bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study of the effect of crack distribution on the failure mechanism of sandstone specimens based on inclination angles and number of parallel flaws
Authors: Pang Jiewen , He Yongliang , Han Qiaoyun , Ba Deyang , Sun Xiaoyuan
Published: March 2024

Discontinuous joints are prevalent in engineered rock masses and play a significant role in the stability of the rock mass. This study aims to analyze the impact of the inclination angle and number of prefabricated flaws on the crack evolution and failure pattern of sandstone specimens. Uniaxial compression tests, along with acoustic emission technology and digital image technology, were employed to monitor and analyze the effects. The findings indicate that: (1) With the increase in the flaw inclination angle, the damage mode of the specimen transitions from tensile to compressive-shear failure. The localized high-strain region on the surface of the specimen predicts the propagation path for the formation of macroscopic cracks. (2) When the number of prefabricated flaws is small, the flaws mainly expand through tensile wing cracks. As the number of flaws increases, the inner flaw tip does not produce cracks. Instead, the failure of the entire specimen occurs along the direction of the outer flaw's tensile wing crack, with the inner flaw running through it. (3) The winged tensile crack is the first crack to appear in all rock samples, regardless of the flaw initiation angles. Finally, the stress intensity factor at the crack tip under uniaxial compression conditions, without considering the closure effect, was expressed based on fracture mechanics theory. The crack initiation angle was then calculated. The results of the theoretical calculation of the initiation angle were found to be consistent with the test results. These research findings can serve as theoretical references and provide insights into the failure mechanisms of cracked rocks and the development of disaster control methods in rock engineering.
Heterogeneity and agency in the contemporary food regime in Switzerland: among the food from nowhere, somewhere, and here sub-regimes
Authors: Stotten Rike
Published: March 2024

This study empirically illuminates the contemporary food regime in Switzerland to understand the organisation of food production, distribution, and consumption. From the perspective of food regime theory, it highlights in detail the (inter)relationships in the food regime between the food from nowhere, somewhere, and here sub-regimes using empirical means. Heterogeneous structures, processes, and relations that coexist within an umbrella food regime are examined. To address the criticisms of food regime theory ignoring social agency, this study further reveals collective agency and addresses the role of alternative food systems within the food regime in Switzerland. In-depth document analysis and subsequent qualitative data collection relying on expert interviews were performed. This study illustrates the collective agency shaping the contemporary food regime in Switzerland, encompassing private companies, relevant media, as well as associations and unions involved in farming, processing, and consumption. These influential entities and actor-networks advance different sub-regimes of food from nowhere, somewhere, and here that reflect the heterogeneity of the contemporary food regime in Switzerland. However, the data did not provide sufficient information to determine the collective agency of actors within the alternative food system. The dynamics of the food regime are shaped by contested social practices, which are influenced and interpreted through social agency. This results in an overlap of the sub-regimes that has led to strong counter-movements within the contemporary food regime in Switzerland.
Contrasting Regulation of Phaseolus vulgaris Root Hydraulic Properties Under Drought and Saline Conditions by Three Arbuscular Mycorrhizal Fungal Species From Soils with Divergent Moisture Regime
Authors: Erice Gorka , Cano Custodia , Bago Alberto , Ruíz-Lozano Juan Manuel , Aroca Ricardo
Published: March 2024

Purpose

Arbuscular mycorrhizal fungi (AMF) may help plants to overcome abiotic stresses, in part by improving their water uptake capacity. However how different AMF isolated from different climatic regions regulate plant abiotic stress tolerance and water uptake capacity is barely studied. The aim of this study was to reveal how three AMF isolated from two Mediterranean climate locations contrasting in annual precipitation, modify bean (Phaseolus vulgaris L.) root hydraulic properties facing drought and salinity.

Methods

Rhizophagus intraradices (Ri) and Funneliformis mosseae (Fm) were isolated from a humid area, whereas Claroideoglomus etunicatum (Ce) was isolated from a dry location. All plants (inoculated or not) were subjected to four days of withholding water or salt treatment. Root hydraulic properties including root hydraulic conductivity and aquaporin expression and abundance were determined.

Results

All three AMF isolate induced significant differences in plant physiology regardless their different mycorrhizal colonization extent. Drought treatment diminished root hydraulic conductivity and only Fm inoculated plants featured measurable amount of sap exudate. After salt irrigation, AMF inoculation counterbalanced the drop of root hydraulic conductivity. In such situation two AMF, Fm and Ce, presented lowered phosphorylated (Ser-283) PIP2 AQP amount. AQP gene expression highlighted the importance of PvPIP1;2 and PvPIP2;3 plasticity in plants facing osmotic stress. After drought treatment AMF species from the humid location, Ri and Fm, improved plant water status and Fm enhanced root hydraulic conductivity, whereas all AMF performed similarly after salt irrigation, enhancing stomatal conductance and root hydraulic conductivity.

