bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring the Basal Friction Law From Long Term Changes of Glacier Length, Thickness and Velocity on an Alpine Glacier
Authors: Gilbert A. , Gimbert F. , Gagliardini O. , Vincent C. 
Published: August 2023

AbstractBasal sliding of glaciers and ice sheets remains a source of uncertainty in simulating the long‐term evolution of ice masses. In particular, the response of ice flow to changes in driving stress depends strongly on the value of the exponent m in nonlinear friction laws (e.g., Weertman's law), which is poorly constrained by observations. Here we constrain the friction law at a natural scale on Argentière Glacier (French Alps, hard‐bed), taking advantage of well‐resolved observations of glacier mass balance, geometry and basal sliding over time spans that include large changes in driving stress. By combining three different independent methods based on (a) surface velocity inversion, (b) transient length change modeling, and (c) direct local sliding measurements, we consistently find a value of m = 3.1 ± 0.3. We suggest that Weertman's law is suitable for modeling the long‐term evolution of hard‐bedded glaciers and ice sheets.
Polymeric and biological membranes for organ-on-a-chip devices
Authors: Corral-Nájera Kendra , Chauhan Gaurav , Serna-Saldívar Sergio O. , Martínez-Chapa Sergio O. , Aeinehvand Mohammad Mahdi 
Published: August 2023

AbstractMembranes are fundamental elements within organ-on-a-chip (OOC) platforms, as they provide adherent cells with support, allow nutrients (and other relevant molecules) to permeate/exchange through membrane pores, and enable the delivery of mechanical or chemical stimuli. Through OOC platforms, physiological processes can be studied in vitro, whereas OOC membranes broaden knowledge of how mechanical and chemical cues affect cells and organs. OOCs with membranes are in vitro microfluidic models that are used to replace animal testing for various applications, such as drug discovery and disease modeling. In this review, the relevance of OOCs with membranes is discussed as well as their scaffold and actuation roles, properties (physical and material), and fabrication methods in different organ models. The purpose was to aid readers with membrane selection for the development of OOCs with specific applications in the fields of mechanistic, pathological, and drug testing studies. Mechanical stimulation from liquid flow and cyclic strain, as well as their effects on the cell’s increased physiological relevance (IPR), are described in the first section. The review also contains methods to fabricate synthetic and ECM (extracellular matrix) protein membranes, their characteristics (e.g., thickness and porosity, which can be adjusted depending on the application, as shown in the graphical abstract), and the biological materials used for their coatings. The discussion section joins and describes the roles of membranes for different research purposes and their advantages and challenges.
Cell type-specific NRBF2 orchestrates autophagic flux and adult hippocampal neurogenesis in chronic stress-induced depression
Authors: Zhang Shao-Qi , Deng Qiao , Zhu Qi , Hu Zhuang-Li , Long Li-Hong , Wu Peng-Fei , He Jin-Gang , Chen Hong-Sheng , Yue Zhenyu , Lu Jia-Hong , Wang Fang , Chen Jian-Guo 
Published: August 2023

AbstractDysfunctional autophagy and impairment of adult hippocampal neurogenesis (AHN) each contribute to the pathogenesis of major depressive disorder (MDD). However, whether dysfunctional autophagy is linked to aberrant AHN underlying MDD remains unclear. Here we demonstrate that the expression of nuclear receptor binding factor 2 (NRBF2), a component of autophagy-associated PIK3C3/VPS34-containing phosphatidylinositol 3-kinase complex, is attenuated in the dentate gyrus (DG) under chronic stress. NRBF2 deficiency inhibits the activity of the VPS34 complex and impairs autophagic flux in adult neural stem cells (aNSCs). Moreover, loss of NRBF2 disrupts the neurogenesis-related protein network and causes exhaustion of aNSC pool, leading to the depression-like phenotype. Strikingly, overexpressing NRBF2 in aNSCs of the DG is sufficient to rescue impaired AHN and depression-like phenotype of mice. Our findings reveal a significant role of NRBF2-dependent autophagy in preventing chronic stress-induced AHN impairment and suggest the therapeutic potential of targeting NRBF2 in MDD treatment.
Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA
Authors: Block Matthias F. , Delley Cyrille L. , Keller Lena M. L. , Stuehlinger Timo T. , Weber-Ban Eilika 
Published: August 2023

AbstractPupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover.
Skeletal metalation of lactams through a carbonyl-to-nickel-exchange logic
Authors: Zhong Hongyu , Egger Dominic T. , Gasser Valentina C. M. , Finkelstein Patrick , Keim Loris , Seidel Merlin Z. , Trapp Nils , Morandi Bill 
Published: August 2023

