL-1. Therefore, IL-10/DEL-1 axis supports emergency granulopoiesis, prevents neutropenia and promotes sepsis survival in early life.
A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Authors: Scalabrin Simone , Magris Gabriele , Liva Mario , Vitulo Nicola , Vidotto Michele , Scaglione Davide , Del Terra Lorenzo , Ruosi Manuela Rosanna , Navarini Luciano , Pellegrino Gloria , Berny Mier y Teran Jorge Carlos , Toniutti Lucile , Suggi Liverani Furio , Cerutti Mario , Di Gaspero Gabriele , Morgante Michele
Published: January 2024

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid speciesCoffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species,Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.
Exosomal secreted SCIMP regulates communication between macrophages and neutrophils in pneumonia
Authors: Pei Xiaolei , Liu Li , Wang Jieru , Guo Changyuan , Li Qingqing , Li Jia , Ren Qian , Ma Runzhi , Zheng Yi , Zhang Yan , Liu Li , Zheng Danfeng , Wang Pingzhang , Jiang Ping , Feng Xiaoming , Jiang Erlie , Wang Ying , Feng Sizhou
Published: January 2024

In pneumonia, the deficient or delayed pathogen clearance can lead to pathogen proliferation and subsequent overactive immune responses, inducing acute lung injury (ALI). While screening human genome coding genes using our peripheral blood cell chemotactic platform, we unexpectedly find SLP adaptor and CSK interacting membrane protein (SCIMP), a protein with neutrophil chemotactic activity secreted during ALI. However, the specific role of SCIMP in ALI remains unclear. In this study, we investigate the secretion of SCIMP in exosomes (SCIMPexo) by macrophages after bacterial stimulation, both in vitro and in vivo. We observe a significant increase in the levels of SCIMPexoin bronchoalveolar lavage fluid and serum of pneumonia patients. We also find that bronchial perfusion with SCIMPexoor SCIMP N-terminal peptides increases the survival rate of the ALI model. This occurs due to the chemoattraction and activation of peripheral neutrophils dependent on formyl peptide receptor 1/2 (FPR1/2). Conversely, exosome suppressors and FPR1/2 antagonists decrease the survival rate in the lethal ALI model.Scimp-deficient andFpr1/2-deficient mice also have lower survival rates and shorter survival times than wild-type mice. However, bronchial perfusion of SCIMP rescuesScimp-deficient mice but notFpr1/2-deficient mice. Collectively, our findings suggest that the macrophage-SCIMP-FPRs-neutrophil axis plays a vital role in the innate immune process underlying ALI.
AKT1 phosphorylation of cytoplasmic ME2 induces a metabolic switch to glycolysis for tumorigenesis
Authors: Chen Taiqi , Xie Siyi , Cheng Jie , Zhao Qiao , Wu Hong , Jiang Peng , Du Wenjing
Published: January 2024

Many types of tumors feature aerobic glycolysis for meeting their increased energetic and biosynthetic demands. However, it remains still unclear how this glycolytic phenomenon is achieved and coordinated with other metabolic pathways in tumor cells in response to growth stimuli. Here we report that activation of AKT1 induces a metabolic switch to glycolysis from the mitochondrial metabolism via phosphorylation of cytoplasmic malic enzyme 2 (ME2), named ME2fl (fl means full length), favoring an enhanced glycolytic phenotype. Mechanistically, in the cytoplasm, AKT1 phosphorylates ME2fl at serine 9 in the mitochondrial localization signal peptide at the N-terminus, preventing its mitochondrial translocation. Unlike mitochondrial ME2, which accounts for adjusting the tricarboxylic acid (TCA) cycle, ME2fl functions as a scaffold that brings together the key glycolytic enzymes phosphofructokinase (PFKL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase M2 (PKM2), as well as Lactate dehydrogenase A (LDHA), to promote glycolysis in the cytosol. Thus, through phosphorylation of ME2fl, AKT1 enhances the glycolytic capacity of tumor cells in vitro and in vivo, revealing an unexpected role for subcellular translocation switching of ME2 mediated by AKT1 in the metabolic adaptation of tumor cells to growth stimuli.
Acoustic and language-specific sources for phonemic abstraction from speech
Authors: Mai Anna , Riès Stephanie , Ben-Haim Sharona , Shih Jerry J. , Gentner Timothy Q.
Published: January 2024

