bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality Prediction and Model Explanation of Resistance Spot Welding Process Under Varying Fit-Up Conditions
Authors: Lyu Tianle , Xia Yunjun , Li Yongbing , Wang Songlin 
Published: September 2023

Abstract
This paper focuses on the challenge of online predicting resistance spot welding (RSW) quality, which is affected by the fit-up condition that inevitably varies in production due to assembly deviation but is rarely considered in previous research. To address this gap, this paper develops online prediction models for RSW quality based on multi-sensing signal features. Four widely-used machine learning regression models, namely multiple linear regression (MLR), Gaussian process regression (GPR), support vector regression (SVR), and multilayer perceptron regression (MLPR) were trained on datasets with varying fit-up conditions. The models’ adaptabilities to input signals and their generalizations to different fit-up conditions were assessed. Specifically, SHAP values were adopted to determine the contribution of each signal feature for model interpretation, and the t-SNE method was utilized to explain the influence of fit-up conditions on the model performance. The results demonstrated that the GPR model has the best prediction performance, with an accuracy of 92.2% and RMSE of 0.591 mm. Among the 26 features, welding current, heat input, and average electrode displacement exhibit the highest universality for varying conditions. When only limited signals are allowed as input, resistance together with displacement signals can achieve the best prediction. However, the model generalizations to varying conditions are low, particularly to the edge proximity condition. Therefore, it is important to minimize the discrepancy between the training and test datasets to improve the model generalization.
Machine Learning-Based Modeling of Electric-Field-Assisted Direct Ink Writing (EDIW) Process
Authors: Chen Yinong , Deshpande Anupam Ajit , Joyee Erina Baynojir , Pan Yayue 
Published: September 2023

Abstract
Direct ink writing (DIW) is an extrusion-based additive manufacturing technology. It has gained wide attentions in both industry and research because of its simple design and versatile platform. In electric-field-assisted Direct Ink Writing (eDIW) processes, an external electric field is added between the nozzle and the printing substrate to manipulate the ink-substrate wetting dynamics and therefore optimize the ink printability. eDIW was found effective in printing liquids that are typically difficult to print in the conventional DIW processes. In this paper, an eDIW process modeling system based on machine learning (ML) algorithms is developed. The system is found effective in predicting eDIW printing geometry under varied process parameter settings. Image processing approaches to collect experiment data are developed. Accuracies of different machine learning algorithms for predicting printing results and trace width are compared and discussed. The capabilities, applications and limitations of the presented machine learning-based modeling approach are presented.
An exhaustive multiple knockout approach to understanding cell wall hydrolase function in
Bacillus subtilis
Authors: Wilson Sean A. , Tank Raveen K. J. , Hobbs Jamie K. , Foster Simon J. , Garner Ethan C. 
Published: September 2023

ABSTRACT

Most bacteria are surrounded by their cell wall, containing a highly cross-linked protective envelope of peptidoglycan. To grow, bacteria must continuously remodel their wall, inserting new material and breaking old bonds. Bond cleavage is performed by cell wall hydrolases, allowing the wall to expand. Understanding the functions of individual hydrolases has been impeded by their redundancy: single knockouts usually present no phenotype. We used an exhaustive multiple-knockout approach to determine the minimal set of hydrolases required for growth in
Bacillus subtilis
. We identified 42 candidate hydrolases. Strikingly, we were able to remove all but two of these genes in a single strain; this “∆40” strain shows only a mild reduction in growth rate, indicating that none of the 40 hydrolases are necessary for growth. The ∆40 strain does not detectably shed old wall, suggesting that turnover is not essential for growth. The remaining hydrolases in the ∆40 strain are LytE and CwlO, previously shown to be synthetically lethal. Either can be removed in ∆40, indicating that either hydrolase alone is sufficient for cell growth. Screening of environmental conditions and biochemistry revealed that LytE activity is inhibited by Mg
2+
and that RlpA-like proteins may stimulate LytE activity. Together, these results suggest that the only essential function of cell wall hydrolases in
B
.
subtilis
is to enable cell growth by expanding the wall and that LytE or CwlO alone are sufficient for this function. These experiments introduce the ∆40 strain as a tool to study hydrolase activity and regulation in
B. subtilis
.

IMPORTANCE

In order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall— cell wall hydrolases—has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in
Bacillus subtilis
and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of
B. subtilis
in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the ∆40 strain is a research tool to characterize hydrolases, using it to identify three “helper” hydrolases that act in certain stress conditions.
Species and condition shape the mutational spectrum in experimentally evolved biofilms
Authors: Hu Guohai , Wang Yue , Liu Xin , Strube Mikael Lenz , Wang Bo , Kovács Ákos T. 
Published: September 2023

ABSTRACT

Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from the
Bacillus
genus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences of
Bacillus thuringiensis
are critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Furthermore, our results suggest that the population size might be an important driver of evolution. Together, these results provide the first comprehensive mutational landscape of two bacterial species’ biofilms that is adapted to an abiotic and biotic surface.

