bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography
Authors: Bauda Elda , Gallet Benoit , Moravcova Jana , Effantin Gregory , Chan Helena , Novacek Jiri , Jouneau Pierre-Henri , Rodrigues Christopher D. A. , Schoehn Guy , Moriscot Christine , Morlot Cecile
Published: February 2024

Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
Eliciting parental preferences and values for the return of additional findings from genomic sequencing
Authors: Goranitis Ilias , Meng Yan , Martyn Melissa , Best Stephanie , Bouffler Sophie , Bombard Yvonne , Gaff Clara , Stark Zornitza
Published: February 2024

Health economic evidence is needed to inform the design of high-value and cost-effective processes for returning genomic results from analyses for additional findings (AF). This study reports the results of a discrete-choice experiment designed to elicit preferences for the process of returning AF results from the perspective of parents of children with rare conditions and to estimate the value placed on AF analysis. Overall, 94 parents recruited within the Australian Genomics and Melbourne Genomics programmes participated in the survey, providing preferences in a total of 1128 choice scenarios. Statistically significant preferences were identified for the opportunity to change the choices made about AF; receiving positive AF in person from a genetic counsellor; timely access to a medical specialist and high-quality online resources; receiving automatic updates through a secure online portal if new information becomes available; and lower costs. For AF uptake rates ranging between 50–95%, the mean per person value from AF analysis was estimated at AU$450–$1700 (US$300–$1140). The findings enable the design of a value-maximising process of analysis for AF in rare-disease genomic sequencing.
Harmonic memory signals in the human cerebral cortex induced by semantic relatedness of words
Authors: Noguchi Yasuki
Published: February 2024

When we memorize multiple words simultaneously, semantic relatedness among those words assists memory. For example, the information about “apple”, “banana,” and “orange” will be connected via a common concept of “fruits” and become easy to retain and recall. Neural mechanisms underlying this semantic integration in verbal working memory remain unclear. Here I used electroencephalography (EEG) and investigated neural signals when healthy human participants memorized five nouns semantically related (Sem trial) or not (NonSem trial). The regularity of oscillatory signals (8–30 Hz) during the retention period was found to be lower in NonSem than Sem trials, indicating that memorizing words unrelated to each other induced a non-harmonic (irregular) waveform in the temporal cortex. These results suggest that (i) semantic features of a word are retained as a set of neural oscillations at specific frequencies and (ii) memorizing words sharing a common semantic feature produces harmonic brain responses through a resonance or integration (sharing) of the oscillatory signals.
Operando film-electrochemical EPR spectroscopy tracks radical intermediates in surface-immobilized catalysts
Authors: Seif-Eddine Maryam , Cobb Samuel J. , Dang Yunfei , Abdiaziz Kaltum , Bajada Mark A. , Reisner Erwin , Roessler Maxie M.
Published: February 2024

The development of surface-immobilized molecular redox catalysts is an emerging research field with promising applications in sustainable chemistry. In electrocatalysis, paramagnetic species are often key intermediates in the mechanistic cycle but are inherently difficult to detect and follow by conventional in situ techniques. We report a new method, operando film-electrochemical electron paramagnetic resonance spectroscopy (FE-EPR), which enables mechanistic studies of surface-immobilized electrocatalysts. This technique enables radicals formed during redox reactions to be followed in real time under flow conditions, at room temperature and in aqueous solution. Detailed insight into surface-immobilized catalysts, as exemplified here through alcohol oxidation catalysis by a surface-immobilized nitroxide, is possible by detecting active-site paramagnetic species sensitively and quantitatively operando, thereby enabling resolution of the reaction kinetics. Our finding that the surface electron-transfer rate, which is of the same order of magnitude as the rate of catalysis (accessible from operando FE-EPR), limits catalytic efficiency has implications for the future design of better surface-immobilized catalysts.
Harmonizing government responses to the COVID-19 pandemic
Authors: Cheng Cindy , Messerschmidt Luca , Bravo Isaac , Waldbauer Marco , Bhavikatti Rohan , Schenk Caress , Grujic Vanja , Model Tim , Kubinec Robert , Barceló Joan
Published: February 2024

Public health and safety measures (PHSM) made in response to the COVID-19 pandemic have been singular, rapid, and profuse compared to the content, speed, and volume of normal policy-making. Not only can they have a profound effect on the spread of the disease, but they may also have multitudinous secondary effects, in both the social and natural worlds. Unfortunately, despite the best efforts by numerous research groups, existing data on COVID-19 PHSM only partially captures their full geographical scale and policy scope for any significant duration of time. This paper introduces our effort to harmonize data from the eight largest such efforts for policies made before September 21, 2021 into the taxonomy developed by the CoronaNet Research Project in order to respond to the need for comprehensive, high quality COVID-19 data. In doing so, we present a comprehensive comparative analysis of existing data from different COVID-19 PHSM datasets, introduce our novel methodology for harmonizing COVID-19 PHSM data, and provide a clear-eyed assessment of the pros and cons of our efforts.
ShetlandsUAVmetry: unmanned aerial vehicle-based photogrammetric dataset for Antarctic environmental research
Authors: Román Alejandro , Navarro Gabriel , Tovar-Sánchez Antonio , Zarandona Pedro , Roque-Atienza David , Barbero Luis
Published: February 2024

