bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards geospatially-resolved public-health surveillance via wastewater sequencing
Authors: Tierney Braden T. , Foox Jonathan , Ryon Krista A. , Butler Daniel , Damle Namita , Young Benjamin G. , Mozsary Christopher , Babler Kristina M. , Yin Xue , Carattini Yamina , Andrews David , Lucaci Alexander G. , Solle Natasha Schaefer , Kumar Naresh , Shukla Bhavarth , Vidović Dušica , Currall Benjamin , Williams Sion L. , Schürer Stephan C. , Stevenson Mario , Amirali Ayaaz , Beaver Cynthia Campos , Kobetz Erin , Boone Melinda M. , Reding Brian , Laine Jennifer , Comerford Samuel , Lamar Walter E. , Tallon John J. , Wain Hirschberg Jeremy , Proszynski Jacqueline , Al Ghalith Gabriel , Can Kurt Kübra , Sharkey Mark E. , Church George M. , Grills George S. , Solo-Gabriele Helena M. , Mason Christopher E.
Published: September 2024

Wastewater is a geospatially- and temporally-linked microbial fingerprint of a given population, making it a potentially valuable tool for tracking public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (N = 2238 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County, USA, from 2020-2022. We used targeted amplicon sequencing to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with positive PCR tests from University students and Miami-Dade hospital patients. Additionally, in bulk metatranscriptomic data, we demonstrate that the bacterial content of different wastewater sampling locations serving small population sizes can be used to detect putative, host-derived microorganisms that themselves have known associations with human health and diet. We also detect multiple enteric pathogens (e.g., Norovirus) and characterize viral diversity across sites. Moreover, we observed an enrichment of antimicrobial resistance genes (ARGs) in hospital wastewater; antibiotic-specific ARGs correlated to total prescriptions of those same antibiotics (e.g Ampicillin, Gentamicin). Overall, this effort lays the groundwork for systematic characterization of wastewater that can potentially influence public health decision-making.
Nur77 protects the bladder urothelium from intracellular bacterial infection
Authors: Collins Christina A. , Waller Chevaughn , Batourina Ekaterina , Kumar Lokesh , Mendelsohn Cathy L. , Gilbert Nicole M.
Published: September 2024

Intracellular infections by Gram-negative bacteria are a significant global health threat. The nuclear receptor Nur77 (also called TR3, NGFI-B, or NR4A1) was recently shown to sense cytosolic bacterial lipopolysaccharide (LPS). However, the potential role for Nur77 in controlling intracellular bacterial infection has not been examined. Here we show that Nur77 protects against intracellular infection in the bladder by uropathogenic Escherichia coli (UPEC), the leading cause of urinary tract infections (UTI). Nur77 deficiency in mice promotes the formation of UPEC intracellular bacterial communities (IBCs) in the cells lining the bladder lumen, leading to persistent infection in bladder tissue. Conversely, treatment with a small-molecule Nur77 agonist, cytosporone B, inhibits invasion and enhances the expulsion of UPEC from human urothelial cells in vitro, and significantly reduces UPEC IBC formation and bladder infection in mice. Our findings reveal a new role for Nur77 in control of bacterial infection and suggest that pharmacologic agonism of Nur77 function may represent a promising antibiotic-sparing therapeutic approach for UTI.
Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq
Authors: Noble Joyce Carol , Lentini Antonio , Hagemann-Jensen Michael , Sandberg Rickard , Reinius Björn
Published: September 2024

Single-cell RNA-sequencing (scRNAseq) is revolutionizing biomedicine, propelled by advances in methodology, ease of use, and cost reduction of library preparation. Over the past decade, there have been remarkable technical improvements in most aspects of single-cell transcriptomics. Yet, little to no progress has been made in advancing RNase inhibition despite maintained RNA integrity being critical during cell collection, storage, and cDNA library generation. Here, we demonstrate that a synthetic thermostable RNase inhibitor (SEQURNA) yields single-cell libraries of equal or superior quality compared to ubiquitously used protein-based recombinant RNase inhibitors (RRIs). Importantly, the synthetic RNase inhibitor provides additional unique improvements in reproducibility and throughput, enables new experimental workflows including retained RNase inhibition throughout heat cycles, and can reduce the need for dry-ice transports. In summary, replacing RRIs represents a substantial advancement in the field of single-cell transcriptomics.
An assessment of the species diversity and disease potential of Pythium communities in Europe
Authors: Boie Wilken , Schemmel Markus , Ye Wanzhi , Hasler Mario , Goll Melanie , Verreet Joseph-Alexander , Cai Daguang
Published: September 2024

Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.
Enhancing the efficiency of high-order harmonics with two-color non-collinear wave mixing in silica
Authors: Roscam Abbing Sylvianne D. C. , Kuzkova Nataliia , van der Linden Roy , Campi Filippo , de Keijzer Brian , Morice Corentin , Zhang Zhuang-Yan , van der Geest Maarten L. S. , Kraus Peter M.
Published: September 2024