AbstractClassical metalation reactions such as the metal-halogen exchange have had a transformative impact on organic synthesis owing to their broad applicability in building carbon-carbon bonds from carbon-halogen bonds. Extending the metal-halogen exchange logic to a metal-carbon exchange would enable the direct modification of carbon frameworks with new implications in retrosynthetic analysis. However, such a transformation requires the selective cleavage of highly inert chemical bonds and formation of stable intermediates amenable to further synthetic elaborations, hence its development has remained considerably challenging. Here we introduce a skeletal metalation strategy that allows lactams, a prevalent motif in bioactive molecules, to be readily converted into well-defined, synthetically useful organonickel reagents. The reaction features a selective activation of unstrained amide C–N bonds mediated by an easily prepared Ni(0) reagent, followed by CO deinsertion and dissociation under mild room temperature conditions in a formal carbonyl-to-nickel-exchange process. The underlying principles of this unique reactivity are rationalized by organometallic and computational studies. The skeletal metalation is further applied to a direct CO excision reaction and a carbon isotope exchange reaction of lactams, underscoring the broad potential of metal-carbon exchange logic in organic synthesis.
Operando monitoring of thermal runaway in commercial lithium-ion cells via advanced lab-on-fiber technologies
Authors: Mei Wenxin , Liu Zhi , Wang Chengdong , Wu Chuang , Liu Yubin , Liu Pengjie , Xia Xudong , Xue Xiaobin , Han Xile , Sun Jinhua , Xiao Gaozhi , Tam Hwa-yaw , Albert Jacques , Wang Qingsong , Guo Tuan 
Published: August 2023

AbstractOperando monitoring of complex physical and chemical activities inside rechargeable lithium-ion batteries during thermal runaway is critical to understanding thermal runaway mechanisms and giving early warning of safety-related failure. However, most existing sensors cannot survive during such extremely hazardous thermal runaway processes (temperature up to 500 °C accompanied by fire and explosion). To address this, we develop a compact and multifunctional optical fiber sensor (12 mm in length and 125 µm in diameter) capable of insertion into commercial 18650 cells to continuously monitor internal temperature and pressure effects during cell thermal runaway. We observe a stable and reproducible correlation between the cell thermal runaway and the optical response. The sensor’s signal shows two internal pressure peaks corresponding to safety venting and initiation of thermal runaway. Further analysis reveals that a scalable solution for predicting imminent thermal runaway is the detection of the abrupt turning range of the differential curves of cell temperature and pressure, which corresponds to an internal transformation between the cell reversible and irreversible reactions. By raising an alert even before safety venting, this new operando measurement tool can provide crucial capabilities in cell safety assessment and warning of thermal runaway.
Readiness for Parkinson’s disease genetic testing and counseling in patients and their relatives in urban settings in the Dominican Republic
Authors: Hackl Margaret , Cook Lola , Wetherill Leah , Walsh Laurence E. , Delk Paula , De León Rebeca , Carbonell Janfreisy , Vicioso Rossy Cruz , Hodges Priscila Delgado 
Published: August 2023

AbstractGenetic testing for Parkinson’s disease (PD) is increasing globally, and genetic counseling is an important service that provides information and promotes understanding about PD genetics and genetic testing. PD research studies have initiated outreach to underrepresented regions in North America, including regions in Latin America, such as the Dominican Republic (DR); some studies may include return of genetic test results. Thus, understanding what individuals know about PD, genetic testing for PD, and their interest in speaking with a genetic counselor, is crucial when assessing readiness. In this cross-sectional study, a survey was distributed to people with Parkinson’s disease (PwP) and their unaffected biological relatives in the DR. Questions assessed genetics knowledge, attitude toward genetic testing, and interest in genetic testing and counseling. Of 45 participants, 69% scored the maximum on the attitude scale, indicating an overall positive attitude toward genetic testing; 95% indicated interest in genetic testing for PD, and 98% were at least somewhat interested in meeting with a genetic counselor. The mean PD genetics knowledge score was similar to previously published data. Through free text responses, participants expressed a desire to know more about PD treatment and management, prevention, cause, and their personal risk for PD. These results provide further evidence of readiness for genetic testing in this country but also underscore some gaps in knowledge that should be addressed with targeted educational efforts, as part of building genetic testing and counseling capacities.
Identifying the mediating role of socioeconomic status on the relationship between schizophrenia and major depressive disorder: a Mendelian randomisation analysis
Authors: Xu Qiang , Cai Mengjing , Ji Yuan , Ma Juanwei , Liu Jiawei , Zhao Qiyu , Chen Yayuan , Zhao Yao , Zhang Yijing , Wang He , Guo Lining , Xue Kaizhong , Wang Zirui , Liu Mengge , Wang Chunyang , Zhu Dan , Liu Feng 
Published: August 2023

