bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender and Political Seniority: Three Measures
Authors: Muriaas Ragnhild , Stavenes Torill
Published: September 2023

This article offers an innovative way of understanding gender balance in parliaments. Motivated by research documenting how newcomers are disadvantaged during their first term in office, while senior members enjoy certain privileges, we want to find out how common women are among senior members of parliaments. We launch an institutional approach comprising three seniority measures to study gender gaps in political endurance to find out whether, where, and when men are more likely than women to be parliamentary seniors. Our analysis using data from seven countries in Western Europe and two countries in North America (1965–2020) shows very high gender gaps across the three measures. Thus, despite an increased level of female representation, women still constitute a small part of the exclusive group of senior members of parliament. Our findings extend the research documenting that women and men largely have equally long parliamentary careers, emphasizing the need to understand gender balance in multidimensional terms.
Stress Constraints From Shear‐Wave Analysis in Shallow Sediments at an Actively Seeping Pockmark on the W‐Svalbard Margin
Authors: Singhroha Sunny , Schramm Bettina , Plaza‐Faverola Andreia , Domel Przemyslaw , Dannowski Anke , Cooke Frances , Bünz Stefan
Published: September 2023

Mechanisms related to sub‐seabed fluid flow processes are complex and inadequately understood. Petrophysical properties, availability of gases, topography, stress directions, and various geological parameters determine the location and intensity of leakage which change over time. From tens of seafloor pockmarks mapped along Vestnesa Ridge on the west‐Svalbard margin, only six show persistent present‐day seepage activity in sonar data. To investigate the causes of such restricted gas seepage, we conducted a study of anisotropy within the conduit feeding one of these active pockmarks (i.e., Lunde Pockmark). Lunde is ∼400–500 m in diameter, and atop a ∼300–400 m wide seismic chimney structure. We study seismic anisotropy using converted S‐wave data from 22 ocean‐bottom seismometers (OBSs) located in and around the pockmark. We investigate differences in symmetry plane directions in anisotropic media using null energy symmetries in transverse components. Subsurface stress distribution affects fault/fracture orientations and seismic anisotropy, and we use S‐wave and high‐resolution 3D seismic data to infer stress regimes in and around the active seep site and study the effect of stresses on seepage. We observe the occurrence of changes in dominant fault/fracture and horizontal stress orientations in and around Lunde Pockmark and conclude minimum (NE‐SW) and maximum (SE‐NW) horizontal stress directions. Our analysis indicates a potential correlation between hydrofractures and horizontal stresses, with up to a ∼32% higher probability of alignment of hydrofractures and faults perpendicular to the inferred minimum horizontal stress direction beneath the Lunde Pockmark area.
Caribbean Marine Heatwaves, Marine Cold Spells, and Co‐Occurrence of Bleaching Events
Authors: Cetina‐Heredia P. , Allende‐Arandía M. E.
Published: September 2023

Marine heatwaves (MHWs) and Cold Spells (marine cold spells (MCSs)) are events of extreme positive and negative temperature anomalies, that last 5 days or longer. These events have been diagnosed across oceans from sea surface temperatures (SSTs) and recognized to affect ecosystems' health worldwide. Some studies have focused on the extent, evolution, and drivers of specifically intense and long‐lasting regional MHW events. Although extreme temperature anomalies could lead to coral bleaching, mortality, and ecosystems' shift from healthy to barren reefs, no studies have focused on MHWs and MCSs in the Caribbean Sea. This study characterizes them in the Caribbean Sea, explores simultaneous thermal‐stress and coral response, and reveals prevailing environmental conditions during their occurrence. We use four decades of SSTs observed daily and a recently published database of worldwide coral bleaching events. We found bleaching events occurring simultaneously with both MCSs and MHWs, often with extreme events of mild intensity and typical duration. We find a positive long‐term trend in MHWs' frequency, consistent not only with global warming, but also with the Atlantic Meridional Mode. There is a clear seasonal signal with MHWs occurring more often in summer and MCSs in autumn‐winter. Our results suggest MHWs and MCSs development is related to El Niño/La Niña conditions, respectively. Finally, we identify intense extreme temperature events that span large areas as candidates for future studies on their dynamics. Our results are relevant for the development of MHWs and MCSs forecasts applied to conservation strategies and ecosystem‐based management of marine resources, particularly in reef systems.
Implicit Algorithm for Threshold Stream Power Incision Model
Authors: Braun Jean , Deal Eric
Published: September 2023