Conclusion

Under drought conditions, the AMF isolates from humid regions were the ones that most effectively improved plant water relations. However, under salt stress, all three AMF isolates exhibited similar behavior. Therefore, to some extent, the climatic origin of the AMF could have influenced the response of host plants to drought stress, suggesting that those originating from dry areas may not necessarily be the most efficient.
The ethical wisdom of AI developers
Authors: Griffin Tricia A. , Green Brian P. , Welie Jos V.M.
Published: March 2024

This paper explores ethical wisdom in the artificial intelligence (AI) developer community. Despite robust literature about the need for virtue ethics approaches in AI development, little research has directly engaged with the developer community about their progress in this regard. We have thus conducted semi-structured interviews with a worldwide cohort of 40 developers, which focused on their awareness of ethics issues, how they navigate ethical challenges, and the barriers they encounter in developing ethical wisdom. We find developers are largely aware of the ethical territories they must navigate and the moral dilemmas they personally encounter, but they face limited and inconsistent resources for ethical guidance or training. Furthermore, there are significant barriers inhibiting the development of ethical wisdom in the AI developer community, including the industry’s fixation on innovation, the narrow scope of technical practice, limited provisions for reflection and dialogue, and incentive structures that prioritize profits and prestige. The paper concludes by emphasizing the need to address the gap in domain-specific ethical skill and provides recommendations for organizations, educators, and the AI developer community.
Genome-wide analysis of the PME gene family reveals its role in suppressing fruit lignification in pear
Authors: Zhang Fanhang , Wang Qi , Yuan Kaili , Xie Zhihua , Qi Kaijie , Li Wen , Gong Xin , Zhang Shaoling , Tao Shutian
Published: March 2024

In pears, the presence of stone cells adversely affects fruit quality. Pectin methylesterase (PME) plays various roles in plant biology, including lignin biosynthesis. However, only a limited fraction has been functionally characterized, and the distribution and function of PME in many Rosaceae trees remain unexplored. In this study, we identified 396 putative PME family candidate genes, with 81 in Pyrus bretschneideri, 92 in Malus domestica, 62 in Fragaria vesca, 65 in Prunus mume, 15 in Pyrus communis, and 81 in Pyrus pyrifolia. Leveraging insights from model plants, we categorized PME family genes into four groups. Additionally, the evolution of the PME gene family was shaped by various gene duplication events, primarily dispersed duplication, influenced by purifying selection. A specific gene, Pbr031522.1, designated PbPME35, emerged as a candidate associated with lignin biosynthesis in pear fruits, supported by RNA-seq data. The role of PbPME35 in repressing lignification was validated through its overexpression in pear callus and Arabidopsis. Overall, our findings highlight the ability of PbPME35 to reduce lignin content in pear fruit by downregulating the expression levels of lignin biosynthesis genes. These findings provide new insights into the characteristics of PME genes and their role in regulating lignification in pear fruits.
A study on the interpretation and application of the ‘International Concern Provisions’ of Chinese Coast Guard Law
Authors: Cui Haoran
Published: March 2024

The Chinese Coast Guard Law was adopted and came into force in 2021. This has prompted discussion in the wider international community. This paper first interprets the ‘International Concern Provisions’, including ‘areas under the jurisdiction of China’, ‘forcible measures against illegal acts of foreign warships and government vessels’, and ‘the nature of coast guard agency’. The concept of those waters under Chinese jurisdiction denotes the scope of maritime rights as authorized by the United Nations Convention on the Law of the Sea and the waters it claims by historical precedent. It is concluded that the Chinese Coast Guard has the right to use weapons according to domestic law, but it should still align with international law and customs when taking forcible measures against any illegal acts committed by foreign warships or government vessels. The main duties of the Chinese Coast Guard are to protect maritime rights and enforce the law. The Chinese Coast Guard agency has the dual attributes of being part of the national armed forces and a law enforcement authority. China should improve the concept of ‘maritime rights protection and law enforcement’, promote the connection between the Chinese Coast Guard Law and other maritime domestic laws, and strive for better understanding and recognition in the international community while safeguarding extant maritime rights and interests.
Revolution, War, and Cholera in 1848–49: The Case of Hungary
Authors: Fazekas Csaba
Published: March 2024

This paper investigates the events and lessons from the 1848–49 cholera epidemic in Hungary. For contemporaries, the ongoing revolution and civil war pushed the devastation of the cholera epidemic into the background, even though the death rate was similar to that of the earlier 1831 infection. The epidemic hit the country in a period when the revolutionary Hungarian state was waging a war of self-defense. This article strives to refute the historiographic view that the movements of the different armies had a considerable influence on the development of the epidemic. Instead, this article argues that the cholera epidemic was a demographic crisis unfolding in the background of war, but for the most part independently of it. It mattered that most people of that time had already directly experienced cholera and that the Hungarian government did not want to cause panic with restrictive measures. In 1848, cholera was not a “mobilizing factor,” but in 1849 it contributed to the demoralization of the hinterland and frequently appeared in the political propaganda of the civil war.
Thiamine deficiency as a cause of anorexia in terminally ill cancer patients: A case of possible gastrointestinal beriberi
Authors: Hayashi Eriko , Matuura Tetsuya , Takano Junko , Morofushi Kaori , Toriizuka Kaori , Onishi Hideki
Published: March 2024

Objectives

Anorexia in cancer patients has a variety of causes and impairs patients’ quality of life. However, there have been few reports of thiamine deficiency (TD) playing a role in anorexia during palliative care. The objective of this report was to describe such a case.

