bluuebunny/crossref_metadata_2025_split huggingface dataset:
The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction
Authors: Saharkhiz Saber , Mostafavi Mehrnaz , Birashk Amin , Karimian Shiva , Khalilollah Shayan , Jaferian Sohrab , Yazdani Yalda , Alipourfard Iraj , Huh Yun Suk , Farani Marzieh Ramezani , Akhavan-Sigari Reza 
Published: July 2024

AbstractIn recent years, there has been a notable increase in the scientific community's interest in rational protein design. The prospect of designing an amino acid sequence that can reliably fold into a desired three-dimensional structure and exhibit the intended function is captivating. However, a major challenge in this endeavor lies in accurately predicting the resulting protein structure. The exponential growth of protein databases has fueled the advancement of the field, while newly developed algorithms have pushed the boundaries of what was previously achievable in structure prediction. In particular, using deep learning methods instead of brute force approaches has emerged as a faster and more accurate strategy. These deep-learning techniques leverage the vast amount of data available in protein databases to extract meaningful patterns and predict protein structures with improved precision. In this article, we explore the recent developments in the field of protein structure prediction. We delve into the newly developed methods that leverage deep learning approaches, highlighting their significance and potential for advancing our understanding of protein design.
Carbon-based nanomaterials cause toxicity by oxidative stress to the liver and brain in Sprague–Dawley rats
Authors: Xu Ying-Ying , Jin Chan , Wu Meng , Zhou Jian-Ye , Wei Hui-Ling 
Published: July 2024

AbstractCarbon-based nanomaterials have important research significance in various disciplines, such as composite materials, nanoelectronic devices, biosensors, biological imaging, and drug delivery. Recently, the human and ecological risks associated with carbon-based nanomaterials have received increasing attention. However, the biological safety of carbon based nanomaterials has not been systematically studied. In this study, we used different types of carbon materials, namely, graphene oxide (GO), single-walled carbon nanotubes (SWCNTs), and multiwalled carbon nanotubes (MWCNTs), as models to observe their distribution and oxidative damage in vivo. The results of Histopathological and ultrastructural examinations indicated that the liver and lungs were the main accumulation targets of these nanomaterials. SR-$$\upmu$$
μ
-XRF analysis revealed that SWCNTs and MWCNTs might be present in the brain. This shows that the three types of carbon-based nanomaterials could cross the gas–blood barrier and eventually reach the liver tissue. In addition, SWCNTs and MWCNTs could cross the blood–brain barrier and accumulate in the cerebral cortex. The increase in ROS and MDA levels and the decrease in GSH, SOD, and CAT levels indicated that the three types of nanomaterials might cause oxidative stress in the liver. This suggests that direct instillation of these carbon-based nanomaterials into rats could induce ROS generation. In addition, iron (Fe) contaminants in these nanomaterials were a definite source of free radicals. However, these nanomaterials did not cause obvious damage to the rat brain tissue. The deposition of selenoprotein in the rat brain was found to be related to oxidative stress and Fe deficiency. This information may support the development of secure and reasonable applications of the studied carbon-based nanomaterials.
Groundwater Recharge Potential Index and artificial groundwater recharge in the alluvial soils of the middle Ganga Basin
Authors: Arya Vinay , Rao Mavidnam Someshwar 
Published: July 2024

AbstractRecent studies prove the faster depletion of groundwater is a cause of concern in the middle Ganga basin. Most of the groundwater-related studies in the middle Ganga basin deal with groundwater levels and quality aspects. The past studies on groundwater potential are confined to arid and humid zones of India, which leaves ample space for semi-humid to semi-arid, frost-prone, and alluvial region. The basin has alluvial soil due to sediments deposited by the river Ganga. In this study, eight thematic maps were prepared for the assessment of the groundwater recharge potential. These maps are; rainfall, geomorphology, slope, drainage density, lineament density, lithology, Land Use/Land Cover (LULC), and Groundwater Fluctuation (GWF). The weighted overlay of these thematic maps gave the Groundwater Recharge Potential Zone (GWRPZ) map representing the spatial variation of the Groundwater Recharge Potential Index (GWRPI) in the basin, whose value varies from 0.071 to 0.309. A total of 92 artificial groundwater recharge sites have been identified using specialized GIS processes taking into account stream network. The Analytic Hierarchy Process (AHP) based weights classification offers a robust framework for prioritizing and understanding the relative significance of factors affecting groundwater recharge. Alluvial soils are capable of holding large amount of water, and are overlaid by large aquifers. A large number of wells and tube wells have led to the over-extraction of groundwater in the region. This is the reason of the study being carried out despite being a region infested with large aquifers.
Water-saving control system based on multiple intelligent algorithms
Authors: Liu Fengnian , Yu Xiang , Tang Junya 
Published: July 2024

