bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-photon nanoprobes based on bioorganic nanoarchitectonics with a photo-oxidation enhanced emission mechanism
Authors: Li Shukun , Chang Rui , Zhao Luyang , Xing Ruirui , van Hest Jan C. M. , Yan Xuehai
Published: August 2023

Two-photon absorption (TPA) fluorescence imaging holds great promise in diagnostics and biomedicine owing to its unparalleled spatiotemporal resolution. However, the adaptability and applicability of currently available TPA probes, which act as a critical element for determining the imaging contrast effect, is severely challenged by limited photo-luminescence in vivo. This is particularly a result of uncontrollable aggregation that causes fluorescence quenching, and inevitable photo-oxidation in harsh physiological milieu, which normally leads to bleaching of the dye. Herein, we describe the remarkably enhanced TPA fluorescence imaging capacity of self-assembling near-infrared (NIR) cyanine dye-based nanoprobes (NPs), which can be explained by a photo-oxidation enhanced emission mechanism. Singlet oxygen generated during photo-oxidation enables chromophore dimerization to form TPA intermediates responsible for enhanced TPA fluorescence emission. The resulting NPs possess uniform size distribution, excellent stability, more favorable TPA cross-section and anti-bleaching ability than a popular TPA probe rhodamine B (RhB). These properties of cyanine dye-based TPA NPs promote their applications in visualizing blood circulation and tumoral accumulation in real-time, even to cellular imaging in vivo. The photo-oxidation enhanced emission mechanism observed in these near-infrared cyanine dye-based nanoaggregates opens an avenue for design and development of more advanced TPA fluorescence probes.
Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers
Authors: Deng Ting , Su Shichen , Yuan Xun , He Jinqiu , Huang Ying , Ma Jinbiao , Wang Jia
Published: August 2023

Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated RNAi pathway plays important roles in defending against viral infections and protecting genome integrity. During the maturation of siRNAs, two cofactors can regulate DmDcr-2’s functions: Loqs-PD that is required for dsRNA processing, and R2D2 that is essential for the subsequent loading of siRNAs into effector Ago2 to form RISC complexes. However, due to the lack of structural information, it is still unclear whether R2D2 and Loqs-PD affect the functions of DmDcr-2 simultaneously. Here we present several cryo-EM structures of DmDcr-2/R2D2/Loqs-PD complex bound to dsRNAs with various lengths by the Helicase domain. These structures revealed that R2D2 and Loqs-PD can bind to different regions of DmDcr-2 without interfering with each other. Furthermore, the cryo-EM results demonstrate that these complexes can form large oligomers and assemble into fibers. The formation and depolymerization of these oligomers are associated with ATP hydrolysis. These findings provide insights into the structural mechanism of DmDcr-2 and its cofactors during siRNA processing.
Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling
Authors: Vierra Nicholas C. , Ribeiro-Silva Luisa , Kirmiz Michael , van der List Deborah , Bhandari Pradeep , Mack Olivia A. , Carroll James , Le Monnier Elodie , Aicher Sue A. , Shigemoto Ryuichi , Trimmer James S.
Published: August 2023

Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.
Discovery and construction of surface kagome electronic states induced by p-d electronic hybridization in Co3Sn2S2
Authors: Huang Li , Kong Xianghua , Zheng Qi , Xing Yuqing , Chen Hui , Li Yan , Hu Zhixin , Zhu Shiyu , Qiao Jingsi , Zhang Yu-Yang , Cheng Haixia , Cheng Zhihai , Qiu Xianggang , Liu Enke , Lei Hechang , Lin Xiao , Wang Ziqiang , Yang Haitao , Ji Wei , Gao Hong-Jun
Published: August 2023

Kagome-lattice materials possess attractive properties for quantum computing applications, but their synthesis remains challenging. Herein, based on the compelling identification of the two cleavable surfaces of Co3Sn2S2, we show surface kagome electronic states (SKESs) on a Sn-terminated triangular Co3Sn2S2surface. Such SKESs are imprinted by verticalp-delectronic hybridization between the surface Sn (subsurface S) atoms and the buried Co kagome-lattice network in the Co3Sn layer under the surface. Owing to the subsequent lateral hybridization of the Sn and S atoms in a corner-sharing manner, the kagome symmetry and topological electronic properties of the Co3Sn layer is proximate to the Sn surface. The SKESs and both hybridizations were verified via qPlus non-contact atomic force microscopy (nc-AFM) and density functional theory calculations. The construction of SKESs with tunable properties can be achieved by the atomic substitution of surface Sn (subsurface S) with other group III-V elements (Se or Te), which was demonstrated theoretically. This work exhibits the powerful capacity of nc-AFM in characterizing localized topological states and reveals the strategy for synthesis of large-area transition-metal-based kagome-lattice materials using conventional surface deposition techniques.
A cage-on-MOF strategy to coordinatively functionalize mesoporous MOFs for manipulating selectivity in adsorption and catalysis
Authors: Liang Yu , Yang Xiaoxin , Wang Xiaoyu , Guan Zong-Jie , Xing Hang , Fang Yu
Published: August 2023