The emission of high-order harmonics from solids under intense laser-pulse irradiation is revolutionizing our understanding of strong-field solid-light interactions, while simultaneously opening avenues towards novel, all-solid, coherent, short-wavelength table-top sources with tailored emission profiles and nanoscale light-field control. To date, broadband spectra in solids have been generated well into the extreme-ultraviolet (XUV), but the comparatively low conversion efficiency in the XUV range achieved under optimal conditions still lags behind gas-based high-harmonic generation (HHG) sources. Here, we demonstrate that two-color high-order harmonic wave mixing in a fused silica solid is more efficient than solid HHG driven by a single color. This finding has significant implications for compact XUV sources where gas-based HHG is not feasible, as solid XUV wave mixing surpasses solid-HHG in performance. Moreover, our results enable utilizing solid high-order harmonic wave mixing as a probe of structure or material dynamics of the generating solid, which will enable reducing measurement times compared to the less efficient regular solid HHG. The emission intensity scaling that follows perturbative optical wave mixing, combined with the angular separation of the emitted frequencies, makes our approach a decisive step for all-solid coherent XUV sources and for studying light-engineered materials.
Computer-aided drug design to generate a unique antibiotic family
Authors: Barden Christopher J. , Wu Fan , Fernandez-Murray J. Pedro , Lu Erhu , Sun Shengguo , Taylor Marcia M. , Rushton Annette L. , Williams Jason , Tavasoli Mahtab , Meek Autumn , Reddy Alla Siva , Doyle Lisa M. , Sagamanova Irina , Sivamuthuraman Kovilpitchai , Boudreau Robert T. M. , Byers David M. , Weaver Donald F. , McMaster Christopher R.
Published: September 2024

The World Health Organization has identified antibiotic resistance as one of the three greatest threats to human health. The need for antibiotics is a pressing matter that requires immediate attention. Here, computer-aided drug design is used to develop a structurally unique antibiotic family targeting holo-acyl carrier protein synthase (AcpS). AcpS is a highly conserved enzyme essential for bacterial survival that catalyzes the first step in lipid synthesis. To the best of our knowledge, there are no current antibiotics targeting AcpS making this drug development program of high interest. We synthesize a library of > 700 novel compounds targeting AcpS, from which 33 inhibit bacterial growth in vitro at ≤ 2 μg/mL. We demonstrate that compounds from this class have stand-alone activity against a broad spectrum of Gram-positive organisms and synergize with colistin to enable coverage of Gram-negative species. We demonstrate efficacy against clinically relevant multi-drug resistant strains in vitro and in animal models of infection in vivo including a difficult-to-treat ischemic infection exemplified by diabetic foot ulcer infections in humans. This antibiotic family could form the basis for several multi-drug-resistant antimicrobial programs.
Assessing semantic interoperability in environmental sciences: variety of approaches and semantic artefacts
Authors: Di Muri Cristina , Pulieri Martina , Raho Davide , Muresan Alexandra N. , Tarallo Andrea , Titocci Jessica , Nestola Enrica , Basset Alberto , Mazzoni Sabrina , Rosati Ilaria
Published: September 2024

The integration and reuse of digital research products can be only ensured through the adoption of machine-actionable (meta)data standards enriched with semantic artefacts. This study compiles 540 semantic artefacts in environmental sciences to: i. examine their coverage in scientific domains and topics; ii. assess key aspects of their FAIRness; and iii. evaluate management and governance concerns. The analyses showed that the majority of semantic artefacts concern the terrestrial biosphere domain, and that a small portion of the total failed to meet the FAIR principles. For example, 5.5% of semantic artefacts were not available in semantic catalogues, 8% were not built with standard model languages and formats, 24.6% were published without usage licences and 22.4% without version information or with divergent versions across catalogues in which they were available. This investigation discusses common semantic practices, outlines existing gaps and suggests potential solutions to address semantic interoperability challenges in some of the resources originally designed to guarantee it.
Comparison of basal ganglia regions across murine brain atlases using metadata models and the Waxholm Space
Authors: Kleven H. , Schlegel U. , Groenewegen H. J. , Leergaard T. B. , Bjerke I. E.
Published: September 2024

The murine basal ganglia regions are targets for research into complex brain functions such as motor control and habit formation. However, there are several ways to name and annotate these regions, posing challenges for interpretation and comparison of data across studies. Here, we give an overview of basal ganglia terms and boundaries in the literature and reference atlases, and describe the criteria used for annotating these regions in the Waxholm Space rat brain atlas. We go on to compare basal ganglia annotations in stereotaxic rat brain atlases and the Allen Mouse brain Common Coordinate Framework to those in the Waxholm Space rat brain atlas. We demonstrate and describe considerable differences in the terms and boundaries of most basal ganglia regions across atlases and their versions. We also register information about atlases and regions in the openMINDS metadata framework, facilitating integration of data in neuroscience databases. The comparisons of terms and boundaries across rat and mouse atlases support analysis and interpretation of existing and new data from the basal ganglia.
BASEPROD: The Bardenas Semi-Desert Planetary Rover Dataset
Authors: Gerdes Levin , Wiese Tim , Castilla Arquillo Raúl , Bielenberg Laura , Azkarate Martin , Leblond Hugo , Wilting Felix , Ortega Cortés Joaquín , Bernal Alberto , Palanco Santiago , Pérez del Pulgar Carlos
Published: September 2024