We present an O(n) complexity and implicit algorithm for the two‐dimensional solution of the stream power incision model (SPIM) enriched by a discharge threshold term and taking into account variability in rainfall and thus discharge. The algorithm is based on the formulation developed by Deal et al. (2018, https://doi.org/10.1002/2017jf004393) and the generalization of the FastScape algorithm (Braun & Willett, 2013, https://doi.org/10.1016/j.geomorph.2012.10.008) where the slope is approximated by first‐order accurate finite difference. We consider a variety of discharge thresholds that vary in their dependence on channel slope. The algorithm requires finding the root of a non‐linear equation using a Newton‐Raphson iterative scheme. We show that the convergence of this scheme is unconditional, except for a narrow range of model parameters where the threshold increases with the slope and for low discharge variability. We also show that the rate of convergence of the iterative scheme is directly proportional to the slope exponent n in the SPIM. We compare the algorithm to analytical solutions and to numerical solutions obtained using a higher‐order finite difference scheme. We show that the accuracy of the FastScape algorithm and its generalization presented here is comparable to other schemes for values of n > 1. We also confirm that the FastScape algorithm and its generalization to variable discharge + threshold conditions does not need to satisfy the CFL condition and provides an accurate solution for both small and very long time steps. We finally use the new algorithm to quantify how the existence of an erosional threshold strongly affects the length of the post‐orogenic decay of mountain belts.
A deformability-based biochip for precise label-free stratification of metastatic subtypes using deep learning
Authors: Hua Haojun , Zou Shangjie , Ma Zhiqiang , Guo Wang , Fong Ching Yin , Khoo Bee Luan
Published: September 2023

Cellular deformability is a promising biomarker for evaluating the physiological state of cells in medical applications. Microfluidics has emerged as a powerful technique for measuring cellular deformability. However, existing microfluidic-based assays for measuring cellular deformability rely heavily on image analysis, which can limit their scalability for high-throughput applications. Here, we develop a parallel constriction-based microfluidic flow cytometry device and an integrated computational framework (ATMQcD). The ATMQcD framework includes automatic training set generation, multiple object tracking, segmentation, and cellular deformability quantification. The system was validated using cancer cell lines of varying metastatic potential, achieving a classification accuracy of 92.4% for invasiveness assessment and stratifying cancer cells before and after hypoxia treatment. The ATMQcD system also demonstrated excellent performance in distinguishing cancer cells from leukocytes (accuracy = 89.5%). We developed a mechanical model based on power-law rheology to quantify stiffness, which was fitted with measured data directly. The model evaluated metastatic potentials for multiple cancer types and mixed cell populations, even under real-world clinical conditions. Our study presents a highly robust and transferable computational framework for multiobject tracking and deformation measurement tasks in microfluidics. We believe that this platform has the potential to pave the way for high-throughput analysis in clinical applications, providing a powerful tool for evaluating cellular deformability and assessing the physiological state of cells.
Neonatal mortality and video assessment of resuscitation in four district hospitals in Pemba, Tanzania
Authors: Holm-Hansen Charlotte Carina , Lund Stine , Skytte Tine Bruhn , Molenaar Jil , Steensgaard Christina Nadia , Mohd Ulfat Amour , Mzee Said , Ali Said Mouhammed , Kjærgaard Jesper , Greisen Gorm , Sorensen Jette Led , Poulsen Anja
Published: September 2023

Background

We aimed to assess risk factors for neonatal mortality, quality of neonatal resuscitation (NR) on videos and identify potential areas for improvement.

Methods

This prospective cohort study included women in childbirth and their newborns at four district hospitals in Pemba, Tanzania. Videos were analysed for quality-of-care. Questionnaires on quality-of-care indicators were answered by health workers (HW) and women. Risk factors for neonatal mortality were analysed in a binomial logistic regression model.

Results

1440 newborns were enrolled. 34 newborns died within the neonatal period (23.6 per 1000 live births). Ninety neonatal resuscitations were performed, 20 cases on video. Positive pressure ventilation (PPV) was inadequate in 15 cases (75%). Half (10/20) did not have PPV initiated within the first minute, and in one case (5.0%), no PPV was performed. PPV was not sustained in 16/20 (80%) newborns. Of the 20 videos analysed, death occurred in 10 newborns: 8 after resuscitation attempts and two within the first 24 h. Most of HW 49/56 (87.5%) had received training in NR.

Conclusions

Video analysis of NR revealed significant deviations from guidelines despite 87.5% of HW being trained in NR. Videos provided direct evidence of gaps in the quality of care and areas for future education, particularly effective PPV.

Impact

Neonatal mortality in Pemba is 23.6 per 1000 livebirths, with more than 90% occurring in the first 24 h of life.

Video assessment of neonatal resuscitation revealed deviations from guidelines and can add to understanding challenges and aid intervention design.

The present study using video assessment of neonatal resuscitation is the first one performed at secondary-level hospitals where many of the world’s births are conducted.

Almost 90% of the health workers had received training in neonatal resuscitation, and the paper can aid intervention design by understanding the actual challenges in neonatal resuscitation.
Polygenic risk scores of lithium response and treatment resistance in major depressive disorder
Authors: Xiong Ying , Karlsson Robert , Song Jie , Kowalec Kaarina , Rück Christian , Sigström Robert , Jonsson Lina , Clements Caitlin C. , Andersson Evelyn , Boberg Julia , Lewis Cathryn M. , Sullivan Patrick F. , Landén Mikael , Lu Yi
Published: September 2023

