bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple method to prepare carbon-based mesoporous materials by coal gasification of fine slag and its application in phenol adsorption
Authors: Guo Lei , Zhang Tong , Dai Xiaomin , Cao Baowei , Xu Yunhua , Yang Yonglin 
Published: October 2023

Abstract
Phenol is a common organic pollutant that is difficult to degrade and widely exists in all kinds of wastewater. In this study, an economical and environmentally friendly alternative process for phenol-containing wastewater has been developed using porous nano-adsorption material (PNAM) prepared from coal gasification fine slag. The morphology, crystal structure, surface functional groups, gap structure, and specific surface area of PNAM were characterized by SEM, XRD, FT-IR, and BET. The effects of adsorbent dosage, temperature, pH, and reaction time on adsorption were further investigated. In addition, the adsorption kinetics, thermodynamics, and adsorption mechanism were explored. The results show that the surface area of PNAM is high, up to 602 m2 g−1, and the pore volume is 0.507 cm3 g−1. Adsorption processes mainly occur in mesopores between 2 and 5 nm, including physical and chemical adsorption, and here chemical adsorption plays a significant role. The adsorption rate of phenol in a 1000 mg l−1 simulated phenol solution by PNAM reaches 96.14%, while the unit adsorption capacity is 32.045 mg g−1. As a result, it is expected that employing coal gasification fine slag to prepare adsorption materials for phenol-containing wastewater treatment may be an economically feasible and environmentally sustainable strategy.
Contamination reduction for 150 mm SiC substrates by integrating CMP and Post-CMP cleaning
Authors: Hsieh Chi-Hsiang , Lee Ming-Hsun , Chen Chao-Chang A , Tu Chang-Ching , Kuo Hao-Chung 
Published: October 2023

Abstract
The quality of silicon carbide (SiC) substrates has great influence on the quality of the epitaxial layers atop. During the epitaxial growth, crystallographic defects and substrate contaminations may transform to various surface defects, such as carrots, polytype inclusions and scratches, which are detrimental to the performance and reliability of SiC devices. In general, chemical mechanical polishing (CMP) and post-CMP cleaning are the last two steps before the epitaxial growth, playing critical roles in controlling the scratch and contamination levels on the SiC substrates. In this article, the methods for reducing the aluminum (Al) and manganese (Mn) metal contaminations as well as other surface particle contaminations are investigated. We found that different commercial CMP slurries may lead to different contamination levels. Most importantly, by adding a scrubber cleaning step prior to the conventional RCA cleaning process, the contamination levels can be greatly reduced, achieving the quality for mass production.
Monitoring of thermo-cycles in fibre laser welding of duplex stainless steel 2205 sheets and its correlation with microstructures and mechanical properties
Authors: Ahmad Gulshad Nawaz , Singh Nirmal Kumar , Tripathi Brajendra Nath , Askari Syed Sadique Anwer , Pandey Shatrudhan , Zare Ali , Hasnain S M Mozammil 
Published: October 2023

Abstract
The study reports the influence of change in the heat supplied (43 J mm−1 to 18.5 J mm−1) on the microstructures as well as mechanical properties of weld joints obtained by welding of Duplex stainless steel 2205 using fibre laser. In-process thermal monitoring of the molten weld pool was carried out using IR pyrometer. Cooling rates (i.e. solidification and solid) were calculated from the thermo-profiles of weld pool, and it increases with the decrease in heat input. From the optical images, it is observed that columnar grains originated from the fusion zone walls and merged at the center. Since, solidification front velocity is comparable on both sides’ leads to a central edge. Ferrite phase content observed in fusion zone microstructure, increases with the increase in solid cooling rate. The result suggests that the joints fabricated at lowest heat input displayed highest tensile strength. The maximum tensile strength been reported to be 872.5 ± 10.8 MPa, and failure occurred at parent metal. Tensile strength of weld joints of DSS 2205 was found to have improved with increasing cooling rate. Higher cooling rate results in the formation of fine dendritic grains as well as higher ferrite content in the weld metal.
Design and analysis of multi-material structures of 3D printed implants of mandible
Authors: K Kalaithendral , Karuppudaiyan S , Roy Sandipan 
Published: October 2023

