bluuebunny/crossref_metadata_2025 huggingface dataset:
A survey of second-life batteries based on techno-economic perspective and applications-based analysis
Authors: Iqbal Huma , Sarwar Sohail , Kirli Desen , Shek Jonathan K. H. , Kiprakis Aristides E.
Published: April 2023

The penetration of electrical vehicles (EVs) is exponentially rising to decarbonize the transport sector resulting in the research problem regarding the future of their retired batteries. Landfill disposal poses an environmental hazard, therefore, recycling or reusing them as second-life batteries (SLBs) are the inevitable options. Reusing the EV batteries with significant remaining useful life in stationary storage applications maximizes the economic benefits while extending the useful lifetime before recycling. Following a critical review of the research in SLBs, the key areas were identified as accurate State of Health (SOH) estimation, optimization of health indicators, battery life cycle assessment including repurposing, End-Of-Life (EOL) extension techniques and significance of first-life degradation data on ageing in second-life applications. The inconsistencies found in the reviewed literature showed that the absence of degradation data from first as well as second life, has a serious impact on accurate remaining useful life (RUL) prediction and SOH estimation. This review, for the first time, critically surveyed the recent studies in the field of identification, selection and control of application-based health indicators in relation to the accurate SOH estimation, offering future research directions in this emerging research area. In addition to the technical challenges, this paper also analyzed the economic perspective of SLBs, highlighting the impact of accuracy in second-life SOH estimation and RUL extension on their projected revenue in stationary storage applications. Lack of standard business model based on future market trends of energy and battery pricing and governing policies for SLBs are identified as urgent research gaps.
Temporal effects on death by suicide: empirical evidence and possible molecular correlates
Authors: Bhagar R. , Le-Niculescu H. , Roseberry K. , Kosary K. , Daly C. , Ballew A. , Yard M. , Sandusky G. E. , Niculescu A. B.
Published: April 2023

Popular culture and medical lore have long postulated a connection between full moon and exacerbations of psychiatric disorders. We wanted to empirically analyze the hypothesis that suicides are increased during the period around full moons. We analyzed pre-COVID suicides from the Marion County Coroner’s Office (n = 776), and show that deaths by suicide are significantly increased during the week of the full moon (p = 0.037), with older individuals (age ≥ 55) showing a stronger effect (p = 0.019). We also examined in our dataset which hour of the day (3–4 pm, p = 0.035), and which month of the year (September, p = 0.09) show the most deaths by suicide. We had blood samples on a subset of the subjects (n = 45), which enabled us to look at possible molecular mechanisms. We tested a list of top blood biomarkers for suicidality (n = 154) from previous studies of ours 7, to assess which of them are predictive. The biomarkers for suicidality that are predictive of death by suicide during full moon, peak hour of day, and peak month of year, respectively, compared to outside of those periods, appear to be enriched in circadian clock genes. For full moon it is AHCYL2, ACSM3, AK2, and RBM3. For peak hour it is GSK3B, AK2, and PRKCB. For peak month it is TBL1XR1 and PRKCI. Half of these genes are modulated in expression by lithium and by valproate in opposite direction to suicidality, and all of them are modulated by depression and alcohol in the same direction as suicidality. These data suggest that there are temporal effects on suicidality, possibly mediated by biological clocks, pointing to changes in ambient light (timing and intensity) as a therapeutically addressable target to decrease suicidality, that can be coupled with psychiatric pharmacological and addiction treatment preventive interventions.
Effects of Long-Term Aerobic Exercise on Perivascular Adipose Tissue Function and Akt/eNOS/NO Pathway in Obese Rats
Authors: Wang Chaoge , Zhou Jie , Gao Dongdong , Wang Yarong , Guo Lianmeng , Liang Wenhao , Shi Niujin , Cheng Ran , Wang Han , Huang Junhao , Liao Jingwen , Hu Min
Published: April 2023

Background

Perivascular adipose tissue (PVAT) in obesity critically contributes to vascular dysfunction, which might be restored by long-term exercise. Protein kinase B/nitric oxide synthase/nitric oxide (Akt/eNOS/NO) down-regulation within PVAT might be involved in the impaired anti-contractile function of arteries. Therefore, the present study evaluated the effect of long-term aerobic exercise on PVAT function and the potential regulator during this process.

Methods

Male Sprague Dawley rats were divided into normal diet control group (NC), normal diet exercise group (NE), high-fat diet control group (HC), and high-fat diet exercise group (HE) (n = 12 in each group). Upon the establishment of obesity (20 weeks of high-fat diet), exercise program was performed on a treadmill for 17 weeks. After the intervention, circulating biomarkers and PVAT morphology were evaluated. Vascular contraction and relaxation were determined with or without PVAT. Production of NO and the phosphorylations of Akt (Ser473) and eNOS (Ser1177) within PVAT were quantified.