Treatment response and resistance in major depressive disorder (MDD) are suggested to be heritable. Due to significant challenges in defining treatment-related phenotypes, our understanding of their genetic bases is limited. This study aimed to derive a stringent definition of treatment resistance and to investigate the genetic overlap between treatment response and resistance in MDD. Using electronic medical records on the use of antidepressants and electroconvulsive therapy (ECT) from Swedish registers, we derived the phenotype of treatment-resistant depression (TRD) and non-TRD within ~4500 individuals with MDD in three Swedish cohorts. Considering antidepressants and lithium are first-line treatment and augmentation used for MDD, respectively, we generated polygenic risk scores (PRS) of antidepressants and lithium response for individuals with MDD and evaluated their associations with treatment resistance by comparing TRD with non-TRD. Among 1778 ECT-treated MDD cases, nearly all (94%) used antidepressants before their first ECT and the vast majority had at least one (84%) or two (61%) antidepressants of adequate duration, suggesting these MDD cases receiving ECT were resistant to antidepressants. We did not observe a significant difference in the mean PRS of antidepressant response between TRD and non-TRD; however, we found that TRD cases had a significantly higher PRS of lithium response compared to non-TRD cases (OR = 1.10–1.12 under various definitions). The results support the evidence of heritable components in treatment-related phenotypes and highlight the overall genetic profile of lithium-sensitivity in TRD. This finding further provides a genetic explanation for lithium efficacy in treating TRD.
Psychological interventions for the prevention of depression relapse: systematic review and network meta-analysis
Authors: Zhou Yurong , Zhao Defeng , Zhu Xiaotong , Liu Lu , Meng Ming , Shao Xiaojun , Zhu Xueyan , Xiang Jing , He Jiali , Zhao Yimeng , Yuan Yuman , Gao Rui , Jiang Lin , Zhu Gang
Published: September 2023

Depression is highly prevalent and easily relapses. Psychological interventions are effective for the prevention of depression relapse. This systematic review and network meta-analysis aimed to compare the efficacy at the same follow-up time points of psychological interventions in depression. We searched PubMed, Embase, and PsycINFO via OVID, and the Cochrane Library published up to December 12, 2021, and PubMed up to July 1, 2022. The primary outcome was depression relapse, considering the same time points that were extracted on survival curves or relapse curves. The study protocol was registered with PROSPERO, CRD42022343327. A total of 2,871 patients were included from 25 RCTs. Mindfulness-based cognitive therapy (MBCT) was significantly better than placebo at the 3 months, the 6 months, and the 9 months at follow-up. Cognitive behavioral therapy (CBT) was significantly better than treatment as usual at the 3 months, the 9 months, the 12 months, and the 15 months at follow-up. CBT was significantly better than placebo at the 21 months and the 24 months at follow-up. Behavioral activation therapy was significantly better than placebo at the 21 months and the 24 months at follow-up. Interpersonal psychotherapy was significantly better than placebo at the 24-month follow-up. All psychological interventions included in the study were significantly better than supportive counseling most of the time. The results were robust in various sensitivity and subgroup analyses. In conclusion, MBCT had a continuous effect in preventing relapse of depression. CBT had the longest but not continuous effect in preventing relapse of depression. The effects of behavioral activation therapy and interpersonal therapy for the prevention of depression appeared late. All psychological interventions included in the study were more effective than supportive counseling. More evidence is needed from large comparative trials that provide long-term follow-up data.
Synthesis of a covalent organic framework with hetero-environmental pores and its medicine co-delivery application
Authors: Ji Wenyan , Zhang Pai , Feng Guangyuan , Cheng Yuan-Zhe , Wang Tian-Xiong , Yuan Daqiang , Cha Ruitao , Ding Xuesong , Lei Shengbin , Han Bao-Hang
Published: September 2023

The topology type and the functionalization of pores play an important role in regulating the performance of covalent organic frameworks. Herein, we designed and synthesized the covalent organic framework with hetero-environmental pores using predesigned asymmetrical dialdehyde monomer. According to the results of structural characterization, crystallinity investigation, and theoretical calculation, the hetero-environmental pores of the obtained framework are regarded as the alternant arrangement. The distinctive hetero pore structure leads the designed material to show more advantages as compared with control materials in loading both hydrophobic and hydrophilic antibiotics for wound healing. This dual-antibiotic strategy can expand the antibacterial range as compared with the single antibiotic one, and reduce the generation of drug resistance. In summary, this strategy for designing covalent organic frameworks with hetero-environmental pores can extend the structural variety and provide a pathway for improving the practical application performance of these materials.
Defining the condensate landscape of fusion oncoproteins
Authors: Tripathi Swarnendu , Shirnekhi Hazheen K. , Gorman Scott D. , Chandra Bappaditya , Baggett David W. , Park Cheon-Gil , Somjee Ramiz , Lang Benjamin , Hosseini Seyed Mohammad Hadi , Pioso Brittany J. , Li Yongsheng , Iacobucci Ilaria , Gao Qingsong , Edmonson Michael N. , Rice Stephen V. , Zhou Xin , Bollinger John , Mitrea Diana M. , White Michael R. , McGrail Daniel J. , Jarosz Daniel F. , Yi S. Stephen , Babu M. Madan , Mullighan Charles G. , Zhang Jinghui , Sahni Nidhi , Kriwacki Richard W.
Published: September 2023

Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
Perivascular niche cells sense thrombocytopenia and activate hematopoietic stem cells in an IL-1 dependent manner
Authors: Luis Tiago C. , Barkas Nikolaos , Carrelha Joana , Giustacchini Alice , Mazzi Stefania , Norfo Ruggiero , Wu Bishan , Aliouat Affaf , Guerrero Jose A. , Rodriguez-Meira Alba , Bouriez-Jones Tiphaine , Macaulay Iain C. , Jasztal Maria , Zhu Guangheng , Ni Heyu , Robson Matthew J. , Blakely Randy D. , Mead Adam J. , Nerlov Claus , Ghevaert Cedric , Jacobsen Sten Eirik W.
Published: September 2023

Hematopoietic stem cells (HSCs) residing in specialized niches in the bone marrow are responsible for the balanced output of multiple short-lived blood cell lineages in steady-state and in response to different challenges. However, feedback mechanisms by which HSCs, through their niches, sense acute losses of specific blood cell lineages remain to be established. While all HSCs replenish platelets, previous studies have shown that a large fraction of HSCs are molecularly primed for the megakaryocyte-platelet lineage and are rapidly recruited into proliferation upon platelet depletion. Platelets normally turnover in an activation-dependent manner, herein mimicked by antibodies inducing platelet activation and depletion. Antibody-mediated platelet activation upregulates expression of Interleukin-1 (IL-1) in platelets, and in bone marrow extracellular fluid in vivo. Genetic experiments demonstrate that rather than IL-1 directly activating HSCs, activation of bone marrow Lepr+ perivascular niche cells expressing IL-1 receptor is critical for the optimal activation of quiescent HSCs upon platelet activation and depletion. These findings identify a feedback mechanism by which activation-induced depletion of a mature blood cell lineage leads to a niche-dependent activation of HSCs to reinstate its homeostasis.
NLRP6 potentiates PI3K/AKT signalling by promoting autophagic degradation of p85α to drive tumorigenesis
Authors: Zhi Feng , Li Bowen , Zhang Chuanxia , Xia Fan , Wang Rong , Xie Weihong , Cai Sihui , Zhang Dawei , Kong Ren , Hu Yiqiao , Yang Yilin , Peng Ya , Cui Jun
Published: September 2023

The PI3K/AKT pathway plays an essential role in tumour development. NOD-like receptors (NLRs) regulate innate immunity and are implicated in cancer, but whether they are involved in PI3K/AKT pathway regulation is poorly understood. Here, we report that NLRP6 potentiates the PI3K/AKT pathway by binding and destabilizing p85α, the regulatory subunit of PI3K. Mechanistically, NLRP6 recruits the E3 ligase RBX1 to p85α and ubiquitinates lysine 256 on p85α, which is recognized by the autophagy cargo receptor OPTN, causing selective autophagic degradation of p85α and subsequent activation of the PI3K/AKT pathway by reducing PTEN stability. We further show that loss of NLRP6 suppresses cell proliferation, colony formation, cell migration, and tumour growth in glioblastoma cells in vitro and in vivo. Disruption of the NLRP6/p85α interaction using the Pep9 peptide inhibits the PI3K/AKT pathway and generates potent antitumour effects. Collectively, our results suggest that NLRP6 promotes p85α degradation via selective autophagy to drive tumorigenesis, and the interaction between NLRP6 and p85α can be a promising therapeutic target for tumour treatment.
An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides
Authors: Ghosh Pritha , Raj Nishant , Verma Hitesh , Patel Monika , Chakraborti Sohini , Khatri Bhavesh , Doreswamy Chandrashekar M. , Anandakumar S. R. , Seekallu Srinivas , Dinesh M. B. , Jadhav Gajanan , Yadav Prem Narayan , Chatterjee Jayanta
Published: September 2023

Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
Computational remodeling of an enzyme conformational landscape for altered substrate selectivity
Authors: St-Jacques Antony D. , Rodriguez Joshua M. , Eason Matthew G. , Foster Scott M. , Khan Safwat T. , Damry Adam M. , Goto Natalie K. , Thompson Michael C. , Chica Roberto A.
Published: September 2023

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.
The neglected role of abandoned cropland in supporting both food security and climate change mitigation
Authors: Zheng Qiming , Ha Tim , Prishchepov Alexander V. , Zeng Yiwen , Yin He , Koh Lian Pin
Published: September 2023

Despite the looming land scarcity for agriculture, cropland abandonment is widespread globally. Abandoned cropland can be reused to support food security and climate change mitigation. Here, we investigate the potentials and trade-offs of using global abandoned cropland for recultivation and restoring forests by natural regrowth, with spatially-explicit modelling and scenario analysis. We identify 101 Mha of abandoned cropland between 1992 and 2020, with a capability of concurrently delivering 29 to 363 Peta-calories yr-1 of food production potential and 290 to 1,066 MtCO2 yr-1 of net climate change mitigation potential, depending on land-use suitability and land allocation strategies. We also show that applying spatial prioritization is key to maximizing the achievable potentials of abandoned cropland and demonstrate other possible approaches to further increase these potentials. Our findings offer timely insights into the potentials of abandoned cropland and can inform sustainable land management to buttress food security and climate goals.
Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex
Authors: Yuan Ling , Han Yaoyao , Zhao Jiazheng , Zhang Yixiao , Sun Yadong
Published: September 2023

