bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimisation of the depth range of UIV on cohesive sediment (fluid mud) flows
Authors: Brouwers Bart , van Beeck Jeroen , Lataire Evert 
Published: June 2024

AbstractUltrasound Image Velocimetry (UIV) is a technique that enables the monitoring of flows in natural high-density cohesive sediments, also known as fluid mud. Using conventional medical ultrasound imaging equipment, the depth range of UIV in mud is however too limited. This manuscript discusses how this depth range can be improved based on the results of experimental UIV measurements in fluid mud. The results show that the depth range limitation is determined by the pixel brightness of the generated speckle pattern images. Since pixel brightness is a measure of the intensity of the backscattered signals, it degrades with increasing depth due to the attenuation of the ultrasound radiation by the mud. The rate at which ultrasound is attenuated by fluid mud is constant and is governed by the density of the mud and the applied ultrasound frequency. A greater depth range can thus be achieved by reducing attenuation and increasing the intensity of the emitted ultrasound. The former was confirmed by the results of experiments with variable mud density and ultrasound frequency. Flexibility of both parameters is however restricted, allowing only a limited increase in depth range. Another experiment confirmed an additional increase in depth range when a higher ultrasound intensity is applied. Patient safety measures of medical ultrasound imaging equipment, however restrict the intensity of the emitted ultrasound. To increase the depth range even further, potential solutions are therefore suggested, such as the use of high-power non-medical ultrasound imaging equipment or a novel procedure for processing the acquired acoustic data.
A Concrete Syntax Transformation Approach for Software Language Processing
Authors: Lano Kevin , Xue Qiaomu , Haughton Howard 
Published: June 2024

AbstractIn this paper we present an approach for software language processing tasks such as code generation, reverse-engineering and refactoring, based upon text-to-text (T2T) transformations expressed using theconcrete syntaxof the source and target software languages. The goal of the approach is to provide simpler and more usable techniques for specifying such tasks, compared to model-to-model (M2M) or model-to-text (M2T) transformation approaches. We evaluate the approach on language processing tasks of domain-specific language (DSL) tool support, software abstraction, model transformation, reverse engineering and program translation, and show that it can be effective for these tasks.
Clinically proven natural products in aid of treating Parkinson's disease: a comprehensive review
Authors: Roni Md Abul Hasan , Jami Md. Abu Bakar Siddique , Hoque Sajidul , Al Hasibuzzaman Md. , Banu Kazi Hamida , Rozina  , Ansari Farzana , Sohel Md , Ashifuzzaman Md. , Joy Ferdous-Ul-Haque , Hossain Md. Solaiman , Huda Nazmul , Mostaq Md. Saqline , Amin Mohammad Nurul , Yunus Mohd Yusri Bin Mohd 
Published: June 2024

AbstractParkinson's disease (PD) is a neurodegenerative disorder that is caused by degeneration of nerve cells in the part of the brain called the substantia nigra, which controls movement. Although there is some considerable evidence with conventional drugs for PD, treating patients becomes increasingly difficult due to their short- and long-term adverse effects and other restrictions. This dire circumstance emphasizes the need for an innovative, strong alternative treatment for PD. Plants and natural products are considered one of the most important sources of bioactive molecules against a wide range of health disorders. With mechanistic insights, this systematic review explains the efficacy of clinically proven natural products in managing PD. This review is based on comprehensive literature searches from PubMed, Science Direct, Scopus, and Google Scholar databases using the keywords- “plants or natural products in Parkinson's”, “plants or herbs used in Parkinson's treatment”, or keywords that are similar to those. Natural products that have been clinically proven for their anti-Parkinson effect have only been selected for this study, and the products are- Mucuna pruriens, Caffeine, Camellia sinensis or green tea leaves, and a traditional Chinese herbal called Jiawei-Liujunzi Tang. In comparison to currently available medications, we firmly feel that the mentioned clinically proven natural products would be more effective at treating PD while having fewer adverse effects. However, further study is required to confirm their exact mechanism of action.
Properties of concrete using water from the Padma River and the Shitalakshya River, Bangladesh
Authors: Hasan Md. Mahmudul , Adnan Raofur , Shafiquzzaman Md. , Azad Md. Izharul Haque , Pial Md. Asaduzzaman , Rahman Shohanur , Tonmoy Zakaria Hassan , Roy Nayan , Islam Tony 
Published: June 2024

