bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated management of groundwater quantity, physicochemical properties, and microbial quality in West Nile delta using a new MATLAB code and geographic information system mapping
Authors: Shehata Mohamed , Zaid Samir M. , Al-Goul Soha T. , Shami Ashwag , Al Syaad Khalid M. , Ahmed Ahmed Ezzat , Mostafa Yasser S. , Al-Quwaie Diana A. , Ashkan Mada F. , Alqahtani Fatimah S. , Hassan Yusuf A. , Taha Taha F. , El-Tarabily Khaled A. , AbuQamar Synan F. 
Published: April 2024

AbstractGroundwater is an excellent alternative to freshwater for drinking, irrigation, and developing arid regions. Agricultural, commercial, industrial, residential, and municipal activities may affect groundwater quantity and quality. Therefore, we aimed to use advanced methods/techniques to monitor the piezometric levels and collect groundwater samples to test their physicochemical and biological characteristics. Our results using software programs showed two main types of groundwater: the most prevalent was the Na–Cl type, which accounts for 94% of the groundwater samples, whereas the Mg–Cl type was found in 6% of samples only. In general, the hydraulic gradient values, ranging from medium to low, could be attributed to the slow movement of groundwater. Salinity distribution in groundwater maps varied between 238 and 1350 mg L−1. Although lower salinity values were observed in northwestern wells, higher values were recorded in southern ones. The collected seventeen water samples exhibited brackish characteristics and were subjected to microbial growth monitoring. Sample WD12 had the lowest total bacterial count (TBC) of 4.8 ± 0.9 colony forming unit (CFU mg L−1), while WD14 had the highest TBC (7.5 ± 0.5 CFU mg L−1). None of the tested water samples, however, contained pathogenic microorganisms. In conclusion, the current simulation models for groundwater drawdown of the Quaternary aquifer system predict a considerable drawdown of water levels over the next 10, 20, and 30 years with the continuous development of the region.
Establishing a reference focal plane using convolutional neural networks and beads for brightfield imaging
Authors: Chalfoun Joe , Lund Steven P. , Ling Chenyi , Peskin Adele , Pierce Laura , Halter Michael , Elliott John , Sarkar Sumona 
Published: April 2024

AbstractRepeatability of measurements from image analytics is difficult, due to the heterogeneity and complexity of cell samples, exact microscope stage positioning, and slide thickness. We present a method to define and use a reference focal plane that provides repeatable measurements with very high accuracy, by relying on control beads as reference material and a convolutional neural network focused on the control bead images. Previously we defined a reference effective focal plane (REFP) based on the image gradient of bead edges and three specific bead image features. This paper both generalizes and improves on this previous work. First, we refine the definition of the REFP by fitting a cubic spline to describe the relationship between the distance from a bead’s center and pixel intensity and by sharing information across experiments, exposures, and fields of view. Second, we remove our reliance on image features that behave differently from one instrument to another. Instead, we apply a convolutional regression neural network (ResNet 18) trained on cropped bead images that is generalizable to multiple microscopes. Our ResNet 18 network predicts the location of the REFP with only a single inferenced image acquisition that can be taken across a wide range of focal planes and exposure times. We illustrate the different strategies and hyperparameter optimization of the ResNet 18 to achieve a high prediction accuracy with an uncertainty for every image tested coming within the microscope repeatability measure of 7.5 µm from the desired focal plane. We demonstrate the generalizability of this methodology by applying it to two different optical systems and show that this level of accuracy can be achieved using only 6 beads per image.
The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago
Authors: Yaworsky Peter M. , Nielsen Emil S. , Nielsen Trine K. 
Published: April 2024

AbstractNeanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.
Key HPI axis receptors facilitate light adaptive behavior in larval zebrafish
Authors: Lee Han B. , Shams Soaleha , Dang Thi Viet Ha , Boyum Grace E. , Modhurima Rodsy , Hall Emma M. , Green Izzabella K. , Cervantes Elizabeth M. , Miguez Fernando E. , Clark Karl J. 
Published: April 2024