Removal of introns from transfer RNA precursors (pre-tRNAs) occurs in all living organisms. This is a vital phase in the maturation and functionality of tRNA. Here we present a 3.2 Å-resolution cryo-EM structure of an active human tRNA splicing endonuclease complex bound to an intron-containing pre-tRNA. TSEN54, along with the unique regions of TSEN34 and TSEN2, cooperatively recognizes the mature body of pre-tRNA and guides the anticodon-intron stem to the correct position for splicing. We capture the moment when the endonucleases are poised for cleavage, illuminating the molecular mechanism for both 3′ and 5′ cleavage reactions. Two insertion loops from TSEN54 and TSEN2 cover the 3′ and 5′ splice sites, respectively, trapping the scissile phosphate in the center of the catalytic triad of residues. Our findings reveal the molecular mechanism for eukaryotic pre-tRNA recognition and cleavage, as well as the evolutionary relationship between archaeal and eukaryotic TSENs.
Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane
Authors: Park Si Hoon , Han Juhyun , Jeong Byung-Cheon , Song Ju Han , Jang Se Hwan , Jeong Hyeongseop , Kim Bong Heon , Ko Young-Gyu , Park Zee-Yong , Lee Kyung Eun , Hyun Jaekyung , Song Hyun Kyu
Published: September 2023

Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles at the site of membrane damage, but the underlying molecular mechanisms remain poorly understood. Here we present the structure of Mus musculus TRIM72, a complete model of a TRIM E3 ubiquitin ligase. We demonstrated that the interaction between TRIM72 and phosphatidylserine-enriched membranes is necessary for its oligomeric assembly and ubiquitination activity. Using cryogenic electron tomography and subtomogram averaging, we elucidated a higher-order model of TRIM72 assembly on the phospholipid bilayer. Combining structural and biochemical techniques, we developed a working molecular model of TRIM72, providing insights into the regulation of RING-type E3 ligases through the cooperation of multiple domains in higher-order assemblies. Our findings establish a fundamental basis for the study of TRIM E3 ligases and have therapeutic implications for diseases associated with membrane repair.
A synthetic data set to benchmark anti-money laundering methods
Authors: Jensen Rasmus Ingemann Tuffveson , Ferwerda Joras , Jørgensen Kristian Sand , Jensen Erik Rathje , Borg Martin , Krogh Morten Persson , Jensen Jonas Brunholm , Iosifidis Alexandros
Published: September 2023

Bank transactions are highly confidential. As a result, there are no real public data sets that can be used to investigate and compare anti-money laundering (AML) methods in banks. This severely limits research on important AML problems such as efficiency, effectiveness, class imbalance, concept drift, and interpretability. To address the issue, we present SynthAML: a synthetic data set to benchmark statistical and machine learning methods for AML. The data set builds on real data from Spar Nord, a systemically important Danish bank, and contains 20,000 AML alerts and over 16 million transactions. Experimental results indicate that performance on SynthAML can be transferred to the real world. As use cases, we present and discuss open problems in the AML literature.
A novel signature for predicting prognosis and immune landscape in cutaneous melanoma based on anoikis-related long non-coding RNAs
Authors: Zhang Miao , Zuo Yuzhi , Guo Jian , Yang Lushan , Wang Yizhi , Tan Meiyun , Guo Xing
Published: September 2023

Anoikis is a unique form of apoptosis associated with vascularization and distant metastasis in cancer. Eliminating anoikis resistance in tumor cells could be a promising target for improving the prognosis of terminal cancer patients. However, current studies have not elaborated on the prognosis effect of anoikis-related long non-coding RNAs (lncRNAs) in cutaneous melanoma. Pre-processed data, including RNA sequences and clinical information, were retrieved from TCGA and GTEx databases. After a series of statistical analyses, anoikis-related lncRNAs with prognostic significance were identified, and a unique risk signature was constructed. Risk scores were further analyzed in relation to the tumor microenvironment, tumor immune dysfunction and exclusion, immune checkpoint genes, and RNA methylation genes. The indicators were also used to predict the potentially sensitive anti-cancer drugs. An anoikis-related lncRNAs risk signature consisting of LINC01711, POLH-AS1, MIR205HG, and LINC02416 was successfully established in cutaneous melanoma. Overall survival and progression-free survival of patients were strongly linked with the risk score, independently of other clinical factors. The low-risk group exhibited a more beneficial immunological profile, was less affected by RNA methylation, and was more sensitive to the majority of anti-cancer drugs, all of which indicated a better prognostic outcome. The 4 hub lncRNAs may be fundamental to studying the mechanism of anoikis in cutaneous melanoma and provide personalized therapy for salvaging drug resistance.
On asymmetry of magnetic activity and plasma flow temperature in Jupiter’s magnetosphere
Authors: Kaminker Vitaliy
Published: September 2023