Spoken language comprehension requires abstraction of linguistic information from speech, but the interaction between auditory and linguistic processing of speech remains poorly understood. Here, we investigate the nature of this abstraction using neural responses recorded intracranially while participants listened to conversational English speech. Capitalizing on multiple, language-specific patterns where phonological and acoustic information diverge, we demonstrate the causal efficacy of the phoneme as a unit of analysis and dissociate the unique contributions of phonemic and spectrographic information to neural responses. Quantitive higher-order response models also reveal that unique contributions of phonological information are carried in the covariance structure of the stimulus-response relationship. This suggests that linguistic abstraction is shaped by neurobiological mechanisms that involve integration across multiple spectro-temporal features and prior phonological information. These results link speech acoustics to phonology and morphosyntax, substantiating predictions about abstractness in linguistic theory and providing evidence for the acoustic features that support that abstraction.
Durvalumab plus pazopanib combination in patients with advanced soft tissue sarcomas: a phase II trial
Authors: Cho Hee Jin , Yun Kum-Hee , Shin Su-Jin , Lee Young Han , Kim Seung Hyun , Baek Wooyeol , Han Yoon Dae , Kim Sang Kyum , Ryu Hyang Joo , Lee Joohee , Cho Iksung , Go Heounjeong , Ko Jiwon , Jung Inkyung , Jeon Min Kyung , Rha Sun Young , Kim Hyo Song
Published: January 2024

We aimed to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 inhibitor, durvalumab, in metastatic and/or recurrent soft tissue sarcoma (STS). In this single-arm phase 2 trial (NCT03798106), treatment consisted of pazopanib 800 mg orally once a day and durvalumab 1500 mg once every 3 weeks. Primary outcome was overall response rate (ORR) and secondary outcomes included progression-free survival (PFS), overall survival, disease control rate, immune-related response criteria, and safety. The ORR was 30.4% and the trial met the pre-specified endpoint. The median PFS was 7.7 months (95% confidence interval: 5.7–10.4). The common treatment-related adverse events of grades 3–4 included neutropenia (9 [19.1%]), elevated aspartate aminotransferase (7 [14.9%]), alanine aminotransferase (5 [10.6%]), and thrombocytopenia (4 [8.5%]). In a prespecified transcriptomic analysis, the B lineage signature was a significant key determinant of overall response (P = 0.014). In situ analysis also showed that tumours with high CD20+ B cell infiltration and vessel density had a longer PFS (P = 6.5 × 10−4) than those with low B cell infiltration and vessel density, as well as better response (50% vs 12%, P = 0.019). CD20+ B cell infiltration was identified as the only independent predictor of PFS via multivariate analysis. Durvalumab combined with pazopanib demonstrated promising efficacy in an unselected STS cohort, with a manageable toxicity profile.
Dithiine-linked metalphthalocyanine framework with undulated layers for highly efficient and stable H2O2 electroproduction
Authors: Zhi Qianjun , Jiang Rong , Yang Xiya , Jin Yucheng , Qi Dongdong , Wang Kang , Liu Yunpeng , Jiang Jianzhuang
Published: January 2024

Realization of stable and industrial-level H2O2 electroproduction still faces great challenge due large partly to the easy decomposition of H2O2. Herein, a two-dimensional dithiine-linked phthalocyaninato cobalt (CoPc)-based covalent organic framework (COF), CoPc-S-COF, was afforded from the reaction of hexadecafluorophthalocyaninato cobalt (II) with 1,2,4,5-benzenetetrathiol. Introduction of the sulfur atoms with large atomic radius and two lone-pairs of electrons in the C-S-C linking unit leads to an undulated layered structure and an increased electron density of the Co center for CoPc-S-COF according to a series of experiments in combination with theoretical calculations. The former structural effect allows the exposition of more Co sites to enhance the COF catalytic performance, while the latter electronic effect activates the 2e− oxygen reduction reaction (2e− ORR) but deactivates the H2O2 decomposition capability of the same Co center, as a total result enabling CoPc-S-COF to display good electrocatalytic H2O2 production performance with a remarkable H2O2 selectivity of >95% and a stable H2O2 production with a concentration of 0.48 wt% under a high current density of 125 mA cm−2 at an applied potential of ca. 0.67 V versus RHE for 20 h in a flow cell, representing the thus far reported best H2O2 synthesis COFs electrocatalysts.
Folding pathway of a discontinuous two-domain protein
Authors: Agam Ganesh , Barth Anders , Lamb Don C.
Published: January 2024