Functionalizing porous materials with capping agents generates hybrid materials with enhanced properties, while the challenge is how to improve the selectivity and maintain the porosity of the parent framework. Herein, we developed a “Cage-on-MOF” strategy to tune the recognition and catalytic properties of MOFs without impairing their porosity. Two types of porous coordination cages (PCCs) of opposite charges containing secondary binding groups were developed to coordinatively functionalize two distinct porous MOFs, namely MOF@PCC nanocomposites. We demonstrated that the surface-capped PCCs can act as “modulators” to effectively tune the surface charge, stability, and adsorption behavior of different host MOF particles. More importantly, the MOF@PCCs can serve as selective heterogeneous catalysts for condensation reactions to achieve reversed product selectivity and excellent recyclability. This work sets the foundation for using molecular cages as porous surface-capping agents to functionalize and manipulate another porous material, without affecting the intrinsic properties of the parent framework.
Behavioural individuality determines infection risk in clonal ant colonies
Authors: Li Zimai , Bhat Bhoomika , Frank Erik T. , Oliveira-Honorato Thalita , Azuma Fumika , Bachmann Valérie , Parker Darren J. , Schmitt Thomas , Economo Evan P. , Ulrich Yuko
Published: August 2023

In social groups, infection risk is not distributed evenly across individuals. Individual behaviour is a key source of variation in infection risk, yet its effects are difficult to separate from other factors (e.g., age). Here, we combine epidemiological experiments with chemical, transcriptomic, and automated behavioural analyses in clonal ant colonies, where behavioural individuality emerges among identical workers. We find that: (1) Caenorhabditis-related nematodes parasitise ant heads and affect their survival and physiology, (2) differences in infection emerge from behavioural variation alone, and reflect spatially-organised division of labour, (3) infections affect colony social organisation by causing infected workers to stay in the nest. By disproportionately infecting some workers and shifting their spatial distribution, infections reduce division of labour and increase spatial overlap between hosts, which should facilitate parasite transmission. Thus, division of labour, a defining feature of societies, not only shapes infection risk and distribution but is also modulated by parasites.
QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
Authors: Wang Xi , Li Juan , Han Linqian , Liang Chengyong , Li Jiaxin , Shang Xiaoyang , Miao Xinxin , Luo Zi , Zhu Wanchao , Li Zhao , Li Tianhuan , Qi Yongwen , Li Huihui , Lu Xiaoduo , Li Lin
Published: August 2023

Genetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.
Sea-ice decline could keep zooplankton deeper for longer
Authors: Flores Hauke , Veyssière Gaëlle , Castellani Giulia , Wilkinson Jeremy , Hoppmann Mario , Karcher Michael , Valcic Lovro , Cornils Astrid , Geoffroy Maxime , Nicolaus Marcel , Niehoff Barbara , Priou Pierre , Schmidt Katrin , Stroeve Julienne
Published: August 2023

As Arctic sea ice deteriorates, more light enters the ocean, causing largely unknown effects on the ecosystem. Using an autonomous biophysical observatory, we recorded zooplankton vertical distribution under Arctic sea ice from dusk to dawn of the polar night. Here we show that zooplankton ascend into the under-ice habitat during autumn twilight, following an isolume of 2.4 × 10−4 W m−2. We applied this trigger isolume to CMIP6 model outputs accounting for incoming radiation after sunset and before sunrise of the polar night. The models project that, in about three decades, the total time spent by zooplankton in the under-ice habitat could be reduced by up to one month, depending on geographic region. This will impact zooplankton winter survival, the Arctic foodweb, and carbon and nutrient fluxes. These findings highlight the importance of biological processes during the twilight periods for predicting change in high-latitude ecosystems.
Digitization of the Australian Parliamentary Debates, 1998–2022
Authors: Katz Lindsay , Alexander Rohan
Published: August 2023

Public knowledge of what is said in parliament is a tenet of democracy, and a critical resource for political science research. In Australia, following the British tradition, the written record of what is said in parliament is known as Hansard. While the Australian Hansard has always been publicly available, it has been difficult to use for the purpose of large-scale macro- and micro-level text analysis because it has only been available as PDFs or XMLs. Following the lead of the Linked Parliamentary Data project which achieved this for Canada, we provide a new, comprehensive, high-quality, rectangular database that captures proceedings of the Australian parliamentary debates from 1998 to 2022. The database is publicly available and can be linked to other datasets such as election results. The creation and accessibility of this database enables the exploration of new questions and serves as a valuable resource for both researchers and policymakers.
Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration
Authors: Song Young Hoon , Chung Eun-Sung , Shahid Shamsuddin , Kim Yeonjoo , Kim Dongkyun
Published: August 2023

