bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity
Authors: Sun Yu H. , Cui Hongxiao , Song Chi , Shen Jiafei Teng , Zhuo Xiaoyu , Wang Ruoqiao Huiyi , Yu Xiaohui , Ndamba Rudo , Mu Qian , Gu Hanwen , Wang Duolin , Murthy Gayathri Guru , Li Pidong , Liang Fan , Liu Lei , Tao Qing , Wang Ying , Orlowski Sara , Xu Qi , Zhou Huaijun , Jagne Jarra , Gokcumen Omer , Anthony Nick , Zhao Xin , Li Xin Zhiguo 
Published: February 2023

AbstractUnlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.
Proteasome inhibition targets the KMT2A transcriptional complex in acute lymphoblastic leukemia
Authors: Kamens Jennifer L. , Nance Stephanie , Koss Cary , Xu Beisi , Cotton Anitria , Lam Jeannie W. , Garfinkle Elizabeth A. R. , Nallagatla Pratima , Smith Amelia M. R. , Mitchell Sharnise , Ma Jing , Currier Duane , Wright William C. , Kavdia Kanisha , Pagala Vishwajeeth R. , Kim Wonil , Wallace LaShanale M. , Cho Ji-Hoon , Fan Yiping , Seth Aman , Twarog Nathaniel , Choi John K. , Obeng Esther A. , Hatley Mark E. , Metzger Monika L. , Inaba Hiroto , Jeha Sima , Rubnitz Jeffrey E. , Peng Junmin , Chen Taosheng , Shelat Anang A. , Guy R. Kiplin , Gruber Tanja A. 
Published: February 2023

AbstractRearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.
Engineering nanoscale H supply chain to accelerate methanol synthesis on ZnZrOx
Authors: Lee Kyungho , Mendes Paulo C. D. , Jeon Hyungmin , Song Yizhen , Dickieson Maxim Park , Anjum Uzma , Chen Luwei , Yang Tsung-Cheng , Yang Chia-Min , Choi Minkee , Kozlov Sergey M. , Yan Ning 
Published: February 2023

AbstractMetal promotion is the most widely adopted strategy for enhancing the hydrogenation functionality of an oxide catalyst. Typically, metal nanoparticles or dopants are located directly on the catalyst surface to create interfacial synergy with active sites on the oxide, but the enhancement effect may be compromised by insufficient hydrogen delivery to these sites. Here, we introduce a strategy to promote a ZnZrOxmethanol synthesis catalyst by incorporating hydrogen activation and delivery functions through optimized integration of ZnZrOxand Pd supported on carbon nanotube (Pd/CNT). The CNT in the Pd/CNT + ZnZrOxsystem delivers hydrogen activated on Pd to a broad area on the ZnZrOxsurface, with an enhancement factor of 10 compared to the conventional Pd-promoted ZnZrOxcatalyst, which only transfers hydrogen to Pd-adjacent sites. In CO2hydrogenation to methanol, Pd/CNT + ZnZrOxexhibits drastically boosted activity—the highest among reported ZnZrOx-based catalysts—and excellent stability over 600 h on stream test, showing potential for practical implementation.
Electroacupuncture improves swallowing function in a post-stroke dysphagia mouse model by activating the motor cortex inputs to the nucleus tractus solitarii through the parabrachial nuclei
Authors: Yao Lulu , Ye Qiuping , Liu Yun , Yao Shuqi , Yuan Si , Xu Qin , Deng Bing , Tang Xiaorong , Shi Jiahui , Luo Jianyu , Wu Junshang , Wu Zhennan , Liu Jianhua , Tang Chunzhi , Wang Lin , Xu Nenggui 
Published: February 2023