Dataset acquisitions devised specifically for robotic planetary exploration are key for the advancement, evaluation, and validation of novel perception, localization, and navigation methods in representative environments. Originating in the Bardenas semi-desert in July 2023, the data presented in this Data Descriptor is primarily aimed at Martian exploration and contains relevant rover sensor data from approximately 1.7km of traverses, a high-resolution 3D map of the test area, laser-induced breakdown spectroscopy recordings of rock samples along the rover path, as well as local weather data. In addition to optical cameras and inertial sensors, the rover features a thermal camera and six force-torque sensors. This setup enables, for example, the study of future localization, mapping, and navigation techniques in unstructured terrains for improved Guidance, Navigation, and Control (GNC). The main features of this dataset are the combination of scientific and engineering instrument data, as well as the inclusion of the thermal camera and force-torque sensors in particular.
Gamma rays impact on 2D-MoS2 in water solution
Authors: Singh Manjot , Bianco Davide , Adam Jaber , Capaccio Angela , Clemente Stefania , Del Sorbo Maria Rosaria , Feoli Chiara , Kaur Jasneet , Nappi Carmela , Panico Mariarosaria , Rusciano Giulia , Rossi Manuela , Sasso Antonio , Valadan Mohammadhassan , Cuocolo Alberto , Battista Edmondo , Netti Paolo Antonio , Altucci Carlo
Published: September 2024

Two-dimensional transition metal dichalcogenides, particularly MoS2, are interesting materials for many applications in aerospace research, radiation therapy and bioscience more in general. Since in many of these applications MoS2-based nanomaterials can be placed in an aqueous environment while exposed to ionizing radiation, both experimental and theoretical studies of their behaviour under these conditions is particularly interesting. Here, we study the effects of tiny imparted doses of 511 keV photons to MoS2 nanoflakes in water solution. To the best of our knowledge, this is the first study in which ionizing radiation on 2D-MoS2 occurs in water. Interestingly, we find that, in addition to the direct interaction between high-energy photons and nanoflakes, reactive chemical species, generated by γ-photons induced radiolysis of water, come into play a relevant role. A radiation transport Monte Carlo simulation allowed determining the elements driving the morphological and spectroscopical changes of 2D-MoS2, experimentally monitored by SEM microscopy, DLS, Raman and UV–vis spectroscopy, AFM, and X-ray photoelectron techniques. Our study demonstrates that radiolysis products affect the Molybdenum oxidation state, which is massively changed from the stable + 4 and + 6 states into the rarer and more unstable + 5. These findings will be relevant for radiation-based therapies and diagnostics in patients that are assuming drugs or contrast agents containing 2D-MoS2 and for aerospace biomedical applications of 2DMs investigating their actions into living organisms on space station or satellites.
Third-party punishment-like behavior in a rat model
Authors: Mikami Kanta , Kigami Yuka , Doi Tomomi , Choudhury Mohammed E. , Nishikawa Yuki , Takahashi Rio , Wada Yasuyo , Kakine Honoka , Kawase Mayuu , Hiyama Nanae , Yano Hajime , Abe Naoki , Nishihara Tasuku , Tanaka Junya
Published: September 2024

Third-party punishment (TPP) is an altruistic behavior or sense willing to punish transgressors as a third party not directly involved in the transgression. TPP is observed worldwide, regardless of tradition and culture, and is essential for morality in human society. Moreover, even preverbal infants display TPP-like judgement, suggesting that TPP is evolutionarily conserved and innate. Thus, it is possible that non-human animals display TPP-like behavior, although TPP has been said to be human-specific. We investigated whether or not male mature Wistar rats displayed TPP-like behaviors when they witnessed deadly aggression by an unknown aggressive mouse toward another unknown victim mouse. Normally reared rats did not display TPP-like behaviors, but rats reared with extensive affectionate handling by human caretakers as beloved pets contacted the unknown aggressive mice in a gentle manner leading to reduced aggression toward the unknown victim mice, even when the aggressive mice fought back. Furthermore, the handled rats touched unknown rat pups that were drowning in water and anesthesia-induced comatose rats more frequently than control rats. These findings suggest a possibility that TPP is not in fact human-specific and innate but rather an acquired behavior that flourishes in affectionate circumstances.
A novel computational signal processing framework towards multimodal vital signs extraction using neck-worn wearable devices
Authors: Abdulsadig Rawan S. , Rodriguez-Villegas Esther
Published: September 2024