Abstract
Significant advances in 3D printing technology have paved the way for improvements in the integrity and biological characteristics of polymer implants. The principal objective of this research is the construction of a heterogeneous implant structure using a multi-material approach and 3D printing. Due to their advantageous strength-to-weight ratio, biocompatible polymers have an increasing application in the field of medicine. The osteo-integration process, in which implants bind to the bone over time, can be made more effective by incorporating these materials into implants. In this work, we focused especially on analyzing the strength and integrity of polymer material implants that were created using a combination of different materials, and their stress distribution, and the deformation of these multi-material structures when they were subjected to physiological loading through finite element analysis. The evidence from the frontal bite condition has led to some fascinating conclusions. The variations in stress were observed in homogenous structures, with values ranging from 37.42 MPa for the TPU to 41.07 MPa for the PETG. In contrast, stress distributions in multi-material constructions ranged from 52.31 MPa (in the case of TPU +TPU) to 73.55 MPa (in the case of PLA+ PCL). Similarly, the maximum deformation in homogeneous constructions ranged from 0.81mm (PLA) to 6.85mm (PCL). The deformation of multi-material structures composed of several different materials ranged from 0.68mm (PLA+ PLA) to 5.74 mm (PCL+PCL).These findings provide conclusive evidence that multi-material architectures have a considerable impact on known stress and strain levels. Particularly noteworthy is the fact that the combination of PLA+PLA and PLA+PETG displayed deformation that was equivalent to that of the intact bone model while having lower stress levels. The results of this study provide useful information that can be used to select optimal multi-material combinations that can be 3D printed for implants.
Assessing dynamic energy efficiency in the organization for economic Co-operation and development (OECD) countries and China during COVID-19
Authors: Wu Dan , Hung Fang-Chen , Lin I-Fang , Lu Ching-Cheng 
Published: October 2023

Abstract
According to the October 2021 Glasgow Climate Agreement reaffirming the cooling goals of the Paris Agreement and the Glasgow Leaders Declaration on Forests and Land Use, this research applies the Super-D-DDF model to non-oriented variable returns to scale to evaluate the Organization for Economic Cooperation and Development (OECD) and China (38 countries in total), collect important production and energy variables from 2016 to 2020, and measure the total efficiency of energy dynamics and its changes during COVID-19. The empirical results are as follows. (1) Comparing energy efficiency from 2016 to 2018 and 2019 to 2020 (during COVID-19), we find that most countries (22 countries) changed from high efficiency to low efficiency, showing a decrease in energy efficiency. (2) The emissions of carbon dioxide in China in 2020 are close to the sum of OECD carbon dioxide emissions, highlighting that the energy policy in China should be adjusted appropriately. (3) From 2016 to 2020, the forest area of various countries has a significant impact on overall energy efficiency performance. In line with the United Nations’ policy goals, countries should adjust forest protection policies to effectively reduce carbon emissions.
OffRisk: a docker image for annotating CRISPR off-target sites in the human genome
Authors: Barkai Gil-ad , Malul Tal , Eliaz Yossi , Eyal Eran , Veksler-Lublinsky Isana 
Published: October 2023

Abstract

Summary
The CRISPR-Cas9 system has been adapted to achieve targeted genome editing as well as transcriptional control by customizing 20-nt guide RNA (gRNA) molecules for desired regions in the target genome. Designing gRNAs must consider nonspecific and unintended binding, known as off-targets, since these may have potentially harmful effects. To assist in gRNA design, we have developed OffRisk. This Docker-based tool annotates off-target sites in the human genome and assigns them a potential risk label by incorporating functional and regulatory information at different molecular levels.

Availability and implementation
OffRisk is available at https://github.com/IsanaVekslerLublinsky/OffRisk and https://github.com/IsanaVekslerLublinsky/OffRisk-ui (including code, user guide, docker installation guide, and running examples).
All processed datasets are available at https://zenodo.org/record/8289271.
Aliro: an automated machine learning tool leveraging large language models
Authors: Choi Hyunjun , Moran Jay , Matsumoto Nicholas , Hernandez Miguel E , Moore Jason H 
Published: October 2023

Abstract

Motivation
Biomedical and healthcare domains generate vast amounts of complex data that can be challenging to analyze using machine learning tools, especially for researchers without computer science training.

Results
Aliro is an open-source software package designed to automate machine learning analysis through a clean web interface. By infusing the power of large language models, the user can interact with their data by seamlessly retrieving and executing code pulled from the large language model, accelerating automated discovery of new insights from data. Aliro includes a pre-trained machine learning recommendation system that can assist the user to automate the selection of machine learning algorithms and its hyperparameters and provides visualization of the evaluated model and data.