AbstractWater conservation has become a global problem as the population increases. In many densely populated cities in China, leaks from century-old pipe works have been widespread. However, entirely eradicating the issues involves replacing all water networks, which is costly and time-consuming. This paper proposed an AI-enabled water-saving control system with three control modes: time division control, flow regulation, and critical point control according to actual flow. Firstly, based on the current leaking situation of water supply networks in China and the capability level of China’s water management, a water-saving technology integrating PID control and a series of deep learning algorithms was proposed. Secondly, a multi-jet control valve was designed to control pressure and reduce water distribution network cavitation. This technology has been successfully applied in industrial settings in China and has achieved gratifying water-saving results.
Halide solid-state electrolyte achieving high ionic conductivity by engineering nanocrystals
Authors: Bashir Sajid , Liu Jingbo Louise 
Published: July 2024

AbstractLithium-ion battery (LIB) technologies utilize liquid electrolytes, which can cause safety issues due to electrolyte leakage, uncontrolled side reactions between the liquid electrolyte and electrode, dendrite formation, and flammability of the liquid components with air. These problems can be minimized using solid-state electrolytes (SSEs) containing the functionality of an electrolyte. Our research discovery meets the urgent requirement of developing rapid ionic conductive solid-state electrolytes for lithium metal battery applications, emphasizing safe operation and high energy density. The breakthrough lies in the functionalization and tunability of monoclinic doped Li3InCl6-based solid electrolytes to achieve desirable structural and high ionic conductivity (> 0.15 S cm−1). We report four formulations of solid-state electrolytes obtained using modified sol–gel synthesis and used to assemble symmetrical half cells for electrochemical impedance spectroscopic (EIS) analyses in the frequency ranging from 10–2 to 106 Hz under five different temperatures (15–55 °C). The EIS data of non-doped, F-, Ce-, and Mo-doped electrolytes showed R1 (solid-electrolyte) ranging from 0.05 to 0.10 Ohm and R2 (interfacial) resistance varying from 0.05 to 1.25 Ohm, resulting in superionic conductivity (0.15–0.45 S cm−1), equivalent to the commercially available liquid electrolyte and evidenced two magnitudes increase compared to the published data.
Graphical abstract
PANoptosis-based molecular subtype and prognostic model predict survival and immune landscape in esophageal cancer
Authors: Liu Zheming , Liu Jiahui , Liao Fuben , Li Wei , Wang Jing , Zhang Chi 
Published: July 2024

Abstract
Purpose
To establish a prognostic model to predict the survival of patients with esophageal cancer (EC).

Methods
We extracted the expression profiles of prognostic-related genes and clinicopathological data from TCGA and GEO databases. Subsequently, a comprehensive bioinformatics analysis was conducted to construct a prognostic model utilizing LASSO and multivariate Cox regression. The stability of the risk signature was validated through Kaplan-Meier and ROC curve analyses on the training, internal testing, and external testing sets. Furthermore, we developed a nomogram that incorporates the risk score and clinical features to predict the suvival. Additionally, a nomogram incorporating the risk score and relevant clinical parameters was developed to enhance survivorship prediction. Furthermore, we delved into exploring the correlation between the risk score and immune cell abundance, expression of cancer checkpoints, as well as responses to immunotherapy and chemotherapeutic agents.