Results

Metabolic abnormalities, systemic inflammation, and circulating adipokines in obesity were significantly restored by long-term aerobic exercise (P < 0.05). The anti-contractile effect of PVAT was significantly enhanced by exercise in obese rats (P < 0.05), which was accompanied by a significant reduction in the PVAT mass and lipid droplet area (P < 0.05). Furthermore, the production of NO was significantly increased, and phosphorylation levels of Akt (Ser473) and eNOS (Ser1177) were also significantly promoted in PVAT by long-term aerobic exercise (P < 0.05).

Conclusion

Long-term aerobic exercise training restored PVAT morphology and anti-contractile function in obese rats, and enhanced the activation of the Akt/eNOS/NO signaling pathway in PVAT.
Controlling Uncertainty in Coalition Governments
Authors: Sozzi Fabio
Published: April 2023

Multiparty governments are based on delegation and compromises but, at the same time, coalition parties have at their disposal several legislative instruments to keep tabs on their partners. Whereas previous studies focused on policy divisiveness and issue salience as main factors able to explain parliamentary scrutiny, in this article we suggest uncertainty as a complementary factor. In particular, we theorize that the use of parliamentary questions (PQs) is a function not only of policy characteristics but also of actors involved in coalition governance. When ministers increase intra-coalition uncertainty, cabinet parties use PQs to extract information from ministers and to reduce uncertainty in policy implementation. Statistical analyses of all written and oral parliamentary questions in the Italian Chamber of Deputies between 2006 and 2018 support our main hypothesis that when intra-coalition uncertainty increases, coalition parties ask more questions of ‘hostile’ ministers.
Testing the National Identity Argument in a Time of Crisis – Evidence from Israel
Authors: Ariely Gal
Published: April 2023

This article explores the national identity argument in unsettled times by using the COVID-19 pandemic as a test case. It uses a longitudinal survey among Jewish Israelis to examine whether the pandemic influenced levels of national identity and solidarity and whether it altered their relationship. The findings indicate a clear reduction in levels of solidarity, national attachment, and national chauvinism over time. They also show that the positive connection between national attachment and solidarity grew stronger, while the connection between national chauvinism and solidarity became weaker and insignificant. These findings provide complex evidence for the national identity argument.
Modelling maize yield impacts of improved water and fertilizer management in southern Africa using cropping system model coupled to an agro-hydrological model at field and catchment scale
Authors: Lam Q. D. , Rötter R. P. , Rapholo E. , Ayisi K. , Nelson W. C. D. , Odhiambo J. , Foord S.
Published: April 2023

This study quantifies the effect of fertilizer and irrigation management on water use efficiency (WUE), crop growth and crop yield in sub-humid to semi-arid conditions of Limpopo Province, South Africa. An approach of coupling a cropping system model (DSSAT) with an agro-hydrological model (SWAT) was developed and applied to simulate crop yield at the field and catchment scale. Simulation results indicated that the application of fertilizer has a greater positive effect on maize yield than irrigation. WUE ranged from 0.10–0.57 kg/m3 (rainfed) to 0.84–1.39 kg/m3 (irrigated) and was positively correlated with fertilizer application rate. The combined application of the variants with deficit irrigation and fertilizer rate (120:60 kg N:P/ha) for maize turned out to be the best option, giving the highest WUE and increasing average yield by up to 5.7 t/ha compared to no fertilization and rainfed cultivation (1.3 t/ha). The simulated results at the catchment scale showed the considerable spatial variability of maize yield across agricultural fields with different soils, slopes and climate conditions. The average annual simulated maize yield across the catchment corresponding to the highest WUE ranged from 4.0 to 7.0 t/ha. The yield gaps ranged from 3.0 to 6.0 t/ha under deficit irrigation combined with 120N:60P kg/ha and ranged from 0.2 to 1.5 t/ha when only applying deficit irrigation but no fertilizer. This information can support regional decision makers to find appropriate interventions that aim at improving crop yield and WUE for catchments/regions.
The relationship between Porphyromonas gingivalis and oesophageal squamous cell carcinoma: a literature review
Authors: Kong Jinyu , Liu Yiwen , Qian Mengfan , Xing Ling , Gao Shegan
Published: April 2023