Methods

An 82-year-old woman with advanced cervical cancer was admitted for palliative care because of progressive disease. One month after admission, she developed myoclonus on the left side, difficulty speaking, slurred speech, and drooping of the left corner of the mouth, with no consciousness disturbance. She also developed nausea and complained of decreased dietary intake for more than 2 weeks.

Results

The patient’s thiamine level, which had been measured 2 weeks earlier, was 27 ng/ml, which was below the normal range, and 100 mg of thiamine was administered intravenously. After 2 hours, the patient’s neurological findings resolved, and her dietary intake improved from 30% to 40% of meals to 90% to 100%. Subsequently, the patient did not experience similar symptoms, and her clinical course was stable. Based on the patient’s clinical course, gastrointestinal beriberi was diagnosed.

Significance of results

This case shows that TD may cause anorexia. Many patients who receive palliative care have decreased dietary intake. Consequently, such patients may present with gastrointestinal beriberi, as in the present case. Appropriate diagnosis and treatment may contribute to increasing such patients’ quality of life. It may be necessary to differentiate TD from other conditions as a cause of anorexia in patients receiving palliative care.
Snowfall Replenishes Groundwater Loss in the Great Basin of the Western United States, but Cannot Compensate for Increasing Aridification
Authors: Hall Dorothy K. , Loomis Bryant D. , DiGirolamo Nicolo E. , Forman Barton A.
Published: March 2024

There has been an acceleration of groundwater loss in the Great Basin (GB) of the western U.S. as determined from total water storage (TWS) measurements from the GRACE/FO satellite missions. From 2002 to 2023, there was a loss of TWS in the GB of ∼68.7 km3 which is more than six times the current volume of the Lake Mead Reservoir. In this arid/semi‐arid region, groundwater is the primary factor contributing to the decade‐scale decline in TWS. Stronger declining trends are found in the western versus the eastern GB. Snow loading is the major cause of seasonal fluctuations of TWS in the GB. Despite annual replenishment of groundwater by snow, the downward trend persists even in notable snow years. Likely causes include declining snow mass, upstream water diversions and increased evaporation/sublimation due to increasing temperatures. Dire consequences for humans and wildlife are associated with this large loss of groundwater.
A Framework for Evaluating Geomagnetic Indices Forecasting Models
Authors: Collado‐Villaverde Armando , Muñoz Pablo , Cid Consuelo
Published: March 2024

The use of Deep Learning models to forecast geomagnetic storms is achieving great results. However, the evaluation of these models is mainly supported on generic regression metrics (such as the Root Mean Squared Error or the Coefficient of Determination), which are not able to properly capture the specific particularities of geomagnetic storms forecasting. Particularly, they do not provide insights during the high activity periods. To overcome this issue, we introduce the Binned Forecasting Error to provide a more accurate assessment of models' performance across the different intensity levels of a geomagnetic storm. This metric facilitates a robust comparison of different forecasting models, presenting a true representation of a model's predictive capabilities while being resilient to different storms duration. In this direction, for enabling fair comparison among models, it is important to standardize the sets of geomagnetic storms for model training, validation and testing. To do this, we have started from the current sets used in the literature for forecasting the SYM‐H, enriching them with newer storms not considered previously, focusing not only on disturbances caused by Coronal Mass Ejections but also addressing High‐Speed Streams. To operationalize the evaluation framework, a comparative study is conducted between a baseline neural network model and a persistence model, showcasing the effectiveness of the new metric in evaluating forecasting performance during intense geomagnetic storms. Finally, we propose the use of preliminary measurements from ACE to evaluate the model performance in settings closer to an operational real‐time scenario, where the forecasting models are expected to operate.
METTL3-dependent m6A modification of PSEN1 mRNA regulates craniofacial development through the Wnt/β-catenin signaling pathway
Authors: Ma Lan , Zhou Xi , Yao Siyue , Zhang Xinyu , Mao Ji , Vona Barbara , Fan Liwen , Lou Shu , Li Dandan , Wang Lin , Pan Yongchu
Published: March 2024

