bluuebunny/crossref_metadata_2025 huggingface dataset:
The Devil and Democracy in the Global South: Hugo Chávez's Transnational Populism
Authors: Simon Joshua , Parody Gina
Published: December 2023

In this article, we argue that the speeches and policy documents from the later period of Hugo Chávez's presidency exemplify ‘transnational populism’, a form of populist discourse that defies the close association between populism and nationalism that frames the scholarly literatures on both populism and Chávez. We explain why Chávez's populism took this distinctive form by reference to the history of international political thought in Latin America and the political context surrounding the creation of the Alianza Bolivariana para los Pueblos de Nuestra América (Bolivarian Alliance for the Peoples of Our America, ALBA). We suggest that while transnational populism may actually amplify the threat that other scholars have argued populist leaders pose to democratic institutions, it also offers an important corrective to how scholars think about the relationship between populism, democracy and international politics, suggesting that international institutions capable of restraining powerful states are essential to stabilising democracies in the Global South.
Eleven vowels of Imilike Igbo including ATR and RTR schwa
Authors: Akinbo Samuel , Ozburn Avery , Nweya Gerald , Pulleyblank Douglas
Published: December 2023

In this paper, we examine the acoustics of vowels in the Imilike [ìmìlìkè] dialect of Igbo (Igboid, Niger-Congo), which has not previously been done. While Standard Igbo has eight vowels, previous auditorily-based research has identified eleven vowels in Imilike. Like Standard Igbo, Imilike contrasts vowels in Advanced/Retracted Tongue Root (ATR vs. RTR). We find that there are eleven vowels, distinguished most reliably by F1, B1, energy (dB) of voiced sound below 500Hz and duration. The results of this study also suggest that RTR vowels in Imilike might involve the laryngeal constriction and movement that accompany pharyngealization. The ATR and RTR schwas have similar phonological distribution and acoustic patterns as the other ATR and RTR vowels in the language.
Development of trait-specific genetic stocks derived from wild Cicer species as novel sources of resistance to important diseases for chickpea improvement
Authors: Sharma Shivali , Sharma Mamta
Published: December 2023

Low level of resistance to major diseases such as ascochyta blight (AB), botrytis grey mould (BGM) and dry root rot (DRR) in the cultivated chickpea genepool necessitates harnessing wild Cicer species. Sixty-eight accessions belonging to eight annual wild Cicer species and seven chickpea cultivars were screened for AB, BGM and DRR under controlled environmental conditions over the years. Intra-accession variability was observed among wild Cicer accessions for each disease. Hence, progenies of single resistant plants were selected for further evaluations and the trait-specific genetic stocks (TGS) were developed for each disease after re-screening following the single seed descent method. For AB, a high level of resistance was identified in four accessions belonging to tertiary genepool species, ICC 17334 (Cicer judaicum), ICC 17302, ICC 17308 and ICC 20177 (C. bijugum). Nine accessions, ICC 17160, ICC 17264, ICC 17270, ICC 20170, ICC 20186, ICC 20225, ICC 20247, ICC 20251 and IG 72941 of primary (C. reticulatum) and one accession, ICC 20190 of secondary (C. echinospermum) genepool species were resistant to BGM whereas, four accessions, ICC 20187 (C. reticulatum) and ICC 20218, ICC 20244 and ICC 20257 (C. echinospermum) were resistant to DRR. Development and utilization of these TGS in chickpea pre-breeding will assist in developing disease-resistant chickpea cultivars with broad genetic base.
Adjoint Inversion of Near‐Field Pressure Gauge Recordings for Rapid and Accurate Tsunami Source Characterization
Authors: Xie Yuqing , Mohanna Saeed , Meng Lingsen , Zhou Tong , Ho Tung‐Cheng
Published: December 2023

We explore the potential of the adjoint‐state tsunami inversion method for rapid and accurate near‐field tsunami source characterization using S‐net, an array of ocean bottom pressure gauges. Compared to earthquake‐based methods, this method can obtain more accurate predictions for the initial water elevation of the tsunami source, including potential secondary sources, leading to accurate water height and wave run‐up predictions. Unlike finite‐fault tsunami source inversions, the adjoint method achieves high‐resolution results without requiring densely gridded Green's functions, reducing computation time. However, optimal results require a dense instrument network with sufficient azimuthal coverage. S‐net meets these requirements and reduces data collection time, facilitating the inversion and timely issuance of tsunami warnings. Since the method has not yet been applied to dense, near‐field data, we test it on synthetic waveforms of the 2011 Mw 9.0 Tohoku earthquake and tsunami, including triggered secondary sources. The results indicate that with a static source model without noise, using the first 5 min of the waveforms yields a favorable performance with an average accuracy score of 93%, and the largest error of predicted wave amplitudes ranges between −5.6 and 1.9 m. Using the first 20 min, secondary sources were clearly resolved. We also demonstrate the method's applicability using S‐net recordings of the 2016 Mw 6.9 Fukushima earthquake. The findings suggest that lower‐magnitude events require a longer waveform duration for accurate adjoint inversion. Moreover, the estimated stress drop obtained from inverting our obtained tsunami source, assuming uniform slip, aligns with estimations from recent studies.
Atypical cell death and insufficient matrix organization in long-bone growth plates from Tric-b-knockout mice
Authors: Ichimura Atsuhiko , Miyazaki Yuu , Nagatomo Hiroki , Kawabe Takaaki , Nakajima Nobuhisa , Kim Ga Eun , Tomizawa Masato , Okamoto Naoki , Komazaki Shinji , Kakizawa Sho , Nishi Miyuki , Takeshima Hiroshi
Published: December 2023

