bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus)
Authors: Oosting Tom , Martínez-García Lourdes , Ferrari Giada , Verry Alexander J. F. , Scarsbrook Lachie , Rawlence Nicolas J. , Wellenreuther Maren , Star Bastiaan , Ritchie Peter A. 
Published: December 2022

AbstractGlacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water
Authors: Onvlee Jolijn , Trippel Sebastian , Küpper Jochen 
Published: December 2022

AbstractInteractions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible – paving the way for the complete chemical-reactivity experiment.
A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex
Authors: Rutkauskas Marius , Songailiene Inga , Irmisch Patrick , Kemmerich Felix E. , Sinkunas Tomas , Siksnys Virginijus , Seidel Ralf 
Published: December 2022

AbstractCRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy
Authors: Zhu Junmeng , Ke Yaohua , Liu Qin , Yang Ju , Liu Fangcen , Xu Ruihan , Zhou Hang , Chen Aoxing , Xiao Jie , Meng Fanyan , Yu Lixia , Li Rutian , Wei Jia , Liu Baorui 
Published: December 2022

AbstractIn situ vaccination is a promising strategy to convert the immunosuppressive tumor microenvironment into an immunostimulatory one with limited systemic exposure and side effect. However, sustained clinical benefits require long-term and multidimensional immune activation including innate and adaptive immunity. Here, we develop a probiotic food-grade Lactococcus lactis-based in situ vaccination (FOLactis) expressing a fusion protein of Fms-like tyrosine kinase 3 ligand and co-stimulator OX40 ligand. Intratumoural delivery of FOLactis contributes to local retention and sustained release of therapeutics to thoroughly modulate key components of the antitumour immune response, such as activation of natural killer cells, cytotoxic T lymphocytes, and conventional-type-1-dendritic cells in the tumors and tumor-draining lymph nodes. In addition, intratumoural administration of FOLactis induces a more robust tumor antigen-specific immune response and superior systemic antitumour efficacy in multiple poorly immune cell-infiltrated and anti-PD1-resistant tumors. Specific depletion of different immune cells reveals that CD8+ T and natural killer cells are crucial to the in situ vaccine-elicited tumor regression. Our results confirm that FOLactis displays an enhanced antitumour immunity and successfully converts the ‘cold’ tumors to ‘hot’ tumors.
Multi-angular polarimetric remote sensing to pinpoint global aerosol absorption and direct radiative forcing
Authors: Chen Cheng , Dubovik Oleg , Schuster Gregory L. , Chin Mian , Henze Daven K. , Lapyonok Tatyana , Li Zhengqiang , Derimian Yevgeny , Zhang Ying 
Published: December 2022

AbstractQuantitative estimations of atmospheric aerosol absorption are rather uncertain due to the lack of reliable information about the global distribution. Because the information about aerosol properties is commonly provided by single-viewing photometric satellite sensors that are not sensitive to aerosol absorption. Consequently, the uncertainty in aerosol radiative forcing remains one of the largest in the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC AR5 and AR6). Here, we use multi-angular polarimeters (MAP) to provide constraints on emission of absorbing aerosol species and estimate global aerosol absorption optical depth (AAOD) and its climate effect. Our estimate of modern-era mid-visible AAOD is 0.0070 that is higher than IPCC by a factor of 1.3-1.8. The black carbon instantaneous direct radiative forcing (BC DRF) is +0.33 W/m2 [+0.17, +0.54]. The MAP constraint narrows the 95% confidence interval of BC DRF by a factor of 2 and boosts confidence in its spatial distribution.
Single-molecule characterization of subtype-specific β1 integrin mechanics
Authors: Jo Myung Hyun , Li Jing , Jaumouillé Valentin , Hao Yuxin , Coppola Jessica , Yan Jiabin , Waterman Clare M. , Springer Timothy A. , Ha Taekjip 
Published: December 2022