Oesophageal cancer is the most common gastrointestinal malignancy in China and one of the major causes of death due to cancer worldwide. The occurrence of oesophageal cancer is a multifactor, multistage, and multistep process influenced by heredity, the environment, and microorganisms. Specifically, bacterial infection may be involved in the process of tissue carcinogenesis by directly or indirectly influencing tumour occurrence and development. Porphyromonas gingivalis is an important pathogen causing periodontitis, and periodontitis can promote the occurrence of various tumours. An increasing number of studies to date have shown that P. gingivalis plays an important role in the occurrence and development of oesophageal cancer. Overall, exploring how P. gingivalis promotes oesophageal cancer occurrence and development and how it affects the prognosis of these patients is of great importance for the diagnosis, prevention, and treatment of this type of cancer. Herein, the latest progress is reviewed.
Barriers to advance care planning among patients with advanced serious illnesses: A national survey of health-care professionals in Singapore
Authors: Malhotra Chetna , Chaudhry Isha
Published: April 2023

Objectives

To assess the barriers that health-care professionals (HCPs) face in having advance care planning (ACP) conversations with patients suffering from advanced serious illnesses and to provide care consistent with patients’ documented preferences.

Methods

We conducted a national survey of HCPs trained in facilitating ACP conversations in Singapore between June and July 2021. HCPs responded to hypothetical vignettes about a patient with an advanced serious illness and rated the importance of barriers (HCP-, patient-, and caregiver-related) in (i) conducting and documenting ACP conversations and (ii) providing care consistent with documented preferences.

Results

Nine hundred eleven HCPs trained in facilitating ACP conversations responded to the survey; 57% of them had not facilitated any in the last 1 year. HCP factors were reported as the topmost barriers to facilitating ACP. These included lack of allocated time to have ACP conversations and ACP facilitation being time-consuming. Patient’s refusal to engage in ACP conversations and family experiencing difficulty in accepting patient’s poor prognosis were the topmost patient- and caregiver-related factors. Non-physician HCPs were more likely than physicians to report being fearful of upsetting the patient/family and lack of confidence in facilitating ACP conversations. About 70% of the physicians perceived caregiver factors (surrogate wanting a different course of treatment and family caregivers being conflicted about patients’ care) as barriers to providing care consistent with preferences.

Significance of results

Study findings suggest that ACP conversations be simplified, ACP training framework be improved, awareness regarding ACP among patients, caregivers, and general public be increased, and ACP be made widely accessible.
Ocean Warm Skin Signals Observed by Saildrone at High Latitudes
Authors: Jia Chong , Minnett Peter J.
Published: April 2023

The existence of a cool sea surface skin layer in the global ocean during both day and night is generally recognized. However, a warm skin should be present if the total surface net heat flux () were to be from the atmosphere into ocean. Saildrone, an advanced uncrewed surface vehicle, has been shown to be able to provide sufficiently accurate sea skin temperature (SSTskin) and subsurface temperature (SSTdepth) data at high latitudes. Using those SST data along with meteorological parameters from a Saildrone deployed in the Arctic in the summer of 2019, some warm skin layers were identified due to the gain resulting from the combined effect of positive air‐sea temperature difference, humid surface air and cloudy skies. Furthermore, most warm skins here were found during and shortly after rainfall events. It is essential to incorporate the ability to simulate warm skin layers in the present cool skin models.
Solar Wind Protons in the Diamagnetic Cavity at Comet 67P/Churyumov‐Gerasimenko
Authors: Goetz Charlotte , Scharré Lucie , Wedlund Cyril Simon , Moeslinger Anja , Nilsson Hans , Odelstad Elias , Taylor Matthew G. G. T. , Volwerk Martin
Published: April 2023

The plasma environment at a comet can be divided into different regions with distinct plasma characteristics. Two such regions are the solar wind ion cavity, which refers to the part of the outer coma that does not contain any solar wind ions anymore; and the diamagnetic cavity, which is the region of unmagnetized plasma in the innermost coma. From theory and previous observations, it was thought that under usual circumstances no solar wind ion should be observable near or inside of the diamagnetic cavity. For the first time, we report on five observations that show that protons near solar wind energies can also be found inside the diamagnetic cavity. We characterize these proton signatures, where and when they occur, and discuss possible mechanisms that could lead to protons penetrating the inner coma and traversing the diamagnetic cavity boundary. By understanding these observations, we hope to better understand the interaction region of the comet with the solar wind under nonstandard conditions. The protons detected inside the diamagnetic cavity have directions and energies consistent with protons of solar wind origin. The five events occur only at intermediate gas production rates and low cometocentric distances. Charge transfer reactions, high solar wind dynamic pressure and a neutral gas outburst can be ruled out as causes. We suggest that the anomalous appearance of protons in the diamagnetic cavity is due to a specific solar wind configuration where the solar wind velocity is parallel to the interplanetary magnetic field, thus inhibiting mass‐loading and deflection.
Intestinal mucus components and secretion mechanisms: what we do and do not know
Authors: Song Chunyan , Chai Zhenglong , Chen Si , Zhang Hui , Zhang Xiaohong , Zhou Yuping
Published: April 2023