Reliable projection of evapotranspiration (ET) is important for planning sustainable water management for the agriculture field in the context of climate change. A global dataset of monthly climate variables was generated to estimate potential ET (PET) using 14 General Circulation Models (GCMs) for four main shared socioeconomic pathways (SSPs). The generated dataset has a spatial resolution of 0.5° × 0.5° and a period ranging from 1950 to 2100 and can estimate historical and future PET using the Penman-Monteith method. Furthermore, this dataset can be applied to various PET estimation methods based on climate variables. This paper presents that the dataset generated to estimate future PET could reflect the greenhouse gas concentration level of the SSP scenarios in latitude bands. Therefore, this dataset can provide vital information for users to select appropriate GCMs for estimating reasonable PETs and help determine bias correction methods to reduce between observation and model based on the scale of climate variables in each GCM.
Label-free tumor cells classification using deep learning and high-content imaging
Authors: Piansaddhayanon Chawan , Koracharkornradt Chonnuttida , Laosaengpha Napat , Tao Qingyi , Ingrungruanglert Praewphan , Israsena Nipan , Chuangsuwanich Ekapol , Sriswasdi Sira
Published: August 2023

Many studies have shown that cellular morphology can be used to distinguish spiked-in tumor cells in blood sample background. However, most validation experiments included only homogeneous cell lines and inadequately captured the broad morphological heterogeneity of cancer cells. Furthermore, normal, non-blood cells could be erroneously classified as cancer because their morphology differ from blood cells. Here, we constructed a dataset of microscopic images of organoid-derived cancer and normal cell with diverse morphology and developed a proof-of-concept deep learning model that can distinguish cancer cells from normal cells within an unlabeled microscopy image. In total, more than 75,000 organoid-drived cells from 3 cholangiocarcinoma patients were collected. The model achieved an area under the receiver operating characteristics curve (AUROC) of 0.78 and can generalize to cell images from an unseen patient. These resources serve as a foundation for an automated, robust platform for circulating tumor cell detection.
Tamoxifen associated to the conservative CKD treatment promoted additional antifibrotic effects on experimental hypertensive nephrosclerosis
Authors: Fanelli Camilla , Francini Ana L. R. , Celestrino Giovanna A. , Teles Flávio , Barbosa Ana P. , Noda Paloma , Iannuzzi Leandro R. , Guzzo Cristiane R. , Ornellas Felipe M. , Noronha Irene L.
Published: August 2023

CKD progression depends on the activation of an intricate set of hemodynamic and inflammatory mechanisms, promoting renal leukocyte infiltration, inflammation and fibrosis, leading to renal function loss. There are currently no specific drugs to detain renal fibrogenesis, which is a common end-point for different nephropathies. Clinical therapy for CKD is mostly based on the management of hypertension and proteinuria, partially achieved with renin–angiotensin–aldosterone system (RAAS) blockers, and the control of inflammation by immunosuppressive drugs. The aim of the present study was to verify if the administration of tamoxifen (TAM), an estrogen receptor modulator, clinically employed in the treatment of breast cancer and predicted to exert antifibrotic effects, would promote additional benefits when associated to a currently used therapeutic scheme for the conservative management of experimental CKD. Wistar rats underwent the NAME model of hypertensive nephrosclerosis, obtained by daily oral administration of a nitric oxide synthesis inhibitor, associated to dietary sodium overload. The therapeutic association of TAM to losartan (LOS), and mofetil mycophenolate (MMF) effectively reduced the severe hypertension, marked albuminuria and glomerular damage exhibited by NAME animals. Moreover, the association also succeeded in limiting renal inflammation in this model, and promoted further reduction of ECM interstitial accumulation and renal fibrosis, compared to the monotherapies. According to our results, the association of TAM to the currently used conservative treatment of CKD added significant antifibrotic effects both in vivo and in vitro, and may represent an alternative to slow the progression of chronic nephropathy.
Multiphoton microscopy is a nondestructive label-free approach to investigate the 3D structure of gas cell walls in bread dough
Authors: Castanha Nanci , Challois Sylvain , Grenier David , Le-Bail Patricia , Dubreil Laurence , Lucas Tiphaine
Published: August 2023

During the different steps of bread-making, changes in the microstructure of the dough, particularly in the gas cell walls (GCW), have a major influence on the final bread crumb texture. Investigation of the spatial conformation of GCWs is still a challenge because it requires both high resolutions and 3D depth imaging. The originality of the present work lies in the use of label-free non-destructive multiphoton microscopy (NLOM) to image the 3D structure of GCWs, shedding light on their behavior and organization in wheat bread dough. We demonstrated that second and third harmonic generation (SHG, THG) allow imaging, respectively, of starch granules and interfaces in bread dough, while the gluten matrix was detected via two-photon excitation fluorescence (TPEF). Last, a distinction between the gluten network and starch granules was achieved using gluten endogenous fluorescence (EF) imaging, while the position, size, and 3D orientation of starch granules in GCWs were determined from harmonic imaging, made possible by the acquisition of backward and forward SHG with linear polarization. These innovative experiments highlight the strengths of NLOM for a label-free characterization of bread dough microstructure for the first time, in order to understand the role of starch granules in dough stabilization.
A new distinguishing attack on reduced round ChaCha permutation
Authors: Dey Chandan , Sarkar Santanu
Published: August 2023