TRIC-A and TRIC-B proteins form homotrimeric cation-permeable channels in the endoplasmic reticulum (ER) and nuclear membranes and are thought to contribute to counterionic flux coupled with store Ca2+ release in various cell types. Serious mutations in the TRIC-B (also referred to as TMEM38B) locus cause autosomal recessive osteogenesis imperfecta (OI), which is characterized by insufficient bone mineralization. We have reported that Tric-b-knockout mice can be used as an OI model; Tric-b deficiency deranges ER Ca2+ handling and thus reduces extracellular matrix (ECM) synthesis in osteoblasts, leading to poor mineralization. Here we report irregular cell death and insufficient ECM in long-bone growth plates from Tric-b-knockout embryos. In the knockout growth plate chondrocytes, excess pro-collagen fibers were occasionally accumulated in severely dilated ER elements. Of the major ER stress pathways, activated PERK/eIF2α (PKR-like ER kinase/ eukaryotic initiation factor 2α) signaling seemed to inordinately alter gene expression to induce apoptosis-related proteins including CHOP (CCAAT/enhancer binding protein homologous protein) and caspase 12 in the knockout chondrocytes. Ca2+ imaging detected aberrant Ca2+ handling in the knockout chondrocytes; ER Ca2+ release was impaired, while cytoplasmic Ca2+ level was elevated. Our observations suggest that Tric-b deficiency directs growth plate chondrocytes to pro-apoptotic states by compromising cellular Ca2+-handling and exacerbating ER stress response, leading to impaired ECM synthesis and accidental cell death.
Epidemic graph diagrams as analytics for epidemic control in the data-rich era
Authors: Valdano Eugenio , Colombi Davide , Poletto Chiara , Colizza Vittoria
Published: December 2023

COVID-19 highlighted modeling as a cornerstone of pandemic response. But it also revealed that current models may not fully exploit the high-resolution data on disease progression, epidemic surveillance and host behavior, now available. Take the epidemic threshold, which quantifies the spreading risk throughout epidemic emergence, mitigation, and control. Its use requires oversimplifying either disease or host contact dynamics. We introduce the epidemic graph diagrams to overcome this by computing the epidemic threshold directly from arbitrarily complex data on contacts, disease and interventions. A grammar of diagram operations allows to decompose, compare, simplify models with computational efficiency, extracting theoretical understanding. We use the diagrams to explain the emergence of resistant influenza variants in the 2007–2008 season, and demonstrate that neglecting non-infectious prodromic stages of sexually transmitted infections biases the predicted epidemic risk, compromising control. The diagrams are general, and improve our capacity to respond to present and future public health challenges.
An updated nuclear-physics and multi-messenger astrophysics framework for binary neutron star mergers
Authors: Pang Peter T. H. , Dietrich Tim , Coughlin Michael W. , Bulla Mattia , Tews Ingo , Almualla Mouza , Barna Tyler , Kiendrebeogo Ramodgwendé Weizmann , Kunert Nina , Mansingh Gargi , Reed Brandon , Sravan Niharika , Toivonen Andrew , Antier Sarah , VandenBerg Robert O. , Heinzel Jack , Nedora Vsevolod , Salehi Pouyan , Sharma Ritwik , Somasundaram Rahul , Van Den Broeck Chris
Published: December 2023

The multi-messenger detection of the gravitational-wave signal GW170817, the corresponding kilonova AT2017gfo and the short gamma-ray burst GRB170817A, as well as the observed afterglow has delivered a scientific breakthrough. For an accurate interpretation of all these different messengers, one requires robust theoretical models that describe the emitted gravitational-wave, the electromagnetic emission, and dense matter reliably. In addition, one needs efficient and accurate computational tools to ensure a correct cross-correlation between the models and the observational data. For this purpose, we have developed the Nuclear-physics and Multi-Messenger Astrophysics framework NMMA. The code allows incorporation of nuclear-physics constraints at low densities as well as X-ray and radio observations of isolated neutron stars. In previous works, the NMMA code has allowed us to constrain the equation of state of supranuclear dense matter, to measure the Hubble constant, and to compare dense-matter physics probed in neutron-star mergers and in heavy-ion collisions, and to classify electromagnetic observations and perform model selection. Here, we show an extension of the NMMA code as a first attempt of analyzing the gravitational-wave signal, the kilonova, and the gamma-ray burst afterglow simultaneously. Incorporating all available information, we estimate the radius of a 1.4M⊙ neutron star to be $$R=11.9{8}_{-0.40}^{+0.35}$$
R
=
11.9