AbstractAs a traditional medical therapy, stimulation at the Lianquan (CV23) acupoint, located at the depression superior to the hyoid bone, has been shown to be beneficial in dysphagia. However, little is known about the neurological mechanism by which this peripheral stimulation approach treats for dysphagia. Here, we first identified a cluster of excitatory neurons in layer 5 (L5) of the primary motor cortex (M1) that can regulate swallowing function in male mice by modulating mylohyoid activity. Moreover, we found that focal ischemia in the M1 mimicked the post-stroke dysphagia (PSD) pathology, as indicated by impaired water consumption and electromyographic responses in the mylohyoid. This dysfunction could be rescued by electroacupuncture (EA) stimulation at the CV23 acupoint (EA-CV23) in a manner dependent on the excitatory neurons in the contralateral M1 L5. Furthermore, neuronal activation in both the parabrachial nuclei (PBN) and nucleus tractus solitarii (NTS), which was modulated by the M1, was required for the ability of EA-CV23 treatment to improve swallowing function in male PSD model mice. Together, these results uncover the importance of the M1-PBN-NTS neural circuit in driving the protective effect of EA-CV23 against swallowing dysfunction and thus reveal a potential strategy for dysphagia intervention.
Cross-protective antibodies against common endemic respiratory viruses
Authors: Cabán Madelyn , Rodarte Justas V. , Bibby Madeleine , Gray Matthew D. , Taylor Justin J. , Pancera Marie , Boonyaratanakornkit Jim 
Published: February 2023

AbstractRespiratory syncytial virus (RSV), human metapneumovirus (HMPV), and human parainfluenza virus types one (HPIV1) and three (HPIV3) can cause severe disease and death in immunocompromised patients, the elderly, and those with underlying lung disease. A protective monoclonal antibody exists for RSV, but clinical use is limited to high-risk infant populations. Hence, therapeutic options for these viruses in vulnerable patient populations are currently limited. Here, we present the discovery, in vitro characterization, and in vivo efficacy testing of two cross-neutralizing monoclonal antibodies, one targeting both HPIV3 and HPIV1 and the other targeting both RSV and HMPV. The 3 × 1 antibody is capable of targeting multiple parainfluenza viruses; the MxR antibody shares features with other previously reported monoclonal antibodies that are capable of neutralizing both RSV and HMPV. We obtained structures using cryo-electron microscopy of these antibodies in complex with their antigens at 3.62 Å resolution for 3 × 1 bound to HPIV3 and at 2.24 Å for MxR bound to RSV, providing a structural basis for in vitro binding and neutralization. Together, a cocktail of 3 × 1 and MxR could have clinical utility in providing broad protection against four of the respiratory viruses that cause significant morbidity and mortality in at-risk individuals.
Ultrarobust subzero healable materials enabled by polyphenol nano-assemblies
Authors: Wang Nan , Yang Xin , Zhang Xinxing 
Published: February 2023

AbstractBio-inspired self-healing materials hold great promise for applications in wearable electronics, artificial muscles and soft robots, etc. However, self-healing at subzero temperatures remains a great challenge because the reconstruction of interactions will experience resistance of the frozen segments. Here, we present an ultrarobust subzero healable glassy polymer by incorporating polyphenol nano-assemblies with a large number of end groups into polymerizable deep eutectic solvent elastomers. The combination of multiple dynamic bonds and rapid secondary relaxations with low activation energy barrier provides a promising method to overcome the limited self-healing ability of glassy polymers, which can rarely be achieved by conventional dynamic cross-linking. The resulted material exhibits remarkably improved adhesion force at low temperature (promotes 30 times), excellent mechanical properties (30.6 MPa) and desired subzero healing efficiencies (85.7% at −20 °C). We further demonstrated that the material also possesses reliable cryogenic strain-sensing and functional-healing ability. This work provides a viable approach to fabricate ultrarobust subzero healable glassy polymers that are applicable for winter sports wearable devices, subzero temperature-suitable robots and artificial muscles.
Illumination of a progressive allosteric mechanism mediating the glycine receptor activation
Authors: Shi Sophie , Lefebvre Solène N. , Peverini Laurie , Cerdan Adrien H. , Milán Rodríguez Paula , Gielen Marc , Changeux Jean-Pierre , Cecchini Marco , Corringer Pierre-Jean 
Published: February 2023