Craniofacial malformations, often associated with syndromes, are prevalent birth defects. Emerging evidence underscores the importance of m6A modifications in various bioprocesses such as stem cell differentiation, tissue development, and tumorigenesis. Here, in vivo, experiments with zebrafish models revealed that mettl3-knockdown embryos at 144 h postfertilization exhibited aberrant craniofacial features, including altered mouth opening, jaw dimensions, ethmoid plate, tooth formation and hypoactive behavior. Similarly, low METTL3 expression inhibited the proliferation and migration of BMSCs, HEPM cells, and DPSCs. Loss of METTL3 led to reduced mRNA m6A methylation and PSEN1 expression, impacting craniofacial phenotypes. Co-injection of mettl3 or psen1 mRNA rescued the level of Sox10 fusion protein, promoted voluntary movement, and mitigated abnormal craniofacial phenotypes induced by mettl3 knockdown in zebrafish. Mechanistically, YTHDF1 enhanced the mRNA stability of m6A-modified PSEN1, while decreased METTL3-mediated m6A methylation hindered β-catenin binding to PSEN1, suppressing Wnt/β-catenin signaling. Pharmacological activation of the Wnt/β-catenin pathway partially alleviated the phenotypes of mettl3 morphant and reversed the decreases in cell proliferation and migration induced by METTL3 silencing. This study elucidates the pivotal role of METTL3 in craniofacial development via the METTL3/YTHDF1/PSEN1/β-catenin signaling axis.
Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE
Authors: Portela Pilar C. , Shipps Catharine C. , Shen Cong , Srikanth Vishok , Salgueiro Carlos A. , Malvankar Nikhil S.
Published: March 2024

Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s−1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s−1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner
Authors: ElBeck Zaher , Hossain Mohammad Bakhtiar , Siga Humam , Oskolkov Nikolay , Karlsson Fredrik , Lindgren Julia , Walentinsson Anna , Koppenhöfer Dominique , Jarvis Rebecca , Bürli Roland , Jamier Tanguy , Franssen Elske , Firth Mike , Degasperi Andrea , Bendtsen Claus , Menzies Robert I. , Streckfuss-Bömeke Katrin , Kohlhaas Michael , Nickel Alexander G. , Lund Lars H. , Maack Christoph , Végvári Ákos , Betsholtz Christer
Published: March 2024

While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.
Mapping human tissues with highly multiplexed RNA in situ hybridization
Authors: Kalhor Kian , Chen Chien-Ju , Lee Ho Suk , Cai Matthew , Nafisi Mahsa , Que Richard , Palmer Carter R. , Yuan Yixu , Zhang Yida , Li Xuwen , Song Jinghui , Knoten Amanda , Lake Blue B. , Gaut Joseph P. , Keene C. Dirk , Lein Ed , Kharchenko Peter V. , Chun Jerold , Jain Sanjay , Fan Jian-Bing , Zhang Kun
Published: March 2024

In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
Balancing competing effects of tissue growth and cytoskeletal regulation during Drosophila wing disc development
Authors: Kumar Nilay , Rangel Ambriz Jennifer , Tsai Kevin , Mim Mayesha Sahir , Flores-Flores Marycruz , Chen Weitao , Zartman Jeremiah J. , Alber Mark
Published: March 2024

How a developing organ robustly coordinates the cellular mechanics and growth to reach a final size and shape remains poorly understood. Through iterations between experiments and model simulations that include a mechanistic description of interkinetic nuclear migration, we show that the local curvature, height, and nuclear positioning of cells in the Drosophila wing imaginal disc are defined by the concurrent patterning of actomyosin contractility, cell-ECM adhesion, ECM stiffness, and interfacial membrane tension. We show that increasing cell proliferation via different growth-promoting pathways results in two distinct phenotypes. Triggering proliferation through insulin signaling increases basal curvature, but an increase in growth through Dpp signaling and Myc causes tissue flattening. These distinct phenotypic outcomes arise from differences in how each growth pathway regulates the cellular cytoskeleton, including contractility and cell-ECM adhesion. The coupled regulation of proliferation and cytoskeletal regulators is a general strategy to meet the multiple context-dependent criteria defining tissue morphogenesis.
Extended stop codon context predicts nonsense codon readthrough efficiency in human cells
Authors: Mangkalaphiban Kotchaphorn , Fu Lianwu , Du Ming , Thrasher Kari , Keeling Kim M. , Bedwell David M. , Jacobson Allan
Published: March 2024

Protein synthesis terminates when a stop codon enters the ribosome’s A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. Seeking to understand readthrough regulation we used a machine learning approach to analyze readthrough efficiency data from published HEK293T ribosome profiling experiments and compared it to comparable yeast experiments. We obtained evidence for the conservation of identities of the stop codon, its context, and 3’-UTR length (when termination is compromised), but not the P-site codon, suggesting a P-site tRNA role in readthrough regulation. Models trained on data from cells treated with the readthrough-promoting drug, G418, accurately predicted readthrough of premature termination codons arising from CFTR nonsense alleles that cause cystic fibrosis. This predictive ability has the potential to aid development of nonsense suppression therapies by predicting a patient’s likelihood of improvement in response to drugs given their nonsense mutation sequence context.
Structure of an open KATP channel reveals tandem PIP2 binding sites mediating the Kir6.2 and SUR1 regulatory interface
Authors: Driggers Camden M. , Kuo Yi-Ying , Zhu Phillip , ElSheikh Assmaa , Shyng Show-Ling
Published: March 2024