8

−
0.40

+
0.35

km.
Full hardware implementation of neuromorphic visual system based on multimodal optoelectronic resistive memory arrays for versatile image processing
Authors: Zhou Guangdong , Li Jie , Song Qunliang , Wang Lidan , Ren Zhijun , Sun Bai , Hu Xiaofang , Wang Wenhua , Xu Gaobo , Chen Xiaodie , Cheng Lan , Zhou Feichi , Duan Shukai
Published: December 2023

In-sensor and near-sensor computing are becoming the next-generation computing paradigm for high-density and low-power sensory processing. To fulfil a high-density and efficient neuromorphic visual system with fully hierarchical emulation of the retina and visual cortex, emerging multimodal neuromorphic devices for multi-stage processing and a fully hardware-implemented system with versatile image processing functions are still lacking and highly desirable. Here we demonstrate an emerging multimodal-multifunctional resistive random-access memory (RRAM) device array based on modified silk fibroin protein (MSFP), exhibiting both optoelectronic RRAM (ORRAM) mode featured by unique negative and positive photoconductance memory and electrical RRAM (ERRAM) mode featured by analogue resistive switching. A full hardware implementation of the artificial visual system with versatile image processing functions is realised for the first time, including ORRAM mode array for the in-sensor image pre-processing (contrast enhancement, background denoising, feature extraction) and ERRAM mode array for near-sensor high-level image recognition, which hugely improves the integration density, and simply the circuit design and the fabrication and integration complexity.
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics
Authors: Bittremieux Wout , Avalon Nicole E. , Thomas Sydney P. , Kakhkhorov Sarvar A. , Aksenov Alexander A. , Gomes Paulo Wender P. , Aceves Christine M. , Caraballo-Rodríguez Andrés Mauricio , Gauglitz Julia M. , Gerwick William H. , Huan Tao , Jarmusch Alan K. , Kaddurah-Daouk Rima F. , Kang Kyo Bin , Kim Hyun Woo , Kondić Todor , Mannochio-Russo Helena , Meehan Michael J. , Melnik Alexey V. , Nothias Louis-Felix , O’Donovan Claire , Panitchpakdi Morgan , Petras Daniel , Schmid Robin , Schymanski Emma L. , van der Hooft Justin J. J. , Weldon Kelly C. , Yang Heejung , Xing Shipei , Zemlin Jasmine , Wang Mingxun , Dorrestein Pieter C.
Published: December 2023

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or “suspects,” were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
Adult stem cell activity in naked mole rats for long-term tissue maintenance
Authors: Montazid Shamir , Bandyopadhyay Sheila , Hart Daniel W. , Gao Nan , Johnson Brian , Thrumurthy Sri G. , Penn Dustin J. , Wernisch Bettina , Bansal Mukesh , Altrock Philipp M. , Rost Fabian , Gazinska Patrycja , Ziolkowski Piotr , Hayee Bu’Hussain , Liu Yue , Han Jiangmeng , Tessitore Annamaria , Koth Jana , Bodmer Walter F. , East James E. , Bennett Nigel C. , Tomlinson Ian , Irshad Shazia
Published: December 2023

The naked mole rat (NMR), Heterocephalus glaber, the longest-living rodent, provides a unique opportunity to explore how evolution has shaped adult stem cell (ASC) activity and tissue function with increasing lifespan. Using cumulative BrdU labelling and a quantitative imaging approach to track intestinal ASCs (Lgr5+) in their native in vivo state, we find an expanded pool of Lgr5+ cells in NMRs, and these cells specifically at the crypt base (Lgr5+CBC) exhibit slower division rates compared to those in short-lived mice but have a similar turnover as human LGR5+CBC cells. Instead of entering quiescence (G0), NMR Lgr5+CBC cells reduce their division rates by prolonging arrest in the G1 and/or G2 phases of the cell cycle. Moreover, we also observe a higher proportion of differentiated cells in NMRs that confer enhanced protection and function to the intestinal mucosa which is able to detect any chemical imbalance in the luminal environment efficiently, triggering a robust pro-apoptotic, anti-proliferative response within the stem/progenitor cell zone.
Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina
Authors: Lyu Pin , Iribarne Maria , Serjanov Dmitri , Zhai Yijie , Hoang Thanh , Campbell Leah J. , Boyd Patrick , Palazzo Isabella , Nagashima Mikiko , Silva Nicholas J. , Hitchcock Peter F. , Qian Jiang , Hyde David R. , Blackshaw Seth
Published: December 2023

Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes through Müller glia (MG) reprogramming and asymmetric cell division that produces a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, do MG reprogram to a developmental retinal progenitor cell (RPC) state? Second, to what extent does regeneration recapitulate retinal development? And finally, does loss of different retinal cell subtypes induce unique MG regeneration responses? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. Here we show that injury induces MG to reprogram to a state similar to late-stage RPCs. However, there are major transcriptional differences between MGPCs and RPCs, as well as major transcriptional differences between activated MG and MGPCs when different retinal cell subtypes are damaged. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes.
Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis
Authors: Patitucci Cecilia , Hernández-Camacho Juan Diego , Vimont Elodie , Yde Sonny , Cokelaer Thomas , Chaze Thibault , Giai Gianetto Quentin , Matondo Mariette , Gazi Anastasia , Nemazanyy Ivan , Stroud David A. , Hock Daniella H. , Donnarumma Erminia , Wai Timothy
Published: December 2023