AbstractPentameric ligand-gated ion channel mediate signal transduction at chemical synapses by transiting between resting and open states upon neurotransmitter binding. Here, we investigate the gating mechanism of the glycine receptor fluorescently labeled at the extracellular-transmembrane interface by voltage-clamp fluorometry (VCF). Fluorescence reports a glycine-elicited conformational change that precedes pore opening. Low concentrations of glycine, partial agonists or specific mixtures of glycine and strychnine trigger the full fluorescence signal while weakly activating the channel. Molecular dynamic simulations of a partial agonist bound-closed Cryo-EM structure show a highly dynamic nature: a marked structural flexibility at both the extracellular-transmembrane interface and the orthosteric site, generating docking properties that recapitulate VCF data. This work illuminates a progressive propagating transition towards channel opening, highlighting structural plasticity within the mechanism of action of allosteric effectors.
Global ocean redox changes before and during the Toarcian Oceanic Anoxic Event
Authors: Kunert Alexandra , Kendall Brian 
Published: February 2023

AbstractMesozoic oceanic anoxic events are recognized as widespread deposits of marine organic-rich mudrocks temporally associated with mass extinctions and large igneous province emplacement. The Toarcian Oceanic Anoxic Event is one example during which expanded ocean anoxia is hypothesized in response to environmental perturbations associated with emplacement of the Karoo–Ferrar igneous province. However, the global extent of total seafloor anoxia and the relative extent of euxinic (anoxic and sulfide-rich) and non-euxinic anoxic conditions during the Toarcian Oceanic Anoxic Event are poorly constrained. Here we present estimates of the global total anoxic and euxinic seafloor areas before and during the Toarcian Oceanic Anoxic Event based on rhenium and molybdenum enrichments, respectively, in organic-rich mudrocks of the Fernie Formation (British Columbia, Canada). We find that mass balance models depict an expansion of up to ~7% total seafloor anoxia, which was dominated by euxinia, at the onset of the Toarcian Oceanic Anoxic Event, followed by a contraction before the end of the event. The global ocean redox trends revealed by the rhenium data mirrors the collapse and recovery patterns of global ammonite and foraminiferal biodiversity.
Reversible transformations between the non-porous phases of a flexible coordination network enabled by transient porosity
Authors: Nikolayenko Varvara I. , Castell Dominic C. , Sensharma Debobroto , Shivanna Mohana , Loots Leigh , Forrest Katherine A. , Solanilla-Salinas Carlos J. , Otake Ken-ichi , Kitagawa Susumu , Barbour Leonard J. , Space Brian , Zaworotko Michael J. 
Published: February 2023

AbstractFlexible metal–organic materials that exhibit stimulus-responsive switching between closed (non-porous) and open (porous) structures induced by gas molecules are of potential utility in gas storage and separation. Such behaviour is currently limited to a few dozen physisorbents that typically switch through a breathing mechanism requiring structural contortions. Here we show a clathrate (non-porous) coordination network that undergoes gas-induced switching between multiple non-porous phases through transient porosity, which involves the diffusion of guests between discrete voids through intra-network distortions. This material is synthesized as a clathrate phase with solvent-filled cavities; evacuation affords a single-crystal to single-crystal transformation to a phase with smaller cavities. At 298 K, carbon dioxide, acetylene, ethylene and ethane induce reversible switching between guest-free and gas-loaded clathrate phases. For carbon dioxide and acetylene at cryogenic temperatures, phases showing progressively higher loadings were observed and characterized using in situ X-ray diffraction, and the mechanism of diffusion was computationally elucidated.
A rapid realist review of universal interventions to promote inclusivity and acceptance of diverse sexual and gender identities in schools
Authors: Schlief Merle , Stefanidou Theodora , Wright Talen , Levy Grace , Pitman Alexandra , Lewis Gemma 
Published: February 2023