Damage to the colon mucus barrier, the first line of defense against microorganisms, is an important determinant of intestinal diseases such as inflammatory bowel disease and colorectal cancer, and disorder in extraintestinal organs. The mucus layer has attracted the attention of the scientific community in recent years, and with the discovery of new mucosal components, it has become increasingly clear that the mucosal barrier is a complex system composed of many components. Moreover, certain components are jointly involved in regulating the structure and function of the mucus barrier. Therefore, a comprehensive and systematic understanding of the functional components of the mucus layer is clearly warranted. In this review, we summarize the various functional components of the mucus layer identified thus far and describe their unique roles in shaping mucosal structure and function. Furthermore, we detail the mechanisms underlying mucus secretion, including baseline and stimulated secretion. In our opinion, baseline secretion can be categorized into spontaneous Ca2+ oscillation-mediated slow and continuous secretion and stimulated secretion, which is mediated by massive Ca2+ influx induced by exogenous stimuli. This review extends the current understanding of the intestinal mucus barrier, with an emphasis on host defense strategies based on fortification of the mucus layer.
Monolithic integration of embedded III-V lasers on SOI
Authors: Wei Wen-Qi , He An , Yang Bo , Wang Zi-Hao , Huang Jing-Zhi , Han Dong , Ming Ming , Guo Xuhan , Su Yikai , Zhang Jian-Jun , Wang Ting
Published: April 2023

Silicon photonic integration has gained great success in many application fields owing to the excellent optical device properties and complementary metal-oxide semiconductor (CMOS) compatibility. Realizing monolithic integration of III-V lasers and silicon photonic components on single silicon wafer is recognized as a long-standing obstacle for ultra-dense photonic integration, which can provide considerable economical, energy-efficient and foundry-scalable on-chip light sources, that has not been reported yet. Here, we demonstrate embedded InAs/GaAs quantum dot (QD) lasers directly grown on trenched silicon-on-insulator (SOI) substrate, enabling monolithic integration with butt-coupled silicon waveguides. By utilizing the patterned grating structures inside pre-defined SOI trenches and unique epitaxial method via hybrid molecular beam epitaxy (MBE), high-performance embedded InAs QD lasers with monolithically out-coupled silicon waveguide are achieved on such template. By resolving the epitaxy and fabrication challenges in such monolithic integrated architecture, embedded III-V lasers on SOI with continuous-wave lasing up to 85 °C are obtained. The maximum output power of 6.8 mW can be measured from the end tip of the butt-coupled silicon waveguides, with estimated coupling efficiency of approximately -6.7 dB. The results presented here provide a scalable and low-cost epitaxial method for the realization of on-chip light sources directly coupling to the silicon photonic components for future high-density photonic integration.
Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs
Authors: Perini Samuel , Filosi Michele ,   The Italian Autism Network, Allibrio Giovanni , Basadonne Ilaria , Benvenuto Arianna , Buono Serafino , Bravaccio Carmela , Casonato Carlo , Ceppi Elisa , Curatolo Paolo , Bernardina Bernardo Dalla , Da Ros Lucio , Darra Francesca , Eusebi Anna , Gabellone Alessandra , De Giacomo Andrea , Distefano Grazia , Donno Federica , Elia Maurizio , Fazzi Elisa , Gatta Michela , Giusto Stefania , Grittani Serenella , Lanzarini Evamaria , Malerba Giovanni , Mani Elisa , Manzi Barbara , Margari Lucia , Marzulli Lucia , Masi Gabriele , Mattei Paola , Mazzone Luigi , Molteni Massimo , Muglia Pierandrea , Musumeci Sebastiano , Narzisi Antonio , Pascotto Antonio , Pari Cinzia , Parmeggiani Antonia , Petruzzelli Maria Giuseppina , Raffagnato Alessia , Ratti Emiliangelo , Rossaro Maria Paola , Riccio Maria Pia , Rizzini Paolo , Scifo Renato , Siracusano Martina , Tancredi Raffaella , Tiberti Alessandra , Trabetti Elisabetta , Traverso Annalisa , Venuti Paola , Zoccante Leonardo , Zuddas Alessandro , Domenici Enrico
Published: April 2023