Pulse rate (PR) and respiratory rate (RR) are two of the most important vital signs. Monitoring them would benefit from easy-to-use technologies. Hence, wearable devices would, in principle, be ideal candidates for such systems. The neck, although highly susceptible to artifacts, presents an attractive location for a diverse pool of physiological biomarkers monitoring purposes such as airflow sensing in a non-obstructive manner. This paper presents a methodology for PR and RR estimation using photoplethysmography (PPG) and accelerometry (Acc) sensors placed on the neck. Neck PPG and Acc signals were recorded from 22 healthy participants for RR estimation, where the resting subjects performed guided breathing following a visual metronome. Neck PPG signals were obtained from 16 healthy participants who breathed through an altitude generator machine in order to acquire a wider range of PR readings while at rest. The proposed methodology was able to provide rate estimates via a combination of recursive FFT-based dominance scoring coupled with an exponentially weighted moving average (EWMA)-driven aggregation scheme. The recursion aimed at bypassing sudden intra-window amplitude deviations caused by momentary artifacts, while the EWMA-based aggregation was utilized for handling inter-window artifact-induced deviations. To further improve estimation stability and confidence, estimates were calculated in the form of rate bands taking into account the relevant clinically acceptable error margins, and results when considering rate values and rate bands are presented and discussed. The framework was able to achieve an overall pulse rate value accuracy of $$93.67\pm 7.64$$

93.67
±
7.64

% within the clinically acceptable ± 5 BPM with reference to the gold-standard reference devices while providing an overall respiratory rate value accuracy within the clinically appropriate ± 3 BrPM of $$94.94\pm 3.56$$

94.94
±
3.56

% with reference to the guiding visual metronome, and $$88.4\pm 7.63$$

88.4
±
7.63

% with respect to the gold-standard reference device. The proposed methodology achieves acceptable PR and RR estimation capabilities, even when signals are acquired from an unusual location such as the neck. This work introduces novel ideas that can lead to the development of medical device outputs for PR and RR monitoring, especially capitalizing on the advantages of the neck as a multi-modal physiological monitoring location.
PCR-based RFLP and ERIC-PCR patterns of Helicobacter pylori strains linked to multidrug resistance in Egypt
Authors: Abdulrahman Mohammed S. , Mansy Moselhy S. , Al-Ghreib Kamel A. , Johar Dina , Zaky Samy
Published: September 2024

H. pylori infects approximately 50% of the world’s population that causes chronic gastritis, and may lead to peptic ulcer disease (PUD). H. pylori-induced chronic infections are associated with gastric adenocarcinoma and low-grade gastric lymphoma. In Egypt, H. pylori strains are widespread and became resistant to antimicrobial agents, thus advanced typing methods are needed to differentiate infectious strains that are resistant to antibiotics, and therefore earlier prognosis and infection control. The main objectives were (i) to determine susceptibility of infectious H. pylori strains to some antimicrobial agents that are currently used in eradication therapy in Egypt; (ii) to identify diverse strains commonly detected in the gastrointestinal (GIT) endoscopy units in Egypt through phenotypic and genotypic analyses. In this observational study we isolated 167 isolates from 232 gastric biopsies (antrum and corpus) of patients who were admitted to the upper GIT endoscopy units in five governmental Egyptian hospitals. Antimicrobial susceptibility patterns were investigated using Kirby Bauer disc diffusion and agar dilution Minimum Inhibitory Concentrations (MICs) methods. Phenotypic characterization was based on biotyping and antibiogram typing techniques. Genotypic characterization was carried out using PCR-based Restriction Fragment Length Polymorphism (RFLP) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR analyses. H. pylori isolates were highly resistant to diverse antimicrobial agents including Metronidazole, Fluoroquinolones, Macrolides, Amoxycillin, Tetracycline and Gentamicin. Two factors contributed to the increased resistance of H. pylori to the conventional therapy seen in Egypt: (i) Metronidazole and Amoxycillin are inexpensive and available drugs being abused by patients; (ii) the regional prescribing practice of Macrolids commonly used to treat upper respiratory and urinary tract infections. Five different biotypes were identified depending on the ability of the isolates to synthesize different enzymes. Nine antibiogram types were identified. PCR-RFLP analysis revealed fifteen different fingerprints while ERIC-PCR revealed 22 fingerprints. Biotyping alone or in combination with antibiogram typing are highly useful molecular tools in the prognosis of strain relatedness. PCR-RFLP and ERIC-PCR acquired good discriminatory power for identifying H. pylori infectious sub-types.
Preliminary study on heart response and locomotor parameters in Donkeys (Equus asinus) during exercise using fitness tracker (Equimetre)
Authors: Khamis Taleb Al , Shawaf Turke , El-Deeb Wael , Almubarak Adel , Al-Ali Mohammed Ali , Almuaqqil Meshari , AlAiyan Ahmad , Homeida Abdelgadir M.
Published: September 2024