It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.
Systematic determination of a material’s magnetic ground state from first principles
Authors: Tellez-Mora Andres , He Xu , Bousquet Eric , Wirtz Ludger , Romero Aldo H.
Published: January 2024

We present a self-consistent method based on first-principles calculations to determine the magnetic ground state of materials, regardless of their dimensionality. Our methodology is founded on satisfying the stability conditions derived from the linear spin wave theory (LSWT) by optimizing the magnetic structure iteratively. We demonstrate the effectiveness of our method by successfully predicting the experimental magnetic structures of NiO, FePS3, FeP, MnF2, FeCl2, and CuO. In each case, we compared our results with available experimental data and existing theoretical calculations reported in the literature. Finally, we discuss the validity of the method and the possible extensions.
Electricity and natural gas tariffs at United States wastewater treatment plants
Authors: Chapin Fletcher T. , Bolorinos Jose , Mauter Meagan S.
Published: January 2024

Wastewater treatment plants (WWTPs) are large electricity and natural gas consumers with untapped potential to recover carbon-neutral biogas and provide energy services for the grid. Techno-economic analysis of emerging energy recovery and management technologies is critical to understanding their commercial viability, but quantifying their energy cost savings potential is stymied by a lack of well curated, nationally representative electricity and natural gas tariff data. We present a dataset of electricity tariffs for the 100 largest WWTPs in the Clean Watershed Needs Survey (CWNS) and natural gas tariffs for the 54 of 100 WWTPs with on-site cogeneration. We manually collected tariffs from each utility’s website and implemented data checks to ensure their validity. The dataset includes facility metadata, electricity tariffs, and natural gas tariffs (where cogeneration is present). Tariffs are current as of November 2021. We provide code for technical validation along with a sample simulation.
A real-world dataset of group emotion experiences based on physiological data
Authors: Bota Patrícia , Brito Joana , Fred Ana , Cesar Pablo , Silva Hugo
Published: January 2024

Affective computing has experienced substantial advancements in recognizing emotions through image and facial expression analysis. However, the incorporation of physiological data remains constrained. Emotion recognition with physiological data shows promising results in controlled experiments but lacks generalization to real-world settings. To address this, we present G-REx, a dataset for real-world affective computing. We collected physiological data (photoplethysmography and electrodermal activity) using a wrist-worn device during long-duration movie sessions. Emotion annotations were retrospectively performed on segments with elevated physiological responses. The dataset includes over 31 movie sessions, totaling 380 h+ of data from 190+ subjects. The data were collected in a group setting, which can give further context to emotion recognition systems. Our setup aims to be easily replicable in any real-life scenario, facilitating the collection of large datasets for novel affective computing systems.
Mass spectrometry-based proteomics data from thousands of HeLa control samples
Authors: Webel Henry , Perez-Riverol Yasset , Nielsen Annelaura Bach , Rasmussen Simon
Published: January 2024

Here we provide a curated, large scale, label free mass spectrometry-based proteomics data set derived from HeLa cell lines for general purpose machine learning and analysis. Data access and filtering is a tedious task, which takes up considerable amounts of time for researchers. Therefore we provide machine based metadata for easy selection and overview along the 7,444 raw files and MaxQuant search output. For convenience, we provide three filtered and aggregated development datasets on the protein groups, peptides and precursors level. Next to providing easy to access training data, we provide a SDRF file annotating each raw file with instrument settings allowing automated reprocessing. We encourage others to enlarge this data set by instrument runs of further HeLa samples from different machine types by providing our workflows and analysis scripts.
A consolidated and geolocated facility list in Senegal from triangulating secondary data
Authors: Gueye Daouda M. , Ly Alioune Badara , Gueye Babacar , Ndour Papa Ibrahima , Fullman Nancy , Liu Patrick Y. , Mbaye Khadim , Diallo Aliou , Diatta Ibrahima , Diatta Saly Amos , Mane Mouhamadou Moustapha , Ikilezi Gloria , Sarr Moussa
Published: January 2024