Hepatic steatosis is the result of imbalanced nutrient delivery and metabolism in the liver and is the first hallmark of Metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD is the most common chronic liver disease and involves the accumulation of excess lipids in hepatocytes, inflammation, and cancer. Mitochondria play central roles in liver metabolism yet the specific mitochondrial functions causally linked to MASLD remain unclear. Here, we identify Mitochondrial Fission Process 1 protein (MTFP1) as a key regulator of mitochondrial and metabolic activity in the liver. Deletion of Mtfp1 in hepatocytes is physiologically benign in mice yet leads to the upregulation of oxidative phosphorylation (OXPHOS) activity and mitochondrial respiration, independently of mitochondrial biogenesis. Consequently, liver-specific knockout mice are protected against high fat diet-induced steatosis and metabolic dysregulation. Additionally, Mtfp1 deletion inhibits mitochondrial permeability transition pore opening in hepatocytes, conferring protection against apoptotic liver damage in vivo and ex vivo. Our work uncovers additional functions of MTFP1 in the liver, positioning this gene as an unexpected regulator of OXPHOS and a therapeutic candidate for MASLD.
Cyclosporine A-resistant CAR-T cells mediate antitumour immunity in the presence of allogeneic cells
Authors: Zhang Yixi , Fang Hongyu , Wang Guocan , Yuan Guangxun , Dong Ruoyu , Luo Jijun , Lyu Yu , Wang Yajie , Li Peng , Zhou Chun , Yin Weiwei , Xiao Haowen , Sun Jie , Zeng Xun
Published: December 2023

Chimeric antigen receptor (CAR)-T therapy requires autologous T lymphocytes from cancer patients, a process that is both costly and complex. Universal CAR-T cell treatment from allogeneic sources can overcome this limitation but is impeded by graft-versus-host disease (GvHD) and host versus-graft rejection (HvGR). Here, we introduce a mutated calcineurin subunit A (CNA) and a CD19-specific CAR into the T cell receptor α constant (TRAC) locus to generate cells that are resistant to the widely used immunosuppressant, cyclosporine A (CsA). These immunosuppressant-resistant universal (IRU) CAR-T cells display improved effector function in vitro and anti-tumour efficacy in a leukemia xenograft mouse model in the presence of CsA, compared with CAR-T cells carrying wild-type CNA. Moreover, IRU CAR-T cells retain effector function in vitro and in vivo in the presence of both allogeneic T cells and CsA. Lastly, CsA withdrawal restores HvGR, acting as a safety switch that can eliminate IRU CAR-T cells. These findings demonstrate the efficacy of CsA-resistant CAR-T cells as a universal, ‘off-the-shelf’ treatment option.
Metallic micronutrients are associated with the structure and function of the soil microbiome
Authors: Dai Zhongmin , Guo Xu , Lin Jiahui , Wang Xiu , He Dan , Zeng Rujiong , Meng Jun , Luo Jipeng , Delgado-Baquerizo Manuel , Moreno-Jiménez Eduardo , Brookes Philip C. , Xu Jianming
Published: December 2023

The relationship between metallic micronutrients and soil microorganisms, and thereby soil functioning, has been little explored. Here, we investigate the relationship between metallic micronutrients (Fe, Mn, Cu, Zn, Mo and Ni) and the abundance, diversity and function of soil microbiomes. In a survey across 180 sites in China, covering a wide range of soil conditions the structure and function of the soil microbiome are highly correlated with metallic micronutrients, especially Fe, followed by Mn, Cu and Zn. These results are robust to controlling for soil pH, which is often reported as the most important predictor of the soil microbiome. An incubation experiment with Fe and Zn additions for five different soil types also shows that increased micronutrient concentration affects microbial community composition and functional genes. In addition, structural equation models indicate that micronutrients positively contribute to the ecosystem productivity, both directly (micronutrient availability to plants) and, to a lesser extent, indirectly (via affecting the microbiome). Our findings highlight the importance of micronutrients in explaining soil microbiome structure and ecosystem functioning.
Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics
Authors: Liu Andrew Bo , Lee Daniel , Jalihal Amogh Prabhav , Hanage William P. , Springer Michael
Published: December 2023

Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Air travel monitoring does not accelerate outbreak detection in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.
VWCE modulates amino acid-dependent mTOR signaling and coordinates with KICSTOR to recruit GATOR1 to the lysosomes
Authors: Zhao Tianyu , Guan Yuanyuan , Xu Chenchen , Wang Dong , Guan Jialiang , Liu Ying
Published: December 2023