The study of the functioning and responses of Antarctica to the current climate change scenario is a priority and a challenge for the scientific community aiming to predict and mitigate impacts at a regional and global scale. Due to the difficulty of obtaining aerial data in such extreme, remote, and difficult-to-reach region of the planet, the development of remote sensing techniques with Unmanned Aerial Vehicles (UAVs) has revolutionized polar research. ShetlandsUAVmetry comprises original datasets collected by UAVs during the Spanish Antarctic Campaign 2021–2022 (January to March 2022), along with the photogrammetric products resulting from their processing. It includes data recorded during twenty-eight distinct UAV flights at various study sites on Deception and Livingston islands (South Shetland Islands, Antarctica) and consists of a total of 15,691 high-resolution optical RGB captures. In addition, this dataset is accompanied by additional associated files that facilitate its use and accessibility. It is publicly accessible and can be downloaded from the figshare data repository.
Pollen viability and longevity in Juniperus taxa native to Slovakia
Authors: Galgóci Martin , Kormuťák Andrej , Klobučník Miroslav , Gömöry Dušan , Lukáčik Ivan , Boleček Peter
Published: February 2024

Pollen viability, dispersion ability and longevity during deep-freezer storage were studied in three Juniperus taxa distributed in Slovakia. All these characteristics of pollen are closely related to the pollination and/or fertilization success of the junipers in nature. Pollen viability varied considerably between the three populations of J. communis and one population of each, J. sibirica and J. communis var. intermedia. Pollen germination rate ranged between 40.75% and 75.06%, and pollen tube length between 30.32 and 40.41 µm. A clear tendency indicates a higher germination rate of J. communis pollen from lower altitudes and reduced germination of J. sibirica and J. communis var. intermedia pollen from higher altitudes. The dispersion potential of the J. communis pollen during its shedding seems relatively low. In 2021, pollen cloud density was diluted at 68.1% at the 4 m distance from the test shrub, in 2022 of 52.1% at the 17 m distance from the pollen source. A deep-freezer storage of juniper pollen in a double-walled polyethylene bag with silica gel was not efficient enough, as indicated by the drop of pollen germination rate of 31.2% in J. communis and of 79.4% in J. sibirica during a 1-year storage period at − 81 °C.
Identification and characterization of intact glycopeptides in human urine
Authors: Garcia-Marques Fernando , Fuller Keely , Bermudez Abel , Shamsher Nikhiya , Zhao Hongjuan , Brooks James D. , Flory Mark R. , Pitteri Sharon J.
Published: February 2024

Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of glycoproteins in human urine using LC–MS/MS-based intact glycopeptide analysis, providing both the identification of protein glycosites and characterization of the glycan composition at specific glycosites. Gene enrichment analysis reveals differences in biological processes, cellular components, and molecular functions in the urine glycoproteome versus the urine proteome, as well as differences based on the major glycan class observed on proteins. Meta-heterogeneity of glycosylation is examined on proteins to determine the variation in glycosylation across multiple sites of a given protein with specific examples of individual sites differing from the glycosylation trends in the overall protein. Taken together, this dataset represents a potentially valuable resource as a baseline characterization of glycoproteins in human urine for future urine glycoproteomics studies.
Rhythmic motor behavior explains individual differences in grammar skills in adults
Authors: Kim Hyun-Woong , Kovar Jessica , Bajwa Jesper Singh , Mian Yasir , Ahmad Ayesha , Mancilla Moreno Marisol , Price Theodore J. , Lee Yune Sang
Published: February 2024

A growing body of literature has reported the relationship between music and language, particularly between individual differences in perceptual rhythm skill and grammar competency in children. Here, we investigated whether motoric aspects of rhythm processing—as measured by rhythmic finger tapping tasks—also explain the rhythm-grammar connection in 150 healthy young adults. We found that all expressive rhythm skills (spontaneous, synchronized, and continued tapping) along with rhythm discrimination skill significantly predicted receptive grammar skills on either auditory sentence comprehension or grammaticality well-formedness judgment (e.g., singular/plural, past/present), even after controlling for verbal working memory and music experience. Among these, synchronized tapping and rhythm discrimination explained unique variance of sentence comprehension and grammaticality judgment, respectively, indicating differential associations between different rhythm and grammar skills. Together, we demonstrate that even simple and repetitive motor behavior can account for seemingly high-order grammar skills in the adult population, suggesting that the sensorimotor system continue to support syntactic operations.
Flexible metallic core–shell nanostructured electrodes for neural interfacing
Authors: Rodilla Beatriz L. , Arché-Núñez Ana , Ruiz-Gómez Sandra , Domínguez-Bajo Ana , Fernández-González Claudia , Guillén-Colomer Clara , González-Mayorga Ankor , Rodríguez-Díez Noelia , Camarero Julio , Miranda Rodolfo , López-Dolado Elisa , Ocón Pilar , Serrano María C. , Pérez Lucas , González M. Teresa
Published: February 2024