The welfare of donkeys remains a compelling subject for researchers, with limited literature available on the response of the donkey cardiovascular system during strenuous exercise. The study aimed to address two primary objectives. Firstly, to assess the reliability of wearable devices in detecting heart rate (HR) and ECG readings. Secondly, to determine HR, locomotor and cardiac troponin 1 (cTnI) levels in donkeys during exercise. A total of seven donkeys were outfitted with two systems for ECG measurements, namely Equimetre and the Standard base apex, to enable a comparison between the two. Additionally, fifteen apparently healthy donkeys equipped with Equimetre were divided into two groups: the race group (R), consisting of donkeys trained for racing, and the non-race group (NR), comprising donkeys used for regular riding. The results indicated a level of agreement between the two devices in intervals R-R (P =  < 0.0001), S-T (P = 0.0002), Q-T(P = 0.0003), P-R (P = 0.0037), segment P-R (P = 0.0023) and HR (P =  < 0.0001) at rest. This suggested that Equimetre can provide a level of accepted ECG reading in donkey. No significant difference in heart response and locomotor parameters between donkey groups, although this finding needs further studies to verify it and to understand the dynamics of donkey. This study demonstrates the feasibility of Equimetre in detection HR and present initial data of heart response and locomotor in donkeys during exercise.
A simulation-based analysis of optical read-out for electrochemical reactions using composite vortex beams
Authors: Kumar Nirjhar , Arora Ankit , Krishnan Ananth
Published: September 2024

We propose an optical read-out method for extracting faradaic current in electrochemical (EC) reactions and analyze its performance using opto-EC simulations. Our approach utilizes structured electrodes to generate composite optical vortex (COV) beams upon optical illumination. Through opto-EC simulations, we demonstrate that the EC reaction of 10 mM potassium ferricyanide induces a refractive index (RI) change, $$\Delta$$
Δ
RI, of approximately $$10^{-4}$$

10

-
4

RI units, leading to the rotation of the COV beam’s intensity profile with a peak rotation of $$40^{\circ }$$

40
∘

. This rotation’s magnitude is proportional to $$\Delta$$
Δ
RI, while the rate correlates with the faradaic current ($$I_f$$

I
f

) density responsible for $$\Delta$$
Δ
RI. As the opto-EC information is from bulk $$\Delta$$
Δ
RI, it remains unaffected by interfering non-faradaic components at the interface and is advantageous for studying intermediate species and bulk homogeneous reactions. Furthermore, as rotation depends on $$I_f$$

I
f

density rather than $$I_f$$

I
f

itself, this method proves beneficial in low $$I_f$$

I
f

scenarios, such as when employing micro-electrodes to decrease solution resistance or obtain localized EC data. Even in low $$I_f$$

I
f

density scenarios, like monitoring slow EC reactions, our method enables signal amplification by accumulating rotation over time. This interdisciplinary approach holds promise for advancing EC research and addressing critical challenges across various fields, including energy storage, corrosion protection, environmental remediation, and biomedical sciences.
Comparative study of machine learning and statistical survival models for enhancing cervical cancer prognosis and risk factor assessment using SEER data
Authors: Kolasseri Anjana Eledath , B Venkataramana
Published: September 2024

Cervical cancer is a common malignant tumor of the female reproductive system and the leading cause of death among women worldwide. The survival prediction method can be used to effectively analyze the time to event, which is essential in any clinical study. This study aims to bridge the gap between traditional statistical methods and machine learning in survival analysis by revealing which techniques are most effective in predicting survival, with a particular emphasis on improving prediction accuracy and identifying key risk factors for cervical cancer. Women with cervical cancer diagnosed between 2013 and 2015 were included in our study using data from the Surveillance, Epidemiology, and End Results (SEER) database. Using this dataset, the study assesses the performance of Weibull, Cox proportional hazards models, and Random Survival Forests in terms of predictive accuracy and risk factor identification. The findings reveal that machine learning models, particularly Random Survival Forests (RSF), outperform traditional statistical methods in both predictive accuracy and the discernment of crucial prognostic factors, underscoring the advantages of machine learning in handling complex survival data. However, for a survival dataset with a small number of predictors, statistical models should be used first. The study finds that RSF models enhance survival analysis with more accurate predictions and insights into survival risk factors but highlights the need for larger datasets and further research on model interpretability and clinical applicability.
Effects on upper masonry structures caused by double-line parallel shield cutting group pile construction
Authors: Zhu Xiang , Ma Shi-ju , Hong Kai-rong , Ding Yong-gang
Published: September 2024

The effects on the upper masonry structure and the construction parameters of shield cutting piles were studied during shield construction, focusing on a shield interval of Zhengzhou Metro Line 5. The study utilized the actual engineering case of left and right double-lane shields superimposed on cutting cement soil group pile composite foundations beneath masonry structures. Findings revealed that masonry structures within approximately 30 m (5.0 times the tunnel diameter) were impacted before and after shield cut pile construction, resulting in deflection and twisting deformations of houses along the central axes of the left and right tunnel lines. Implementation of “clay shock” grouting outside the shield shell, radial grouting through small conduits, shield tail synchronous grouting, and secondary reinforcement grouting effectively mitigated the disturbance caused by shield construction to the ground. When shield cut piles passed beneath masonry structures, pressure on the soil chamber, total thrust, and cutterhead speed were consistently controlled. Furthermore, the cutterhead torque was appropriately reduced, and slurry injection volume increased, contributing to better control of house settlement.
New carnivorous sponges (Porifera: Cladorhizidae) from Western Australia, collected by a Remotely Operated Vehicle (ROV)
Authors: Ekins Merrick , Wilson Nerida G.
Published: September 2024