This work concentrates on differential-linear distinguishing attacks on the prominent ARX-based permutation ChaCha. Here, we significantly improve the 7-round differential-linear distinguisher for ChaCha permutation by introducing a new path of linear approximation. We first introduce a new single-bit differential distinguisher for the 3.5th round of the permutation that assists us in inventing a new path for the differential-linear distinguisher. We show that one can distinguish a 7-round ChaCha permutation with time complexity of $$2^{207}$$

2
207

. This improves the recent work of Coutinho et al. (in: Advances in Cryptology—ASIACRYPT 2022—28nd International Conference on the Theory and Application of Cryptology and Information Security, Taipei, Taiwan, December 5–9, 2012, Springer, 2022), which achieved time complexity $$2^{214}$$

2
214

. We also propose a distinguisher for the 7.25-round of ChaCha permutation and this is the first distinguishing attack for more than 7-round of ChaCha permutation. We provide theoretical proofs and the corresponding experimental results for the linear approximations that we use for differential-linear distinguisher. We point out that the existing multibit distinguishing attacks on the cipher ChaCha are invalid. These attacks are worked only for the ChaCha permutation.
Applying negative ions and an electric field to countermeasure droplets/aerosol transmission without hindering communication
Authors: Kanda Kaito , Nishimura Hisaaki , Koiso Takuya , Takemoto Kousuke , Nakagoe Kazuma , Yamada Tetsuya , Takahashi Masaharu , Hanafusa Mariko , Kawahara Tomoki , Yanagida Yasuko , Kuramochi Jin , Fujiwara Takeo
Published: August 2023

In the COVID-19 pandemic, lockdown and acryl partitions were adopted as countermeasures against droplets/aerosol infections; however, these countermeasures restrict communication. In this study, a blocking device was developed using negative ions and an electric field. The device blocks mists simulating droplets/aerosol by a maximum of 89% but transmits light and sound, which is important for communication. The device demonstrated effective blocking performance for aerosol, including the COVID-19 virus spread from patients in a clinic. Our device can help prevent infections without disrupting communication.
Post-Covid condition and clinic characteristics associated with SARS-CoV-2 infection: a 2-year follow-up to Brazilian cases
Authors: da Silva Nayara Sousa , de Araújo Nathália Kelly , dos Santos Katiusse Alves , de Souza Karla Simone Costa , de Araújo Jéssica Nayara Góes , Cruz Marina Sampaio , Parra Esteban J. , Silbiger Vivian Nogueira , Luchessi André Ducati
Published: August 2023

Until January 2023, Brazil recorded 37 million COVID-19 cases despite the decrease in mortality due to mass vaccination efforts against COVID-19. The infection continues to challenge researchers and health professionals with the persistent symptoms and onset manifestations after the acute phase of the disease, namely Post-Covid Condition (PCC). Being one of the countries with the highest infection rate, Brazil must prepare for a growing number of patients with chronic health consequences of COVID-19. Longitudinal studies that follow patients over extended periods are crucial in understanding the long-term impacts of COVID-19, including potential health consequences and the effects on quality of life. We describe the clinical profile of a cohort of COVID-19 patients infected during the first year of the pandemic in Brazil and a follow-up after two years to investigate the health impacts of SARS-CoV-2 infection. The first wave of SARS-CoV-2 infection in Brazil featured extensive drug misuse, notably the ineffective COVID kit comprised of ivermectin, antimalarials and azithromycin, and elevated in-hospital mortality. In the second phase of the study, Post-Covid Condition was reported by symptomatic COVID-19 subjects across different severity levels two years after infection. Long haulers are more likely to be women, previously hospitalized, and reported a range of symptoms from muscle pain to cognitive deficit. Our longitudinal study is essential to inform public health authorities to develop strategies and policies to control the spread of the virus and mitigate its impacts on society.
Retrospective study of COVID-19 experiences in elite multinational aquatic athletes
Authors: Juhász Vencel , Csulak Emese , Szabó Liliána , Ocsovszky Zsófia , Balla Dorottya , Nagy György , Zorzi Alessandro , Hoepelman Andy I. M. , Merkely Béla , Vágó Hajnalka , Sydó Nóra ,   World Aquatics, Sports Medicine Committee, van den Hoogenband Cees-Rein , Gerrard David , Boyd Kevin , Magnusson Christer , Merkely Béla , Miller Jim , Shahpar Farhad Moradi , Ortiz Edgar , Varvodic Josip , Wang Xinzhai , Cherif Mohamed Yahia ,   World Aquatics, COVID-19 Task Force, Diop Mohamed , Gerrard David , van den Hoogenband Cees-Rein
Published: August 2023