Electrodes with nanostructured surface have emerged as promising low-impedance neural interfaces that can avoid the charge‐injection restrictions typically associated to microelectrodes. In this work, we propose a novel approximation, based on a two-step template assisted electrodeposition technique, to obtain flexible nanostructured electrodes coated with core–shell Ni–Au vertical nanowires. These nanowires benefit from biocompatibility of the Au shell exposed to the environment and the mechanical properties of Ni that allow for nanowires longer and more homogeneous in length than their only-Au counterparts. The nanostructured electrodes show impedance values, measured by electrochemical impedance spectroscopy (EIS), at least 9 times lower than those of flat reference electrodes. This ratio is in good accordance with the increased effective surface area determined both from SEM images and cyclic voltammetry measurements, evidencing that only Au is exposed to the medium. The observed EIS profile evolution of Ni–Au electrodes over 7 days were very close to those of Au electrodes and differently from Ni ones. Finally, the morphology, viability and neuronal differentiation of rat embryonic cortical cells cultured on Ni–Au NW electrodes were found to be similar to those on control (glass) substrates and Au NW electrodes, accompanied by a lower glial cell differentiation. This positive in-vitro neural cell behavior encourages further investigation to explore the tissue responses that the implantation of these nanostructured electrodes might elicit in healthy (damaged) neural tissues in vivo, with special emphasis on eventual tissue encapsulation.
Excreta flow mapping along the sanitation service chain, a case of Kombolcha town, Ethiopia
Authors: Endris Seid , Kebede Andinet , Assefa Eshetu , Ali Almayehu , Desale Tewodrose
Published: February 2024

Poor management of fecal sludge (FSM) presents significant risks to public health and the environment. This study employed qualitative and quantitative data collection methods, along with the Shit Flow Diagram (SFD) data analyzing tool to investigate FSM patterns in Kombolcha town, Ethiopia. The findings indicate that 75.7% of housing unites in the town are shared toilets, with multiple households sharing a single facility. The primary toilet technologies used include cistern flush toilets (2.1%), pour/manual flush toilets (19.8%), ventilated improved pit latrines (11.1%), pit latrines with slabs (56.4%), and pit latrines without slabs (10.6%). However, 98.5% of these toilet types had either unlined or only partially lined containments. Furthermore, only 37% of households practice safe pit or sludge tank emptying. As a result, only 17% of fecal sludge goes through the sanitation value chain and is effectively treated, while 39% remains onsite and unemptied, and the remaining 44% is disposed of in a manner that poses risks to the environment and public health. The study highlights the significant public health and environmental risks associated with the high reliance on shared toilets, the prevalence of inadequately lined toilet types, and the low adoption of proper fecal sludge management practices. Addressing these challenges requires the implementation of sanitation bylaws and building code regulations that prioritize hygienic standards and promote improved toilet technologies.
Revealing the associated microflora hosted by the globally significant parasite Trichostrongylus colubriformis
Authors: Paz Erwin A. , Chua Eng Guan , Palmer Dieter G. , Greeff Johan C. , Liu Shimin , Cheuquemán Carolina , Hassan Shamshad Ul , Martin Graeme B. , Tay Chin Yen
Published: February 2024

Trichostrongylus colubriformis is a parasitic helminth that primarily infects small ruminants, causing substantial economic losses in the livestock industry. Exploring the microbiome of this helminth might provide insights into the potential influence of its microbial community on the parasite’s survival. We characterised the intestinal microbiome of T. colubriformis that had been collected from the duodenum of sheep, and compared the helminth microbiome with the duodenal microbiome of its host, aiming to identify contributions from the helminth’s environment. At the same time, we explored the isolation of fastidious organisms from the harvested helminth. Primary alpha and beta diversity analyses of bacterial species revealed statistically significant differences between the parasite and the host, in terms of species richness and ecological composition. 16S rRNA differential abundance analysis showed that Mycoplasmoides and Stenotrophomonas were significantly present in T. colubriformis but not in the duodenal microbiome of the sheep. Furthermore, two bacteria, Aeromonas caviae and Aeromonas hydrophila, were isolated from T. colubriformis. Examinations of the genome highlight differences in genome size and profiles of antimicrobial resistance genes. Our results suggest that T. colubriformis carries a specific bacterial community that could be supporting the helminth’s long-term survival in the host’s digestive system.
Shared attention in virtual immersive reality enhances electrophysiological correlates of implicit sensory learning
Authors: Sarasso Pietro , Ronga Irene , Piovesan Francesca , Barbieri Paolo , Del Fante Elena , De Luca Daniela , Bechis Ludovico , Osello Anna , Sacco Katiuscia
Published: February 2024

Shared attention effects on learning and memory demonstrate that experiences are amplified when we are not alone. Virtual reality poses new challenges to the study of co-presence. Above all, is coattending together with someone else’s avatar in an immersive VR setting comparable with shared experiences at a neural processing level? In the present study we investigate shared attention effects in VR for the first time. We recorded mismatch negativities (MMN) during an auditory roving paradigm, a well-known index of implicit perceptual learning. EEG responses to deviant and standard sounds were registered while subjects were alone (Solo condition) or together (Other condition) with a virtual avatar (Virtual scenario) or physically present confederate (Physical scenario). We found an overall main effect of co-presence on MMN revealed by a point-by-point 2 × 2 ANOVA, thereby replicating previous studies on physical co-presence. Additionally, we found no significant interaction between the scenario (Physical vs. Virtual) and co-presence (Solo vs. Other). Our results indicate that virtual immersive co-presence mimics physical co-presence.
Deep learning assisted XRF spectra classification
Authors: Andric Velibor , Kvascev Goran , Cvetanovic Milos , Stojanovic Sasa , Bacanin Nebojsa , Gajic-Kvascev Maja
Published: February 2024