Results
In this study, we successfully identified 19 prognosis-related genes out of a pool of 65 PANoptosis-related genes (PRGs) sourced from existing literature. Through consensus clustering analysis, we classified patients into two distinct groups as PANcluster A and B. Furthermore, the risk score derived from the five PANoptosis-related signatures emerged as an independent prognostic factor among patients with EC. To enhance the prognostic accuracy, we devised a nomogram integrating the risk score with clinical risk characteristics, enabling the prediction of 1-year, 2-year, and 3-year overall survival (OS) rates. Notably, individuals classified in the high-risk group demonstrated poorer prognoses compared to their low-risk counterparts. Furthermore, the risk score displayed substantial correlations with immune cell abundance, expression levels of cancer checkpoints, and responses to immunotherapy and chemotherapeutic agents. These pivotal findings underscore the significance of considering PANoptosis-related patterns in improving prognostic assessment and predicting treatment responses in patients diagnosed with esophageal cancer.

Conclusion
We constructed a reliable prognostic risk model for EC utilizing five PRGs. The developed nomogram serves as a valuable tool in predicting patient outcomes, offering crucial insights that can inform and guide treatment decisions for individuals diagnosed with EC.
Band engineering in two-dimensional porphyrin- and phthalocyanine-based covalent organic frameworks: insight from molecular design
Authors: Ni Xiaojuan , Brédas Jean-Luc 
Published: July 2024

AbstractTwo-dimensional covalent organic frameworks (2D COFs) represent an emerging class of crystalline polymeric networks, characterized by their tunable architectures and porosity, synthetic adaptability, and interesting optical, magnetic, and electrical properties. The incorporation of porphyrin (Por) or phthalocyanine (Pc) core units into 2D COFs provides an ideal platform for exploring the relationship between the COF geometric structure and its electronic properties in the case of tetragonal symmetry. In this work, on the basis of tight-binding models and density functional theory calculations, we describe the generic types of electronic band structures that can arise in tetragonal COFs. Three tetragonal lattice symmetries are examined: the basic square lattice, the Lieb lattice, and the checkerboard lattice. The potential topological characteristics of each lattice are explored. The Por-/Pc-based COFs exhibit characteristic band dispersions that are directly linked to their lattice symmetries and the nature of the frontier molecular orbitals of their building units. We show that the band dispersions in these COFs can be tailored by choosing specific symmetries of the molecular building units and/or by modulating the relative energies of the core and linker units. These strategies can be extended to a wide array of COFs, offering an effective approach to engineering their electronic properties.
Advancements in the understanding and management of histiocytic neoplasms
Authors: Koh Kyung-Nam , Yoon Su Hyun , Kang Sung Han , Kim Hyery , Im Ho Joon 
Published: July 2024

AbstractHistiocytic neoplasms are rare diseases involving macrophages, dendritic cells, and monocytes. They include Langerhans cell histiocytosis (LCH), Erdheim-Chester disease (ECD), Rosai-Dorfman disease (RDD), juvenile xanthogranuloma (JXG), and histiocytic sarcoma. Histiocytic neoplasms are characterized by varied clinical courses and prognoses, necessitating a nuanced understanding of their classification, epidemiology, and clinical manifestations. Genetic studies have revealed somatic mutations, predominantly in the MAPK pathway, suggesting a clonal neoplastic nature. This review covers the current understanding of histiocytic neoplasms, molecular pathophysiology, with a particular focus on mutations in genes such as BRAF, MAP2K1, and the PI3K-AKT signaling pathways, and evolving treatment strategies, especially focusing on LCH, ECD, RDD, and JXG. The treatment landscape has evolved with advancements in targeted therapies. BRAF inhibitors, such as vemurafenib and dabrafenib, have shown efficacy, especially in high-risk LCH cases; however, challenges remain, including relapse post-treatment discontinuation, and adverse effects. MEK inhibitors have also demonstrated effectiveness, and cobimetinib has recently been approved for use in adults. Further research is required to determine the optimal treatment duration and strategies for managing therapy interruptions. Advancements in molecular genetics and targeted therapies have revolutionized the management of histiocytic neoplasms. However, ongoing research is crucial for optimizing patient outcomes.
Evolutionary constrained multi-objective optimization: a review
Authors: Liang Jing , Lin Hongyu , Yue Caitong , Ban Xuanxuan , Yu Kunjie 
Published: July 2024

