bluuebunny/crossref_metadata_2025_split huggingface dataset:
Air quality related equity implications of U.S. decarbonization policy
Authors: Picciano Paul , Qiu Minghao , Eastham Sebastian D. , Yuan Mei , Reilly John , Selin Noelle E. 
Published: September 2023

AbstractClimate policies that target greenhouse gas emissions can improve air quality by reducing co-emitted air pollutant emissions. However, the extent to which climate policy could contribute to the targets of reducing existing pollution disparities across different populations remains largely unknown. We quantify potential air pollution exposure reductions under U.S. federal carbon policy, considering implications of resulting health benefits for exposure disparities across U.S. racial/ethnic groups. We focus on policy cases that achieve reductions of 40-60% in 2030 economy-wide carbon dioxide (CO2) emissions, when compared with 2005 emissions. The 50% CO2 reduction policy case reduces average fine particulate matter (PM2.5) exposure across racial/ethnic groups, with greatest benefit for non-Hispanic Black (−0.44 μg/m3) and white populations (−0.37 μg/m3). The average exposure disparity for racial/ethnic minorities rises from 12.4% to 13.1%. Applying an optimization approach to multiple emissions reduction scenarios, we find that no alternate combination of reductions from different CO2 sources would substantially mitigate exposure disparities. Results suggest that CO2-based strategies for this range of reductions are insufficient for fully mitigating PM2.5 exposure disparities between white and racial/ethnic minority populations; addressing disparities may require larger-scale structural changes.
Evolutionary origin of genomic structural variations in domestic yaks
Authors: Liu Xinfeng , Liu Wenyu , Lenstra Johannes A. , Zheng Zeyu , Wu Xiaoyun , Yang Jiao , Li Bowen , Yang Yongzhi , Qiu Qiang , Liu Hongyu , Li Kexin , Liang Chunnian , Guo Xian , Ma Xiaoming , Abbott Richard J. , Kang Minghui , Yan Ping , Liu Jianquan 
Published: September 2023

AbstractYak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.
The isocyanide SN2 reaction
Authors: Patil Pravin , Zheng Qiang , Kurpiewska Katarzyna , Dömling Alexander 
Published: September 2023

AbstractThe SN2 nucleophilic substitution reaction is a vital organic transformation used for drug and natural product synthesis. Nucleophiles like cyanide, oxygen, nitrogen, sulfur, or phosphorous replace halogens or sulfonyl esters, forming new bonds. Isocyanides exhibit unique C-centered lone pair σ and π* orbitals, enabling diverse radical and multicomponent reactions. Despite this, their nucleophilic potential in SN2 reactions remains unexplored. We have uncovered that isocyanides act as versatile nucleophiles in SN2 reactions with alkyl halides. This yields highly substituted secondary amides through in situ nitrilium ion hydrolysis introducing an alternative bond break compared to classical amide synthesis. This novel 3-component process accommodates various isocyanide and electrophile structures, functional groups, scalability, late-stage drug modifications, and complex compound synthesis. This reaction greatly expands chemical diversity, nearly doubling the classical amid coupling’s chemical space. Notably, the isocyanide nucleophile presents an unconventional Umpolung amide carbanion synthon (R-NHC(-) = O), an alternative to classical amide couplings.
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Authors: Nakato Ryuichiro , Sakata Toyonori , Wang Jiankang , Nagai Luis Augusto Eijy , Nagaoka Yuya , Oba Gina Miku , Bando Masashige , Shirahige Katsuhiko 
Published: September 2023

AbstractCohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer–promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.
Dynamically tuning friction at the graphene interface using the field effect
Authors: Greenwood Gus , Kim Jin Myung , Nahid Shahriar Muhammad , Lee Yeageun , Hajarian Amin , Nam SungWoo , Espinosa-Marzal Rosa M. 
Published: September 2023