EDXRF spectrometry is a well-established and often-used analytical technique in examining materials from which cultural heritage objects are made. The analytical results are traditionally subjected to additional multivariate analysis for archaeometry studies to reduce the initial data’s dimensionality based on informative features. Nowadays, artificial intelligence (AI) techniques are used more for this purpose. Different soft computing techniques are used to improve speed and accuracy. Choosing the most suitable AI method can increase the sustainability of the analytical process and postprocessing activities. An autoencoder neural network has been designed and used as a dimension reduction tool of initial $$40 \times 2048$$

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data collected in the raw EDXRF spectra, containing information about the selected points’ elemental composition on the canvas paintings’ surface. The autoencoder network design enables the best possible reconstruction of the original EDXRF spectrum and the most informative feature extraction, which has been used for dimension reduction. Such configuration allows for efficient classification algorithms and their performances. The autoencoder neural network approach is more sustainable, especially in processing time consumption and experts’ manual work.
Characterization of graded 6-Hydroxydopamine unilateral lesion in medial forebrain bundle of mice
Authors: Cui Juntao , Zhao Di , Xu Manman , Li Zheheng , Qian Junliang , Song Ning , Wang Jun , Xie Junxia
Published: February 2024

Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease, with a progressive loss of dopaminergic cells and fibers. The purpose of this study was to use different doses of 6-hydroxydopamine (6-OHDA) injection into the medial forebrain bundle (MFB) of mice to mimic the different stages of the disease and to characterize in detail their motor and non-motor behavior, as well as neuropathological features in the nigrostriatal pathway. MFB were injected with 0.5 μg, 1 μg, 2 μg of 6-OHDA using a brain stereotaxic technique. 6-OHDA induced mitochondrial damage dose-dependently, as well as substantia nigra pars compacta (SNpc) tyrosine hydroxylase-positive (TH+) cell loss and striatal TH fiber loss. Activation of astrocytes and microglia in the SNpc and striatum were consistently observed at 7 weeks, suggesting a long-term glial response in the nigrostriatal system. Even with a partial or complete denervation of the nigrostriatal pathway, 6-OHDA did not cause anxiety, although depression-like behavior appeared. Certain gait disturbances were observed in 0.5 μg 6-OHDA lesioned mice, and more extensive in 1 μg group. Despite the loss of more neurons from 2 μg 6-OHDA, there was no further impairment in behaviors compared to 1 μg 6-OHDA. Our data have implications that 1 μg 6-OHDA was necessary and sufficient to induce motor and non-motor symptoms in mice, thus a valuable mouse tool to explore disease progression and new treatment in PD.
Potential Alzheimer’s early biomarkers in a transgenic rat model and benefits of diazoxide/dibenzoylmethane co-treatment on spatial memory and AD-pathology
Authors: Wallace Charles H. , Oliveros Giovanni , Xie Lei , Serrano Peter , Rockwell Patricia , Figueiredo-Pereira Maria
Published: February 2024

Alzheimer’s disease (AD) is the major form of dementia prevalent in older adults and with a high incidence in females. Identification of early biomarkers is essential for preventive intervention to delay its progression. Furthermore, due to its multifactorial nature, a multi-target approach could be therapeutically beneficial. Our studies included 4- (pre-pathology) and 11-month (mild-pathology) TgF344-AD rats, a transgenic Alzheimer’s model that exhibits age-dependent AD progression. We identified two potential early biomarker genes for AD, early growth response 2 (EGR2) and histone 1H2AA (HIST1H2AA), in the hippocampus of 4-month females. Out of 17,168 genes analyzed by RNA sequencing, expression of these two genes was significantly altered in 4-month TgF344-AD rats compared to wild-type littermates. We also evaluated co-treatment with diazoxide (DZ), a potassium channel activator, and dibenzoylmethane (DIB), which inhibits eIF2α-P activity, on TgF344-AD and wild-type rats. DZ/DIB-treatment mitigated spatial memory deficits and buildup of hippocampal Aβ plaques and tau PHF in 11-month TgF344-AD rats but had no effect on wild-type littermates. To our knowledge, this preclinical study is the first to report EGR2 and HIST1H2AA as potential AD biomarkers in females, and the benefits of DZ/DIB-treatment in AD. Evaluations across multiple AD-related models is warranted to corroborate our findings.
Nanoscale morphology, optical dynamics and gas sensor of porous silicon
Authors: Ghaderi Atefeh , Sabbaghzadeh Jamshid , Dejam Laya , Behzadi Pour Ghobad , Moghimi Emad , Matos Robert S. , da Fonseca Filho Henrique Duarte , Țălu Ștefan , Salehi shayegan Amirhossein , Aval Leila Fekri , Astani Doudaran Mahdi , Sari Amirhossein , Solaymani Shahram
Published: February 2024

We investigated the multifaceted gas sensing properties of porous silicon thin films electrodeposited onto (100) oriented P-type silicon wafers substrates. Our investigation delves into morphological, optical properties, and sensing capabilities, aiming to optimize their use as efficient gas sensors. Morphological analysis revealed the development of unique surfaces with distinct characteristics compared to untreated sample, yielding substantially rougher yet flat surfaces, corroborated by Minkowski Functionals analysis. Fractal mathematics exploration emphasized that despite increased roughness, HF/ethanol-treated surfaces exhibit flatter attributes compared to untreated Si sample. Optical approaches established a correlation between increased porosity and elevated localized states and defects, influencing the Urbach energy value. This contributed to a reduction in steepness values, attributed to heightened dislocations and structural disturbances, while the transconductance parameter decreases. Simultaneously, porosity enhances the strength of electron‒phonon interaction. The porous silicon thin films were further tested as effective gas sensors for CO2 and O2 vapors at room temperature, displaying notable changes in electrical resistance with varying concentrations. These findings bring a comprehensive exploration of some important characteristics of porous silicon surfaces and established their potential for advanced industrial applications.
Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants
Authors: Viktorsson Charlotte , Portugal Ana Maria , Falck-Ytter Terje
Published: February 2024