Discs of plasma around giant planets are natural laboratories that contain within mechanisms of transferring and keeping energy into the plasma and magnetic field system. Various missions to Jovian planets observed that expansion of plasmadiscs is not adiabatic and plasma temperature is increasing with radial distance. Magnetometer measurements from Juno mission were examined to determine plausibility of turbulent fluctuations as the plasma heating mechanism. Extensive azimuthal map of magnetic activity in Jupiter’s nightside plasmadisc is presented. Observations show that magnetic activity is distributed asymmetrically, with active and quiet regions. This is similar to the asymmetrical distribution of activity observed in Saturn’s magnetosphere. However, comprehensive study of temperature measurements showed that the only systematic change of temperature in magnetospheres of giant planets is in the radial direction. Observed breakfrequency in the magnetometer time series is systematically greater than the ion cyclotron frequency. Examination of the power spectrum points to that the kinetic energy of the corotating plasma as a source of increase of plasma temperature. This study shows that turbulent fluctuations themselves are not good candidates as a plasma heating mechanism. External pressure fluctuation however, can be used to convert kinetic energy of the plasma flow into thermal.
Studies on the mechanical and thermal stability of Calotropis gigantea fibre-reinforced bran nano particulates epoxy composite
Authors: Raja Thandavamoorthy , Devarajan Yuvarajan , Thanappan Subash
Published: September 2023

In recent trends, the usage of synthetic materials has been reduced by introducing natural fibres for lightweight applications. In this study, Madar (Calotropis gigantea) fibre is selected for the reinforcement phase (40%), and the epoxy polymer is blended with bran filler selected as a matrix material. To calculate hybrid composite mechanical characteristics, five composite laminates with different fibre/filler weight ratios were made. The results show that when the weight ratio of madar fibre increased, the superior mechanical properties were observed in the composite laminate sample (A), such as tensile strength (20.85 MPa), flexural strength (24.14 MPa), impact energy absorption (23 J) compared with an increasing the weight ratio of bran nanofiller to this composite material. At the same time, increasing bran nanofillers can improve thermal stability up to 445 °C of degrading temperature. To analyse the surface interaction between the madar fibres, bran nanofillers, and epoxy matrix by conducting the scanning electron microscope (SEM) analysis before subjecting to the mechanical test and also to identify the failure mode by conducting the SEM test after the laminates are broken during the mechanical tests of the hybrid composite.
Topological phase transition in the antiferromagnetic topological insulator MnBi$$_2$$Te$$_4$$ from the point of view of axion-like state realization
Authors: Shikin A. M. , Estyunina T. P. , Eryzhenkov A. V. , Zaitsev N. L. , Tarasov A. V.
Published: September 2023

This work aims to study the conditions of topological phase transition (TPT) between the topological and trivial states in the antiferromagnetic topological insulator (AFM TI) MnBi$$_2$$

2

Te$$_4$$

4

and propose some theory about the relationship of this TPT with the possibility of axion-like state realization in this material. Using the density functional approach we have analyzed the changes in the electronic and spin structure of topological surface states (TSSs) and the nearest conduction and valence bands (CB and VB) including the changes in the bulk band gap as well as the Dirac point (DP) gap in TSSs under variation of the spin-orbit coupling strength in the region of the TPT for infinite crystal and slab with a surface both. We have shown that in both cases the TPT occurs with inversion of the contributions of the Bi-$$p_z$$

p
z

and Te-$$p_z$$

p
z

states of different parity at the gap edges related to change in the gap sign. In the case of surface calculations, the Bi-$$p_z$$

p
z

and Te-$$p_z$$

p
z

states at the edges of the bulk band gap and their inversion at the TPT point are transformed into the TSSs with an energy gap at the DP. In this case the TPT takes place without closing the band gap, i.e. with a “jump” through zero and the formation of the nonzero gap during such a transition. Our calculations show that the TPT point is also characterized by an inversion of the out-of-plane spin polarization $$s_z$$

s
z

at the $$\Gamma$$
Γ
point for lower and upper parts of the Dirac cone and a significant spatial redistribution of the TSSs between the surface and the bulk. We suppose that the nonzero Dirac gap can have some relationship with the formation of the axion-like state, which presumably couples nonmagnetic spin-orbit and magnetic contributions at the boundary between the topological and trivial phases for a system with parameters close to the TPT conditions. A practically realized system is proposed - the AFM TI with a stoichiometry close to that of MnBi$$_2$$

2

Te$$_2$$

2

Se$$_2$$

2

with partial (about 50%) substitution of Te atoms for Se atoms in MnBi$$_2$$

2

Te$$_4$$

4

which can be an experimental platform for the implementation and experimental analysis of the TPT and the corresponding possibility of the axion-like state realization in Condensed Matter. Besides, such system could serve as a good platform for studying the dynamic axion effect, where the axion field fluctuations are maximised when a small external field is applied to the system which state is close to the TPT.
Fabrication of new composite NCuTiO2/CQD for photocatalytic degradation of ciprofloxacin and pharmaceutical wastewater treatment: degradation pathway, toxicity assessment
Authors: Noroozi Roghayeh , Gholami Mitra , Oskoei Vahide , Hesami Arani Mohsen , Mousavifard Seyedeh Azar , Nguyen Le Binh , Fattahi Mehdi
Published: September 2023