AbstractSolving constrained multi-objective optimization problems (CMOPs) is challenging due to the simultaneous consideration of multiple conflicting objectives that need to be optimized and complex constraints that need to be satisfied. To address this class of problems, a large number of constrained multi-objective evolutionary algorithms (CMOEAs) have been designed. This paper presents a comprehensive review of state-of-the-art algorithms for solving CMOPs. First, the background knowledge and concepts of evolutionary constrained multi-objective optimization are presented. Then, some classic constraint handling technologies (CHTs) are introduced, and the advantages and limitations of each CHT are discussed. Subsequently, based on the mechanisms used by these algorithms, the CMOEAs are classified into six categories, each of which is explained in detail. Following that, the benchmark test problems used to evaluate the algorithm’s performance are reviewed. Moreover, the experimental comparison and performance analysis of different types of algorithms are carried out on different test problems with different characteristics. Finally, some of the challenges and future research directions in evolutionary constrained multi-objective optimization are discussed.
Safeguarding Asian tapir habitat in Sumatra, Indonesia
Authors: Pinondang Irene M.R. , Deere Nicolas J. , Voigt Maria , Ardiantiono  , Subagyo Agus , Moßbrucker Alexander , Fardilla Antika , Chandradewi Desy S. , Surahmat Fahrudin , Widodo Febri A. , Fredriksson Gabriella , Wibisono Hariyo T. , Supriatna Jatna , Lubis M. Irfansyah , Asmita Nuri , Sunarto  , Lidra Tengku , Ariyanto Tomi , Albert Wido R. , Novarino Wilson , Pusparini Wulan , Dinata Yoan , Struebig Matthew J. 
Published: July 2024

AbstractThe Asian tapir Tapirus indicus is the only tapir species in Southeast Asia. It is declining across its range and is categorized as Endangered on the IUCN Red List. The forests of Sumatra are critical to Asian tapir conservation as they contain some of the last remaining populations of the species, yet conservation efforts are hindered by a lack of information on habitat suitability. We collated camera-trap data from nine landscapes across 69,500 km2 of Sumatran rainforest to help predict suitable habitat for Asian tapirs on the island. Predictions from Bayesian occupancy models demonstrated that tapir occupancy was greatest in forests below 600 m elevation and exclusively in forests with high aboveground biomass. Forests around the Barisan Mountains on the west of Sumatra provide the most suitable habitat for the species. Only 36% of the most critical habitat (i.e. 80th percentile of predicted occupancy values, or above) for tapirs is formally protected for conservation, with much of the remainder found in forests allocated to watershed protection (35%) or logging (23%). We highlight several key areas in Sumatra where tapir conservation could be bolstered, such as by leveraging existing conservation efforts for other charismatic flagships species on the island.
The Impact of Velocity Update Frequency on Time Accuracy for Mantle Convection Particle Methods
Authors: Trim S. J. , Butler S. L. , Spiteri R. J. 
Published: July 2024

AbstractComputing the velocity field is an expensive process for mantle convection codes. This has implications for particle methods used to model the advection of quantities such as temperature or composition. A common choice for the numerical treatment of particle trajectories is classical fourth‐order explicit Runge–Kutta (ERK4) integration, which involves a velocity computation at each of its four stages. To reduce the cost per time step, it is possible to evaluate the velocity for a subset of the four time integration stages. We explore two such alternative schemes, in which velocities are only computed for: (a) stage 1 on odd‐numbered time steps and stages 2–4 for even‐numbered time steps, and (b) stage 1 for all time steps. A theoretical analysis of stability and accuracy is presented for all schemes. It was found that the alternative schemes are first‐order accurate with stability regions different from that of ERK4. The efficiency and accuracy of the alternate schemes were compared against ERK4 in four test problems covering isothermal, thermal, and thermochemical flows. Exact solutions were used as reference solutions when available. In agreement with theory, the alternate schemes were observed to be first‐order accurate for all test problems. Accordingly, they may be used to efficiently compute solutions to within modest error tolerances. For small error tolerances, however, ERK4 was the most efficient.
First Results of Mars Express—ExoMars Trace Gas Orbiter Mutual Radio Occultation
Authors: Parrott Jacob , Svedhem Håkan , Witasse Olivier , Wilson Colin , Müller‐Wodarg Ingo , Cardesín‐Moinelo Alejandro , Schmitz Peter , Godfrey James , Reboud Olivier , Geiger Bernhard , Sánchez‐Cano Beatriz , Nava Bruno , Migoya‐Orué Yenca 
Published: July 2024