The last two decades have reinvigorated systematic research on predatory sponges, mainly fuelled by advances in technology that have facilitated collection in deep-water habitats. This research presents six new species of carnivorous sponges from the family Cladorhizidae Dendy, 1922 from the western continental margin of Australia. The new species are Abyssocladia johnhooperi nov. sp., Abyssocladia aurora nov. sp., Abyssocladia janusi nov. sp., Axoniderma challengeri nov. sp., Cladorhiza vanessaekins nov. sp. and Nullarbora ningalooa nov. sp.. This material was collected by ROV during expeditions FK200308 to the Ningaloo Canyons expedition off the mid-west coast near Ningaloo, and FK200126 to the Southwest Australian canyons expedition, in Western Australia. These and other expeditions by the Schmidt Ocean Institute in 2020–21 formed a campaign around Australia’s deep sea and mesophotic environments, which has vastly increased our understanding of biodiversity in these habitats.
Adipose gene expression profiles in Northern Finncattle, Mirandesa cattle, Yakutian cattle and commercial Holstein cattle
Authors: Ruvinskiy Daniil , Amaral Andreia , Weldenegodguad Melak , Ammosov Innokentyi , Honkatukia Mervi , Lindeberg Heli , Peippo Jaana , Popov Ruslan , Soppela Päivi , Stammler Florian , Uimari Pekka , Ginja Catarina , Kantanen Juha , Pokharel Kisun
Published: September 2024

The drastic change in global climate has led to in-depth studies of the geneticresources of native cattle adapted to challenging environments. Native cattle breeds may harbor unique genetic mechanisms that have enabled them adapt to their given environmental conditions. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the differential gene expression profiles in three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle. A total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n = 26), metacarpal adipose tissue (n = 26), tailhead adipose tissue (n = 26) and prescapular adipose tissue (n = 3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such as NR4A3, TEKT3, and FGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, and IL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of the TPRG1 gene in three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency. The highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues among breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue.
Estimating the distribution of reedbed in Britain demonstrates challenges of remotely sensing rare land cover types at large spatial scales
Authors: Davies Jacob G. , Dytham Calvin , Robinson Robert A. , Beale Colin M.
Published: September 2024

Common Reed Phragmites australis, globally one of the mostly widely distributed wetland plants, is important for biodiversity and for humans. However, like most wetland plant communities, reedbed has rarely been mapped at large geographical scales, restricting the information available to study reed’s range dynamics or inform its management. Using Sentinel-2 data and machine learning, we aimed to produce the first published remotely-sensed reedbed map of Britain; however, accuracy as assessed by field validation was relatively low (AUC = 0.671), with many false positives (commission error of 93.4%). A similar workflow carried out in Google Earth Engine, using nearly an order of magnitude more images, gave a lower commission error but a disproportionately higher omission error. Using the known commission and omission error, we estimate that in 2015–2017 ~ 7800 ha of Britain was reedbed. Our study highlights the enduring barriers to accurate land cover classification at large spatial scales. Even with a ‘big data’ approach, reflectance error and ecological factors such as confusion land cover types and geographical variation in temporal reflectance function will probably continue to limit the size of area for which land cover can be classified accurately, therefore limiting the utility of remote sensing for ecologists.
Clustered ARPE-19 cells distinct in mitochondrial membrane potential may play a pivotal role in cell differentiation
Authors: Miyatani Takafumi , Tanaka Hiroshi , Numa Kosaku , Uehara Asako , Otsuki Yohei , Hamuro Junji , Kinoshita Shigeru , Sotozono Chie
Published: September 2024

Age-related macular degeneration (AMD) is associated with the dysfunction and degeneration of retinal pigment epithelium (RPE) cells. Here, we examined how the formation and expansions of cell clusters are regulated by the differentiation of the RPE　cells. In this study, ARPE-19 cells were cultivated in standard or differentiation media, i.e., without or with nicotinamide, to evaluate the spreading of cell clusters specified with differentiated cell phenotypes. Mitochondria membrane potential (MMP) and the distribution of the RPE cell clusters was also monitored with or without rotenone, a mitochondrial electron transport chain (ETC) complex I inhibitor. Cultured ARPE-19 cells generated scattered cell clusters composed mostly of smaller size cells expressing the differentiation markers mouse anti-cellular retinaldehyde–binding protein (CRALBP) and Bestrophin only in differentiation medium. After the increase of the number of clusters, the clusters appeared to paracellularly merge, resulting in expansion of the area occupied by the clusters. Of note, the cells within the clusters selectively had high MMP and were in accordance with the expression of RPE differentiation markers. Rotenone repressed the formation of the clusters and decreased intracellular MMP. The above results suggest that clustering of RPE cells with functional mitochondria plays a pivotal role in RPE cell differentiation process and the ETC complex I inhibition greatly influences the composition of RPE cells that are degenerated or differentiation disposed.
Value creation of copra meal mannan into functional manno-oligosaccharides (β-MOS) using the mannanase Bacillus man B (BlMan26B)
Authors: Cuong Nguyen Cao , Haltrich Dietmar , Min Thae Thae , Nguyen Thu-Ha , Yamabhai Montarop
Published: September 2024