This study assessed the experiences of elite aquatic athletes with coronavirus disease 2019 (COVID-19) during the first World Championship conducted without social distancing and an isolation “bubble”. An online questionnaire was completed by 812 athletes (22.7 ± 5.9 years, 467 females) to provide data on demographics, sports activity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates, symptoms, reinfection, vaccination status, and psychological aspects. The answers revealed that 49.4% of athletes had experienced SARS-CoV-2 infection. The infection rates varied significantly across different aquatic sports, with open water swimmers having the lowest (28%) and water polo players (67%) and artistic swimmers (61%) having the highest infection rates (p < 0.0001). The majority reported mild (51%) or moderate (27%) symptoms, while 16% remained asymptomatic. Reinfection occurred in 13%, and 10% of initial infections led to long COVID, with fatigue (65%) and shortness of breath (48%) being the most common long-term symptoms. Significantly, 92% of athletes received at least two vaccine doses and reported a positive vaccination experience (median score of 8 out of 10 for each shot). Mood changes and subjective performance drops significantly correlated with the overall experience scores (rho: 0.617, p < 0.0001, and rho: 0.466, p < 0.0001, respectively). In conclusion, most athletes experienced a benign disease course despite a relatively high infection rate. This study provides valuable insights into the COVID-19 experiences of elite aquatic athletes. The findings emphasize the importance of vaccination initiatives, monitoring psychological well-being and the need to fortify athletes’ resilience in the face of future health challenges.
Divergent responses of native and invasive macroalgae to submarine groundwater discharge
Authors: Richards Donà Angela , Smith Celia M. , Bremer Leah L.
Published: August 2023

Marine macroalgae are important indicators of healthy nearshore groundwater dependent ecosystems (GDEs), which are emergent global conservation priorities. Submarine groundwater discharge (SGD) supports abundant native algal communities in GDEs via elevated but naturally derived nutrients. GDEs are threatened by anthropogenic nutrient inputs that pollute SGD above ambient levels, favoring invasive algae. Accordingly, this case study draws on the GDE conditions of Kona, Hawai‘i where we evaluated daily photosynthetic production and growth for two macroalgae; a culturally valued native (Ulva lactuca) and an invasive (Hypnea musciformis). Manipulative experiments—devised to address future land-use, climate change, and water-use scenarios for Kona—tested algal responses under a natural range of SGD nutrient and salinity levels. Our analyses demonstrate that photosynthesis and growth in U. lactuca are optimal in low-salinity, high-nutrient waters, whereas productivity for H. musciformis appears limited to higher salinities despite elevated nutrient subsidies. These findings suggest that reductions in SGD via climate change decreases in rainfall or increased water-use from the aquifer may relax physiological constraints on H. musciformis. Collectively, this study reveals divergent physiologies of a native and an invasive macroalga to SGD and highlights the importance of maintaining SGD quantity and quality to protect nearshore GDEs.
Mechanical stimuli activate gene expression via a cell envelope stress sensing pathway
Authors: Harper Christine E. , Zhang Wenyao , Lee Junsung , Shin Jung-Ho , Keller Megan R. , van Wijngaarden Ellen , Chou Emily , Wang Zhaohong , Dörr Tobias , Chen Peng , Hernandez Christopher J.
Published: August 2023

Mechanosensitive mechanisms are often used to sense damage to tissue structure, stimulating matrix synthesis and repair. While this kind of mechanoregulatory process is well recognized in eukaryotic systems, it is not known whether such a process occurs in bacteria. In Vibrio cholerae, antibiotic-induced damage to the load-bearing cell wall promotes increased signaling by the two-component system VxrAB, which stimulates cell wall synthesis. Here we show that changes in mechanical stress within the cell envelope are sufficient to stimulate VxrAB signaling in the absence of antibiotics. We applied mechanical forces to individual bacteria using three distinct loading modalities: extrusion loading within a microfluidic device, direct compression and hydrostatic pressure. In all cases, VxrAB signaling, as indicated by a fluorescent protein reporter, was increased in cells submitted to greater magnitudes of mechanical loading, hence diverse forms of mechanical stimuli activate VxrAB signaling. Reduction in cell envelope stiffness following removal of the endopeptidase ShyA led to large increases in cell envelope deformation and substantially increased VxrAB response, further supporting the responsiveness of VxrAB. Our findings demonstrate a mechanosensitive gene regulatory system in bacteria and suggest that mechanical signals may contribute to the regulation of cell wall homeostasis.
The stem region of group A transferase is crucial for its specificity, and its alteration promotes heterologous Forssman synthase activity
Authors: Cid Emili , Yamamoto Miyako , Barrero Laura , Yamamoto Fumiichiro
Published: August 2023

Some stem region mutants of human blood group A transferase (hAT) possess Forssman synthase (FS) activity, but very little is known about the mechanisms responsible for this enzymatic crosstalk. We performed confocal microscopy and image analysis to determine whether different intra-Golgi localization was accountable for this acquired activity. We also performed structural modeling and mutational and normal mode analyses. We introduced new mutations in the stem region and tested its FS and AT activities. No differences in subcellular localization were found between hAT and FS-positive mutants. AlphaFold models of hAT and mFS (mouse Forssman synthase) showed that the hAT stem region has a tether-like stem region, while in mFS, it encircles its catalytic domain. In silico analysis of FS-positive mutants indicated that stem region mutations induced structural changes, decreasing interatomic interactions and mobility of hAT that correlated with FS activity. Several additional mutations introduced in that region also bestowed FS activity without altering the AT activity: hAT 37–55 aa substitution by mFS 34–52, 37–55 aa deletion, and missense mutations: S46P, Q278Y, and Q286M. Stem region structure, mobility, and interactions are crucial for hAT specificity. Moreover, stem region mutations can lead to heterologous Forssman activity without changes in the catalytic machinery.
Predicting elastic and plastic properties of small iron polycrystals by machine learning
Authors: Mińkowski Marcin , Laurson Lasse
Published: August 2023