While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations
Authors: Yahia Ashraf , Hamed Ahlam A. A. , Mohamed Inaam N. , Elseed Maha A. , Salih Mustafa A. , El-sadig Sarah M. , Siddig Hassab Elrasoul , Nasreldien Ali Elsir Musa , Abdullah Mohamed Ahmed , Elzubair Maha , Omer Farouk Yassen , Bakhiet Aisha Motwakil , Abubaker Rayan , Abozar Fatima , Adil Rawaa , Emad Sara , Musallam Mhammed Alhassan , Eltazi Isra Z. M. , Omer Zulfa , Malik Hiba , Mohamed Mayada O. E. , Elhassan Ali A. , Mohamed Eman O. E. , Ahmed Ahmed K. M. A. , Ahmed Elhami A. A. , Eltaraifee Esraa , Hussein Bidour K. , Abd Allah Amal S. I. , Salah Lina , Nimir Mohamed , Tag Elseed Omnia M. , Elhassan Tasneem E. A. , Elbashier Abubakr , Alfadul Esraa S. A. , Fadul Moneeb , Ali Khalil F. , Taha Shaimaa Omer M. A. , Bushara Elfatih E. , Amin Mutaz , Koko Mahmoud , Ibrahim Muntaser E. , Ahmed Ammar E. , Elsayed Liena E. O. , Stevanin Giovanni
Published: April 2023

Hereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52–59% (31–35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.
Retinoic acid signaling modulation guides in vitro specification of human heart field-specific progenitor pools
Authors: Zawada Dorota , Kornherr Jessica , Meier Anna B. , Santamaria Gianluca , Dorn Tatjana , Nowak-Imialek Monika , Ortmann Daniel , Zhang Fangfang , Lachmann Mark , Dreßen Martina , Ortiz Mariaestela , Mascetti Victoria L. , Harmer Stephen C. , Nobles Muriel , Tinker Andrew , De Angelis Maria Teresa , Pedersen Roger A. , Grote Phillip , Laugwitz Karl-Ludwig , Moretti Alessandra , Goedel Alexander
Published: April 2023

Cardiogenesis relies on the precise spatiotemporal coordination of multiple progenitor populations. Understanding the specification and differentiation of these distinct progenitor pools during human embryonic development is crucial for advancing our knowledge of congenital cardiac malformations and designing new regenerative therapies. By combining genetic labelling, single-cell transcriptomics, and ex vivo human-mouse embryonic chimeras we uncovered that modulation of retinoic acid signaling instructs human pluripotent stem cells to form heart field-specific progenitors with distinct fate potentials. In addition to the classical first and second heart fields, we observed the appearance of juxta-cardiac field progenitors giving rise to both myocardial and epicardial cells. Applying these findings to stem-cell based disease modelling we identified specific transcriptional dysregulation in first and second heart field progenitors derived from stem cells of patients with hypoplastic left heart syndrome. This highlights the suitability of our in vitro differentiation platform for studying human cardiac development and disease.
Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota
Authors: Jaunet-Lahary Titouan , Shimamura Tatsuro , Hayashi Masahiro , Nomura Norimichi , Hirasawa Kouta , Shimizu Tetsuya , Yamashita Masao , Tsutsumi Naotaka , Suehiro Yuta , Kojima Keiichi , Sudo Yuki , Tamura Takashi , Iwanari Hiroko , Hamakubo Takao , Iwata So , Okazaki Kei-ichi , Hirai Teruhisa , Yamashita Atsuko
Published: April 2023

An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.
Nanoscale thermodynamics needs the concept of a disjoining chemical potential
Authors: Dong W.
Published: April 2023

Disjoining pressure was discovered by Derjaguin in 1930’s, which describes the difference between the pressure of a strongly confined fluid and the corresponding one in a bulk phase. It has been revealed recently that the disjoining pressure is at the origin of distinct differential and integral surface tensions for strongly confined fluids. Here we show how the twin concept, disjoining chemical potential, arises in a reminiscent way although it comes out eighty years later. This twin concept advances our understanding of nanoscale thermodynamics. Ensemble-dependence (or environment-dependence) is one hallmark of thermodynamics of small systems. We show that integral surface tension is ensemble-dependent while differential surface tension is not. Moreover, two generalized Gibbs-Duhem equations involving integral surface tensions are derived, as well as two additional adsorption equations relating surface tensions to adsorption-induced strains. All the results obtained in this work further evidence that an approach alternative of Hill’s nanothermodynamics is possible, by extending Gibbs surface thermodynamics instead of resorting to Hill’s replica trick. Moreover, we find a compression-expansion hysteresis without any underlying phase transition.
Cellular differentiation into hyphae and spores in halophilic archaea
Authors: Tang Shu-Kun , Zhi Xiao-Yang , Zhang Yao , Makarova Kira S. , Liu Bing-Bing , Zheng Guo-Song , Zhang Zhen-Peng , Zheng Hua-Jun , Wolf Yuri I. , Zhao Yu-Rong , Jiang Song-Hao , Chen Xi-Ming , Li En-Yuan , Zhang Tao , Chen Pei-Ru , Feng Yu-Zhou , Xiang Ming-Xian , Lin Zhi-Qian , Shi Jia-Hui , Chang Cheng , Zhang Xue , Li Rui , Lou Kai , Wang Yun , Chang Lei , Yin Min , Yang Ling-Ling , Gao Hui-Ying , Zhang Zhong-Kai , Tao Tian-Shen , Guan Tong-Wei , He Fu-Chu , Lu Yin-Hua , Cui Heng-Lin , Koonin Eugene V. , Zhao Guo-Ping , Xu Ping
Published: April 2023

Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
Cellcano: supervised cell type identification for single cell ATAC-seq data
Authors: Ma Wenjing , Lu Jiaying , Wu Hao
Published: April 2023

Computational cell type identification is a fundamental step in single-cell omics data analysis. Supervised celltyping methods have gained increasing popularity in single-cell RNA-seq data because of the superior performance and the availability of high-quality reference datasets. Recent technological advances in profiling chromatin accessibility at single-cell resolution (scATAC-seq) have brought new insights to the understanding of epigenetic heterogeneity. With continuous accumulation of scATAC-seq datasets, supervised celltyping method specifically designed for scATAC-seq is in urgent need. Here we develop Cellcano, a computational method based on a two-round supervised learning algorithm to identify cell types from scATAC-seq data. The method alleviates the distributional shift between reference and target data and improves the prediction performance. After systematically benchmarking Cellcano on 50 well-designed celltyping tasks from various datasets, we show that Cellcano is accurate, robust, and computationally efficient. Cellcano is well-documented and freely available at https://marvinquiet.github.io/Cellcano/.
MAIT cell inhibition promotes liver fibrosis regression via macrophage phenotype reprogramming
Authors: Mabire Morgane , Hegde Pushpa , Hammoutene Adel , Wan Jinghong , Caër Charles , Sayegh Rola Al , Cadoux Mathilde , Allaire Manon , Weiss Emmanuel , Thibault-Sogorb Tristan , Lantz Olivier , Goodhardt Michèle , Paradis Valérie , de la Grange Pierre , Gilgenkrantz Hélène , Lotersztajn Sophie
Published: April 2023

Recent data have shown that liver fibrosis can regress even at later stages of cirrhosis and shifting the immune response from pro-inflammatory towards a resolutive profile is considered as a promising option. The immune regulatory networks that govern the shift of the inflammatory phenotype and thus potential reversal of liver fibrosis are lesser known. Here we show that in precision-cut human liver slices obtained from patients with end-stage fibrosis and in mouse models, inhibiting Mucosal-Associated Invariant T (MAIT) cells using pharmacological or antibody-driven approaches, limits fibrosis progression and even regresses fibrosis, following chronic toxic- or non-alcoholic steatohepatitis (NASH)-induced liver injury. Mechanistic studies, combining RNA sequencing, in vivo functional studies (performed in male mice) and co-culture experiments indicate that disruption of the MAIT cell-monocyte/macrophage interaction results in resolution of fibrosis both by increasing the frequency of restorative Ly6Clo at the expenses of pro-fibrogenic Ly6Chi monocyte-derived macrophages and promoting an autophagic phenotype in both subsets. Thus, our data show that MAIT cell activation and the consequential phenotype shift of liver macrophages are important pathogenic features of liver fibrosis and could be targeted by anti-fibrogenic therapy.
Parabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice
Authors: Zhao Qi , Dai Man-Yun , Huang Ruo-Yue , Duan Jing-Yi , Zhang Ting , Bao Wei-Min , Zhang Jing-Yi , Gui Shao-Qiang , Xia Shu-Min , Dai Cong-Ting , Tang Ying-Mei , Gonzalez Frank J. , Li Fei
Published: April 2023

Parabacteroides distasonis (P. distasonis) plays an important role in human health, including diabetes, colorectal cancer and inflammatory bowel disease. Here, we show that P. distasonis is decreased in patients with hepatic fibrosis, and that administration of P. distasonis to male mice improves thioacetamide (TAA)- and methionine and choline-deficient (MCD) diet-induced hepatic fibrosis. Administration of P. distasonis also leads to increased bile salt hydrolase (BSH) activity, inhibition of intestinal farnesoid X receptor (FXR) signaling and decreased taurochenodeoxycholic acid (TCDCA) levels in liver. TCDCA produces toxicity in mouse primary hepatic cells (HSCs) and induces mitochondrial permeability transition (MPT) and Caspase-11 pyroptosis in mice. The decrease of TCDCA by P. distasonis improves activation of HSCs through decreasing MPT-Caspase-11 pyroptosis in hepatocytes. Celastrol, a compound reported to increase P. distasonis abundance in mice, promotes the growth of P. distasonis with concomitant enhancement of bile acid excretion and improvement of hepatic fibrosis in male mice. These data suggest that supplementation of P. distasonis may be a promising means to ameliorate hepatic fibrosis.
Single-shot polarimetry of vector beams by supervised learning
Authors: Pierangeli Davide , Conti Claudio
Published: April 2023