AbstractThe vertebrate stress response (SR) is mediated by the hypothalamic–pituitary–adrenal (HPA) axis and contributes to generating context appropriate physiological and behavioral changes. Although the HPA axis plays vital roles both in stressful and basal conditions, research has focused on the response under stress. To understand broader roles of the HPA axis in a changing environment, we characterized an adaptive behavior of larval zebrafish during ambient illumination changes. Genetic abrogation of glucocorticoid receptor (nr3c1) decreased basal locomotor activity in light and darkness. Some key HPI axis receptors (mc2r [ACTH receptor], nr3c1), but not nr3c2 (mineralocorticoid receptor), were required to adapt to light more efficiently but became dispensable when longer illumination was provided. Such light adaptation was more efficient in dimmer light. Our findings show that the HPI axis contributes to the SR, facilitating the phasic response and maintaining an adapted basal state, and that certain adaptations occur without HPI axis activity.
Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR
Authors: Nakamura Tomoka , Takita Teisuke , Kuwata Kohei , Mizutani Kimihiko , Mikami Bunzo , Nakamura Satoshi , Yasukawa Kiyoshi 
Published: April 2024

AbstractXynR is a thermostable alkaline GH10 xylanase, for which we have previously examined the effects of saturation mutagenesis at position 315 on enzyme alkaliphily, and found that at pH 10, the activities of variants could be ordered as follows: T315Q > T315S = T315N > T315H = wild-type XynR (WT) > 15 other variants. In this study, we sought to elucidate the mechanisms underlying the variable activity of these different variants. Crystallographic analysis revealed that the Ca2+ ion near position 315 in WT was absent in the T315Q variant. We accordingly hypothesized that the enhancement of alkaliphily in T315Q, and probably also in the T315H, T315N, and T315S variants, could be ascribed to an activity-stability trade-off associated with a reduction in stability due to the lack of this Ca2+ ion. Consistent with expectations, the alkaline resistance of T315H, T315N, T315Q, and T315S, evaluated through the pH-dependence of stability at 0 mM CaCl2 under alkaline conditions, was found to be lower than that of WT: the residual activity at pH 11 of WT was 78% while those of T315H, T315N, T315Q, and T315S were 0, 9, 0, and 43%, respectively. In addition, the thermostabilities of these four variants, as assessed using the denaturing temperatures (Tm) at 0 mM CaCl2 based on ellipticity at 222 nm in circular dichroism measurements, were lower than that of WT by 2–8 °C. Furthermore, the Tm values of WT and variants at 5 mM CaCl2 were higher than those at 0 mM CaCl2 by 6–11 °C. Collectively, our findings in this study indicate that mutation of the T residue at position 315 of XynR to H, N, Q, and S causes an increase in the alkaliphily of this enzyme, thereby reducing its stability.
Neuroprotective mechanisms of luteolin in glutamate-induced oxidative stress and autophagy-mediated neuronal cell death
Authors: Vongthip Wudtipong , Nilkhet Sunita , Boonruang Kanokkan , Sukprasansap Monruedee , Tencomnao Tewin , Baek Seung Joon 
Published: April 2024

AbstractNeurodegenerative diseases, characterized by progressive neuronal dysfunction and loss, pose significant health challenges. Glutamate accumulation contributes to neuronal cell death in diseases such as Alzheimer's disease. This study investigates the neuroprotective potential of Albizia lebbeck leaf extract and its major constituent, luteolin, against glutamate-induced hippocampal neuronal cell death. Glutamate-treated HT-22 cells exhibited reduced viability, altered morphology, increased ROS, and apoptosis, which were attenuated by pre-treatment with A. lebbeck extract and luteolin. Luteolin also restored mitochondrial function, decreased mitochondrial superoxide, and preserved mitochondrial morphology. Notably, we first found that luteolin inhibited the excessive process of mitophagy via the inactivation of BNIP3L/NIX and inhibited lysosomal activity. Our study suggests that glutamate-induced autophagy-mediated cell death is attenuated by luteolin via activation of mTORC1. These findings highlight the potential of A. lebbeck as a neuroprotective agent, with luteolin inhibiting glutamate-induced neurotoxicity by regulating autophagy and mitochondrial dynamics.
Research on factor analysis and method for evaluating grouting effects using machine learning
Authors: Li Wenxin , Chen Juntao , Zhu Jun , Ji Xinbo , Fu Ziqun 
Published: April 2024