Deformation of crystalline materials is an interesting example of complex system behaviour. Small samples typically exhibit a stochastic-like, irregular response to externally applied stresses, manifested as significant sample-to-sample variation in their mechanical properties. In this work we study the predictability of the sample-dependent shear moduli and yield stresses of a large set of small cube-shaped iron polycrystals generated by Voronoi tessellation, by combining molecular dynamics simulations and machine learning. Training a convolutional neural network to infer the mapping between the initial polycrystalline structure of the samples and features of the ensuing stress-strain curves reveals that the shear modulus can be predicted better than the yield stress. We discuss our results in the context of the sensitivity of the system’s response to small perturbations of its initial state.
Prophylactic influences of prebiotics on gut microbiome and immune response of heat-stressed broiler chickens
Authors: Sayed Yara , Hassan Mariam , Salem Heba M. , Al-Amry Khaled , Eid Gamal E.
Published: August 2023

Climatic changes and elevated ambient temperature are significant environmental stressors with a negative impact on birds’ physiological, immunological, and behavioral status, increasing their susceptibility to stressors and immunosuppression and consequently increasing intestinal permeability (leaky gut). Prebiotics have been utilized to stop or diminish the harmful effects of stress in chickens. We aimed to evaluate the role of mannan-oligosaccharides, and beta-d-glucan prebiotics supplements in drinking water against experimentally induced heat stress (HS) on broiler chickens and study their impact on birds’ performance, gut microbiome, and immune response. A total of 120 1-day-old Ross broiler chicks were allocated into four groups (30 birds/group), and each group was subdivided into triplicates (10 birds each). The experimental groups were classified as follows; the 1st (G1) control birds, the 2nd (G2) birds exposed experimentally to HS, the 3rd (G3) birds administered prebiotics in drinking water without exposure to HS, and the 4th (G4) birds exposed to HS and administered prebiotics in drinking water. After each vaccination, blood samples and serum samples were collected to evaluate the birds’ immune status. Fecal samples were also collected for the molecular evaluation of the gut microbiome based on the genetic analyses and sequencing of 16S rRNA gene. The results showed that HS has reduced the birds’ performance and badly affected the birds’ immune response and gut microbiome. However, the addition of prebiotics to drinking water, with or without stress, enhanced the growth rate, maintained a normal gut microbiome, and improved immune parameters. Moreover, the usage of prebiotics improved the chicken gut microbiome and alleviated the negative effect of heat stress. Administering prebiotics significantly (p < 0.05) increased the relative abundance of beneficial bacteria and eradicated pathogenic ones in the birds’ gut microbiome. Prebiotics showed a positive effect on the gut microbiome and the immune status of chickens under HS in addition to their efficacy as a growth promoter.
Effect of coconut oil on growth performance, carcass criteria, liver and kidney functions, antioxidants and immunity, and lipid profile of broilers
Authors: Elewa Mohamed S. , Abou-Kassem Diaa E. , El-Hindawy Mohamed M. , Madkour Mahmoud , Elsharkawy Mohamed S. , Afifi Mohamed , Alagawany Mahmoud
Published: August 2023

The aim of this study is to evaluate the beneficial effects of coconut essential oil on growth performance, carcass criteria, antioxidant status, and immune response of broiler chicks. A total of 192 un-sexed 7-days broiler chicks were divided into six treatment sets with four copies of 8 chicks per set. The groups were as follows: (1) basal diet (without additive), (2) basal diet plus 0.5 ml coconut essential oil/kg, (3) basal diet plus 1 ml coconut essential oil/kg, (4) basal diet plus 1.5 ml coconut essential oil/kg, (5) basal diet plus 2 ml coconut essential oil/kg and (6) basal diet plus 2.5 ml coconut essential oil/kg. The results showed that the most prevalent compound in coconut oil is 6-Octadecenoic acid (oleic acid) representing 46.44% followed 2(3H)-Furanone, dihydro-5-pentyl- (CAS) (11.36%), Hexadecanoic acid (CAS) (4.71%), and vanillin (2.53%). Dietary 1 and 1.5 ml of coconut oil improved significantly the body weight and gain of broiler chickens. Dietary supplementation of 1 ml of coconut oil improved significantly liver function compared to control and other treatment groups. The supplementation with 1 ml coconut oil significantly reduced TG and VLDL compared to control and other treatment groups, while no significant differences in TC, HDL, and LDL due to dietary coconut oil. The present findings showed that dietary coconut oil with 1 and 1.5 ml/kg feed improved significantly antioxidants status through increased antioxidant enzymes like SOD and GSH while decreasing significantly MDA levels compared to control and other treatment groups. Therefore, it was concluded that the diets of broiler chickens could be fortified with coconut oil with 1 or 1.5 ml to improve the growth, feed utilization, and antioxidant status of broiler chickens.
Unraveling the key drivers of community composition in the agri-food trade network
Authors: Clemente Gian Paolo , Cornaro Alessandra , Della Corte Francesco
Published: August 2023