States of light encoding multiple polarizations - vector beams - offer unique capabilities in metrology and communication. However, their practical application is limited by the lack of methods for measuring many polarizations in a scalable and compact way. Here we demonstrate polarimetry of vector beams in a single shot without any polarization optics. We map the beam polarization content into a spatial intensity distribution through light scattering and exploit supervised learning for single-shot measurements of multiple polarizations. We characterize structured light encoding up to nine polarizations with accuracy beyond 95% on each Stokes parameter. The method also allows us to classify beams with an unknown number of polarization modes, a functionality missing in conventional techniques. Our findings enable a fast and compact polarimeter for polarization-structured light, a general tool that may radically impact optical devices for sensing, imaging, and computing.
Mapping the pathways of photo-induced ion migration in organic-inorganic hybrid halide perovskites
Authors: Kim Taeyong , Park Soyeon , Iyer Vasudevan , Shaheen Basamat , Choudhry Usama , Jiang Qi , Eichman Gage , Gnabasik Ryan , Kelley Kyle , Lawrie Benjamin , Zhu Kai , Liao Bolin
Published: April 2023

Organic-inorganic hybrid perovskites exhibiting exceptional photovoltaic and optoelectronic properties are of fundamental and practical interest, owing to their tunability and low manufacturing cost. For practical applications, however, challenges such as material instability and the photocurrent hysteresis occurring in perovskite solar cells under light exposure need to be understood and addressed. While extensive investigations have suggested that ion migration is a plausible origin of these detrimental effects, detailed understanding of the ion migration pathways remains elusive. Here, we report the characterization of photo-induced ion migration in perovskites using in situ laser illumination inside a scanning electron microscope, coupled with secondary electron imaging, energy-dispersive X-ray spectroscopy and cathodoluminescence with varying primary electron energies. Using methylammonium lead iodide and formamidinium lead iodide as model systems, we observed photo-induced long-range migration of halide ions over hundreds of micrometers and elucidated the transport pathways of various ions both near the surface and inside the bulk of the samples, including a surprising finding of the vertical migration of lead ions. Our study provides insights into ion migration processes in perovskites that can aid perovskite material design and processing in future applications.
Macroscopic transition metal dichalcogenides monolayers with uniformly high optical quality
Authors: Li Qiuyang , Alfrey Adam , Hu Jiaqi , Lydick Nathanial , Paik Eunice , Liu Bin , Sun Haiping , Lu Yang , Wang Ruoyu , Forrest Stephen , Deng Hui
Published: April 2023

The unique optical properties of transition metal dichalcogenide (TMD) monolayers have attracted significant attention for both photonics applications and fundamental studies of low-dimensional systems. TMD monolayers of high optical quality, however, have been limited to micron-sized flakes produced by low-throughput and labour-intensive processes, whereas large-area films are often affected by surface defects and large inhomogeneity. Here we report a rapid and reliable method to synthesize macroscopic-scale TMD monolayers of uniform, high optical quality. Using 1-dodecanol encapsulation combined with gold-tape-assisted exfoliation, we obtain monolayers with lateral size > 1 mm, exhibiting exciton energy, linewidth, and quantum yield uniform over the whole area and close to those of high-quality micron-sized flakes. We tentatively associate the role of the two molecular encapsulating layers as isolating the TMD from the substrate and passivating the chalcogen vacancies, respectively. We demonstrate the utility of our encapsulated monolayers by scalable integration with an array of photonic crystal cavities, creating polariton arrays with enhanced light-matter coupling strength. This work provides a pathway to achieving high-quality two-dimensional materials over large areas, enabling research and technology development beyond individual micron-sized devices.
Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi
Authors: Gupta Yogesh K. , Marcelino-Guimarães Francismar C. , Lorrain Cécile , Farmer Andrew , Haridas Sajeet , Ferreira Everton Geraldo Capote , Lopes-Caitar Valéria S. , Oliveira Liliane Santana , Morin Emmanuelle , Widdison Stephanie , Cameron Connor , Inoue Yoshihiro , Thor Kathrin , Robinson Kelly , Drula Elodie , Henrissat Bernard , LaButti Kurt , Bini Aline Mara Rudsit , Paget Eric , Singan Vasanth , Daum Christopher , Dorme Cécile , van Hoek Milan , Janssen Antoine , Chandat Lucie , Tarriotte Yannick , Richardson Jake , Melo Bernardo do Vale Araújo , Wittenberg Alexander H. J. , Schneiders Harrie , Peyrard Stephane , Zanardo Larissa Goulart , Holtman Valéria Cristina , Coulombier-Chauvel Flavie , Link Tobias I. , Balmer Dirk , Müller André N. , Kind Sabine , Bohnert Stefan , Wirtz Louisa , Chen Cindy , Yan Mi , Ng Vivian , Gautier Pierrick , Meyer Maurício Conrado , Voegele Ralf Thomas , Liu Qingli , Grigoriev Igor V. , Conrath Uwe , Brommonschenkel Sérgio H. , Loehrer Marco , Schaffrath Ulrich , Sirven Catherine , Scalliet Gabriel , Duplessis Sébastien , van Esse H. Peter
Published: April 2023