AbstractAlthough integrins are known to be mechanosensitive and to possess many subtypes that have distinct physiological roles, single molecule studies of force exertion have thus far been limited to RGD-binding integrins. Here, we show that integrin α4β1 and RGD-binding integrins (αVβ1 and α5β1) require markedly different tension thresholds to support cell spreading. Furthermore, actin assembled downstream of α4β1 forms cross-linked networks in circularly spread cells, is in rapid retrograde flow, and exerts low forces from actin polymerization. In contrast, actin assembled downstream of αVβ1 forms stress fibers linking focal adhesions in elongated cells, is in slow retrograde flow, and matures to exert high forces (>54-pN) via myosin II. Conformational activation of both integrins occurs below 12-pN, suggesting that post-activation subtype-specific cytoskeletal remodeling imposes the higher threshold for spreading on RGD substrates. Multiple layers of single integrin mechanics for activation, mechanotransduction and cytoskeleton remodeling revealed here may underlie subtype-dependence of diverse processes such as somite formation and durotaxis.
Bead-jet printing enabled sparse mesenchymal stem cell patterning augments skeletal muscle and hair follicle regeneration
Authors: Cao Yuanxiong , Tan Jiayi , Zhao Haoran , Deng Ting , Hu Yunxia , Zeng Junhong , Li Jiawei , Cheng Yifan , Tang Jiyuan , Hu Zhiwei , Hu Keer , Xu Bing , Wang Zitian , Wu Yaojiong , Lobie Peter E. , Ma Shaohua 
Published: December 2022

AbstractTransplantation of mesenchymal stem cells (MSCs) holds promise to repair severe traumatic injuries. However, current transplantation practices limit the potential of this technique, either by losing the viable MSCs or reducing the performance of resident MSCs. Herein, we design a “bead-jet” printer, specialized for high-throughput intra-operative formulation and printing of MSCs-laden Matrigel beads. We show that high-density encapsulation of MSCs in Matrigel beads is able to augment MSC function, increasing MSC proliferation, migration, and extracellular vesicle production, compared with low-density bead or high-density bulk encapsulation of the equivalent number of MSCs. We find that the high-density MSCs-laden beads in sparse patterns demonstrate significantly improved therapeutic performance, by regenerating skeletal muscles approaching native-like cell density with reduced fibrosis, and regenerating skin with hair follicle growth and increased dermis thickness. MSC proliferation within 1-week post-transplantation and differentiation at 3 − 4 weeks post-transplantation are suggested to contribute therapy augmentation. We expect this “bead-jet” printing system to strengthen the potential of MSC transplantation.
A circuit from the ventral subiculum to anterior hypothalamic nucleus GABAergic neurons essential for anxiety-like behavioral avoidance
Authors: Yan Jing-Jing , Ding Xiao-Jing , He Ting , Chen Ai-Xiao , Zhang Wen , Yu Zi-Xian , Cheng Xin-Yu , Wei Chuan-Yao , Hu Qiao-Dan , Liu Xiao-Yao , Zhang Yan-Li , He Mengge , Xie Zhi-Yong , Zha Xi , Xu Chun , Cao Peng , Li Haohong , Xu Xiao-Hong 
Published: December 2022

AbstractBehavioral observations suggest a connection between anxiety and predator defense, but the underlying neural mechanisms remain unclear. Here we examine the role of the anterior hypothalamic nucleus (AHN), a node in the predator defense network, in anxiety-like behaviors. By in vivo recordings in male mice, we find that activity of AHN GABAergic (AHNVgat+) neurons shows individually stable increases when animals approach unfamiliar objects in an open field (OF) or when they explore the open-arm of an elevated plus-maze (EPM). Moreover, object-evoked AHN activity overlap with predator cue responses and correlate with the object and open-arm avoidance. Crucially, exploration-triggered optogenetic inhibition of AHNVgat+ neurons reduces object and open-arm avoidance. Furthermore, retrograde viral tracing identifies the ventral subiculum (vSub) of the hippocampal formation as a significant input to AHNVgat+ neurons in driving avoidance behaviors in anxiogenic situations. Thus, convergent activation of AHNVgat+ neurons serves as a shared mechanism between anxiety and predator defense to promote behavioral avoidance.
A growth selection system for the directed evolution of amine-forming or converting enzymes
Authors: Wu Shuke , Xiang Chao , Zhou Yi , Khan Mohammad Saiful Hasan , Liu Weidong , Feiler Christian G. , Wei Ren , Weber Gert , Höhne Matthias , Bornscheuer Uwe T. 
Published: December 2022