In the complex global food system, the dynamics associated with international food trade have become crucial determinants of food security. In this paper, we employ a community detection approach along with a supervised learning technique to explore the evolution of communities in the agri-food trade network and to identify key factors influencing their composition. By leveraging a large dataset that includes both volume and monetary value of trades, we identify similarities between countries and uncover the primary drivers that shape trade dynamics over time. The analysis also takes into account the impact of evolving climate conditions on food production and trading. The results highlight how the network’s topological structure is continuously evolving, influencing the composition of communities over time. Alongside geographical proximity and geo-political relations, our analysis identifies sustainability, climate and food nutrition aspects as emerging factors that contribute to explaining trade relationships. These findings shed light on the intricate interactions within the global food trade system and provide valuable insights into the factors affecting its stability.
Early electrophysiological study variants and their relationship with clinical presentation and outcomes of patients with Guillain-Barré syndrome
Authors: Khedr Eman M. , Shehab Mohamed M. , Mohamed Mohamed Z. , Mohamed Khaled O.
Published: August 2023

This study compared the clinical outcomes of the two main neurophysiological types of Guillain-Barré Syndrome (GBS). Sixty-two GBS patients were examined clinically at onset using Medical Research Council (MRC), Hughes disability scales (HDS), and nerve conduction studies were evaluated in four limbs. The Modified Erasmus GBS outcome score (MEGOS) was assessed 2 weeks after onset. Outcomes were measured after 3 months using MRC and HDS scores. According to electrophysiological data two main groups identified acute inflammatory demyelinating polyneuropathy (AIDP = 31 cases) or acute axonal GBS including inexcitable forms (26 cases). The number of days between onset of weakness and admission was significantly shorter, and gastrointestinal symptoms were significantly higher among the axonal type than AIDP. MRC sum scores at onset and at nadir were significantly worse in the axonal type than in AIDP. Neck muscle weakness, impaired cough reflex, the need for mechanical ventilation, hypoalbuminemia, and hypernatremia were more common in the axonal type. At outcome, 74% of the AIDP were healthy/minor symptoms versus 38.46% of the axonal type. There was a high prevalence of the axonal variant (41.9%) compared with European and North American populations. The axonal type had a significantly worse outcome than AIDP type.
Machine learning models for efficient characterization of Schottky barrier photodiode internal parameters
Authors: Ocaya Richard O. , Akinyelu Andronicus A. , Al-Sehemi Abdullah G. , Dere Ayşegul , Al-Ghamdi Ahmed A. , Yakuphanoğlu Fahrettin
Published: August 2023

We propose ANN-based models to analyze and extract the internal parameters of a Schottky photodiode (SPD) without presenting them with any knowledge of the highly nonlinear thermionic emission (TE) expression of the device current. We train, evaluate and demonstrate the ML models on thirty-six private datasets from three previously published devices, which denote current responses under illumination and ambient temperature of graphene oxide (GO) doped p-Si Schottky barrier diodes (SBDs). The GO doping levels are 0%, 1%, 3%, 5%, and 10%. The illumination ranged from dark (0 mW/cm2) to 30 mW/cm2. The predictions are then made completely at the intensity of 60 mW/cm2. For each diode, some values of the barrier height ($$\phi $$
ϕ
), ideality factor (n), and series resistance ($$R_s$$

R
s

) independently calculated using the Cheung–Cheung method were included in the training dataset. The predictions are done at unspecified intensities on the model development data at 80 and 100 mW/cm2, and on external data at 5% and 20% GO doping which were not part of the development dataset. The ANN achieved a mean square error and mean absolute error score below 0.003 across all datasets. This demonstrates the effective learning capabilities of the ANN models in accurately capturing the photo responses of the photodiodes and accurately predicting the internal parameters of the Schottky Barrier Diodes (SBDs), all without relying on an inherent understanding of the thermionic emission (TE) equation for SBDs. The ANN models achieved high accuracy in this process. The proposed ML models can significantly reduce analysis time in device development cycles and can be applied to other datasets in various fields.
Mutational landscape of intestinal crypt cells after long-term in vivo exposure to high fat diet
Authors: Meyenberg Mathilde , Hakobyan Anna , Papac-Milicevic Nikolina , Göderle Laura , Langner Franziska L. , Markovic Mateo , Lee Ji-Hyun , Koo Bon-Kyoung , Busslinger Georg A. , da Silva Israel Tojal , Binder Christoph J. , Menche Jörg , Loizou Joanna I.
Published: August 2023