A tendency to look at the left side of faces from the observer’s point of view has been found in older children and adults, but it is not known when this face-specific left gaze bias develops and what factors may influence individual differences in gaze lateralization. Therefore, the aims of this study were to estimate gaze lateralization during face observation and to more broadly estimate lateralization tendencies across a wider set of social and non-social stimuli, in early infancy. In addition, we aimed to estimate the influence of genetic and environmental factors on lateralization of gaze. We studied gaze lateralization in 592 5-month-old twins (282 females, 330 monozygotic twins) by recording their gaze while viewing faces and two other types of stimuli that consisted of either collections of dots (non-social stimuli) or faces interspersed with objects (mixed stimuli). A right gaze bias was found when viewing faces, and this measure was moderately heritable (A = 0.38, 95% CI 0.24; 0.50). A left gaze bias was observed in the non-social condition, while a right gaze bias was found in the mixed condition, suggesting that there is no general left gaze bias at this age. Genetic influence on individual differences in gaze lateralization was only found for the tendency to look at the right versus left side of faces, suggesting genetic specificity of lateralized gaze when viewing faces.
Investigation on explainable machine learning models to predict chronic kidney diseases
Authors: Ghosh Samit Kumar , Khandoker Ahsan H.
Published: February 2024

Chronic kidney disease (CKD) is a major worldwide health problem, affecting a large proportion of the world’s population and leading to higher morbidity and death rates. The early stages of CKD sometimes present without visible symptoms, causing patients to be unaware. Early detection and treatments are critical in reducing complications and improving the overall quality of life for people afflicted. In this work, we investigate the use of an explainable artificial intelligence (XAI)-based strategy, leveraging clinical characteristics, to predict CKD. This study collected clinical data from 491 patients, comprising 56 with CKD and 435 without CKD, encompassing clinical, laboratory, and demographic variables. To develop the predictive model, five machine learning (ML) methods, namely logistic regression (LR), random forest (RF), decision tree (DT), Naïve Bayes (NB), and extreme gradient boosting (XGBoost), were employed. The optimal model was selected based on accuracy and area under the curve (AUC). Additionally, the SHAP (SHapley Additive exPlanations) and LIME (Local Interpretable Model-agnostic Explanations) algorithms were utilized to demonstrate the influence of the features on the optimal model. Among the five models developed, the XGBoost model achieved the best performance with an AUC of 0.9689 and an accuracy of 93.29%. The analysis of feature importance revealed that creatinine, glycosylated hemoglobin type A1C (HgbA1C), and age were the three most influential features in the XGBoost model. The SHAP force analysis further illustrated the model’s visualization of individualized CKD predictions. For further insights into individual predictions, we also utilized the LIME algorithm. This study presents an interpretable ML-based approach for the early prediction of CKD. The SHAP and LIME methods enhance the interpretability of ML models and help clinicians better understand the rationale behind the predicted outcomes more effectively.
Probiotic performance of B. subtilis MS. 45 improves aquaculture of rainbow trout Oncorhynchus mykiss during acute hypoxia stress
Authors: Neissi Alireza , Majidi Zahed Hamed , Roshan Reza
Published: February 2024

The aim of this study was to produce mutant strains of Bacillus subtilis with high probiotic performance for use in the aquaculture of rainbow trout Oncorhynchus mykiss. The main strain of B. subtilis (MS) was irradiated with gamma rays (5.3 KGy). Subsequently, the B. subtilis mutant strain no. 45 (MS. 45) was selected for bacterial growth performance, resistance to acidic conditions, resistance to bile salts and antibacterial activity against Aeromonas hydrophila and Pseudomonas fluorescens. After 60 days, the rainbow trout (70.25 ± 3.89 g) fed with MS. 45 and MS were exposed to hypoxia stress (dissolved oxygen = 2 ppm). Subsequently, immune indices (lysozyme, bacterial activity and complement activity), hematological indices [hematocrit, hemoglobin, WBC, RBC, mean corpuscular volume (MCV)] and antioxidant factors (T-AOC, SOD and MDA)) were analyzed after and before hypoxia exposure. The expression of immunological genes (IFN-γ, TNF-α, IL-1β, IL-8) in the intestine and the expression of hypoxia-related genes (HIF-1α, HIF-2α, FIH1) in the liver were compared between the different groups under hypoxia and normoxia conditions. Growth, immunological and antioxidant indices improved in group MS. 45 compared to the other groups. Stress indices and associated immunologic and hypoxia expressions under hypoxia and normoxia conditions improved in MS. 45 compared to the other groups. This resulted in improved growth, immunity and stress responses in fish fed with the microbial supplement of MS. 45 (P < 0.05) under hypoxia and normoxia conditions, (P < 0.05), resulting in a significant improvement in trout aquaculture.
Evaluating the relationship between ocular blood flow and systemic organ blood flow in hemorrhagic shock using a rabbit model
Authors: Watanabe Kento , Shiba Tomoaki , Takahara Akira , Homma Hiroshi , Komatsu Tetsuya , Tanino Yusuke , Nagasawa Yoshinobu , Aimoto Megumi , Hori Yuichi
Published: February 2024