The mechanistic target of rapamycin complex 1 (mTORC1) is a crucial regulator of cell growth. It senses nutrient signals and adjusts cellular metabolism accordingly. Deregulation of mTORC1 has been associated with metabolic diseases, cancer, and aging. Amino acid signals are transduced to mTORC1 through sensor proteins and two protein complexes named GATOR1 and GATOR2. In this study, we identify VWCE (von Willebrand factor C and EGF domains) as a negative regulator of amino acid-dependent mTORC1 signaling. Knockdown of VWCE promotes mTORC1 activity even in the absence of amino acids. VWCE interacts with the KICSTOR complex to facilitate the recruitment of GATOR1 to the lysosomes. Bioinformatic analysis reveals that expression of VWCE is reduced in prostate cancer. More importantly, overexpression of VWCE inhibits the development of prostate cancer. Therefore, VWCE may serve as a potential therapeutic target for the treatment of prostate cancers.
Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica
Authors: Cui Zhiyong , Zhong Yutao , Sun Zhijie , Jiang Zhennan , Deng Jingyu , Wang Qian , Nielsen Jens , Hou Jin , Qi Qingsheng
Published: December 2023

Succinic acid (SA) is an important C4-dicarboxylic acid. Microbial production of SA at low pH results in low purification costs and hence good overall process economics. However, redox imbalances limited SA biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, we engineer the strictly aerobic yeast Yarrowia lipolytica for efficient SA production without pH control. Introduction of the reductive TCA cycle into the cytosol of a succinate dehydrogenase-disrupted yeast strain causes arrested cell growth. Although adaptive laboratory evolution restores cell growth, limited NADH supply restricts SA production. Reconfiguration of the reductive SA biosynthesis pathway in the mitochondria through coupling the oxidative and reductive TCA cycle for NADH regeneration results in improved SA production. In pilot-scale fermentation, the engineered strain produces 111.9 g/L SA with a yield of 0.79 g/g glucose within 62 h. This study paves the way for industrial production of biobased SA.
Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family
Authors: Yang Jiao , Wu Ying , Zhang Pan , Ma Jianxiang , Yao Ying Jun , Ma Yan Lin , Zhang Lei , Yang Yongzhi , Zhao Changmin , Wu Jihua , Fang Xiangwen , Liu Jianquan
Published: December 2023

Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.
A unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis
Authors: Tezuka Takeaki , Mitsuyama Kyota , Date Risa , Ohnishi Yasuo
Published: December 2023

Bacteria of the genus Actinoplanes form sporangia that contain dormant sporangiospores which, upon contact with water, release motile spores (zoospores) through a process called sporangium dehiscence. Here, we set out to study the molecular mechanisms behind sporangium dehiscence in Actinoplanes missouriensis and discover a sigma/anti-sigma system with unique features. Protein σSsdA contains a functional sigma factor domain and an anti-sigma factor antagonist domain, while protein SipA contains an anti-sigma factor domain and an anti-sigma factor antagonist domain. Remarkably, the two proteins interact with each other via the anti-sigma factor antagonist domain of σSsdA and the anti-sigma factor domain of SipA. Although it remains unclear whether the SipA/σSsdA system plays direct roles in sporangium dehiscence, the system seems to modulate oxidative stress responses in zoospores. In addition, we identify a two-component regulatory system (RsdK-RsdR) that represses initiation of sporangium dehiscence.
Storage protein activator controls grain protein accumulation in bread wheat in a nitrogen dependent manner
Authors: Plessis Anne , Ravel Catherine , Risacher Thierry , Duchateau Nathalie , Dardevet Mireille , Merlino Marielle , Torney François , Martre Pierre
Published: December 2023

The expression of cereal grain storage protein (GSP) genes is controlled by a complex network of transcription factors (TFs). Storage protein activator (SPA) is a major TF acting in this network but its specific function in wheat (Triticum aestivum L.) remains to be determined. Here we generated an RNAi line in which expression of the three SPA homoeologs was reduced. In this line and its null segregant we analyzed GSP accumulation and expression of GSP and regulatory TF genes under two regimes of nitrogen availability. We show that down regulation of SPA decreases grain protein concentration at maturity under low but not high nitrogen supply. Under low nitrogen supply, the decrease in SPA expression also caused a reduction in the total quantity of GSP per grain and in the ratio of GSP to albumin-globulins, without significantly affecting GSP composition. The slight reduction in GSP gene expression measured in the SPA RNAi line under low nitrogen supply did not entirely account for the more significant decrease in GSP accumulation, suggesting that SPA regulates additional levels of GSP synthesis. Our results demonstrate a clear role of SPA in the regulation of grain nitrogen metabolism when nitrogen is a limiting resource.
Automated image quality assessment for selecting among multiple magnetic resonance image acquisitions in the German National Cohort study
Authors: Schuppert Christopher , Rospleszcz Susanne , Hirsch Jochen G. , Hoinkiss Daniel C. , Köhn Alexander , von Krüchten Ricarda , Russe Maximilian F. , Keil Thomas , Krist Lilian , Schmidt Börge , Michels Karin B. , Schipf Sabine , Brenner Hermann , Kröncke Thomas J. , Pischon Tobias , Niendorf Thoralf , Schulz-Menger Jeanette , Forsting Michael , Völzke Henry , Hosten Norbert , Bülow Robin , Zaitsev Maxim , Kauczor Hans-Ulrich , Bamberg Fabian , Günther Matthias , Schlett Christopher L.
Published: December 2023