AbstractThe evaluation of grouting effects constitutes a critical aspect of grouting engineering. With the maturity of the grouting project, the workload and empirical characteristics of grouting effect evaluation are gradually revealed. In the context of the Qiuji coal mine’s directional drilling and grouting to limestone aquifer reformation, this study thoroughly analyzes the influencing factors of grouting effects from geological and engineering perspectives, comparing these with various engineering indices associated with drilling and grouting. This led to the establishment of a “dual-process, multi-parameter, and multi-factor” system, employing correlation analysis to validate the selected indices’ reasonableness and scientific merit. Utilizing the chosen indices, eight high-performing machine learning models and three parameter optimization algorithms were employed to develop a model for assessing the effectiveness of directional grouting in limestone aquifers. The model’s efficacy was evaluated based on accuracy, recall, precision, and F-score metrics, followed by practical engineering validation. Results indicate that the “dual-process, multi-parameter, multi-factor” system elucidates the relationship between influencing factors and engineering parameters, demonstrating the intricacy of evaluating grouting effects. Analysis revealed that the correlation among the eight selected indicators—including the proportion of boreholes in the target rock strata, drilling length, leakage, water level, pressure of grouting, mass of slurry injected, permeability properties of limestone aquifers before being grouted, permeability properties of limestone aquifers after being grouted—is not substantial, underscoring their viability as independent indicators for grouting effect evaluation. Comparative analysis showed that the Adaboost machine learning model, optimized via a genetic algorithm, demonstrated superior performance and more accurate evaluation results. Engineering validation confirmed that this model provides a more precise and realistic assessment of grouting effects compared to traditional methods.
Modeling future cliff-front waves during sea level rise and implications for coastal cliff retreat rates
Authors: Matsumoto H. , Dickson M. E. , Stephenson W. J. , Thompson C. F. , Young A. P. 
Published: April 2024

AbstractIt is often assumed that future coastal cliff retreat rates will accelerate as global sea level rises, but few studies have investigated how SLR (sea level rise) might change cliff-front wave dynamics. Using a new simple numerical model, this study simulates the number and type (breaking, broken, or unbroken) of cliff-front waves under future SLR scenarios. Previous research shows breaking waves deliver more energy to cliffs than broken waves, and unbroken waves generate minimal impact. Here, we investigated six cliff-platform profiles from three regions (USA, New Zealand, and UK) with varied tidal ranges and wave climates. Model inputs included 2013–2100 hindcast/forecast incident wave height and tidal water level, and three future SLR scenarios. Results show the number of both cliff-front breaking and broken waves generally increase for a high-elevation (relative to tide) cliff-platform junction. In contrast, breaking/broken wave occurrence decrease by 38–92% for a near-horizontal shore platform with a low-elevation cliff-platform junction under a high SRL scenario, leading to high (96–97%) unbroken wave occurrence. Overall, results suggest the response of cliff-front waves to future SLR is complex and depends on shore platform geometries and SLR scenarios, indicating that future cliff retreat rates may not homogeneously accelerate under SLR.
Vibrotactile enhancement of musical engagement
Authors: Siedenburg Kai , Bürgel Michel , Özgür Elif , Scheicht Christoph , Töpken Stephan 
Published: April 2024

AbstractSound is sensed by the ear but can also be felt on the skin, by means of vibrotactile stimulation. Only little research has addressed perceptual implications of vibrotactile stimulation in the realm of music. Here, we studied which perceptual dimensions of music listening are affected by vibrotactile stimulation and whether the spatial segregation of vibrations improves vibrotactile stimulation. Forty-one listeners were presented with vibrotactile stimuli via a chair’s surfaces (left and right arm rests, back rest, seat) in addition to music presented over headphones. Vibrations for each surface were derived from individual tracks of the music (multi condition) or conjointly by a mono-rendering, in addition to incongruent and headphones-only conditions. Listeners evaluated unknown music from popular genres according to valence, arousal, groove, the feeling of being part of a live performance, the feeling of being part of the music, and liking. Results indicated that the multi- and mono vibration conditions robustly enhanced the nature of the musical experience compared to listening via headphones alone. Vibrotactile enhancement was strong in the latent dimension of ‘musical engagement’, encompassing the sense of being a part of the music, arousal, and groove. These findings highlight the potential of vibrotactile cues for creating intensive musical experiences.
Genetic determinants of plasma protein levels in the Estonian population
Authors: Kalnapenkis Anette , Jõeloo Maarja , Lepik Kaido , Kukuškina Viktorija , Kals Mart , Alasoo Kaur ,   Estonian Biobank Research Team, Metspalu Andres , Milani Lili , Nelis Mari , Hudjashov Georgi , Mägi Reedik , Esko Tõnu , Võsa Urmo 
Published: April 2024

AbstractThe proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184 cis and 94 trans signals for 157 protein traits, which were further fine-mapped to credible sets for 101 cis and 87 trans signals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5 cis and 14 trans associations. CNVs were associated with the levels of 11 proteins (7 cis and 5 trans), examples including a 3q12.1 deletion acting as a hub for multiple trans associations; and a CNV overlapping NAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
Effects of ChatGPT’s AI capabilities and human-like traits on spreading information in work environments
Authors: Jo Hyeon , Park Do-Hyung 
Published: April 2024