ATP-sensitive potassium (KATP) channels, composed of four pore-lining Kir6.2 subunits and four regulatory sulfonylurea receptor 1 (SUR1) subunits, control insulin secretion in pancreatic β-cells. KATP channel opening is stimulated by PIP2 and inhibited by ATP. Mutations that increase channel opening by PIP2 reduce ATP inhibition and cause neonatal diabetes. Although considerable evidence has implicated a role for PIP2 in KATP channel function, previously solved open-channel structures have lacked bound PIP2, and mechanisms by which PIP2 regulates KATP channels remain unresolved. Here, we report the cryoEM structure of a KATP channel harboring the neonatal diabetes mutation Kir6.2-Q52R, in the open conformation, bound to amphipathic molecules consistent with natural C18:0/C20:4 long-chain PI(4,5)P2 at two adjacent binding sites between SUR1 and Kir6.2. The canonical PIP2 binding site is conserved among PIP2-gated Kir channels. The non-canonical PIP2 binding site forms at the interface of Kir6.2 and SUR1. Functional studies demonstrate both binding sites determine channel activity. Kir6.2 pore opening is associated with a twist of the Kir6.2 cytoplasmic domain and a rotation of the N-terminal transmembrane domain of SUR1, which widens the inhibitory ATP binding pocket to disfavor ATP binding. The open conformation is particularly stabilized by the Kir6.2-Q52R residue through cation-π bonding with SUR1-W51. Together, these results uncover the cooperation between SUR1 and Kir6.2 in PIP2 binding and gating, explain the antagonistic regulation of KATP channels by PIP2 and ATP, and provide a putative mechanism by which Kir6.2-Q52R stabilizes an open channel to cause neonatal diabetes.
One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes
Authors: Ye Zilu , Sabatier Pierre , Martin-Gonzalez Javier , Eguchi Akihiro , Lechner Maico , Østergaard Ole , Xie Jingsheng , Guo Yuan , Schultz Lesley , Truffer Rafaela , Bekker-Jensen Dorte B. , Bache Nicolai , Olsen Jesper V.
Published: March 2024

Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamlessly integrates efficient, one-pot sample preparation with precise, narrow-window data-independent acquisition (nDIA) analysis. One-Tip substantially simplifies sample processing, enabling the reproducible identification of >9000 proteins from ~1000 HeLa cells. The versatility of One-Tip is highlighted by nDIA identification of ~6000 proteins in single cells from early mouse embryos. Additionally, the study incorporates the Uno Single Cell Dispenser™, demonstrating the capability of One-Tip in single-cell proteomics with >3000 proteins identified per HeLa cell. We also extend One-Tip workflow to analysis of extracellular vesicles (EVs) extracted from blood plasma, demonstrating its high sensitivity by identifying >3000 proteins from 16 ng EV preparation. One-Tip expands capabilities of proteomics, offering greater depth and throughput across a range of sample types.
Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer
Authors: Bulle Ashenafi , Liu Peng , Seehra Kuljeet , Bansod Sapana , Chen Yali , Zahra Kiran , Somani Vikas , Khawar Iftikhar Ali , Chen Hung-Po , Dodhiawala Paarth B. , Li Lin , Geng Yutong , Mo Chia-Kuei , Mahsl Jay , Ding Li , Govindan Ramaswamy , Davies Sherri , Mudd Jacqueline , Hawkins William G. , Fields Ryan C. , DeNardo David G. , Knoerzer Deborah , Held Jason M. , Grierson Patrick M. , Wang-Gillam Andrea , Ruzinova Marianna B. , Lim Kian-Huat
Published: March 2024

Targeting the mitogen-activated protein kinase (MAPK) cascade in pancreatic ductal adenocarcinoma (PDAC) remains clinically unsuccessful. We aim to develop a MAPK inhibitor-based therapeutic combination with strong preclinical efficacy. Utilizing a reverse-phase protein array, we observe rapid phospho-activation of human epidermal growth factor receptor 2 (HER2) in PDAC cells upon pharmacological MAPK inhibition. Mechanistically, MAPK inhibitors lead to swift proteasomal degradation of dual-specificity phosphatase 6 (DUSP6). The carboxy terminus of HER2, containing a TEY motif also present in extracellular signal-regulated kinase 1/2 (ERK1/2), facilitates binding with DUSP6, enhancing its phosphatase activity to dephosphorylate HER2. In the presence of MAPK inhibitors, DUSP6 dissociates from the protective effect of the RING E3 ligase tripartite motif containing 21, resulting in its degradation. In PDAC patient-derived xenograft (PDX) models, combining ERK and HER inhibitors slows tumour growth and requires cytotoxic chemotherapy to achieve tumour regression. Alternatively, MAPK inhibitors with trastuzumab deruxtecan, an anti-HER2 antibody conjugated with cytotoxic chemotherapy, lead to sustained tumour regression in most tested PDXs without causing noticeable toxicity. Additionally, KRAS inhibitors also activate HER2, supporting testing the combination of KRAS inhibitors and trastuzumab deruxtecan in PDAC. This study identifies a rational and promising therapeutic combination for clinical testing in PDAC patients.
The evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba
Authors: Ding Qi , Guo Nianxin , Gao Lei , McKee Michelle , Wu Dongshan , Yang Jun , Fan Junping , Weng Jing-Ke , Lei Xiaoguang
Published: March 2024