In this research, the photocatalytic degradation of CIP from aqueous solutions using CQD decorated on N-Cu co-doped titania (NCuTCQD) was made during two synthesis steps by sol–gel and hydrothermal methods. The fabricated catalysts were analyzed using various techniques, including XRD, FT-IR, BET, FESEM, EDX, and DRS. The results showed that N and Cu atoms were doped on TiO2and CQD was well deposited on NCuT. The investigation of effective operational parameters demonstrated that the complete removal of ciprofloxacin (CIP: 20 mg/L) could be achieved at pH 7.0, NCuTCQD4wt%: 0.8 g/L, and light intensity: 100 mW/cm2over 60 min reaction time. The O2•–and OH˙ radicals were identified as the primary reactive species during the decontamination process. The synthesized photocatalyst could be recycled after six consecutive cycles of CIP decomposition with an insignificant decrease in performance. Pharmaceutical wastewater was treated through the optimum degradation conditions which showed the photocatalytic degradation eliminated 89% of COD and 75% of TOC within 180 min. In the effluent toxicity evaluation, the EC50values for treated and untreated pharmaceutical wastewater increased from 62.50% to 140%, indicating that the NCuTCQD4wt%/Vis system can effectively reduce the toxic effects of pharmaceutical wastewater on aquatic environments.
Modelling lifespan reduction in an exogenous damage model of generic disease
Authors: Tobin Rebecca , Pridham Glen , Rutenberg Andrew D.
Published: September 2023

We model the effects of disease and other exogenous damage during human aging. Even when the exogenous damage is repaired at the end of acute disease, propagated secondary damage remains. We consider both short-term mortality effects due to (acute) exogenous damage and long-term mortality effects due to propagated damage within the context of a generic network model (GNM) of individual aging that simulates a U.S. population. Across a wide range of disease durations and severities we find that while excess short-term mortality is highest for the oldest individuals, the long-term years of life lost are highest for the youngest individuals. These appear to be universal effects of human disease. We support this conclusion with a phenomenological model coupling damage and mortality. Our results are consistent with previous lifetime mortality studies of atom bomb survivors and post-recovery health studies of COVID-19. We suggest that short-term health impact studies could complement lifetime mortality studies to better characterize the lifetime impacts of disease on both individuals and populations.
Nursery origin of yellowfin tuna in the western Atlantic Ocean: significance of Caribbean Sea and trans-Atlantic migrants
Authors: Rooker Jay R. , Sluis Michelle Zapp , Kitchens Larissa L. , Dance Michael A. , Falterman Brett , Lee Jessica M. , Liu Hui , Miller Nathaniel , Murua Hilario , Rooker Alexandra M. , Saillant Eric , Walter John , David Wells R. J.
Published: September 2023

Natural geochemical markers in the otolith of yellowfin tuna (Thunnus albacares) were used to establish nursery-specific signatures for investigating the origin of fish captured in the western Atlantic Ocean (WAO). Two classes of chemical markers (trace elements, stable isotopes) were used to first establish nursery-specific signatures of age-0 yellowfin tuna from four primary production zones in the Atlantic Ocean: Gulf of Mexico, Caribbean Sea, Cape Verde, and Gulf of Guinea. Next, mixture and individual assignment methods were applied to predict the origin of sub-adult and adult yellowfin tuna from two regions in the WAO (Gulf of Mexico, Mid Atlantic Bight) by relating otolith core signatures (corresponding to age-0 period) to baseline signatures of age-0 fish from each nursery. Significant numbers of migrants from Caribbean Sea and eastern Atlantic Ocean (EAO) production zones (Gulf of Guinea, Cape Verde) were detected in the WAO, suggesting that fisheries in this region were subsidized by outside spawning/nursery areas. Contributions from local production (Gulf of Mexico) were also evident in samples from both WAO fisheries, but highly variable from year to year. High levels of mixing by yellowfin tuna from the different production zones and pronounced interannual trends in nursery-specific contribution rates in the WAO emphasize the complex and dynamic nature of this species’ stock structure and population connectivity. Given that geographic shifts in distribution across national or political boundaries leads to governance and management challenges, this study highlights the need for temporally resolved estimates of nursery origin to refine assessment models and promote the sustainable harvest of this species.
Assessment of environmental and carcinogenic health hazards from heavy metal contamination in sediments of wetlands
Authors: Panda Bibhu Prasad , Mohanta Yugal Kishore , Paul Rakesh , Prusty B. Anjan Kumar , Parida Siba Prasad , Pradhan Abanti , Saravanan Muthupandian , Patowary Kaustuvmani , Jiang Guangming , Joshi Sanket J. , Sarma Hemen
Published: September 2023