AbstractFast screening of enzyme variants is crucial for tailoring biocatalysts for the asymmetric synthesis of non-natural chiral chemicals, such as amines. However, most existing screening methods either are limited by the throughput or require specialized equipment. Herein, we report a simple, high-throughput, low-equipment dependent, and generally applicable growth selection system for engineering amine-forming or converting enzymes and apply it to improve biocatalysts belonging to three different enzyme classes. This results in (i) an amine transaminase variant with 110-fold increased specific activity for the asymmetric synthesis of the chiral amine intermediate of Linagliptin; (ii) a 270-fold improved monoamine oxidase to prepare the chiral amine intermediate of Cinacalcet by deracemization; and (iii) an ammonia lyase variant with a 26-fold increased activity in the asymmetric synthesis of a non-natural amino acid. Our growth selection system is adaptable to different enzyme classes, varying levels of enzyme activities, and thus a flexible tool for various stages of an engineering campaign.
Non-classical ferroptosis inhibition by a small molecule targeting PHB2
Authors: Yang Wei , Mu Bo , You Jing , Tian Chenyu , Bin Huachao , Xu Zhiqiang , Zhang Liting , Ma Ronggang , Wu Ming , Zhang Guo , Huang Chong , Li Linli , Shao Zhenhua , Dai Lunzhi , Désaubry Laurent , Yang Shengyong 
Published: December 2022

AbstractFerroptosis is a new type of programmed cell death characterized by iron-dependent lipid peroxidation. Ferroptosis inhibition is thought as a promising therapeutic strategy for a variety of diseases. Currently, a majority of known ferroptosis inhibitors belong to either antioxidants or iron-chelators. Here we report a new ferroptosis inhibitor, termed YL-939, which is neither an antioxidant nor an iron-chelator. Chemical proteomics revealed the biological target of YL-939 to be prohibitin 2 (PHB2). Mechanistically, YL-939 binding to PHB2 promotes the expression of the iron storage protein ferritin, hence reduces the iron content, thereby decreasing the susceptibility to ferroptosis. We further showed that YL-939 could substantially ameliorate liver damage in a ferroptosis-related acute liver injury model by targeting the PHB2/ferritin/iron axis. Overall, we identified a non-classical ferroptosis inhibitor and revealed a new regulation mechanism of ferroptosis. These findings may present an attractive intervention strategy for ferroptosis-related diseases.
Hemispheric lateralization of semantic processing before and after aripiprazole treatment in first-episode psychosis or ultra-high risk state
Authors: Hwang Tzung-Jeng , Chan Chia-Ta , Hsieh Cheng-Yu , Liu Chih-Min , Liu Chen-Chung , Chien Yi-Ling , Hsieh Ming H. , Lin Yi-Ting , Chou Tai-Li 
Published: December 2022

AbstractWhether aberrant language-related lateralization can be improved after antipsychotic treatment in drug-free patients with first-episode psychosis or ultra-high risk state is little known. We aimed to investigate the improvement in lateralization of semantic processing after antipsychotic treatment and associated clinical and cognitive changes. Twenty-one drug-free patients with first-episode psychosis or ultra-high risk state underwent functional magnetic resonance imaging with a semantic task, neuropsychological testing, and clinical assessments with the Positive and Negative Syndrome Scale before and after 6 weeks of aripiprazole treatment. A lateralization index of the region of interest, i.e., inferior frontal gyrus, was calculated and correlated with the behavioral indices of the semantic task, Positive and Negative Syndrome Scale scores, and language-related neuropsychological test scores. After treatment, the lateralization index of the inferior frontal gyrus was significantly increased, which was related to reduced activation of the right inferior frontal gyrus. The increase in the lateralization index was significantly associated with the increase in verbal fluency score. A higher baseline accuracy of the semantic task was associated with a higher post-treatment lateralization index of the inferior frontal gyrus and greater improvement of the total score and positive subscore of the Positive and Negative Syndrome Scale. Our findings indicated aripiprazole treatment significantly increased semantic processing-related lateralization in the inferior frontal gyrus in drug-free patients with first-episode psychosis or ultra-high risk state. A higher baseline accuracy might predict a higher post-treatment lateralization index and greater symptom improvement.
Area of Habitat maps for the world’s terrestrial birds and mammals
Authors: Lumbierres Maria , Dahal Prabhat Raj , Soria Carmen D. , Di Marco Moreno , Butchart Stuart H. M. , Donald Paul F. , Rondinini Carlo 
Published: December 2022