Biosynthetic enzymes evolutionarily gain novel functions, thereby expanding the structural diversity of natural products to the benefit of host organisms. Diels-Alderases (DAs), functionally unique enzymes catalysing [4 + 2] cycloaddition reactions, have received considerable research interest. However, their evolutionary mechanisms remain obscure. Here, we investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites. Our findings suggest that these DAs have evolved from an ancestor functioning as a flavin adenine dinucleotide (FAD)-dependent oxidocyclase (OC), which catalyses the oxidative cyclisation reactions of isoprenoid-substituted phenolic compounds. Through crystal structure determination, computational calculations, and site-directed mutagenesis experiments, we identified several critical substitutions, including S348L, A357L, D389E and H418R that alter the substrate-binding mode and enable the OCs to gain intermolecular DA activity during evolution. This work provides mechanistic insights into the evolutionary rationale of DAs and paves the way for mining and engineering new DAs from other protein families.
Higher-order Granger reservoir computing: simultaneously achieving scalable complex structures inference and accurate dynamics prediction
Authors: Li Xin , Zhu Qunxi , Zhao Chengli , Duan Xiaojun , Zhao Bolin , Zhang Xue , Ma Huanfei , Sun Jie , Lin Wei
Published: March 2024

Recently, machine learning methods, including reservoir computing (RC), have been tremendously successful in predicting complex dynamics in many fields. However, a present challenge lies in pushing for the limit of prediction accuracy while maintaining the low complexity of the model. Here, we design a data-driven, model-free framework named higher-order Granger reservoir computing (HoGRC), which owns two major missions: The first is to infer the higher-order structures incorporating the idea of Granger causality with the RC, and, simultaneously, the second is to realize multi-step prediction by feeding the time series and the inferred higher-order information into HoGRC. We demonstrate the efficacy and robustness of the HoGRC using several representative systems, including the classical chaotic systems, the network dynamical systems, and the UK power grid system. In the era of machine learning and complex systems, we anticipate a broad application of the HoGRC framework in structure inference and dynamics prediction.
Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Authors: Fang Chao , Jiang Ning , Teresi Scott J. , Platts Adrian E. , Agarwal Gaurav , Niederhuth Chad , Edger Patrick P. , Jiang Jiming
Published: March 2024

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape
Authors: Lozovska Anastasiia , Korovesi Artemis G. , Dias André , Lopes Alexandre , Fowler Donald A. , Martins Gabriel G. , Nóvoa Ana , Mallo Moisés
Published: March 2024

The hindlimb and external genitalia of present-day tetrapods are thought to derive from an ancestral common primordium that evolved to generate a wide diversity of structures adapted for efficient locomotion and mating in the ecological niche occupied by the species. We show that despite long evolutionary distance from the ancestral condition, the early primordium of the mouse external genitalia preserved the capacity to take hindlimb fates. In the absence of Tgfbr1, the pericloacal mesoderm generates an extra pair of hindlimbs at the expense of the external genitalia. It has been shown that the hindlimb and the genital primordia share many of their key regulatory factors. Tgfbr1 controls the response to those factors by modulating the accessibility status of regulatory elements that control the gene regulatory networks leading to the formation of genital or hindlimb structures. Our work uncovers a remarkable tissue plasticity with potential implications in the evolution of the hindlimb/genital area of tetrapods, and identifies an additional mechanism for Tgfbr1 activity that might also contribute to the control of other physiological or pathological processes.
Micro-consolidation occurs when learning an implicit motor sequence, but is not influenced by HIIT exercise
Authors: Brooks Emily , Wallis Sarah , Hendrikse Joshua , Coxon James
Published: March 2024

We investigated if micro-consolidation, a phenomenon recently discovered during the brief rest periods between practice when learning an explicit motor sequence, generalises to learning an implicit motor sequence task. We demonstrate micro-consolidation occurs in the absence of explicit sequence awareness. We also investigated the effect of a preceding bout of high-intensity exercise, as exercise is known to augment the consolidation of new motor skills. Micro-consolidation was not modified by exercise.
Characteristics of germline DNA damage response gene mutations in ovarian cancer in Southwest China
Authors: Fu Kaiyu , Li Qingli , Wang Jie , Zhang Mengpei , Yan Xinyu , Li Kemin , Song Liang , Zhong Lan , Ma Yu , Chen Jinghong , Zeng Jing , Wang Danqing , Shao Di , Zhu Shida , Yin Rutie
Published: March 2024