AbstractDepressive disorder prevalence in patients with schizophrenia has been reported to be 40%. People with low socioeconomic status (SES) are more likely to suffer from schizophrenia and major depressive disorder (MDD). However, the causal relationship between schizophrenia and depression and the potential mediating role of SES remains unclear. Two-sample Mendelian randomization (MR) analyses were conducted to explore the bidirectional causal relationship between schizophrenia and MDD with the largest sample size of European ancestry from public genome-wide association studies (sample size ranged from 130,644 to 480,359). Inverse variance weighted (IVW) method was used as the primary analysis, and several canonical MR methods were used as validation analyses. The mediating role of SES (educational years, household income, employment status, and Townsend deprivation index) was estimated by the two-step MR method. MR analyses showed that genetically predicted schizophrenia was associated with an increased risk of MDD (IVW odds ratio [OR] = 1.137 [95% CI 1.095, 1.181]). Reversely, MDD was also associated with an increased risk of schizophrenia (IVW OR = 1.323 [95% CI 1.118, 1.565]). The mediation analysis via the two-step MR method revealed that the causal effect of schizophrenia on MDD was partly mediated by the Townsend deprivation index with a proportion of 10.27%, but no significant mediation effect was found of SES on the causal effect of MDD on schizophrenia. These results suggest a robust bidirectional causal effect between schizophrenia and MDD. Patients with schizophrenia could benefit from the early and effective intervention of the Townsend deprivation index.
re3data – Indexing the Global Research Data Repository Landscape Since 2012
Authors: Pampel Heinz , Weisweiler Nina Leonie , Strecker Dorothea , Witt Michael , Vierkant Paul , Elger Kirsten , Bertelmann Roland , Buys Matthew , Ferguson Lea Maria , Kindling Maxi , Kotarski Rachael , Petras Vivien 
Published: August 2023

AbstractFor more than ten years, re3data, a global registry of research data repositories (RDRs), has been helping scientists, funding agencies, libraries, and data centers with finding, identifying, and referencing RDRs. As the world’s largest directory of RDRs, re3data currently describes over 3,000 RDRs on the basis of a comprehensive metadata schema. The service allows searching for RDRs of any type and from all disciplines, and users can filter results based on a wide range of characteristics. The re3data RDR descriptions are available as Open Data accessible through an API and are utilized by numerous Open Science services. re3data is engaged in various initiatives and projects concerning data management and is mentioned in the policies of many scientific institutions, funding organizations, and publishers. This article reflects on the ten-year experience of running re3data and discusses ten key issues related to the management of an Open Science service that caters to RDRs worldwide.
Chromosomal level genome assembly of medicinal plant Sophora flavescens
Authors: Qu Zhipeng , Wang Wei , Adelson David L. 
Published: August 2023

AbstractSophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L. . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.
Newborn weight nomograms in selected low and middle-income countries
Authors: Ginsburg Amy Sarah , Jehan Fyezah , Ariff Shabina , Nisar Muhammad Imran , Schaefer Eric , Flaherman Valerie , Shrestha Akina , Dongol Srijana , Laleau Victoria , de Sa Augusto Braima , Co Raimundo , Nankabirwa Victoria 
Published: August 2023

AbstractGrowth impairment is common in low- and middle-income countries (LMIC) and may begin during early infancy, increasing morbidity and mortality. To ensure healthy infant growth, healthcare providers in high-income countries (HIC) track newborn weight change using tools developed and validated in HIC. To understand the utility of these tools for LMIC, we conducted a secondary analysis to compare weight trajectories in the first 5 days of life among newborns born in our LMIC cohort to an existing HIC newborn weight tool designed to track early weight change. Between April 2019 and March 2020, a convenience sample of 741 singleton healthy breastfeeding newborns who weighed ≥ 2000 g at birth were enrolled at selected health facilities in Guinea-Bissau, Nepal, Pakistan, and Uganda. Using a standardized protocol, newborn weights were obtained within 6 h of birth and at 1, 2, 3, 4, and 5 days, and nomograms depicting newborn weight change were generated. The trajectories of early newborn weight change in our cohort were largely similar to published norms derived from HIC infants, with the exceptions that initial newborn weight loss in Guinea-Bissau was more pronounced than HIC norms and newborn weight gain following weight nadir was more pronounced in Guinea-Bissau, Pakistan, and Uganda than HIC norms. These data demonstrate that HIC newborn weight change tools may have utility in LMIC settings.
Emphysema subtyping on thoracic computed tomography scans using deep neural networks
Authors: Xie Weiyi , Jacobs Colin , Charbonnier Jean-Paul , Slebos Dirk Jan , van Ginneken Bram 
Published: August 2023