Availability and implementation
Aliro is deployed by running its custom Docker containers. Aliro is available as open-source from GitHub at: https://github.com/EpistasisLab/Aliro.
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data
Authors: Hsieh Ping-Han , Lopes-Ramos Camila Miranda , Zucknick Manuela , Sandve Geir Kjetil , Glass Kimberly , Kuijjer Marieke Lydia 
Published: October 2023

Abstract

Motivation
Gene co-expression measurements are widely used in computational biology to identify coordinated expression patterns across a group of samples. Coordinated expression of genes may indicate that they are controlled by the same transcriptional regulatory program, or involved in common biological processes. Gene co-expression is generally estimated from RNA-Sequencing data, which are commonly normalized to remove technical variability. Here, we demonstrate that certain normalization methods, in particular quantile-based methods, can introduce false-positive associations between genes. These false-positive associations can consequently hamper downstream co-expression network analysis. Quantile-based normalization can, however, be extremely powerful. In particular, when preprocessing large-scale heterogeneous data, quantile-based normalization methods such as smooth quantile normalization can be applied to remove technical variability while maintaining global differences in expression for samples with different biological attributes.

Results
We developed SNAIL (Smooth-quantile Normalization Adaptation for the Inference of co-expression Links), a normalization method based on smooth quantile normalization specifically designed for modeling of co-expression measurements. We show that SNAIL avoids formation of false-positive associations in co-expression as well as in downstream network analyses. Using SNAIL, one can avoid arbitrary gene filtering and retain associations to genes that only express in small subgroups of samples. This highlights the method’s potential future impact on network modeling and other association-based approaches in large-scale heterogeneous data.

Availability and implementation
The implementation of the SNAIL algorithm and code to reproduce the analyses described in this work can be found in the GitHub repository https://github.com/kuijjerlab/PySNAIL.
Geographical patterns in mandible variation of the common shrew (Sorex araneus) in Europe
Authors: Farková Lucie , Lázaro Javier , Kryštufek Boris , Vohralík Vladimír 
Published: October 2023

Abstract
The common shrew (Sorex araneus) is one of the most studied shrew species of the Western Palaearctic. Despite this, the general drivers underlying morphological variation still remain unclear. Here we provide evidence for contradictory effects of climatic and geographical factors on the mandible of the common shrew. At the continental scale there is a negative correlation between body- and skull-size and latitude and longitude but at regional scales such an association is often not apparent; in fact, in some cases body size and skull size follow the opposite trend and observations at various scales yielded contradictory results. We studied shrew mandibles using geometric morphometrics and tested for correlations of their size and shape with selected geographical and climatic variables. We examined 1155 mandibles from 29 European localities and found significant interpopulation differences in both size and shape. Centroid size negatively correlated with latitude. We also found that centroid size was significantly correlated with altitude and annual precipitation. Our results confirmed an inverse Bergmann’s rule relationship in S. araneus along the transect from the Baltic to the Adriatic Sea. Regarding mandible shape, Slovenian shrews were the most distant from all other studied populations. We discuss how altitude and precipitation can influence the morphology of the common shrew.
Disease from opposing forces in regulatory control
Authors: Frank Steven A 
Published: October 2023

Abstract
Danger requires a strong rapid response. Speedy triggers are prone to false signals. False alarms can be costly, requiring strong negative regulators to oppose the initial triggers. Strongly opposed forces can easily be perturbed, leading to imbalance and disease. For example, immunity and fear response balance strong rapid triggers against widespread slow negative regulators. Diseases of immunity and behavior arise from imbalance. A different opposition of forces occurs in mammalian growth, which balances strong paternally expressed accelerators against maternally expressed suppressors. Diseases of overgrowth or undergrowth arise from imbalance. Other examples of opposing forces and disease include control of dopamine expression and male versus female favored traits.
Nationwide time trends in patients hospitalized for acute coronary syndrome: a worrying generational and social effect among women
Authors: Grave Clémence , Gabet Amélie , Cinaud Alexandre , Tuppin Philippe , Blacher Jacques , Olié Valérie 
Published: October 2023

Abstract

Aims
To estimate the time trends in the annual incidence of patients hospitalized for acute coronary syndrome (ACS) in France from 2009 to 2021 and to analyse the current sex and social differences in ACS, management, and prognosis.

Methods and results
All patients hospitalized for ACS in France were selected from the comprehensive National Health Insurance database. Age-standardized rates were computed overall and according to age group (over or under 65 years), sex, proxy of socioeconomic status, and ACS subtype [ST-segment elevation (STSE) and non-ST-segment elevation]. Patient characteristics and outcomes were described for patients hospitalized in 2019. Differences in management (coronarography, revascularization), and prognosis were analysed by sex, adjusting for cofonders. In 2019, 143,670 patients were hospitalized for ACS, including 53,227 STSE-ACS (mean age = 68.8 years; 32% women). Higher standardized incidence rates among the most socially deprived people were observed. Women were less likely to receive coronarography and revascularization but had a higher excess in-hospital mortality. In 2019, the age-standardized rate for hospitalized ACS patients reached 210 per 100 000 person-year. Between 2009 and 2019, these rates decreased by 11.4% (men: −11.2%; women: −14.0%). Differences in trends of age-standardized incidence rate have been observed according to sex, age, and social status. Middle aged women (45–64 years) showing more unfavourable trends than in other age classes or in men. In addition, among women the temporal trends were more unfavourable as social deprivation increased.