DNA damage response (DDR) pathways are responsible for repairing endogenous or exogenous DNA damage to maintain the stability of the cellular genome, including homologous recombination repair (HRR) pathway, mismatch repair (MMR) pathway, etc. In ovarian cancer, current studies are focused on HRR genes, especially BRCA1/2, and the results show regional and population differences. To characterize germline mutations in DDR genes in ovarian cancer in Southwest China, 432 unselected ovarian cancer patients underwent multi-gene panel testing from October 2016 to October 2020. Overall, deleterious germline mutations in DDR genes were detected in 346 patients (80.1%), and in BRCA1/2 were detected in 126 patients (29.2%). The prevalence of deleterious germline mutations in BRCA2 is higher than in other studies (patients are mainly from Eastern China), and so is the mismatch repair genes. We identified three novel BRCA1/2 mutations, two of which probably deleterious (BRCA1 p.K1622* and BRCA2 p.L2987P). Furthermore, we pointed out that deleterious mutations of FNACD2 and RECQL4 are potential ovarian cancer susceptibility genes and may predispose carriers to ovarian cancer. In conclusion, our study highlights the necessity of comprehensive germline mutation detection of DNA damage response genes in ovarian cancer patients, which is conducive to patient management and genetic counseling.
Limited increases in Arctic offshore oil and gas production with climate change and the implications for energy markets
Authors: Zhang Ying , Msangi Siwa , Edmonds James , Waldhoff Stephanie
Published: March 2024

Climate change impacts on sea ice thickness is opening access to offshore Arctic resources. The degree to which these resources are exploited will depend on sea-ice conditions, technology costs, international energy markets, and the regulatory environment. We use an integrated human-Earth system model, GCAM, to explore the effects of spatial–temporal patterns of sea-ice loss under climate change on future Arctic offshore oil and gas extraction, considering interactions with global energy markets and emission reduction scenarios. We find that under SSP5, a “fossil-fueled development” scenario, the effects of sea-ice loss are larger for Arctic offshore oil production than gas. Under SSP5, future extraction of Arctic offshore oil and gas through 2100 adds roughly 0.8–2.6 EJ/year to oil and gas markets but does not have large impacts on global oil and gas markets. Surprisingly, a low-carbon scenario results in greater Arctic offshore oil production to offset the more emissions-intensive unconventional oil production.
Binocular rivalry reveals differential face processing in congenital prosopagnosia
Authors: Halder Theresa , Ludwig Karin , Schenk Thomas
Published: March 2024

Congenital Prosopagnosia (CP) is an innate impairment in face perception with heterogeneous characteristics. It is still unclear if and to what degree holistic processing of faces is disrupted in CP. Such disruption would be expected to lead to a focus on local features of the face. In this study, we used binocular rivalry (BR) to implicitly measure face perception in conditions that favour holistic or local processing. The underlying assumption is that if stimulus saliency affects the perceptual dominance of a given stimulus in BR, one can deduce how salient a stimulus is for a given group (here: participants with and without CP) based on the measured perceptual dominance. A further open question is whether the deficit in face processing in CP extends to the processing of the facial display of emotions. In experiment 1, we compared predominance of upright and inverted faces displaying different emotions (fearful, happy, neutral) vs. houses between participants with CP (N = 21) and with normal face perception (N = 21). The results suggest that CP observers process emotions in faces automatically but rely more on local features than controls. The inversion of faces, which is supposed to disturb holistic processing, affected controls in a more pronounced way than participants with CP. In experiment 2, we introduced the Thatcher effect in BR by inverting the eye and mouth regions of the presented faces in the hope of further increasing the effect of face inversion. However, our expectations were not borne out by the results. Critically, both experiments showed that inversion effects were more pronounced in controls than in CP, suggesting that holistic face processing is less relevant in CP. We find BR to be a useful implicit test for assessing visual processing specificities in neurological participants.
In silico approaches for the identification of potential allergens among hypothetical proteins from Alternaria alternata and its functional annotation
Authors: Sundararaj Rajamanikandan , Mathimaran Amala , Prabhu Dhamodharan , Ramachandran Balajee , Jeyaraman Jeyakanthan , Muthupandian Saravanan , Asmelash Tsehaye
Published: March 2024