AbstractDynamically controlling friction in micro- and nanoscale devices is possible using applied electrical bias between contacting surfaces, but this can also induce unwanted reactions which can affect device performance. External electric fields provide a way around this limitation by removing the need to apply bias directly between the contacting surfaces. 2D materials are promising candidates for this approach as their properties can be easily tuned by electric fields and they can be straightforwardly used as surface coatings. This work investigates the friction between single layer graphene and an atomic force microscope tip under the influence of external electric fields. While the primary effect in most systems is electrostatically controllable adhesion, graphene in contact with semiconducting tips exhibits a regime of unexpectedly enhanced and highly tunable friction. The origins of this phenomenon are discussed in the context of fundamental frictional dissipation mechanisms considering stick slip behavior, electron-phonon coupling and viscous electronic flow.
Bird clades with less complex appendicular skeletons tend to have higher species richness
Authors: Brinkworth Andrew , Green Emily , Li Yimeng , Oyston Jack , Ruta Marcello , Wills Matthew A. 
Published: September 2023

AbstractSpecies richness is strikingly uneven across taxonomic groups at all hierarchical levels, but the reasons for this heterogeneity are poorly understood. It is well established that morphological diversity (disparity) is decoupled from taxonomic diversity, both between clades and across geological time. Morphological complexity has been much less studied, but there is theory linking complexity with differential diversity across groups. Here we devise an index of complexity from the differentiation of the fore and hind limb pairs for a sample of 983 species of extant birds. We test the null hypothesis that this index of morphological complexity is uncorrelated with clade diversity, revealing a significant and negative correlation between the species richness of clades and the mean morphological complexity of those clades. Further, we find that more complex clades tend to occupy a smaller number of dietary and habitat niches, and that this proxy for greater ecological specialisation correlates with lower species richness. Greater morphological complexity in the appendicular skeleton therefore appears to hinder the generation and maintenance of species diversity. This may result from entrenchment into morphologies and ecologies that are less capable of yielding further diversity.
Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria
Authors: Shimokawa Michiko , Ishiwata Akihiro , Kashima Toma , Nakashima Chiho , Li Jiaman , Fukushima Riku , Sawai Naomi , Nakamori Miku , Tanaka Yuuki , Kudo Azusa , Morikami Sae , Iwanaga Nao , Akai Genki , Shimizu Nobutaka , Arakawa Takatoshi , Yamada Chihaya , Kitahara Kanefumi , Tanaka Katsunori , Ito Yukishige , Fushinobu Shinya , Fujita Kiyotaka 
Published: September 2023

AbstractThe cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of d-arabinose, the enantiomer of the typical l-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-d-arabinanases, GH172 exo-α-d-arabinofuranosidase, and GH116 exo-β-d-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex d-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-d-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these d-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.
Identification of a common ice nucleus on hydrophilic and hydrophobic close-packed metal surfaces
Authors: Chen Pengcheng , Xu Qiuhao , Ding Zijing , Chen Qing , Xu Jiyu , Cheng Zhihai , Qiu Xiaohui , Yuan Bingkai , Meng Sheng , Yao Nan 
Published: September 2023

AbstractEstablishing a general model of heterogeneous ice nucleation has long been challenging because of the surface water structures found on different substrates. Identifying common water clusters, regardless of the underlying substrate, is one of the key steps toward solving this problem. Here, we demonstrate the presence of a common water cluster found on both hydrophilic Pt(111) and hydrophobic Cu(111) surfaces using scanning tunneling microscopy and non-contact atomic force microscopy. Water molecules self-assemble into a structure with a central flat-lying hexagon and three fused pentagonal rings, forming a cluster consisting of 15 individual water molecules. This cluster serves as a critical nucleus during ice nucleation on both surfaces: ice growth beyond this cluster bifurcates to form two-dimensional (three-dimensional) layers on hydrophilic (hydrophobic) surfaces. Our results reveal the inherent similarity and distinction at the initial stage of ice growth on hydrophilic and hydrophobic close-packed metal surfaces; thus, these observations provide initial evidence toward a general model for water-substrate interaction.
A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps
Authors: Forsberg Björn O. , Shah Pranav N. M. , Burt Alister 
Published: September 2023

AbstractCryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction.
Network controllability of structural connectomes in the neonatal brain
Authors: Sun Huili , Jiang Rongtao , Dai Wei , Dufford Alexander J. , Noble Stephanie , Spann Marisa N. , Gu Shi , Scheinost Dustin 
Published: September 2023

AbstractWhite matter connectivity supports diverse cognitive demands by efficiently constraining dynamic brain activity. This efficiency can be inferred from network controllability, which represents the ease with which the brain moves between distinct mental states based on white matter connectivity. However, it remains unclear how brain networks support diverse functions at birth, a time of rapid changes in connectivity. Here, we investigate the development of network controllability during the perinatal period and the effect of preterm birth in 521 neonates. We provide evidence that elements of controllability are exhibited in the infant’s brain as early as the third trimester and develop rapidly across the perinatal period. Preterm birth disrupts the development of brain networks and altered the energy required to drive state transitions at different levels. In addition, controllability at birth is associated with cognitive ability at 18 months. Our results suggest network controllability develops rapidly during the perinatal period to support cognitive demands but could be altered by environmental impacts like preterm birth.
A mechanism that ensures non-selective cytoplasm degradation by autophagy
Authors: Kotani Tetsuya , Sakai Yuji , Kirisako Hiromi , Kakuta Chika , Kakuta Soichiro , Ohsumi Yoshinori , Nakatogawa Hitoshi 
Published: September 2023

AbstractIn autophagy, a membrane cisterna called the isolation membrane expands, bends, becomes spherical, and closes to sequester cytoplasmic constituents into the resulting double-membrane vesicle autophagosome for lysosomal/vacuolar degradation. Here, we discover a mechanism that allows the isolation membrane to expand with a large opening to ensure non-selective cytoplasm sequestration within the autophagosome. A sorting nexin complex that localizes to the opening edge of the isolation membrane plays a critical role in this process. Without the complex, the isolation membrane expands with a small opening that prevents the entry of particles larger than about 25 nm, including ribosomes and proteasomes, although autophagosomes of nearly normal size eventually form. This study sheds light on membrane morphogenesis during autophagosome formation and selectivity in autophagic degradation.
Prosaposin maintains lipid homeostasis in dopamine neurons and counteracts experimental parkinsonism in rodents
Authors: He Yachao , Kaya Ibrahim , Shariatgorji Reza , Lundkvist Johan , Wahlberg Lars U. , Nilsson Anna , Mamula Dejan , Kehr Jan , Zareba-Paslawska Justyna , Biverstål Henrik , Chergui Karima , Zhang Xiaoqun , Andren Per E. , Svenningsson Per 
Published: September 2023

AbstractProsaposin (PSAP) modulates glycosphingolipid metabolism and variants have been linked to Parkinson’s disease (PD). Here, we find altered PSAP levels in the plasma, CSF and post-mortem brain of PD patients. Altered plasma and CSF PSAP levels correlate with PD-related motor impairments. Dopaminergic PSAP-deficient (cPSAPDAT) mice display hypolocomotion and depression/anxiety-like symptoms with mildly impaired dopaminergic neurotransmission, while serotonergic PSAP-deficient (cPSAPSERT) mice behave normally. Spatial lipidomics revealed an accumulation of highly unsaturated and shortened lipids and reduction of sphingolipids throughout the brains of cPSAPDAT mice. The overexpression of α-synuclein via AAV lead to more severe dopaminergic degeneration and higher p-Ser129 α-synuclein levels in cPSAPDAT mice compared to WT mice. Overexpression of PSAP via AAV and encapsulated cell biodelivery protected against 6-OHDA and α-synuclein toxicity in wild-type rodents. Thus, these findings suggest PSAP may maintain dopaminergic lipid homeostasis, which is dysregulated in PD, and counteract experimental parkinsonism.
SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
Authors: Dou Yongchao , Liu Yuejia , Yi Xinpei , Olsen Lindsey K. , Zhu Hongwen , Gao Qiang , Zhou Hu , Zhang Bing 
Published: September 2023

AbstractShotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
Histidine modulates amyloid-like assembly of peptide nanomaterials and confers enzyme-like activity
Authors: Yuan Ye , Chen Lei , Kong Lingfei , Qiu Lingling , Fu Zhendong , Sun Minmin , Liu Yuan , Cheng Miaomiao , Ma Saiyu , Wang Xiaonan , Zhao Changhui , Jiang Jing , Zhang Xinzheng , Wang Liping , Gao Lizeng 
Published: September 2023

AbstractAmyloid-like assembly is not only associated with pathological events, but also leads to the development of novel nanomaterials with unique properties. Herein, using Fmoc diphenylalanine peptide (Fmoc–F–F) as a minimalistic model, we found that histidine can modulate the assembly behavior of Fmoc–F–F and induce enzyme-like catalysis. Specifically, the presence of histidine rearranges the β structure of Fmoc–F–F to assemble nanofilaments, resulting in the formation of active site to mimic peroxidase-like activity that catalyzes ROS generation. A similar catalytic property is also observed in Aβ assembled filaments, which is correlated with the spatial proximity between intermolecular histidine and F-F. Notably, the assembled Aβ filaments are able to induce cellular ROS elevation and damage neuron cells, providing an insight into the pathological relationship between Aβ aggregation and Alzheimer’s disease. These findings highlight the potential of histidine as a modulator in amyloid-like assembly of peptide nanomaterials exerting enzyme-like catalysis.
Clinical blindness in conjunction with childhood bacterial meningitis
Authors: Pelkonen Tuula , Kallio Markku , Latvala Terho , Roine Irmeli , Peltola Heikki 
Published: September 2023

AbstractAlthough rarely reported, bilateral loss of vision is a severe complication of childhood bacterial meningitis. We assessed its frequency in five prospective treatment trials performed in Europe, Latin America, and Angola in 1984–2017. Course of illness, follow-up findings, and child’s sight were recorded. Sight was examined at discharge, and conditions permitting, also at 1–3 months post-hospitalization and in Angola on hospital day 7. Experienced pediatricians diagnosed clinical blindness if the child did not make eye contact, did not blink or move the eyes, or remained unresponsive to bright light or movement of large objects before their eyes. Of 1515 patients, 351, 654, and 510 were from Finland, Latin America, and Angola, respectively. At discharge, blindness was observed in 0 (0%), 8 (1.2%), and 51 (10%) children, respectively. In Angola, 64 children appeared to be blind on day 7; 16 of these children died. Blindness found at discharge in Angola was not invariably irreversible; approximately 40% had restored the sight at follow-up visit. Clinical blindness rarely occurred in isolation and was usually associated with young age and poor general condition at hospital arrival. Various other serious sequelae were common among the survivors with clinical blindness.
Screen time and sleep among medical students in Germany
Authors: Liebig Lukas , Bergmann Antje , Voigt Karen , Balogh Erika , Birkas Béla , Faubl Nora , Kraft Theresa , Schöniger Konrad , Riemenschneider Henna 
Published: September 2023

AbstractMedical students are a vulnerable group for harmful health behaviours due to academic stress. Increased screen time is associated with adverse health behaviour, particularly delayed bedtime, shorter sleep duration and poorer sleep quality. This possible relationship has not yet been examined among medical students in Europe. Medical students at the Technical University of Dresden were invited to participate in an online questionnaire based cross-sectional study. To analyse correlations between screen time and sleep parameters, correlation coefficients, linear regression and mixed-model analysis were calculated. 415 students (average age 24 years, 70% female) were included in the analysis. The students reported an average of 7 h screen time per day and 7.25 h sleep duration per night. Approximately 23% (n = 97) reported sleeping less than 7 h per night and 25% (n = 105) reported fairly to very poor sleep quality. Students who reported more screen time for leisure went to bed significantly later (r = 0.213, p < 0.001). Students who spent more screen time for study/work tended to sleep shorter (r = − 0.108, p < 0.015). There was no significant association between screen time and sleep quality (p = 0.103). The results show a need for educational interventions to promote healthy sleep behaviour and to limit screen time.