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations
Authors: Brown Malory O. , Olagunju Babatunde O. , Giner José-Luis , Welander Paula V.
Published: April 2023

Sterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.
Experimental cheat-sensitive quantum weak coin flipping
Authors: Neves Simon , Yacoub Verena , Chabaud Ulysse , Bozzio Mathieu , Kerenidis Iordanis , Diamanti Eleni
Published: April 2023

As in modern communication networks, the security of quantum networks will rely on complex cryptographic tasks that are based on a handful of fundamental primitives. Weak coin flipping (WCF) is a significant such primitive which allows two mistrustful parties to agree on a random bit while they favor opposite outcomes. Remarkably, perfect information-theoretic security can be achieved in principle for quantum WCF. Here, we overcome conceptual and practical issues that have prevented the experimental demonstration of this primitive to date, and demonstrate how quantum resources can provide cheat sensitivity, whereby each party can detect a cheating opponent, and an honest party is never sanctioned. Such a property is not known to be classically achievable with information-theoretic security. Our experiment implements a refined, loss-tolerant version of a recently proposed theoretical protocol and exploits heralded single photons generated by spontaneous parametric down conversion, a carefully optimized linear optical interferometer including beam splitters with variable reflectivities and a fast optical switch for the verification step. High values of our protocol benchmarks are maintained for attenuation corresponding to several kilometers of telecom optical fiber.
Farrerol directly activates the deubiqutinase UCHL3 to promote DNA repair and reprogramming when mediated by somatic cell nuclear transfer
Authors: Zhang Weina , Wang Mingzhu , Song Zhiwei , Fu Qianzheng , Chen Jiayu , Zhang Weitao , Gao Shuai , Sun Xiaoxiang , Yang Guang , Zhang Qiang , Yang Jiaqing , Tang Huanyin , Wang Haiyan , Kou Xiaochen , Wang Hong , Mao Zhiyong , Xu Xiaojun , Gao Shaorong , Jiang Ying
Published: April 2023

Farrerol, a natural flavanone, promotes homologous recombination (HR) repair to improve genome-editing efficiency, but the specific protein that farrerol directly targets to regulate HR repair and the underlying molecular mechanisms have not been determined. Here, we find that the deubiquitinase UCHL3 is the direct target of farrerol. Mechanistically, farrerol enhanced the deubiquitinase activity of UCHL3 to promote RAD51 deubiquitination, thereby improving HR repair. Importantly, we find that embryos of somatic cell nuclear transfer (SCNT) exhibited defective HR repair, increased genomic instability and aneuploidy, and that the farrerol treatment post nuclear transfer enhances HR repair, restores transcriptional and epigenetic network, and promotes SCNT embryo development. Ablating UCHL3 significantly attenuates farrerol-mediated stimulation in HR and SCNT embryo development. In summary, we identify farrerol as an activator of the deubiquitinase UCHL3, highlighted the importance of HR and epigenetic changes in SCNT reprogramming and provide a feasible method to promote SCNT efficiency.
Direct synthesis of extra-heavy olefins from carbon monoxide and water
Authors: Wang Chuanhao , Du Junjie , Zeng Lin , Li Zhongling , Dai Yizhou , Li Xu , Peng Zijun , Wu Wenlong , Li Hongliang , Zeng Jie
Published: April 2023

Extra-heavy olefins (C12+=), feedstocks to synthesize a wide range of value-added products, are conventionally generated from fossil resources via energy-intensive wax cracking or multi-step processes. Fischer-Tropsch synthesis with sustainably obtained syngas as feed-in provides a potential way to produce C12+=, though there is a trade-off between enhancing C-C coupling and suppressing further hydrogenation of olefins. Herein, we achieve selective production of C12+=via the overall conversion of CO and water, denoted as Kölbel-Engelhardt synthesis (KES), in polyethylene glycol (PEG) over a mixture of Pt/Mo2N and Ru particles. KES provides a continuously high CO/H2 ratio, thermodynamically favoring chain propagation and olefin formation. PEG serves as a selective extraction agent to hinder hydrogenation of olefins. Under an optimal condition, the yield ratio of CO2 to hydrocarbons reaches the theoretical minimum, and the C12+= yield reaches its maximum of 1.79 mmol with a selectivity (among hydrocarbons) of as high as 40.4%.