In magnetic resonance imaging (MRI), the perception of substandard image quality may prompt repetition of the respective image acquisition protocol. Subsequently selecting the preferred high-quality image data from a series of acquisitions can be challenging. An automated workflow may facilitate and improve this selection. We therefore aimed to investigate the applicability of an automated image quality assessment for the prediction of the subjectively preferred image acquisition. Our analysis included data from 11,347 participants with whole-body MRI examinations performed as part of the ongoing prospective multi-center German National Cohort (NAKO) study. Trained radiologic technologists repeated any of the twelve examination protocols due to induced setup errors and/or subjectively unsatisfactory image quality and chose a preferred acquisition from the resultant series. Up to 11 quantitative image quality parameters were automatically derived from all acquisitions. Regularized regression and standard estimates of diagnostic accuracy were calculated. Controlling for setup variations in 2342 series of two or more acquisitions, technologists preferred the repetition over the initial acquisition in 1116 of 1396 series in which the initial setup was retained (79.9%, range across protocols: 73–100%). Image quality parameters then commonly showed statistically significant differences between chosen and discarded acquisitions. In regularized regression across all protocols, ‘structured noise maximum’ was the strongest predictor for the technologists’ choice, followed by ‘N/2 ghosting average’. Combinations of the automatically derived parameters provided an area under the ROC curve between 0.51 and 0.74 for the prediction of the technologists’ choice. It is concluded that automated image quality assessment can, despite considerable performance differences between protocols and anatomical regions, contribute substantially to identifying the subjective preference in a series of MRI acquisitions and thus provide effective decision support to readers.
Naïve, adult, captive chimpanzees do not socially learn how to make and use sharp stone tools
Authors: Bandini Elisa , Tennie Claudio
Published: December 2023

Although once regarded as a unique human feature, tool-use is widespread in the animal kingdom. Some of the most proficient tool-users are our closest living relatives, chimpanzees. These repertoires however consist primarily of tool use, rather than tool manufacture (for later use). Furthermore, most populations of chimpanzees use organic materials, such as sticks and leaves, rather than stones as tools. This distinction may be partly ecological, but it is also important as chimpanzees are often used as models for the evolution of human material culture, the oldest traces of which consist of manufactured sharp stone tools (so-called “flakes”). Thus, examining the conditions (if any) under which chimpanzees may develop flake manufacture and use can provide insight into the drivers of these behaviours in our own lineage. Previous studies on non-human apes’ ability to make and use flakes focused on enculturated apes, giving them full demonstrations of the behaviour immediately, without providing social information on the task in a stepwise manner. Here we tested naïve, captive chimpanzees (N = 4; three potentially enculturated and one unenculturated subject) in a social learning experimental paradigm to investigate whether enculturated and/or unenculturated chimpanzees would develop flake making and use after social information of various degrees (including a human demonstration) was provided in a scaffolded manner. Even though social learning opportunities were provided, neither the unenculturated subject nor any of the potentially enculturated subjects made or used flakes, in stark contrast to previous studies with enculturated apes. These data suggest that flake manufacture and use is outside of our tested group of captive chimpanzees’ individual and social learning repertoires. It also suggests that high levels of enculturation alongside human demonstrations (and/or training) may be required before captive chimpanzees can develop this behaviour.
A novel facile synthesis of metal nitride@metal oxide (BN/Gd2O3) nanocomposite and their antibacterial and anticancer activities
Authors: Mohsin Mayyadah H. , Khashan Khawla S. , Sulaiman Ghassan M. , Mohammed Hamdoon A. , Qureshi Kamal A. , Aspatwar Ashok
Published: December 2023

In this study, a novel core/shell nanocomposite structure (h-BN@Gd2O3 NCs) was created for the first time by combining hexagonal boron nitride (h-BN) with doped gadolinium oxide (Gd2O3) using different laser pulse numbers, i.e., 150, 338, and 772 pulses. We employed various analytical techniques, including mapping analysis, FE-SEM, EDS, HRTEM, SAED, XRD, zeta potential analysis, DLS, FTIR, Raman spectroscopy, and PL measurements, to characterize the synthesized h-BN, c-Gd2O3, and h-BN@Gd2O3 NCs (338 pulses). XRD results indicated hexagonal and cubic crystal structures for BN and Gd2O3, respectively, while EDS confirmed their chemical composition and elemental mapping. Chemical bonds between B–N–Gd, B–N–O, and Gd–O bands at 412, 455, 474, and 520 cm−1 were identified by FTIR analysis. The antimicrobial and anticancer activities of these NCs using agar well diffusion and MTT assays. They exhibited potent antibacterial properties against both Gram-positive and Gram-negative pathogens. Furthermore, NCs have reduced the proliferation of cancerous cells, i.e., human colon adenocarcinoma cells (HT-29) and human breast cancer cells (MCF-7), while not affecting the proliferation of the normal breast cell line (MCF-10). The anticancer efficacy of NCs was validated by the AO/EtBr assay, which confirmed apoptotic cell death. Blood compatibility on human erythrocytes was also confirmed by hemolytic and in vitro toxicity assessments. The compiled results of the study proposed these nanoparticles could be used as a promising drug delivery system and potentially in healthcare applications.
Temperature-dependent Fermi surface probed by Shubnikov–de Haas oscillations in topological semimetal candidates DyBi and HoBi
Authors: Nowakowska Paulina , Pavlosiuk Orest , Wiśniewski Piotr , Kaczorowski Dariusz
Published: December 2023