This study aimed to investigate the feasibility of utilizing noninvasive ocular blood flow measurements as potential indicators of systemic circulation in rabbits experiencing hemorrhagic shock. Using Laser speckle flowgraphy, ocular blood flow indices, relative flow volume (RFV), and mean blur rate in the choroidal area (MBR-CH) were assessed in New Zealand White rabbits (n = 10) subjected to controlled blood removal and return. Hemodynamic parameters and biochemical markers were monitored alongside ocular circulation during blood removal and return phases. Additionally, correlations between ocular parameters and systemic indices were examined. The results indicated that RFV and MBR-CH exhibited significant correlations with renal and intestinal blood flows, with stronger correlations observed during blood removal. Additionally, ocular blood flow changes closely mirrored systemic dynamics, suggesting their potential as real-time indicators of shock progression and recovery. These findings indicate that ocular blood flow measurements may serve as real-time indicators of the systemic circulation status during hemorrhagic shock, offering potential insights into shock management and guiding tailored interventions. Thus, noninvasive ocular blood flow evaluation holds promise as an innovative tool for assessing systemic circulation dynamics during hemorrhagic shock.
Raman enhancement induced by exciton hybridization in molecules and 2D materials
Authors: Kitadai Hikari , Tan Qishuo , Ping Lu , Ling Xi
Published: February 2024

Surface-enhanced Raman spectroscopy (SERS) is a powerful technique for trace-level fingerprinting. Recently, layered two-dimensional (2D) materials have gained significant interest as SERS substrates for providing stable, uniform, and reproducible Raman enhancement with the potential for trace-level detection. Yet, the development of effective 2D SERS substrates is still hindered by the lack of fundamental understanding of the coupling mechanism between target molecules and substrates. Here, we report a systematic excitation-dependent Raman spectroscopy investigation on the coupling between 2D materials such as SnS2, MoS2, WSe2, and graphene and small organic molecules like rhodamine 6G (Rh 6G). Strong coupling between SnS2 and Rh 6G is found due to their degenerate excitons through Raman excitation profiles (REP), leading to the enhancement of Rh 6G vibrational modes that are observable down to 10−13 M. Our study shows that exciton coupling in the substrate-adsorbate complex plays a vital role in the Raman enhancement effect, opening a new route for designing SERS substrates for high sensitivity.
Efferocytosis reprograms the tumor microenvironment to promote pancreatic cancer liver metastasis
Authors: Astuti Yuliana , Raymant Meirion , Quaranta Valeria , Clarke Kim , Abudula Maidinaimu , Smith Olivia , Bellomo Gaia , Chandran-Gorner Vatshala , Nourse Craig , Halloran Christopher , Ghaneh Paula , Palmer Daniel , Jones Robert P. , Campbell Fiona , Pollard Jeffrey W. , Morton Jennifer P. , Mielgo Ainhoa , Schmid Michael C.
Published: February 2024

Pancreatic ductal adenocarcinoma is a highly metastatic disease and macrophages support liver metastases. Efferocytosis, or engulfment of apoptotic cells by macrophages, is an essential process in tissue homeostasis and wound healing, but its role in metastasis is less well understood. Here, we found that the colonization of the hepatic metastatic site is accompanied by low-grade tissue injury and that efferocytosis-mediated clearance of parenchymal dead cells promotes macrophage reprogramming and liver metastasis. Mechanistically, progranulin expression in macrophages is necessary for efficient efferocytosis by controlling lysosomal acidification via cystic fibrosis transmembrane conductance regulator and the degradation of lysosomal cargo, resulting in LXRα/RXRα-mediated macrophage conversion and upregulation of arginase 1. Pharmacological blockade of efferocytosis or macrophage-specific genetic depletion of progranulin impairs macrophage conversion, improves CD8+ T cell functions, and reduces liver metastasis. Our findings reveal how hard-wired functions of macrophages in tissue repair contribute to liver metastasis and identify potential targets for prevention of pancreatic ductal adenocarcinoma liver metastasis.
Natural language processing of multi-hospital electronic health records for public health surveillance of suicidality
Authors: Bey Romain , Cohen Ariel , Trebossen Vincent , Dura Basile , Geoffroy Pierre-Alexis , Jean Charline , Landman Benjamin , Petit-Jean Thomas , Chatellier Gilles , Sallah Kankoe , Tannier Xavier , Bourmaud Aurelie , Delorme Richard
Published: February 2024