Agricultural wastes rich in β-mannan are an important environmental problem in tropical and sub-tropical countries. This research aims at dealing with this and investigates the valorization of mannan-rich copra meal from virgin coconut oil manufacturing into mannan-oligosaccharides (β-MOS) by enzymatic hydrolysis using β-mannanase from Bacillus licheniformis (BlMan26B). Lab-scale process, involving pre-treatment and bioconversion steps, were conducted and evaluated. Lyophilized β-MOS was analyzed and its biological activities were assessed. The size of oligosaccharides obtained ranged from dimers to hexamers with 36.7% conversion yields. The prebiotic effects of β-MOS were demonstrated in comparison with commercial inulin and fructo-oligosaccharides (FOS). In vitro toxicity assays of β -MOS on human dermal fibroblasts and monocytes showed no cytotoxic effect. Interestingly, β-MOS at concentrations ranging from 10 to 200 µg/mL also demonstrated potent anti-inflammatory activity against LPS-induced inflammation of human macrophage THP-1 in a dose-dependent manner. However, at high dose, β-MOS could also stimulate inflammation. Therefore, further investigation must be conducted to ensure its efficacy and safe use in the future. These results indicate that β-MOS have the potential to be used as valued-added health-promoting nutraceutical or feed additive after additional in-depth studies. These finding should be applicable for other agricultural wastes rich in mannan as well.
Modulation of αv integrins by lebecetin, a viper venom-derived molecule, in experimental neuroinflammation and demyelination models
Authors: Neili Nour-elhouda , AbdelKafi-Koubaa Zaineb , Jebali Jed , Kaidi Khouloud , Sahraoui Ghada , Ahmed Melika Ben , Srairi-Abid Najet , Marrakchi Naziha , Doghri Raoudha , ELBini Ines
Published: September 2024

Several neurodegenerative diseases, such as multiple sclerosis and Parkinson’s disease, are linked to alterations in myelin content or structure. Transmembrane receptors such as integrins could be involved in these alterations. In the present study, we investigated the role of αv-integrins in experimental models of neuroinflammation and demyelination with the use of lebecetin (LCT), a C-lectin protein purified from Macrovipera lebetina viper venom, as an αv-integrin modulator. In a model of neuroinflammation, LCT inhibited the upregulation of αv, β3, β5, α5, and β1 integrins, as well as the associated release of pro-inflammatory factor IL-6 and chemokine CXCL-10, and decreased the expression of phosphorylated NfκB. The subsequent “indirect culture” between reactive astrocytes and oligodendrocytes showed a down-regulation of αv and β3 integrins versus upregulation of β1 one, accompanied by a reduced expression of myelin basic protein (MBP). Treatment of oligodendrocytes with LCT rectified the changes in integrin and MBP expression. Through Western blot quantification, LCT was shown to upregulate the expression levels of PI3K and p-mTOR while downregulating expression levels of p-AKT in oligodendrocytes, suggesting the neuroprotective and pro-myelinating effects of LCT may be related to the PI3K/mTor/AKT pathway. Concomitantly, we found that LCT promoted remyelination by tracking the increased expression of MBP in the brains of cuprizone-intoxicated mice. These results point to an involvement of integrins in not only neuroinflammation but demyelination as well. Thus, targeting αv integrins could offer potential therapeutic avenues for the treatment of demyelinating diseases.
Novel 3-dimensional effective regurgitation orifice area quantification serves as a reliable tool to identify severe mitral valve regurgitation
Authors: Harm Tobias , Schwarz Frederic-Joaquim , Zdanyte Monika , Goldschmied Andreas , Baas Livia , Aidery Parwez , Shcherbyna Serhii , Toskas Ioannis , Keller Timea , Kast Isabela , Schreieck Juergen , Geisler Tobias , Gawaz Meinrad Paul , Mueller Karin Anne Lydia
Published: September 2024

A precise quantification of mitral regurgitation (MR) severity is essential for treatment and outcome of patients with MR. 3D echocardiography facilitates estimation of MR but selection of patients with necessity of invasive treatment remains challenging. We investigate effective regurgitation orifice area (EROA) quantification by 3D compared to 2D echocardiography in patients with MR and highlight the improved discrimination of MR severity. We consecutively enrolled fifty patients with primary or secondary and at least moderate MR undergoing 2D and 3D colour Doppler echocardiography prior to transcatheter edge-to-edge repair (TEER). Improved accuracy of MR grading using 3D vena contracta area (VCA) as an estimate of EROA was compared to 2D proximal isovelocity surface area (PISA) quantification method and a multiparameter reference standard. Quantification of EROA remarkably varies between 2D and 3D echocardiography and the discrimination between moderate and severe MR was significantly (p = 0.001) different using 2D PISA or 3D VCA, respectively. 3D VCA correlated significantly (r = 0.501, p < 0.001) better with the pre-defined MR severity. We detected crucial differences in the correct identification of severe MR between 2D and 3D techniques, thus 2D PISA significantly (p < 0.0001) underestimates EROA due to clinical and morphological parameters. The assessment of 3D VCA resulted in improved diagnostic accuracy.
GPT-3.5 altruistic advice is sensitive to reciprocal concerns but not to strategic risk
Authors: Schmidt Eva-Madeleine , Bonati Sara , Köbis Nils , Soraperra Ivan
Published: September 2024