Obesity is a modifiable risk factor in cancer development, especially for gastrointestinal cancer. While the etiology of colorectal cancer is well characterized by the adenoma-carcinoma sequence, it remains unclear how obesity influences colorectal cancer development. Dietary components of a high fat diet along with obesity have been shown to modulate the cancer risk by perturbing the homeostasis of intestinal stem cells, yet how adiposity impacts the development of genomic instability has not been studied. Mutational signatures are a powerful way to understand how a complex biological response impacts genomic stability. We utilized a mouse model of diet-induced obesity to study the mutational landscape of intestinal crypt cells after a 48-week exposure to an experimental high fat diet in vivo. By clonally enriching single crypt derived cells in organoid culture and obtaining whole genome sequences, we analyzed and compared the mutational landscape of intestinal epithelial cells from normal diet and high fat diet mice. Single nucleotide substitution signatures and indel signatures present in our cohort are found equally active in both diet groups and reflect biological processes of normal aging, cellular replication, and oxidative stress induced during organoid culturing. Thus, we demonstrate that in the absence of activating mutations or chemical exposure, high fat diet alone is not sufficient to increase genomic instability.
Public speaking training in front of a supportive audience in Virtual Reality improves performance in real-life
Authors: Kroczek Leon O. H. , Mühlberger Andreas
Published: August 2023

Public speaking is a challenging task that requires practice. Virtual Reality allows to present realistic public speaking scenarios in this regard, however, the role of the virtual audience during practice remains unknown. In the present study, 73 participants completed a Virtual Reality practice session while audience was manipulated to be supportive or unsupportive or presentations were practiced without audience. Importantly, following the virtual practice, participants held the presentation during a real university course via Zoom. We measured emotional experience, self-efficacy, and the subjective evaluation of performance at baseline, after VR practice, and after the real presentation. Additionally, participants’ performance in the real presentation was evaluated by instructors (blinded to condition). Supportive in contrast to unsupportive audiences led to more positive believes about one’s own performance, while there were no changes in beliefs in the group without audience. Importantly, practice in front of a supportive compared to unsupportive audience resulted in a more positive evaluation of speaker confidence in real-life public speaking as rated by the instructors. These results demonstrate an impact of virtual social feedback during public speaking on subsequent subjective performance evaluation. This may increase self-confidence resulting in actual improved public speaking performance in real-life.
Long-range fiber-optic earthquake sensing by active phase noise cancellation
Authors: Noe Sebastian , Husmann Dominik , Müller Nils , Morel Jacques , Fichtner Andreas
Published: August 2023

We present a long-range fiber-optic environmental deformation sensor based on active phase noise cancellation (PNC) in metrological frequency dissemination. PNC sensing exploits recordings of a compensation frequency that is commonly discarded. Without the need for dedicated measurement devices, it operates synchronously with metrological services, suggesting that existing phase-stabilized metrological networks can be co-used effortlessly as environmental sensors. The compatibility of PNC sensing with inline amplification enables the interrogation of cables with lengths beyond 1000 km, making it a potential contributor to earthquake detection and early warning in the oceans. Using spectral-element wavefield simulations that accurately account for complex cable geometry, we compare observed and computed recordings of the compensation frequency for a magnitude 3.9 earthquake in south-eastern France and a 123 km fiber link between Bern and Basel, Switzerland. The match in both phase and amplitude indicates that PNC sensing can be used quantitatively, for example, in earthquake detection and characterization.
Multidrug resistance pattern and molecular epidemiology of pathogens among children with diarrhea in Bangladesh, 2019–2021
Authors: Sharif Nadim , Ahmed Shamsun Nahar , Khandaker Shamim , Monifa Nuzhat Haque , Abusharha Ali , Vargas Debora Libertad Ramírez , Díez Isabel De la Torre , Castilla Angel Gabriel Kuc , Talukder Ali Azam , Parvez Anowar Khasru , Dey Shuvra Kanti
Published: August 2023

Antimicrobial and multidrug resistance (MDR) pathogens are becoming one of the major health threats among children. Integrated studies on the molecular epidemiology and prevalence of AMR and MDR diarrheal pathogens are lacking. A total of 404 fecal specimens were collected from children with diarrhea in Bangladesh from January 2019 to December 2021. We used conventional bacteriologic and molecular sequence analysis methods. Phenotypic and genotypic resistance were determined by disk diffusion and molecular sequencing methods. Fisher’s exact tests with 95% confidence intervals (CIs) was performed. Prevalence of bacterial infection was 63% (251 of 404) among children with diarrhea. E. coli (29%) was the most prevalent. E. coli, Shigella spp., V. cholerae, and Salmonella spp., showed the highest frequency of resistance against ceftriaxone (75–85%), and erythromycin (70–75%%). About 10–20% isolates of E. coli, V. cholerae and Shigella spp. showed MDR against cephem, macrolides, and quinolones. Significant association (p value < 0.05) was found between the phenotypic and genotypic resistance. The risk of diarrhea was the highest among the patients co-infected with E. coli and rotavirus [OR 3.6 (95% CI 1.1–5.4) (p = 0.001)] followed by Shigella spp. and rotavirus [OR 3.5 (95% CI 0.5–5.3) (p = 0.001)]. This study will provide an integrated insight of molecular epidemiology and antimicrobial resistance profiling of bacterial pathogens among children with diarrhea in Bangladesh.