AbstractAccurate identification of emphysema subtypes and severity is crucial for effective management of COPD and the study of disease heterogeneity. Manual analysis of emphysema subtypes and severity is laborious and subjective. To address this challenge, we present a deep learning-based approach for automating the Fleischner Society’s visual score system for emphysema subtyping and severity analysis. We trained and evaluated our algorithm using 9650 subjects from the COPDGene study. Our algorithm achieved the predictive accuracy at 52%, outperforming a previously published method’s accuracy of 45%. In addition, the agreement between the predicted scores of our method and the visual scores was good, where the previous method obtained only moderate agreement. Our approach employs a regression training strategy to generate categorical labels while simultaneously producing high-resolution localized activation maps for visualizing the network predictions. By leveraging these dense activation maps, our method possesses the capability to compute the percentage of emphysema involvement per lung in addition to categorical severity scores. Furthermore, the proposed method extends its predictive capabilities beyond centrilobular emphysema to include paraseptal emphysema subtypes.
Clarifying the composition of the ATP consumption factors required for maintaining ion homeostasis in mouse rod photoreceptors
Authors: Muangkram Yuttamol , Himeno Yukiko , Amano Akira 
Published: August 2023

AbstractTo date, no effective treatment has been established for photoreceptor loss due to energy imbalances, but numerous therapeutic approaches have reported some success in slowing photoreceptor degeneration by downregulating energy demand. However, the detailed mechanisms remain unclear. This study aimed to clarify the composition of ATP consumption factors in photoreceptors in darkness and in light. We introduced mathematical formulas for ionic current activities combined with a phototransduction model to form a new mathematical model for estimating the energy expenditure of each ionic current. The proposed model included various ionic currents identified in mouse rods using a gene expression database incorporating an available electrophysiological recording of each specific gene. ATP was mainly consumed by Na+/K+-ATPase and plasma membrane Ca2+-ATPase pumps to remove excess Na+ and Ca2+. The rod consumed 7 $$\times$$
×
107 molecules of ATP s−1, where 65% was used to remove ions from the cyclic nucleotide-gated channel and 20% from the hyperpolarization-activated current in darkness. Increased light intensity raised the energy requirements of the complex phototransduction cascade mechanisms. Nevertheless, the overall energy consumption was less than that in darkness due to the significant reduction in ATPase activities, where the hyperpolarization-activated current proportion increased to 83%. A better understanding of energy demand/supply may provide an effective tool for investigating retinal pathophysiological changes and analyzing novel therapeutic treatments related to the energy consumption of photoreceptors.
Partially defatted rather than native poppy seeds beneficially alter lipid metabolism in rats fed a high-fat diet
Authors: Koza Jarosław , Jurgoński Adam 
Published: August 2023

AbstractPartially defatted poppy seeds, a by-product of poppy oil cold pressing, could be an interesting dietary supplement for obesity management. The aim of this study was to compare the effects of dietary supplementation with a small amount of native or partially defatted poppy seeds on gastrointestinal function and lipid metabolism in rats fed a high-fat diet. The defatted poppy seeds had, among others, lower fat content and higher fibre and protein content than native poppy seeds. The rats fed with a high-fat diet were characterised by severe metabolic disorders, especially in the liver, and poppy seeds were unable to prevent them. However, depending on the seed form, dietary supplementation with poppy seeds differentially affected the microbial and endogenous lipid metabolism in rats. In the distal intestine, both dietary seed forms stimulated microbial acetate production, and the supplementation with partially defatted poppy seeds additionally inhibited isobutyrate and isovalerate formation, which indicates a reduction in putrefaction. Both dietary seed forms increased cholesterol accumulation in the liver. Only dietary supplementation with partially defatted poppy seeds attenuated visceral fat and hepatic triglyceride accumulations and lowered blood triglyceride concentrations, and at the transcriptional level, the inhibition of SREBP-1c, which upregulates genes responsible for de novo lipogenesis, was additionally observed in this organ. In conclusion, a low and regular consumption of partially defatted poppy seeds may be beneficial in managing obesity-related disorders.