There is an urgent need to monitor the mental health of large populations, especially during crises such as the COVID-19 pandemic, to timely identify the most at-risk subgroups and to design targeted prevention campaigns. We therefore developed and validated surveillance indicators related to suicidality: the monthly number of hospitalisations caused by suicide attempts and the prevalence among them of five known risks factors. They were automatically computed analysing the electronic health records of fifteen university hospitals of the Paris area, France, using natural language processing algorithms based on artificial intelligence. We evaluated the relevance of these indicators conducting a retrospective cohort study. Considering 2,911,920 records contained in a common data warehouse, we tested for changes after the pandemic outbreak in the slope of the monthly number of suicide attempts by conducting an interrupted time-series analysis. We segmented the assessment time in two sub-periods: before (August 1, 2017, to February 29, 2020) and during (March 1, 2020, to June 31, 2022) the COVID-19 pandemic. We detected 14,023 hospitalisations caused by suicide attempts. Their monthly number accelerated after the COVID-19 outbreak with an estimated trend variation reaching 3.7 (95%CI 2.1–5.3), mainly driven by an increase among girls aged 8–17 (trend variation 1.8, 95%CI 1.2–2.5). After the pandemic outbreak, acts of domestic, physical and sexual violence were more often reported (prevalence ratios: 1.3, 95%CI 1.16–1.48; 1.3, 95%CI 1.10–1.64 and 1.7, 95%CI 1.48–1.98), fewer patients died (p = 0.007) and stays were shorter (p < 0.001). Our study demonstrates that textual clinical data collected in multiple hospitals can be jointly analysed to compute timely indicators describing mental health conditions of populations. Our findings also highlight the need to better take into account the violence imposed on women, especially at early ages and in the aftermath of the COVID-19 pandemic.
Targeting the mevalonate or Wnt pathways to overcome CAR T-cell resistance in TP53-mutant AML cells
Authors: Mueller Jan , Schimmer Roman R , Koch Christian , Schneiter Florin , Fullin Jonas , Lysenko Veronika , Pellegrino Christian , Klemm Nancy , Russkamp Norman , Myburgh Renier , Volta Laura , Theocharides Alexandre PA , Kurppa Kari J , Ebert Benjamin L , Schroeder Timm , Manz Markus G , Boettcher Steffen
Published: February 2024

TP53-mutant acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are characterized by chemotherapy resistance and represent an unmet clinical need. Chimeric antigen receptor (CAR) T-cells might be a promising therapeutic option for TP53-mutant AML/MDS. However, the impact of TP53 deficiency in AML cells on the efficacy of CAR T-cells is unknown. We here show that CAR T-cells engaging TP53-deficient leukemia cells exhibit a prolonged interaction time, upregulate exhaustion markers, and are inefficient to control AML cell outgrowth in vitro and in vivo compared to TP53 wild-type cells. Transcriptional profiling revealed that the mevalonate pathway is upregulated in TP53-deficient AML cells under CAR T-cell attack, while CAR T-cells engaging TP53-deficient AML cells downregulate the Wnt pathway. In vitro rational targeting of either of these pathways rescues AML cell sensitivity to CAR T-cell-mediated killing. We thus demonstrate that TP53 deficiency confers resistance to CAR T-cell therapy and identify the mevalonate pathway as a therapeutic vulnerability of TP53-deficient AML cells engaged by CAR T-cells, and the Wnt pathway as a promising CAR T-cell therapy-enhancing approach for TP53-deficient AML/MDS.
Exosomes encapsulated in hydrogels for effective central nervous system drug delivery
Authors: Zakeri Ziba , Heiderzadeh Morteza , Kocaarslan Azra , Metin Ecem , Hosseini Karimi Seyed Nasir , Saghati Sepideh , Vural Atay , Akyoldaş Göktuğ , Baysal Kemal , Yağcı Yusuf , Gürsoy-Özdemir Yasemin , Taşoğlu Savaş , Rahbarghazi Reza , Sokullu Emel
Published: February 2024

The targeted delivery of pharmacologically active molecules, metabolites, and growth factors to the brain parenchyma has become one of the major challenges following the onset of neurodegeneration and pathological conditions.
3D printing of polyvinyl alcohol hydrogels enabled by aqueous two-phase system
Authors: Karyappa Rahul , Nagaraju Nidhi , Yamagishi Kento , Koh Xue Qi , Zhu Qiang , Hashimoto Michinao
Published: February 2024

Embedded 3D printing of PVA hydrogels (PVA-Hy) was demonstrated via alkali-induced physical crosslinking (NaOH, 4% w/w), which was enabled by simultaneous salt-induced stabilization of PVA via aqueous two-phase system (ATPS).
Nanoscale dynamical investigation of the hemoglobin complex with the bacterial protein IsdB: is their interaction stabilized by catch bonds?
Authors: Botti Valentina , De Bei Omar , Marchetti Marialaura , Campanini Barbara , Cannistraro Salvatore , Bettati Stefano , Bizzarri Anna Rita
Published: February 2024

Iron surface determinant B (IsdB) is a surface protein of Staphylococcus aureus that plays essential roles in host cell invasion by mediating both bacterial adhesion and hemic iron acquisition.
Seed-mediated growth synthesis and tunable narrow-band luminescence of quaternary Ag–In–Ga–S alloyed nanocrystals
Authors: Lin Ouyang , Wang Lijin , Xie Xiulin , Wang Shuaibing , Feng Yibo , Xiao Jiawen , Zhang Yu , Tang Aiwei
Published: February 2024

Narrow-band luminescence was observed from Ag–In–Ga–S alloyed nanocrystals were synthesized through a seed-mediated growth and cation exchange strategy, which was originated from the recombination of the conduction band edge to silver vacancy states.
Gram-scale chemical synthesis of galactosyllactoses and their impact on infant gut microbiota in vitro
Authors: Meeusen Evy , Cao Linqiu , Delsing Dianne J. , Groeneveld Andre , Heerikhuisen Margreet , Schuren Frank , Boltje Thomas J.
Published: February 2024