AbstractSpacecraft‐to‐spacecraft radio occultations experiments are being conducted at Mars between Mars Express (MEX) and Trace Gas Orbiter (TGO), the first ever extensive inter‐spacecraft occultations at a planet other than Earth. Here we present results from the first 83 such occultations, conducted between 2 Nov 2020 and 5th of July 2023. Of these, 44 observations have to‐date resulted in the extraction of vertical electron density profiles. These observations are the successful results of a major feasibility study conducted by the European Space Agency to use pre‐existing relay communication equipment for radio science purposes. Mutual radio occultations have numerous advantages over traditional spacecraft‐to‐ground station occultations. In this work, we demonstrate how raw data are transformed into electron density values and validated with models and other instruments.
Gulf Stream Moisture Fluxes Impact Atmospheric Blocks Throughout the Northern Hemisphere
Authors: Mathews J. P. , Czaja A. , Vitart F. , Roberts C. 
Published: July 2024

AbstractIn this study, we explore the impact of oceanic moisture fluxes on atmospheric blocks using the ECMWF IFS. Artificially suppressing surface latent heat flux over the Gulf Stream (GS) region reduces atmospheric blocking frequency across the Northern Hemisphere by up to 30%. Affected blocks show a shorter lifespan (−6%), smaller spatial extent (−10%), and reduced intensity (−0.4%), with an increased number of individual blocking anticyclones (+17%). These findings are robust across various blocking detection thresholds. Analysis reveals a qualitatively consistent response across all resolutions, with Tco639 (∼18 km) showing the largest statistically significant change across all blocking characteristics, although differences between resolutions are not statistically significant. Exploring the broader Rossby wave pattern, we observe that diminished moisture fluxes favor eastward propagation and higher zonal wavenumbers, while air‐sea interactions promote stationary and westward‐propagating waves with zonal wavenumber 3. This study underscores the critical role of the GS in modulating atmospheric blocking.
Geologic and Tectonic Controls on Deep Fracturing, Weathering, and Water Flow in the Central California Coast Range
Authors: Callahan Russell P. , Huang Mong‐Han , Donaldson Amanda , Hudson‐Rasmussen Berit , Zimmer Margaret 
Published: July 2024

AbstractThe creation of fractures in bedrock dictates water movement through the critical zone, controlling weathering, vadose zone water storage, and groundwater recharge. However, quantifying connections between fracturing, water flow, and chemical weathering remains challenging because of limited access to the deep critical zone. Here we overcome this challenge by coupling measurements from borehole drilling, groundwater monitoring, and seismic refraction surveys in the central California Coast Range. Our results show that the subsurface is highly fractured, which may be driven by the regional geologic and tectonic setting. The pervasively fractured rock facilitates infiltration of meteoric water down to a water table that aligns with oxidation in exhumed rock cores and is coincident with the adjacent intermittent first‐order stream channel. This work highlights the need to incorporate deep water flow and weathering due to pervasive fracturing into models of catchment water balances and critical zone weathering, especially in tectonically active landscapes.
Modulation of the Pacific Meridional Mode on the Dipole Pattern of the CONUS Summertime Precipitation
Authors: Affram Grace , Zhang Wei , Hari Vittal , Gao Si , Ratterman Cody , Zhu Langfeng , Gillies Robert R. 
Published: July 2024

AbstractHistorically, the precipitation trend over the past few decades in the Contiguous United States (CONUS) exhibits a “Dry‐West Wet‐East” pattern; this is manifested by recent droughts/floods in the western/eastern US. However, it remains elusive what atmospheric phenomenon has potentially driven such a remarkable, and impactful precipitation pattern. Here we found that a coupled climate mode—the Pacific Meridional Mode (PMM) exerted strong impacts on the precipitation pattern over the CONUS during the summer season. We discovered a significant association between the PMM index and precipitation across the majority of the CONUS; this was manifested as a zonal dipole pattern—negative correlations in the western U.S. along with positive correlations in the eastern and central U.S. Overall, the physical mechanisms based on observations were supported by using Atmospheric Model Intercomparison Project simulations available from the Coupled Model Intercomparison Project Phase 6.