AbstractArea of Habitat (AOH) is “the habitat available to a species, that is, habitat within its range”. It complements a geographic range map for a species by showing potential occupancy and reducing commission errors. AOH maps are produced by subtracting areas considered unsuitable for the species from their range map, using information on each species’ associations with habitat and elevation. We present AOH maps for 5,481 terrestrial mammal and 10,651 terrestrial bird species (including 1,816 migratory bird species for which we present separate maps for the resident, breeding and non-breeding areas). Our maps have a resolution of 100 m. On average, AOH covered 66 ± 28% of the range maps for mammals and 64 ± 27% for birds. The AOH maps were validated independently, following a novel two-step methodology: a modelling approach to identify outliers and a species-level approach based on point localities. We used AOH maps to produce global maps of the species richness of mammals, birds, globally threatened mammals and globally threatened birds.
Chromosomal-level genome assembly of potato tuberworm, Phthorimaea operculella: a pest of solanaceous crops
Authors: Zhang Mengdi , Cheng Xinyue , Lin Runmao , Xie Bingyan , Nauen Ralf , Rondon Silvia I. , Zavala Jorge A. , Palli Subba Reddy , Li Suhua , Xiong Xingyao , Zhou Wenwu , Gao Yulin 
Published: December 2022

AbstractThe potato tuberworm, Phthorimaea operculella Zeller, is an oligophagous pest feeding on crops mainly belonging to the family Solanaceae. It is one of the most destructive pests of potato worldwide and attacks foliage and tubers in the field and in storage. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis. Here, we report on the genome assembly of P. operculella at the chromosomal level. Using Illumina, Nanopore and Hi-C sequencing, a 648.2 Mb genome was generated from 665 contigs, with an N50 length of 3.2 Mb, and 92.0% (596/648.2 Mb) of the assembly was anchored to 29 chromosomes. In total, 16619 genes were annotated, and 92.4% of BUSCO genes were fully represented. The chromosome-level genome of P. operculella will provide a significant resource for understanding the genetic basis for the biological study of this insect, and for promoting the integrative management of this pest in future.
Long-term High Resolution Image Dataset of Antarctic Coastal Benthic Fauna
Authors: Marini Simone , Bonofiglio Federico , Corgnati Lorenzo Paolo , Bordone Andrea , Schiaparelli Stefano , Peirano Andrea 
Published: December 2022

AbstractAntarctica is a remote place, the continent is covered by ice and its surrounding coastal areas are frozen for the majority of the year. Due to its peculiarity the observation of the underwater organisms is particularly difficult, complicated by logistic factors. We present a long-term dataset consisting of 755 images acquired by using a non-invasive, autonomous imaging device and encompassing both the Antarctic daylight and dark periods, including the corresponding transition phases. All images have the same field of view showing the benthic fauna and part of the water column above, including fishes present in the monitored period. All the images are manually annotated after a visual inspection performed by expert biologists. The extended monitoring period and the annotated images make the dataset a valuable benchmark suitable for studying the dynamics of the long-term Antarctic underwater fauna as well as for developing and testing algorithms for automated image analysis focused on the recognition and classification of the Antarctic organisms and the automated analysis of their long-term dynamics.
High-resolution circa-2020 map of urban lakes in China
Authors: Song Chunqiao , Jiang Xingan , Fan Chenyu , Li Linsen 
Published: December 2022

AbstractUrban lakes provide important ecological services to local communities, such as flood mitigation, biodiversity, and recreation. With rapid urbanization, urban lakes are significantly affected by socio-economic development and urgently need attention. Yet there is still a lack of datasets that include tiny urban lakes on a global or national scale. This study aims to produce a high-resolution circa-2020 map of urban lakes (≥0.001 km2) in China. The 10-m-resolution Sentinel-2 imagery and a simple but robust water extraction method was used to generate waterbodies. The accuracy of this national-scale dataset was evaluated by comparing it with manually sampled urban units, with the average accuracy of 81.85% in area and 93.35% in count. The database totally inventories 1.11 × 106 urban lakes in China, with a net area of ~2.13 × 103 km2. Overall, the spatial distribution of urban lakes in China showed strongly heterogeneous characteristics. This dataset will enhance our understanding of the distribution pattern of China’s urban lakes and contribute to better ecological and environmental management as well as sustainable urban development planning.
Introducing ligand GA, a genetic algorithm molecular tool for automated protein inhibitor design
Authors: Chalmers Gordon 
Published: December 2022

AbstractLigand GA is introduced in this work and approaches the problem of finding small molecules inhibiting protein functions by using the protein site to find close to optimal or optimal small molecule binders. Genetic algorithms (GA) are an effective means for approximating or solving computationally hard mathematics problems with large search spaces such as this one. The algorithm is designed to include constraints on the generated molecules from ADME restriction, localization in a binding site, specified hydrogen bond requirements, toxicity prevention from multiple proteins, sub-structure restrictions, and database inclusion. This algorithm and work is in the context of computational modeling, ligand design and docking to protein sites.