AbstractAssessing the impact of river water on concrete properties is an important aspect of the construction industry, especially in regions with significant exposure to riverine environments, like Bangladesh. This study investigated the applicability of river water in concrete manufacturing regarding its compressive strength and density. Water samples were collected from two major rivers (the Padma and the Shitalakshya) in Bangladesh and analyzed for thirty water quality parameters. 168-cylinder specimens were cast and tested for compressive strength after curing for 7, 14, and 28 days. The investigation was also carried out with two different coarse aggregates (brick and stone chips) in the mix design. Curing was performed with fresh and river water separately. Therefore, ten different experimental conditions were explored. The compressive strength of concrete using river water compared to freshwater decreased from 0 to 24%, except for three cases, where strength increased by 4.2%, 7.3%, and 8%. The variation in water quality between the two rivers significantly influenced the reduction in compressive strength. Higher values of pH, total suspended solids, total solids, ammonia, total hardness, alkalinity, and conductivity in the Padma River water led to a greater reduction in compressive strength than using the Shitalakshya River water. The type of coarse aggregate used also had an impact on strength. Both rivers’ water met the concrete production standards; nevertheless, a pre-treatment process is recommended. Successfully using river water in concrete production could reduce the demand for freshwater resources, contributing to the construction industry’s sustainability.
Probabilistic UK Climate Projections Conditioned on Global Warming Levels
Authors: Steptoe Hamish , Murphy James 
Published: June 2024

AbstractProbabilistic projections from the UK Climate Projections 2018 are presented for four global warming levels (GWLs) at 1.5, 2, 3, and 4°C above the 1850–1900 baseline. Our results show how uncertainties associated with climate models and four representative concentration pathways (RCP) emission scenarios translate to UK regional scale changes in maximum temperature and precipitation, with data also available for minimum and mean temperatures, humidity and surface net downward shortwave radiation flux. We compare weighting the likelihood of RCPs based on (hypothetical) policy decisions, against our baseline assumption that each RCP is equally likely. Differences between weighted and unweighted GWL distributions are small, particularly in relation to the full breadth of uncertainties that are incorporated into the probabilistic projections. Finally we quantify the relative importance of scenario, model and internal variability on regional projected GWLs and show that uncertainty associated with an uncertain climate response to forcings dominates at all GWLs.
CellRank 2: unified fate mapping in multiview single-cell data
Authors: Weiler Philipp , Lange Marius , Klein Michal , Pe’er Dana , Theis Fabian 
Published: June 2024

AbstractSingle-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.
Nano bio fertilizer capsules for sustainable agriculture
Authors: Hamed Rinad , Jodeh Shehdeh , Alkowni Raed 
Published: June 2024

AbstractA novel nano bio-fertilizer encapsulation method was developed to crosslink chitosan and alginate with humic acid. These nanocapsules, referred to as (Ch./Alg.HA.NPK) or (Ch./Alg.HA.NPK.PGPRs), were loaded with nanoscale essential agro-nutrients (NPK) and beneficial microorganisms Pseudomonas Fluorescence abbreviated as (P.Fluorescence). Structural and morphological analyses were conducted using FourierTransform Infrared, Thermogravimetric Analysis, Scanning Electron Microscopy, Malvern Zeta NanoSizer, and Zeta potential. Encapsulation efficiency and water retention were also determined compared to control non-crosslinked nanocapsules. The sustained cumulative release of NPK over 30 days was also investigated to 33.2%, 47.8%, and 68.3%, alternatively. The release mechanism, also assessed through the kinetic module of the Korsemeyer- Peppas Mathematical model, demonstrated superior performance compared to non-crosslinked nanocapsules (chitosan/alginate). These results show the potential of the synthesized nanocapsules for environmentally conscious controlled release of NPK and PGPRs, thereby mitigating environmental impact, enhancing plant growth, and reducing reliance on conventional agrochemical fertilizers.
Shallow foundation design: a comparative study of partial safety factors and full probabilistic methods
Authors: Vořechovský Miroslav , Miča Lumír , Boštík Jiří 
Published: June 2024

AbstractIn the past two decades, Europe has witnessed a significant transition in the design codes used for assessing foundation structures, with the widespread adoption of the Eurocodes (EC). This shift remains a pertinent topic within the engineering community, particularly concerning the transition from traditional design methodologies to those prescribed by the Eurocodes, as well as the potential for fully probabilistic design. While the Eurocodes’ methodology is described as probabilistic, it is crucial to recognize that the achievement of the target reliability level is predominantly facilitated through a system of partial safety factors. These factors are integrated into the calculation algorithm as fixed values, rendering the process essentially deterministic. To refine these calculations for more accurate reliability estimates—expressed in terms of failure probability—a genuinely probabilistic framework is required, termed as fully probabilistic computation. This paper aims to elucidate the fully probabilistic calculation approach for the broader professional community, using the geotechnical application of shallow foundations as an illustrative example. We present a comparative analysis of this advanced approach with the standard foundation design according to EC7 and ČSN 731001, the latter being a precursor in Europe for implementing the partial safety factor method. The discussion extends to a practical demonstration of full probabilistic design juxtaposed against the conventional partial safety factor method, using a shallow foundation case study. Furthermore, the paper delves into the impact of the tail behavior of uncertain or spatially varying soil parameters on the theoretical probability of failure, underscoring its significance in foundation design.
Dynamically predicting comprehension difficulties through physiological data and intelligent wearables
Authors: Hijazi Haytham , Gomes Miguel , Castelhano João , Castelo-Branco Miguel , Praça Isabel , de Carvalho Paulo , Madeira Henrique 
Published: June 2024