Rare earth-based monopnictides are among the most intensively studied groups of materials in which extremely large magnetoresistance has been observed. This study explores magnetotransport properties of two representatives of this group, DyBi and HoBi. The extreme magnetoresistance is discovered in DyBi and confirmed in HoBi. At $$T=2$$

T
=
2

 K and in $$B=14$$

B
=
14

 T for both compounds, magnetoresistance reaches the order of magnitude of $$10^4\%$$

10
4

%

. For both materials, standard Kohler’s rule is obeyed only in the temperature range from 50 to 300 K. At lower temperatures, extended Kohler’s rule has to be invoked because carrier concentrations and mobilities strongly change with temperature and magnetic field. This is further proven by the observation of a quite rare temperature-dependence of oscillation frequencies in Shubnikov–de Haas effect. Rate of this dependence clearly changes at Néel temperature, reminiscent of a novel magnetic band splitting. Multi-frequency character of the observed Shubnikov–de Haas oscillations points to the coexistence of electron- and hole-type Fermi pockets in both studied materials. Overall, our results highlight correlation of temperature dependence of the Fermi surface with the magnetotransport properties of DyBi and HoBi.
Urease inhibitors technologies as strategy to mitigate agricultural ammonia emissions and enhance the use efficiency of urea-based fertilizers
Authors: da Fonseca Adrianne Braga , Santos César , Nunes Ana Paula Pereira , Oliveira Damiany Pádua , de Melo Maria Elisa Araújo , Takayama Thalita , Mansur Bethânia Leite , de Jesus Fernandes Thales , do Carmo Alexandrino Gilson , Dias Marcos Altomani Neves , Guelfi Douglas
Published: December 2023

Experiments were conducted to evaluate the stability and degradation of NBPT under storage conditions and to quantify urease activity, ammonia losses by volatilization, and agronomic efficiency of urea treated with different urease inhibitors, measured in the field. Experiments included urea treated with 530 mg NBPT kg−1 (UNBPT) in contact with six P-sources (monoammonium phosphate-MAP; single superphosphate; triple superphosphate; P-Agrocote; P-Phusion; P-Policote), with two P-concentrations (30; 70%); the monitoring four N-technologies (SoILC; Limus; Nitrain; Anvol); and the application of conventional urea (UGRAN) or urea treated with urease inhibitors as topdressing in three maize fields, at three N rates. It is concluded that: the mixture of UNBPT and P-fertilizers is incompatible. When MAP granules were coated to control P-release (P-Agrocote), the degradation of NBPT was moderate (approximately 400 mg kg−1 at the end of the storage test). SoILC and Limus solvent technologies extended the NBPT half-life by up to 3.7 and 4.7 months, respectively. Under field, each inhibition technology reduced urease activity, and lowered the intensity of ammonia emission compared to UGRAN by 50–62%. Our results show that the concentration of NBPT is reduced by up to 53.7% for mixing with phosphates. In addition, even with coatings, the storage of mixtures of urea with NBPT and phosphates should be for a time that does not reduce the efficiency of the inhibitor after application, and this time under laboratory conditions was 168 h. The reduction of NBPT concentration in urea is reduced even in isolated storage, our results showed that the half-life time is variable according to the formulation used, being 4.7, 3.7, 2.8 and 2.7 days for Limus, SoILC, Nitrain and Anvol, respectively. The results of these NBPT formulations in the field showed that the average losses by volatilization in the three areas were: 15%, 16%, 17%, 19% and 39% of the N applied, for SoILC, Anvol, Nitrain, Limus and urea, respectively. The rate of nitrogen application affected all agronomic variables, with varied effects in Ingaí. Even without N, yields were higher than 9200 kg ha−1 of grains. The increase in nitrogen rates resulted in linear increases in production and N removal in Luminárias and Ingaí, but in Lavras, production decreased above 95.6 kg ha−1 of N. The highest production in Lavras (13,772 kg ha−1 of grains) occurred with 100 kg ha−1 of N. The application of Anvol reduced the removal of N in Ingaí.
Combining blood glucose and SpO2/FiO2 ratio facilitates prediction of imminent ventilatory needs in emergency room COVID-19 patients
Authors: Sakai Kazuya , Okoda Kai , Nishii Mototsugu , Saji Ryo , Ogawa Fumihiro , Abe Takeru , Takeuchi Ichiro
Published: December 2023