Having a geolocated list of all facilities in a country – a “master facility list” (MFL) – can provide critical inputs for health program planning and implementation. To the best of our knowledge, Senegal has never had a centralized MFL, though many data sources currently exist within the broader Senegalese data landscape that could be leveraged and consolidated into a single database – a critical first step toward building a full MFL. We collated 12,965 facility observations from 16 separate datasets and lists in Senegal, and applied matching algorithms, manual checking and revisions as needed, and verification processes to identify unique facilities and triangulate corresponding GPS coordinates. Our resulting consolidated facility list has a total of 4,685 facilities, with 2,423 having at least one set of GPS coordinates. Developing approaches to leverage existing data toward future MFL establishment can help bridge data demands and inform more targeted approaches for completing a full facility census based on areas and facility types with the lowest coverage. Going forward, it is crucial to ensure routine updates of current facility lists, and to strengthen government-led mechanisms around such data collection demands and the need for timely data for health decision-making.
Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection
Authors: De Coster T. , Zhao Y. , Tšuiko O. , Demyda-Peyrás S. , Van Soom A. , Vermeesch J. R. , Smits K.
Published: January 2024

In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
Reconstruction algorithms for DNA-storage systems
Authors: Sabary Omer , Yucovich Alexander , Shapira Guy , Yaakobi Eitan
Published: January 2024

Motivated by DNA storage systems, this work presents theDNA reconstruction problem, in which a length-nstring, is passing through theDNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are calledtraces. ADNA reconstruction algorithmis a mapping which receivesttraces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm’s estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for theshortest common supersequenceand thelongest common subsequenceproblems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.
In vivo identification of Drosophila rhodopsin interaction partners by biotin proximity labeling
Authors: Feizy Nilofar , Leuchtenberg Sarah Franziska , Steiner Christine , Würtz Berit , Fliegner Leo , Huber Armin
Published: January 2024

Proteins exert their function through protein–protein interactions. In Drosophila, G protein-coupled receptors like rhodopsin (Rh1) interact with a G protein to activate visual signal transduction and with arrestins to terminate activation. Also, membrane proteins like Rh1 engage in protein–protein interactions during folding within the endoplasmic reticulum, during their vesicular transport and upon removal from the cell surface and degradation. Here, we expressed a Rh1-TurboID fusion protein (Rh1::TbID) in Drosophila photoreceptors to identify in vivo Rh1 interaction partners by biotin proximity labeling. We show that Rh1::TbID forms a functional rhodopsin that mediates biotinylation of arrestin 2 in conditions where arrestin 2 interacts with rhodopsin. We also observed biotinylation of Rh1::TbID and native Rh1 as well as of most visual signal transduction proteins. These findings indicate that the signaling components in the rhabdomere approach rhodopsin closely, within a range of ca. 10 nm. Furthermore, we have detected proteins engaged in the maturation of rhodopsin and elements responsible for the trafficking of membrane proteins, resembling potential interaction partners of Rh1. Among these are chaperons of the endoplasmic reticulum, proteins involved in Clathrin-mediated endocytosis as well as previously unnoticed contributors to rhodopsin transportation, such as Rab32, Vap33, or PIP82.
Relationship between hemolysis and lipid oxidation in red blood cell-spiked fish muscle; dependance on pH and blood plasma
Authors: Ghirmai Semhar , Krona Annika , Wu Haizhou , Whalin James , Axelsson Michael , Undeland Ingrid
Published: January 2024

The relationship between hemolysis and lipid oxidation was explored in red blood cell (RBCs)-spiked washed cod mince (WCM). At pH 6.8 and 3 ± 1 °C, intact RBCs (71 µM Hb) delayed lipid oxidation by 1 day compared to WCM with partly or fully lysed RBCs which oxidized immediately. Intact RBCs also lowered peak peroxide value (PV) and thiobarbituric acid reactive substances (TBARS) with up to 59.5% and 48.1%, respectively. Adding 3% (v/w) blood plasma to RBC-spiked WCM delayed the lipid oxidation onset from 1 to 3–4 days without delaying hemolysis. At pH 6.4 the oxidation onset in RBC-WCM was the same as for pH 6.8 while at pH 7.2–7.6 lipid oxidation was suppressed for 7 days. Micrographs revealed RBC-lysis from day 2 at pH 6.4 but at pH 7.6, RBC stayed intact for ≥ 7 days. Thus, assuring presence of plasma-derived antioxidants and/or elevating muscle pH to avoid hemolysis can aid valorization of blood rich underutilized fish raw materials.
Transient responses of double core-holes generation in all-attosecond pump-probe spectroscopy
Authors: Liu Jianpeng , Li Yongqiang , Hou Yong , Wu Jianhua , Yuan Jianmin
Published: January 2024