AbstractComprehending digital content written in natural language online is vital for many aspects of life, including learning, professional tasks, and decision-making. However, facing comprehension difficulties can have negative consequences for learning outcomes, critical thinking skills, decision-making, error rate, and productivity. This paper introduces an innovative approach to predict comprehension difficulties at the local content level (e.g., paragraphs). Using affordable wearable devices, we acquire physiological responses non-intrusively from the autonomous nervous system, specifically pulse rate variability, and electrodermal activity. Additionally, we integrate data from a cost-effective eye-tracker. Our machine learning algorithms identify ’hotspots’ within the content and regions corresponding to a high cognitive load. These hotspots represent real-time predictors of comprehension difficulties. By integrating physiological data with contextual information (such as the levels of experience of individuals), our approach achieves an accuracy of 72.11% ± 2.21, a precision of 0.77, a recall of 0.70, and an f1 score of 0.73. This study opens possibilities for developing intelligent, cognitive-aware interfaces. Such interfaces can provide immediate contextual support, mitigating comprehension challenges within content. Whether through translation, content generation, or content summarization using available Large Language Models, this approach has the potential to enhance language comprehension.
In silico study to explore the mechanism of Toxoplasma-induced inflammation and target therapy based on sero and salivary Toxoplasma
Authors: Hassanein Faika , Fadel Hewida H. , Shehata Amany I. , Hamdy Noha Alaa , Masoud Inas M. 
Published: June 2024

AbstractWe aimed to assess salivary and seroprevalence of Toxoplasma immunoglobulins in risky populations and evaluate drug docking targeting TgERP. A cross-sectional study was conducted in Alexandria University hospitals’ outpatient clinics. 192 participants were enrolled from September 2022 to November 2023. Anti-Toxoplasma IgG and IgM were determined in serum and saliva by ELISA. An in-Silico study examined TgERP’s protein–protein interactions (PPIs) with pro-inflammatory cytokine receptors, anti-inflammatory cytokine, cell cycle progression regulatory proteins, a proliferation marker, and nuclear envelope integrity-related protein Lamin B1. Our findings revealed that anti-T. gondii IgG were detected in serum (66.1%) and saliva (54.7%), with 2.1% of both samples were positive for IgM. Salivary IgG had 75.59% sensitivity, 86.15% specificity, 91.40% PPV, 64.40% NPP, 79.17% accuracy and fair agreement with serum IgG. On the other hand, the sensitivity, specificity, PPV, NPV, and accuracy in detecting salivary IgM were 75.0%, 99.47%, 75.0%, 99.47%, and 98.96%. AUC 0.859 indicates good discriminatory power. Examined synthetic drugs and natural products can target specific amino acids residues of TgERP that lie at the same binding interface with LB1 and Ki67, subsequently, hindering their interaction. Hence, salivary samples can be a promising diagnostic approach. The studied drugs can counteract the pro-inflammatory action of TgERP.
Increased expression of miR-320b in blood plasma of patients in response to SARS-CoV-2 infection
Authors: de Souza Nicoletti Aline , Berlofa Visacri Marília , Regina da Silva Correa da Ronda Carla , Tiemi Siguemoto Julia , Motta Neri Carolini , Nogueira de Souza Rafael , de Souza Ventura Deise , Eguti Adriana , Ferreira de Souza Silva Lilian , Wesley Perroud Junior Mauricio , Buosi Keini , Jalalizadeh Mehrsa , Dionato Franciele , Dal Col Luciana , Giacomelli Cristiane , Leme Patrícia , Oliveira Reis Leonardo , Augusto dos Santos Luiz , Durán Nelson , José Fávaro Wagner , Luiz da Costa José , Dagli-Hernandez Carolina , Moriel Patricia , de Carvalho Pincinato Eder 
Published: June 2024

