bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractDataset 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

AbstractTwo-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

AbstractThird-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

AbstractPulse 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

AbstractH. 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

AbstractThe 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

AbstractWe 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

AbstractCervical 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

AbstractThe 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

AbstractThe 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.