Sediment contamination jeopardizes wetlands by harming aquatic organisms, disrupting food webs, and reducing biodiversity. Carcinogenic substances like heavy metals bioaccumulate in sediments and expose consumers to a greater risk of cancer. This study reports Pb, Cr, Cu, and Zn levels in sediments from eight wetlands in India. The Pb (51.25 ± 4.46 µg/g) and Cr (266 ± 6.95 µg/g) concentrations were highest in Hirakud, Cu (34.27 ± 2.2 µg/g) in Bhadrak, and Zn (55.45 ± 2.93 µg/g) in Koraput. The mean Pb, Cr, and Cu values in sediments exceeded the toxicity reference value. The contamination factor for Cr was the highest of the four metals studied at Hirakud (CF = 7.60) and Talcher (CF = 6.97). Furthermore, high and moderate positive correlations were observed between Cu and Zn (r = 0.77) and Pb and Cr (r = 0.36), respectively, across all sites. Cancer patients were found to be more concentrated in areas with higher concentrations of Pb and Cr, which are more carcinogenic. The link between heavy metals in wetland sediments and human cancer could be used to make policies that limit people's exposure to heavy metals and protect their health.
Theoretical study on the glycosidic C–C bond cleavage of 3’’-oxo-puerarin
Authors: Choi Jongkeun , Kim Yongho , Eser Bekir Engin , Han Jaehong
Published: September 2023

Puerarin, daidzein C-glucoside, was known to be biotransformed to daidzein by human intestinal bacteria, which is eventually converted to (S)-equol. The metabolic pathway of puerarin to daidzein by DgpABC of Dorea sp. PUE strain was reported as puerarin (1) → 3’’-oxo-puerarin (2) → daidzein (3) + hexose enediolone (C). The second reaction is the cleavage of the glycosidic C–C bond, supposedly through the quinoid intermediate (4). In this work, the glycosidic C–C bond cleavage reaction of 3’’-oxo-puerarin (2) was theoretically studied by means of DFT calculation to elucidate chemical reaction mechanism, along with biochemical energetics of puerarin metabolism. It was found that bioenergetics of puerarin metabolism is slightly endergonic by 4.99 kcal/mol, mainly due to the reaction step of hexose enediolone (C) to 3’’-oxo-glucose (A). The result implied that there could be additional biochemical reactions for the metabolism of hexose enediolone (C) to overcome the thermodynamic energy barrier of 4.59 kcal/mol. The computational study focused on the C–C bond cleavage of 3’’-oxo-puerarin (2) found that formation of the quinoid intermediate (4) was not accessible thermodynamically, rather the reaction was initiated by the deprotonation of 2’’C–H proton of 3’’-oxo-puerarin (2). The 2’’C-dehydro-3’’-oxo-puerarin (2a2C) anionic species produced hexose enediolone (C) and 8-dehydro-daidzein anion (3a8), and the latter quickly converted to daidzein through the daidzein anion (3a7). Our study also explains why the reverse reaction of C-glycoside formation from daidzein (3) and hexose enediolone (C) is not feasible.
The characteristics and influencing factors of spatial network of city-based innovation correlation in China: from the perspective of high tech zones
Authors: Zhang Hong , Jiang Lili , Zhou Jia , Chu Nanchen , Li Fengjiao
Published: September 2023

In the context of “space of flows”, city-based innovation correlation in driving economic growth is no longer limited to the traditional hierarchical structure. It is of great significance to explore Chinese cities innovation association network from the perspective of high-tech zones which gather a large number of innovation resources. Here our report is to provide new ideas for improving the innovation capability of high-tech zones and accelerating the construction of Chinese high-quality innovation system. Here we take 142 cities with high-tech zones as research samples, and explore the characteristics and influencing factors of spatial network of city-based innovation correlation in China, through modified gravity modelsocial, network analysis and QAP analysis. The results show that city-based innovation network is not closely connected, the number of redundant connection channels is low efficiency, showing a four-level spatial pattern of “Z” shaped spindle. Among them, degree centrality of cities in eastern China is higher than that in the western region, the core cities in central China play a bridging role, and western remote cities are easily affected by related cities. Moreover, there are four innovation cohesion subgroups, including the northern hinterland subgroup, the eastern coastal subgroup, the southern subgroup and the western cooperation subgroup. Furthermore, the results of the influencing factors analysis show the differences in administrative level, economic development level, openness to the outside world, and investment in technology are conducive to the innovation association between cities, while the similarities in spatial adjacency and industrial structure will promote the strong innovation association between cities.
Efficient parameter generation for constrained models using MCMC
Authors: Kravtsova Natalia , Chamberlin Helen M. , Dawes Adriana T.
Published: September 2023

Mathematical models of complex systems rely on parameter values to produce a desired behavior. As mathematical and computational models increase in complexity, it becomes correspondingly difficult to find parameter values that satisfy system constraints. We propose a Markov Chain Monte Carlo (MCMC) approach for the problem of constrained model parameter generation by designing a Markov chain that efficiently explores a model’s parameter space. We demonstrate the use of our proposed methodology to analyze responses of a newly constructed bistability-constrained model of protein phosphorylation to perturbations in the underlying protein network. Our results suggest that parameter generation for constrained models using MCMC provides powerful tools for modeling-aided analysis of complex natural processes.