Double core-holes (DCHs) show remarkable and sensitive effects for understanding electron correlations and coherence. With advanced modulation of x-ray free-electron laser (XFEL) facility, we propose the forthcoming all-attosecond XFEL pump-probe spectroscopy can decipher the hidden photon-initiated dynamics of DCHs. The benchmark case of neon is investigated, and norm-nonconserving Monte-Carlo wavefunction method simulates non-Hermitian dynamics among vast states, which shows superiority in efficiency and reliability. In our scheme, population transfer to DCHs is sequentially irradiated by pump and probe laser. By varying time delay, Stark shifts and quantum path interference of resonant lines sensitively emerge at specific interval of two pulses. These ubiquitous multi-channel effects are also observed in phase-fluctuating pulses, derived from extra phases of impulsive Raman processes by pump laser. Non-perturbation absorption/emission verifies the uniquely interchangeable role of two pules in higher intensity. Our results reveal sensitive and robust responses on pulse parameters, which show potential capacity for XFEL attosecond pulse diagnosis and further attosecond-timescale chemical analysis.
Therapy-induced modulation of tumor vasculature and oxygenation in a murine glioblastoma model quantified by deep learning-based feature extraction
Authors: Bauer Nadine , Beckmann Daniel , Reinhardt Dirk , Frost Nicole , Bobe Stefanie , Erapaneedi Raghu , Risse Benjamin , Kiefer Friedemann
Published: January 2024

Glioblastoma presents characteristically with an exuberant, poorly functional vasculature that causes malperfusion, hypoxia and necrosis. Despite limited clinical efficacy, anti-angiogenesis resulting in vascular normalization remains a promising therapeutic approach. Yet, fundamental questions concerning anti-angiogenic therapy remain unanswered, partly due to the scale and resolution gap between microscopy and clinical imaging and a lack of quantitative data readouts. To what extend does treatment lead to vessel regression or vessel normalization and does it ameliorate or aggravate hypoxia? Clearly, a better understanding of the underlying mechanisms would greatly benefit the development of desperately needed improved treatment regimens. Here, using orthotopic transplantation of Gli36 cells, a widely used murine glioma model, we present a mesoscopic approach based on light sheet fluorescence microscopic imaging of wholemount stained tumors. Deep learning-based segmentation followed by automated feature extraction allowed quantitative analyses of the entire tumor vasculature and oxygenation statuses. Unexpectedly in this model, the response to both cytotoxic and anti-angiogenic therapy was dominated by vessel normalization with little evidence for vessel regression. Equally surprising, only cytotoxic therapy resulted in a significant alleviation of hypoxia. Taken together, we provide and evaluate a quantitative workflow that addresses some of the most urgent mechanistic questions in anti-angiogenic therapy.
Relationship between psycho-physiological indicators and task performance under various indoor space designs for telecommuting environment by introducing mixed-reality
Authors: Lee Kyung-Tae , Kim Ju-Hyung
Published: January 2024

The increase in telecommuting during COVID-19 and advances in digital technology have necessitated the establishment of guidelines for maximizing productivity through indoor space design for telecommuters. Additionally, understanding the physiological response of individuals working in indoor spaces has attracted attention. This study applied mixed-reality environment to alter the design of the indoor space in real-time, while monitoring the task performance and representative psycho-physiological indicators (electroencephalogram and heart rate variability) of 30 individuals with telecommuting experience. To this end, four tasks, including spatial memory, attention, execution, and working memory, were conducted, and the psycho-physiological data from these tests were statistically analyzed. The results revealed that the design of the indoor space did not affect the spatial memory; however, the parasympathetic nerves were stimulated in visually non-preferred spaces, thus reducing mental stress and leading to high efficiency in short-term work. According to the Yerkes-Dodson law, the working memory of an individual is generally efficient and physically stable over time if they adjust to a preferred or decision-making space. Thus, the future design of telecommuting spaces must consider the type of work being done, and guidelines for spatial design should be developed by recognizing the psycho-physiological status of users, while increasing efficiency.