AbstractCoronavirus disease 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Recent research has demonstrated how epigenetic mechanisms regulate the host–virus interactions in COVID-19. It has also shown that microRNAs (miRNAs) are one of the three fundamental mechanisms of the epigenetic regulation of gene expression and play an important role in viral infections. A pilot study published by our research group identified, through next-generation sequencing (NGS), that miR-4433b-5p, miR-320b, and miR-16–2-3p are differentially expressed between patients with COVID-19 and controls. Thus, the objectives of this study were to validate the expression of these miRNAs using quantitative real-time polymerase chain reaction (qRT-PCR) and to perform in silico analyses. Patients with COVID-19 (n = 90) and healthy volunteers (n = 40) were recruited. MiRNAs were extracted from plasma samples and validated using qRT-PCR. In addition, in silico analyses were performed using mirPath v.3 software. MiR-320b was the only miRNA upregulated in the case group com-pared to the control group. The in silico analyses indicated the role of miR-320b in the regulation of the KITLG gene and consequently in the inflammatory process. This study confirmed that miR-320b can distinguish patients with COVID-19 from control participants; however, further research is needed to determine whether this miRNA can be used as a target or a biomarker.
Australia’s 2019/20 Black Summer fire weather exceptionally rare over the last 2000 years
Authors: Udy Danielle G. , Vance Tessa R. , Kiem Anthony S. , Holbrook Neil J. , Abram Nerilie 
Published: June 2024

AbstractAustralia’s record-breaking 2019/20 Black Summer fire weather resulted from a combination of natural and anthropogenic climate factors, but the full range of natural variability in fire weather is unknown. We reconstruct southeast Australian fire weather over the Common Era based on an East Antarctic ice core sea-salt aerosol record. This record reflects the Southern Ocean synoptic-scale weather patterns and Antarctic stratospheric polar vortex strength that pre-condition elevated fire danger over southeast Australia. We show that the (a) intensity of the 2019/20 fire weather was unprecedented since 1950 and (b) frequency of above average fire weather seasons from 2010–2020 has only occurred once since 1950 (over 1977–1987), but there are analogues for similar extreme fire danger caused by natural variability in the 2000-year reconstruction. This highlights the need for fire risk mitigation that considers the full range of plausible natural variability in Australia’s fire weather as well as anthropogenic forcing.
Seafloor roughness reduces melting of East Antarctic ice shelves
Authors: Liu Yuhang , Nikurashin Maxim , Peña-Molino Beatriz 
Published: June 2024

AbstractHeat delivered by the ocean circulation is melting the Antarctic ice sheet from below. This melt is largest where warm Circumpolar Deep Water accesses the continental shelf and reaches the ice shelf cavities. Future melt rate projections are based on ocean thermal forcing derived from climate models, which tend to be biased warm around Antarctica. The bias has been attributed to unresolved ocean processes that occur at scales poorly represented in models. Using a high-resolution model of the Denman Glacier region we show that seafloor roughness unresolved in climate models suppresses the impact of warm water on ice sheet melting. Seafloor roughness slows down the shelf circulation, reducing the presence of warm water over the shelf and the heat transport towards the ice cavities. As a result, the total meltwater discharge drops by 4 Gt year−1. Our results suggest a mechanism missing in global ocean and climate models that could reduce the spread in climate projections.
Real-time motion-enabling positron emission tomography of the brain of upright ambulatory humans
Authors: Siva Nanda K. , Bauer Christopher , Glover Colson , Stolin Alexander , Chandi Sonia , Melnick Helen , Marano Gary , Parker Benjamin , Mandich MaryBeth , Lewis James W. , Qi Jinyi , Gao Si , Nott Kaylee , Majewski Stan , Brefczynski-Lewis Julie A. 
Published: June 2024

Abstract
Background
Mobile upright PET devices have the potential to enable previously impossible neuroimaging studies. Currently available options are imagers with deep brain coverage that severely limit head/body movements or imagers with upright/motion enabling properties that are limited to only covering the brain surface.

Methods
In this study, we test the feasibility of an upright, motion-compatible brain imager, our Ambulatory Motion-enabling Positron Emission Tomography (AMPET) helmet prototype, for use as a neuroscience tool by replicating a variant of a published PET/fMRI study of the neurocorrelates of human walking. We validate our AMPET prototype by conducting a walking movement paradigm to determine motion tolerance and assess for appropriate task related activity in motor-related brain regions. Human participants (n = 11 patients) performed a walking-in-place task with simultaneous AMPET imaging, receiving a bolus delivery of F18-Fluorodeoxyglucose.

Results
Here we validate three pre-determined measure criteria, including brain alignment motion artifact of less than <2 mm and functional neuroimaging outcomes consistent with existing walking movement literature.

Conclusions
The study extends the potential and utility for use of mobile, upright, and motion-tolerant neuroimaging devices in real-world, ecologically-valid paradigms. Our approach accounts for the real-world logistics of an actual human participant study and can be used to inform experimental physicists, engineers and imaging instrumentation developers undertaking similar future studies. The technical advances described herein help set new priorities for facilitating future neuroimaging devices and research of the human brain in health and disease.