Pre-trained large language models (LLMs) have garnered significant attention for their ability to generate human-like text and responses across various domains. This study delves into examines the social and strategic behavior of the commonly used LLM GPT-3.5 by investigating its suggestions in well-established behavioral economics paradigms. Specifically, we focus on social preferences, including altruism, reciprocity, and fairness, in the context of two classic economic games: the Dictator Game (DG) and the Ultimatum Game (UG). Our research aims to answer three overarching questions: (1) To what extent do GPT-3.5 suggestions reflect human social preferences? (2) How do socio-demographic features of the advisee and (3) technical parameters of the model influence the suggestions of GPT-3.5? We present detailed empirical evidence from extensive experiments with GPT-3.5, analyzing its responses to various game scenarios while manipulating the demographics of the advisee and the model temperature. Our findings reveal that, in the DG Dictator Game, model suggestions are more altruistic than in humans. We further show that it also picks up on more subtle aspects of human social preferences: fairness and reciprocity. This research contributes to the ongoing exploration of AI-driven systems’ alignment with human behavior and social norms, providing valuable insights into the behavior of pre-trained LLMs and their implications for human-AI interactions. Additionally, our study offers a methodological benchmark for future research examining human-like characteristics and behaviors in language models.
Causal relationships between immunophenotypes, plasma metabolites, and temporomandibular disorders based on Mendelian randomization
Authors: Qiu Danqi , Sun Shuntao
Published: September 2024

While numerous studies have underscored the implication of immune cells and metabolites in temporomandibular disorders (TMD), conclusive evidence for causality remains elusive. Consequently, our aim is to explore the causal connections between immunophenotypes and plasma metabolites in relation to TMD employing a bidirectional Mendelian randomization (MR) approach. Summary statistics data on 731 immunophenotypes (n = 3757) and 1091 plasma metabolites (n = 8299) were obtained from comprehensive genome-wide association studies (GWAS), while TMD data (5668 cases and 205,355 controls) were acquired from the FinnGen Consortium. Bidirectional MR analyses and a two-step MR approach assessed causal relationships and potential intermediaries. Various corrections and sensitivity analyses were utilized to assess the robustness of the findings. Two immunophenotypes and seven metabolites were significantly associated with TMD risk. Specifically, Alpha-hydroxyisovalerate mediated the link between CD33 on CD33dim HLA DR + CD11b + and TMD (β = 0.034, P = 5.95 × 10–5), while CD8 on NKT cells mediated the causal relationship between 5-acetylamino-6-formylamino-3-methyluracil levels and TMD (β = 0.069, P = 5.11 × 10–5). Our findings revealed the causal relationships between immunophenotypes and plasma metabolites on TMD from a genetic perspective, potentially aiding in TMD prevention.
Spectrum aided vision enhancer enhances mucosal visualization by hyperspectral imaging in capsule endoscopy
Authors: Wang Yen-Po , Karmakar Riya , Mukundan Arvind , Tsao Yu-Ming , Sung Te-Chin , Lu Ching-Liang , Wang Hsiang-Chen
Published: September 2024

Narrow-band imaging (NBI) is more efficient in detecting early gastrointestinal cancer than white light imaging (WLI). NBI technology is available only in conventional endoscopy, but unavailable in magnetic-assisted capsule endoscopy (MACE) systems due to MACE’s small size and obstacles in image processing issues. MACE is an easy, safe, and convenient tool for both patients and physicians to avoid the disadvantages of conventional endoscopy. Enabling NBI technology in MACE is mandatory. We developed a novel method to improve mucosal visualization using hyperspectral imaging (HSI) known as Spectrum Aided Visual Enhancer (SAVE, Transfer N, Hitspectra Intelligent Technology Co., Kaohsiung, Taiwan). The technique was developed by converting the WLI image captured by MACE to enhance SAVE images. The structural similarity index metric (SSIM) between the WLI MACE images and the enhanced SAVE images was 91%, while the entropy difference between the WLI MACE images and the enhanced SAVE images was only 0.47%. SAVE algorithm can identify the mucosal break on the esophagogastric junction in patients with gastroesophageal reflux disorder. We successfully developed a novel image-enhancing technique, SAVE, in the MACE system, showing close similarity to the NBI from the conventional endoscopy system. The future application of this novel technology in the MACE system can be promising.