The increasing requirement of mechanical ventilation (MV) due to the novel coronavirus disease (COVID-19) is still a global threat. The aim of this study is to identify markers that can easily stratify the impending use of MV in the emergency room (ER). A total of 106 patients with COVID-19 requiring oxygen support were enrolled. Fifty-nine patients were provided MV 0.5 h (interquartile range: 0.3 to 1.4) post-admission. Clinical and laboratory data before intubation were collected. Using a multivariate logistic regression model, we identified four markers associated with the impending use of MV, including the ratio of peripheral blood oxygen saturation to fraction of inspired oxygen (SpO2/FiO2 ratio), alanine aminotransferase, blood glucose (BG), and lymphocyte counts. Among these markers, SpO2/FiO2 ratio and BG, which can be measured easily and immediately, showed higher accuracy (AUC: 0.88) than SpO2/FiO2 ratio alone (AUC: 0.84), despite no significant difference (DeLong test: P = 0.591). Moreover, even in patients without severe respiratory failure (SpO2/FiO2 ratio > 300), BG (> 138 mg/dL) was predictive of MV use. Measuring BG and SpO2/FiO2 ratio may be a simple and versatile new strategy to accurately identify ER patients with COVID-19 at high risk for the imminent need of MV.
Mechanisms and factors affecting the removal of minocycline from aqueous solutions using graphene-modified resorcinol formaldehyde aerogels
Authors: Yazdanbakhsh Amirhosein , Behzadi Alireza , Moghaddam Armaghan , Salahshoori Iman , Khonakdar Hossein Ali
Published: December 2023

In recent years, concerns about the presence of pharmaceutical compounds in wastewater have increased. Various types of residues of tetracycline family antibiotic compounds, which are widely used, are found in environmental waters in relatively low and persistent concentrations, adversely affecting human health and the environment. In this study, a resorcinol formaldehyde (RF) aerogel was prepared using the sol–gel method at resorcinol/catalyst ratio of 400 and resorcinol/water ratio of 2 and drying at ambient pressure for removing antibiotics like minocycline. Next, RF aerogel was modified with graphene and to increase the specific surface area and porosity of the modified sample and to form the graphene plates without compromising the interconnected porous three-dimensional structure of the aerogel. Also, the pores were designed according to the size of the minocycline particles on the meso- and macro-scale, which bestowed the modified sample the ability to remove a significant amount of the minocycline antibiotic from the aqueous solution. The removal percentage of the antibiotic obtained by UV–vis spectroscopy. Ultimately, the performance of prepared aerogels was investigated under various conditions, including adsorbent doses (4–10 mg), solution pHs (2–12), contact times of the adsorbent with the adsorbate (3–24 h), and initial concentration of antibiotic (40–100 mg/l). The results from the BET test demonstrated that the surface area of the resorcinol formaldehyde aerogel sample, which included 1 wt% graphene (RF-G1), exhibited an augmentation in comparison to the surface area of the pure aerogel. Additionally, it was noted that the removal percentage of minocycline antibiotic for both the unmodified and altered samples was 71.6% and 92.1% at the optimal pH values of 4 and 6, respectively. The adsorption capacity of pure and modified aerogel for the minocycline antibiotic was 358 and 460.5 mg/g, respectively. The adsorption data for the modified aerogel was studied by the pseudo-second-order model and the results obtained from the samples for antibiotic adsorption with this model revealed a favorable fit, which indicated that the chemical adsorption in the rapid adsorption of the antibiotic by the modified aerogel had occurred.
Controlling the Goos-Hänchen shift in a double prism structure using three-level Raman gain medium
Authors: Asiri Saeed , Wang Li-Gang
Published: December 2023

We propose a scheme to control the Goos-Hänchen (GH) shift of TE and TM reflected light beams in a double-prism structure, where a three-level Raman gain medium is filling the gap between the two prisms. We find that it is possible to control the GH shift in this structure by externally adjusting the optical properties of the Raman gain atomic medium while the gap width between the two prisms is fixed. Inspired by recent successful implementation of the double-prism configuration with an air gap to measure the GH shift, we expected that our proposal to control the GH shift can be achieved experimentally and used in different potential applications of the GH shift.
Dissecting the heterogeneity of “in the wild” stress from multimodal sensor data
Authors: Nagaraj Sujay , Goodday Sarah , Hartvigsen Thomas , Boch Adrien , Garg Kopal , Gowda Sindhu , Foschini Luca , Ghassemi Marzyeh , Friend Stephen , Goldenberg Anna
Published: December 2023

Stress is associated with numerous chronic health conditions, both mental and physical. However, the heterogeneity of these associations at the individual level is poorly understood. While data generated from individuals in their day-to-day lives “in the wild” may best represent the heterogeneity of stress, gathering these data and separating signals from noise is challenging. In this work, we report findings from a major data collection effort using Digital Health Technologies (DHTs) and frontline healthcare workers. We provide insights into stress “in the wild”, by using robust methods for its identification from multimodal data and quantifying its heterogeneity. Here we analyze data from the Stress and Recovery in Frontline COVID-19 Workers study following 365 frontline healthcare workers for 4–6 months using wearable devices and smartphone app-based measures. Causal discovery is used to learn how the causal structure governing an individual’s self-reported symptoms and physiological features from DHTs differs between non-stress and potential stress states. Our methods uncover robust representations of potential stress states across a population of frontline healthcare workers. These representations reveal high levels of inter- and intra-individual heterogeneity in stress. We leverage multiple stress definitions that span different modalities (from subjective to physiological) to obtain a comprehensive view of stress, as these differing definitions rarely align in time. We show that these different stress definitions can be robustly represented as changes in the underlying causal structure on and off stress for individuals. This study is an important step toward better understanding potential underlying processes generating stress in individuals.