Conclusion
Despite encouraging overall trends in patients hospitalized for ACS rates, the increasing trends observed among middle-aged women, especially socially deprived women, is worrying. Targeted cardiovascular prevention and close surveillance of this population should be encouraged.
IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes
Authors: Díez Menéndez Carmen , Poczai Peter , Williams Bernardo , Myllys Leena , Amiryousefi Ali 
Published: October 2023

Abstract
High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large sequencing efforts require software tools for routine display of their distinctive quadripartite structure, which is denoted by four junction sites. By concentrating on these junctions and their close vicinity, IRscope has emerged as the standard tool for detection of this structure and creating simplified comparative graphical maps of plastid genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set of functions such as integrated error detection, flexible color schemes, and an upgraded method to detect inverted repeats in genomic sequences. Spanning across the plant tree of life, IRplus allows the quick visualization of various sets of plastid genomes and features, next to smooth interoperability with other widely used annotation file formats and platforms. The IRplus can be accessed at https://irscope.shinyapps.io/IRplus/, and source codes are freely available at https://github.com/AmiryousefiLab/IRplus.
Life Events and Loneliness Transitions Among Middle-Aged and Older Adults Around the World
Authors: Sheftel Mara Getz , Margolis Rachel , Verdery Ashton M 
Published: October 2023

Abstract

Objectives
Adult loneliness is a substantial social problem and a growing point of concern for policymakers around the world. We assess whether the predictors of loneliness onset among middle-aged and older adults vary from country to country in a large array of settings across world regions. Taking a life course perspective, we focus on common life events in our focal age range, including changes in partnership, coresidence, work, and health, and we test whether changes in them have comparable prospective associations with loneliness onset in different countries.

Methods
We draw on respondent-level data from a diversity of world regions surveyed in 7 harmonized cross-national studies in 20 countries, representing 47% of the global population over the age of 50. Our innovative longitudinal approach estimates prospective transition probability models that examine how each life event predicts the transition into loneliness.

Results
Despite substantial variation in the prevalence of loneliness and life events across the range of countries in our sample, our results highlight consistency in the predictors of loneliness transitions. Family and household changes like divorce, coresidence, and especially widowhood are paramount predictors of loneliness transition across settings, with changes in work and health playing more minor and less universal roles.

Discussion
The results demonstrate the importance that family and household connections play in determining loneliness at these ages. These findings suggest that addressing late-life loneliness may require a focus on key life events, especially those concerning changes in families and households.
Locating tectonic tremors with uncertainty estimates: time- and amplitude-difference optimization, wave propagation-based quality control and Bayesian inversion
Authors: Akuhara Takeshi , Yamashita Yusuke , Sugioka Hiroko , Shinohara Masanao 
Published: October 2023

SUMMARYThe accurate location of tectonic tremors helps improve understanding of their underlying physical processes. However, current location methods often do not statistically evaluate uncertainties to a satisfactory degree and do not account for potential biases due to subsurface structures not included in the model. To address these issues, we propose a novel three-step process for locating tectonic tremors. First, the measured time- and amplitude differences between station pairs are optimized to obtain station-specific relative time and amplitude measurements with uncertainty estimates. Secondly, the time– and amplitude–distance relationships in the optimized data are used to roughly estimate the propagation speed (i.e. shear wave velocity) and attenuation strength. Linear regression is applied to each event, and the resulting velocity and attenuation strength are used for quality control. Finally, the tremor location problem is formulated within a Bayesian framework where the model parameters include the source locations, local site delay/amplification factors, shear wave velocity and attenuation strength. The Markov chain Monte Carlo algorithm is used to sample the posterior probability and is augmented by a parallel tempering scheme for an efficient global search. We tested the proposed method on ocean-bottom data indicating an intense episode of tectonic tremors in Kumano-nada within the Nankai Trough subduction zone. The results show that the range of the 95 per cent confidence interval is typically &lt;7 km horizontally and &lt;10 km vertically. A series of experiments with different inversion settings reveals that adopting amplitude data and site correction factors help reduce random error and systematic bias, respectively. Probabilistic sampling allows us to spatially map the probability of a tremor occurring at a given location. The probability map is used to identify lineaments of tremor sources, which provides insights into structural factors that favour tremor activity.