AbstractUniversal interventions to promote inclusivity and acceptance of diverse sexual and gender identities in schools could help to prevent mental health problems in this population. We reviewed evidence and developed programme theories to explain which universal interventions work, for whom, in which contexts and why. We conducted a rapid realist review and extracted data in context–mechanism–outcome configurations, to develop and refine programme theories. We included 53 sources and identified five intervention themes: student pride clubs, inclusive antibullying and harassment policies, inclusive curricula, workshops and staff training. Here, we show that these interventions could work by reducing discrimination, bullying and marginalization. Interventions appear to work best when school staff are trained and the school climate is supportive and may be less effective for boys, gender minority students and bisexual students. Our findings provide guiding principles for schools to develop interventions and should encourage primary research to confirm, refute or refine our programme theories.
Diagnostic, clustering, and immune cell infiltration analysis of m6A regulators in patients with sepsis
Authors: Li Fenghui , Zhang Yuan , Peng Zhiyun , Wang Yingjing , Zeng Zhaoshang , Tang Zhongxiang 
Published: February 2023

AbstractRNA N6-methladenosine (m6A) regulators are required for a variety of biological processes, including immune responses, and increasing evidence indicates that their dysregulation is closely associated with many diseases. However, the potential roles of m6A regulators in sepsis remain unknown. We comprehensively analyzed the transcriptional variations in and interactions of 26 m6A regulators in sepsis based on the Gene Expression Omnibus (GEO) database. A random forest (RF) model and nomogram were established to predict the occurrence and risk of sepsis in patients. Then, two different m6A subtypes were defined by consensus clustering analysis, and we explored the correlation between the subtypes and immune cells. We found that 17 of the 26 m6A regulators were significantly differentially expressed between patients with and without sepsis, and strong correlations among these 17 m6A regulators were revealed. Compared with the support vector machine (SVM) model, the RF model had better predictive ability, and therefore was used to construct a reliable nomogram containing 10 candidate m6A regulators to predict the risk of sepsis in patients. In addition, a consensus clustering algorithm was used to identify two different subtypes of m6A, which helped us distinguish different levels of immune cell infiltration and inflammation in patients with sepsis. Comprehensive analysis of m6A regulators in sepsis revealed their potential roles in sepsis occurrence, immune cell infiltration and inflammation in patients with sepsis. This study may contribute to the development of follow-up treatment strategies for sepsis.
A machine learning pipeline to classify foetal heart rate deceleration with optimal feature set
Authors: Das Sahana , Obaidullah Sk Md , Mahmud Mufti , Kaiser M. Shamim , Roy Kaushik , Saha Chanchal Kumar , Goswami Kaushik 
Published: February 2023

AbstractDeceleration is considered a commonly practised means to assess Foetal Heart Rate (FHR) through visual inspection and interpretation of patterns in Cardiotocography (CTG). The precision of deceleration classification relies on the accurate estimation of corresponding event points (EP) from the FHR and the Uterine Contraction Pressure (UCP). This work proposes a deceleration classification pipeline by comparing four machine learning (ML) models, namely, Multilayer Perceptron (MLP), Random Forest (RF), Naïve Bayes (NB), and Simple Logistics Regression. Towards an automated classification of deceleration from EP using the pipeline, it systematically compares three approaches to create feature sets from the detected EP: (1) a novel fuzzy logic (FL)-based approach, (2) expert annotation by clinicians, and (3) calculated using National Institute of Child Health and Human Development guidelines. The classification results were validated using different popular statistical metrics, including receiver operating characteristic curve, intra-class correlation coefficient, Deming regression, and Bland-Altman Plot. The highest classification accuracy (97.94%) was obtained with MLP when the EP was annotated with the proposed FL approach compared to RF, which obtained 63.92% with the clinician-annotated EP. The results indicate that the FL annotated feature set is the optimal one for classifying deceleration from FHR.
Automatic measurement and prediction of Chinese Grown Pigs weight using multilayer perceptron neural networks
Authors: Ositanwosu Obiajulu Emenike , Huang Qiong , Liang Yun , Nwokoye Chukwunonso H. 
Published: February 2023