Direct exposure to the fungal species Alternaria alternata is a major risk factor for the development of asthma, allergic rhinitis, and inflammation. As of November 23rd 2020, the NCBI protein database showed 11,227 proteins from A. alternata genome as hypothetical proteins (HPs). Allergens are the main causative of several life-threatening diseases, especially in fungal infections. Therefore, the main aim of the study is to identify the potentially allergenic inducible proteins from the HPs in A. alternata and their associated functional assignment for the complete understanding of the complex biological systems at the molecular level. AlgPred and Structural Database of Allergenic Proteins (SDAP) were used for the prediction of potential allergens from the HPs of A. alternata. While analyzing the proteome data, 29 potential allergens were predicted by AlgPred and further screening in SDAP confirmed the allergic response of 10 proteins. Extensive bioinformatics tools including protein family classification, sequence-function relationship, protein motif discovery, pathway interactions, and intrinsic features from the amino acid sequence were used to successfully predict the probable functions of the 10 HPs. The functions of the HPs are characterized as chitin-binding, ribosomal protein P1, thaumatin, glycosyl hydrolase, and NOB1 proteins. The subcellular localization and signal peptide prediction of these 10 proteins has further provided additional information on localization and function. The allergens prediction and functional annotation of the 10 proteins may facilitate a better understanding of the allergenic mechanism of A. alternata in asthma and other diseases. The functional domain level insights and predicted structural features of the allergenic proteins help to understand the pathogenesis and host immune tolerance. The outcomes of the study would aid in the development of specific drugs to combat A. alternata infections.
Extracellular vesicles secreted from mesenchymal stem cells ameliorate renal ischemia reperfusion injury by delivering miR-100-5p targeting FKBP5/AKT axis
Authors: Chen Guo , Li Xinyuan , Zhou Xiang , Li Yang , Yu Haitao , Peng Xiang , Bai Xuesong , Zhang Chunlin , Feng Zhenwei , Mei Yuhua , Li Li , Liu Yu , Gou Xin , Jiang Yuanbin
Published: March 2024

The incidence of acute kidney injury (AKI) due to ischemia–reperfusion (IR) injury is increasing. There is no effective treatment for AKI, and because of this clinical challenge, AKI often progresses to chronic kidney disease, which is closely associated with poor patient outcomes and high mortality rates. Small extracellular vesicles from human umbilical cord mesenchymal stem cells (hUCMSC-sEVs) play increasingly vital roles in protecting tissue function from the effects of various harmful stimuli owing to their specific biological features. In this study, we found that miR-100-5p was enriched in hUCMSC-sEVs, and miR-100-5p targeted FKBP5 and inhibited HK-2 cell apoptosis by activating the AKT pathway. HK-2 cells that were exposed to IR injury were cocultured with hUCMSC-sEVs, leading to an increase in miR-100-5p levels, a decrease in FKBP5 levels, and an increase in AKT phosphorylation at Ser 473 (AKT-473 phosphorylation). Notably, these effects were significantly reversed by transfecting hUCMSCs with an miR-100-5p inhibitor. Moreover, miR-100-5p targeted FKBP5, as confirmed by a dual luciferase reporter assay. In vivo, intravenous infusion of hUCMSC-sEVs into mice suffering from IR injury resulted in significant apoptosis inhibition, functional maintenance and renal histological protection, which in turn decreased FKBP5 expression levels. Overall, this study revealed an effect of hUCMSC-sEVs on inhibiting apoptosis; hUCMSC-sEVs reduced renal IR injury by delivering miR-100-5p to HK-2 cells, targeting FKBP5 and thereby promoting AKT-473 phosphorylation to activate the AKT pathway. This study provides novel insights into the role of hUCMSC-sEVs in the treatment of AKI.
Changes in use and outcomes after fibrinogen concentrate insurance coverage for critical obstetrical hemorrhage: a nationwide questionnaire survey in Japan
Authors: Nii Masafumi , Oda Tomoaki , Morikawa Mamoru , Nakabayashi Yasushi , Adachi Tomoko , Kobayashi Takao , Itakura Atsuo
Published: March 2024

Fibrinogen concentrate (FC) for acquired hypofibrinogenemia associated with critical obstetrical hemorrhage (COH) was covered by public medical insurance in September 2021 in Japan. We aimed to investigate changes in the policy of FC use and its effect on COH after insurance coverage. A primary survey covering September 2020 to August 2021 and a secondary survey covering September 2021 to August 2022 were conducted at 428 higher-level medical facilities. We investigated the policy of FC use in transfusion strategy and the maternal outcomes in COH. Among the hospitals that responded to both surveys, the number of facilities that use FC increased from 51.5 (101/196) to 78.6% (154/196) (P < 0.0001). The number of COH cases treated using FC increased from 14.3 to 24.3% (P < 0.0001) and that transfused with ≥ 10 units of red blood cells (RBCs) decreased from 36.8 to 29.8% (P = 0.001). The incidence of pulmonary edema reduced by 3.7–2.0% (P = 0.021), and transfusion-induced allergy by 1.9–0.7% (P = 0.008). No changes were observed in the incidence of thromboembolism, arterial embolization, or hysterectomy. The increased use of FC after insurance coverage led to changes in the transfusion strategy, which may be associated with decreases in transfusions of RBCs, pulmonary edema, and transfusion-induced allergies.