We report the gram-scale chemical synthesis of 3′-, 4′-, and 6′-galactosyllactose starting from lactose. The impact of these galactosyllactoses on infant gut microbiota was tested in vitro by fermentation experiments using infant faecal samples.
Organocatalytic asymmetric cascade bicyclization: access to chiral polycyclic bisindoles from 2-indolylmethanols and propargylic alcohols
Authors: Zhu Wen-Run , Su Qiong , Deng Xiao-Yi , Ouyang Ze-Long , Weng Jiang , Lu Gui
Published: February 2024

A chiral phosphoric acid-catalyzed asymmetric bis-cyclization of α-indolyl propargylic alcohols with 2-indolylmethanols was realized.
High electrochemical performance of nickel cobaltite@biomass carbon composite (NiCoO@BC) derived from the bark of Anacardium occidentale for supercapacitor application
Authors: Diop Modou , Ndiaye Baye Modou , Dieng Sokhna , Ngom Balla D. , Chaker Mohamed
Published: February 2024

Nickel cobaltite hydroxide NiCo2O4/NiOOH (NiCoO) with biomass carbon (BC) are successfully synthesized using the bark of Anacardium occidentale extract as a carbon source via an energy-saving hydrothermal process. The carbon from biomass greatly enhances the electrochemical performances of NiCoO.
Antineoplastic indole-containing compounds with potential VEGFR inhibitory properties
Authors: Aboshouk Dalia R. , Youssef M. Adel , Bekheit Mohamed S. , Hamed Ahmed R. , Girgis Adel S.
Published: February 2024

VEGF, an important category of tyrosine kinases, and its receptors (VEGFR) are hyper-activated in different cancers. The recently reported indolyl analogs with potential antineoplastic and VEGFR inhibitory properties are highlighted.
Photocatalytic methanol oxidation to formaldehyde in a continuous laboratory plant over Aeroxide P25
Authors: Stubenrauch Florian , Schörner Markus , Bösmann Andreas , Schühle Patrick , Wasserscheid Peter
Published: February 2024

We here report the photochemical synthesis of formaldehyde by gas phase methanol oxidation with oxygen in a sophisticated continuous laboratory setup.
In situ construction of halogen MOF bifunctional catalysts for synergistic removal of NO and Hg0
Authors: Hao Shu , Jiaju Fu , Yuling Liu , Yinhe Wang
Published: February 2024

The denitration process has certain effects on mercury removal, and covalent C–Cl can effectively capture Hg0.
Revealing the effect of conductive carbon materials on the sodium storage performance of sodium iron sulfate
Authors: Zhu Wenqing , Hao Zhiqiang , Shi Xiaoyan , Zhou Xunzhu , Yang Zhuo , Zhang Lingling , Miao Zongcheng , Li Lin , Chou Shu-Lei
Published: February 2024

The Na2Fe2(SO4)3@KB cathode shows excellent electrochemical performance, and the assembled Na2Fe2(SO4)3@KB//hard carbon full cell also exhibits a high operation voltage of 3.5 V and good capacity retention of 77.3% after 100 cycles.
Current advances and future outlook of heterogeneous catalytic transesterification towards biodiesel production from waste cooking oil
Authors: Ghosh Nabanita , Patra Mehulee , Halder Gopinath
Published: February 2024

The demonstration of disposal and utilisation of waste cooking oil as potential feedstock towards biodiesel synthesis by catalytic heterogeneous transesterification.
Fe/Fe3C nanoparticles in situ-doped with carbon nanofibers embedded in rGO as high-performance anode electrocatalysts of microbial fuel cells
Authors: Ren Tingli , Liu Yuanfeng , Lin Xiaoqiu , Li Congju
Published: February 2024

The aerogel structure composed of NCNFs and rGO is conducive to the colonization and extracellular electron transport of microorganisms.
Heterocycles for direct air capture and MOFs prepared from CO2 utilization
Authors: Du Jingcheng , Liu Linghao , Sun Qian , Song Ziye , Yao Ayan , Ma Ji , Chung Tai-Shung , Xu Wei , Zhang Hongjun , Liu Jiangtao
Published: February 2024

Direct air capture via heterocycles and various flexible MOFs prepared from CO2, heterocycles, and Zn clusters.
Water-soluble red fluorescent protein dimers for hypoxic two-photon photodynamic therapy
Authors: Feng Wan , Qian Ying
Published: February 2024

In this study, two water-soluble red fluorescent protein (RFP) dimers, FP2R′ and FP2R′′, were synthesized by linking two phenothiazine-based RFP chromophore analogues through alkyl chains or alkoxy chains for hypoxic two-photon photodynamic therapy.
Plant-derived exosomes: a green approach for cancer drug delivery
Authors: Madhan Shrishti , Dhar Rajib , Devi Arikketh
Published: February 2024

Plant-derived exosomes (PDEs) show promising potential to be developed as a therapeutic agent against cancer, owing to their multiple advantages such as low toxicity, biocompatibility, availability, affordability, etc.
Fermi–Dirac statistics in correlation between electronic entropy and spatial confinement of liquid crystal-perovskite nanohybrids
Authors: Debnath Deejan , Halder Prithish , Saha Barnali , Acharya Himadri , Ghosh Sujit Kumar
Published: February 2024

The concept of Fermi–Dirac statistics has been applied to correlate between the electronic entropy and spatial confinement of liquid crystal-perovskite nanohybrids as model condensed matter systems.