AbstractThe knowledge of body size/weight is necessary for the general growth enhancement of swine as well as for making informed decisions that concern their health, productivity, and yield. Therefore, this work aims to automate the collection of pigs’ body parameters using images from Kinect V2 cameras, and the development of Multilayer Perceptron Neural Network (MLP NN) models to predict their weight. The dataset obtained using 3D light depth cameras contains 9980 pigs across the S21 and S23 breeds, and then grouped into 70:15:15 training, testing, and validation sets, respectively. Initially, two MLP models were built and evaluations revealed that model 1 outperformed model 2 in predicting pig weights, with root mean squared error (RMSE) values of 5.5 and 6.0 respectively. Moreover, employing a normalized dataset, two new models (3 and 4) were developed and trained. Subsequently, models 2, 3, and 4 performed significantly better with a RMSE value of 5.29 compared to model 1, which has a RMSE value of 6.95. Model 3 produced an intriguing discovery i.e. accurate forecasting of pig weights using just two characteristics, age and abdominal circumference, and other error values show corresponding results
Evolution of fissures and pressure discharge of gas caused by mining of the upper protective layer of a coal seam
Authors: Xie Honggao , Li Xijian , Cai Junjie , Wang Shengwei , Feng Cong 
Published: February 2023

AbstractThe evolution of fissures and permeability associated with mining of the upper protective layer of the coal seam is crucial for pressure relief gas drainage of the underlying seam. To understand the influence of mining the upper protective layer on gas drainage within the underlying coal seam, this study utilized the M16 and M18 seams in the Qinglong Coal Mine in Guizhou. Theoretical analysis, discrete element numerical simulation, and field tests were used to characterize the evolution of fractures associated with mining of the upper protective layer and the effects of pressure relief gas drainage within the protected coal seam. The results show that mining-related stress changes controlled the development of fractures, altering the permeability values of coals. An analysis of the crack development in the coal mass caused by mining of the upper protective layer shows that during the initial stage of mining, the produced cracks exhibited a butterfly shape network. Yet, with further development of the mining, these cracks and the stress changes gradually produced an inverted butterfly shape network. According to simulations, the areas of maximum deformation via expansion in the protected coal seam were located near the open cut and the mining end line of the working face. The maximum deformation values were 29.06 and 26.68 mm, respectively, and the corresponding deformation rates were 9.37‰ and 8.61‰, which are greater than the required 3‰. The findings of this study provide a new reference for gas control in pressure relief coal seams under similar working conditions.
Wheat husk-based sorbent as an economical solution for removal of oil spills from sea water
Authors: Omar Basma M. , Abdelgalil Soad A. , Fakhry Hala , Tamer Tamer M. , El-Sonbati Mervat A. 
Published: February 2023

AbstractOil spills are a significant threat to the marine ecosystem that requires immediate removal from the oceanic environment. Many technologies have been employed to clean up oil spills. Of these, adsorption has scored a prominent success due to the high efficiency, economic viability, environmental friendship, and ease of application. The utilization of agricultural waste to produce biosorbents have been considered as an ecofriendly and efficient approach for removing oil. Thus, a new low-cost oil adsorbent was prepared via esterification of the wheat straw (Str) with a hydrophobic benzoyl group, the resulting copolymer (Str-co-Benz) was characterized by FTIR, TGA, DSC, and SEM and used at laboratory scale. The oil spill cleanup process was conducted using a crude oil-natural seawater system under different adsorption conditions such as oil concentration, adsorbent dose, agitation time and speed. Equilibrium studies were performed to determine the capacity of the prepared materials for crude oil adsorption. Langmuir and Freundlich adsorption models were used to describe the experimental isotherms. The reliability of the data was examined and evaluated via application of response surface methodology program. The results showed that oil adsorption followed a pseudo-second-order kinetic model and fitted well with Langmuir model with a maximum adsorption capacity of 10.989 and 12.786 g/g for Str and (Str-co-Benz), respectively. Overall, the modified wheat husk is an effective platform for removing oil from marine ecosystems due to low cost, biodegradability, simple synthesis and fast removal. Moreover, the resulted solid can be used as a fuel in some industrial processes such as steam boilers and brick production incinerators.