AbstractThe rapid proliferation and integration of AI chatbots in office environments, specifically the advanced AI model ChatGPT, prompts an examination of how its features and updates impact knowledge processes, satisfaction, and word-of-mouth (WOM) among office workers. This study investigates the determinants of WOM among office workers who are users of ChatGPT. We adopted a quantitative approach, utilizing a stratified random sampling technique to collect data from a diverse group of office workers experienced in using ChatGPT. The hypotheses were rigorously tested through Structural Equation Modeling (SEM) using the SmartPLS 4. The results revealed that system updates, memorability, and non-language barrier attributes of ChatGPT significantly enhanced knowledge acquisition and application. Additionally, the human-like personality traits of ChatGPT significantly increased both utilitarian value and satisfaction. Furthermore, the study showed that knowledge acquisition and application led to a significant increase in utilitarian value and satisfaction, which subsequently increased WOM. Age had a positive influence on WOM, while gender had no significant impact. The findings provide theoretical contributions by expanding our understanding of AI chatbots' role in knowledge processes, satisfaction, and WOM, particularly among office workers.
Analyzing temperature, humidity, and precipitation trends in six regions of Thailand using innovative trend analysis
Authors: Kliengchuay Wissanupong , Mingkhwan Rachaneekorn , Kiangkoo Nuttapohn , Suwanmanee San , Sahanavin Narut , Kongpran Jira , Aung Htoo Wai , Tantrakarnapa Kraichat 
Published: April 2024

AbstractThe change of temperature and weather parameters is a major concern affecting sustainable development and impacting various sectors, such as agriculture, tourism, and industry. Changing weather patterns and their impact on water resources are important climatic factors that society is facing. In Thailand, climatological features such as ambient temperature, relative humidity, and precipitation play a substantial role in affecting extreme weather events, which cause damage to the economy, agriculture, tourism, and livelihood of people. To investigate recent serious changes in annual trends of temperature, relative humidity, and precipitation in Thailand, this study used the Mann–Kendall (MK) test and innovative trend analysis (ITA) methods. The MK test showed that all six regions had an upward trend in temperature and humidity index (humidex, how hot the weather feels to the average person), while relative humidity and precipitation showed both upward and downward trends across different regions. The ITA method further confirmed the upward trend in temperature and humidex and showed that most data points fell above the 1:1 line. However, the upward trend in most variables was not significant at the 5% level. The southern and eastern regions showed a significant upward trend in relative humidity and humidex at a 5% level of significance according to the MK test. The output of this study can help in the understanding of weather variations and predict future situations and can be used for adaptation strategies.
Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications
Authors: Chang Andrew , Prabhala Sravya , Daneshkhah Ali , Lin Jianan , Subramanian Hariharan , Roy Hemant Kumar , Backman Vadim 
Published: April 2024

AbstractColonoscopy is accurate but inefficient for colorectal cancer (CRC) prevention due to the low (~ 7 to 8%) prevalence of target lesions, advanced adenomas. We leveraged rectal mucosa to identify patients who harbor CRC field carcinogenesis by evaluating chromatin 3D architecture. Supranucleosomal disordered chromatin chains (~ 5 to 20 nm, ~1 kbp) fold into chromatin packing domains (~ 100 to 200 nm, ~ 100 to 1000 kbp). In turn, the fractal-like conformation of DNA within chromatin domains and the folding of the genome into packing domains has been shown to influence multiple facets of gene transcription, including the transcriptional plasticity of cancer cells. We deployed an optical spectroscopic nanosensing technique, chromatin-sensitive partial wave spectroscopic microscopy (csPWS), to evaluate the packing density scaling D of the chromatin chain conformation within packing domains from rectal mucosa in 256 patients with varying degrees of progression to colorectal cancer. We found average packing scaling D of chromatin domains was elevated in tumor cells, histologically normal-appearing cells 4 cm proximal to the tumor, and histologically normal-appearing rectal mucosa compared to cells from control patients (p < 0.001). Nuclear D had a robust correlation with the model of 5-year risk of CRC with r2 = 0.94. Furthermore, rectal D was evaluated as a screening biomarker for patients with advanced adenomas presenting an AUC of 0.85 and 85% sensitivity and specificity. artificial intelligence-enhanced csPWS improved diagnostic performance with AUC = 0.90. Considering the low sensitivity of existing CRC tests, including liquid biopsies, to early-stage cancers our work highlights the potential of chromatin biomarkers of field carcinogenesis in detecting early, significant precancerous colon lesions.