IMPORTANCE

Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved
Bacillus thuringiensis
and
Bacillus subtilis
that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Furthermore, the differences and similarities of adaptive mechanisms in
B. thuringiensis
and
B. subtilis
were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species’ biofilms that is adapted to an abiotic and biotic surface.
Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome
Authors: Mei Jun-Lan , Chai Li-Juan , Zhong Xiao-Zhong , Lu Zhen-Ming , Zhang Xiao-Juan , Wang Song-Tao , Shen Cai-Hong , Shi Jin-Song , Xu Zheng-Hong 
Published: September 2023

ABSTRACT

The fermentation process of strong-flavor
Baijiu
occurs in an underground cellar surrounded by mud, where grains are decomposed and generate new flavor substances. Pit mud microbiome plays a pivotal role in the formation of
Baijiu
flavor, which is positively correlated with cellar age. Previous research on the pit mud microbiome was often conducted for a specific distillery, making it hard to draw a general conclusion to decipher the pit mud microecosystem in such a unique brewing environment. Hence, in this study, we attempt to unravel community formation mechanisms through research in pit mud microbial biogeography based on 12 independent bacterial studies comprising qualified data sets of 302 samples clearly marked with cellar age from five major producing provinces. We found cellar age explained more variations in the bacterial community than geographical region. The bacterial community displayed evident dominant species alternations on a large time scale.
Lactobacillus
was found to be the dominant species in young pit mud (<10 years), while
Caproiciproducens
dominated in aged pit mud. Null model analysis revealed that as pit mud aged, the influence of stochastic and deterministic processes in the bacterial community shifted, and the relative contribution of homogeneous selection increased. Positive correlations dominated the bacterial co-occurrence networks, and the network complexity decreased and stability increased with cellar age. These findings shed new light on the formation of pit mud microbiomes under the impact of long-term batch-to-batch continuous brewing, providing a basis for the evaluation and production of high-quality pit mud.

IMPORTANCE

Baijiu
is a typical example of how humans employ microorganisms to convert grains into new flavors. Mud cellars are used as the fermentation vessel for strong-flavor
Baijiu
(SFB) to complete the decomposition process of grains. The typical flavor of SFB is mainly attributed to the metabolites of the pit mud microbiome. China has a large number of SFB-producing regions. Previous research revealed the temporal profiles of the pit mud microbiome in different geographical regions. However, each single independent study rarely yields a thorough understanding of the pit mud ecosystem. Will the pit mud microbial communities in different production regions exhibit similar succession patterns and structures under the impact of the brewing environment? Hence, we conducted research in pit mud microbial biogeography to uncover the impact of specific environment on the microbial community over a long time scale.
Tracing the evolving dynamics and research hotspots of microbiota and immune microenvironment from the past to the new era
Authors: Huang Runzhi , Yao Yuntao , Tong Xirui , Wang Lei , Qian Weijin , Lu Jianyu , Zhang Wei , Liu Yifan , Wang Siqiao , Xian Shuyuan , Zhu Yushu , Huang Jie , Guo Xinya , Gu Minyi , Lv Hanlin , Bi Wenshuai , Meng Chenwei , Chang Zhengyan , Zhang Jie , Xu Dayuan , Ji Shizhao 
Published: September 2023

ABSTRACT
Gut microbiota can regulate many physiological processes within gastrointestinal tract and other distal sites. Dysbiosis may not only influence chronic diseases like the inflammatory bowel disease (IBD), metabolic disease, tumor and its therapeutic efficacy, but also deteriorate acute injuries. This article aims to review the documents in this field and summarize the research hotspots as well as developing processes. Gut microbiota and immune microenvironment-related documents from 1976 to 2022 were obtained from the Web of Science Core Collection database. Bibliometrics was used to assess the core authors and journals, most contributive countries and affiliations together with hotspots in this field and keyword co-occurrence analysis. Data were visualized to help comprehension. Nine hundred and twelve documents about gut microbiota and immune microenvironment were retrieved, and the annual publications increased gradually. The most productive author, country, and affiliation were “Zitvogel L,” USA and “UNIV TEXAS MD ANDERSON CANC CTR,” respectively. FRONTIERS IN IMMUNOLOGY, CANCERS, and INTERNATIONAL JOURNAL OF MOLECULAR SCIENCE were the periodicals with most publications. Keyword co-occurrence analysis identified three clusters, including gut microbiota, inflammation, and IBD. Combined with the visualized analysis of documents and keyword co-occurrence as well as literature reading, we recognized three key topics of gut microbiota: cancer and therapy; immunity, inflammation and IBD; acute injuries and metabolic diseases. This article revealed researches on gut microbiota and immune microenvironment were growing. More attention should be given to the latest hotspots like gut microbiota, inflammation, IBD, cancer and immunotherapy, acute traumas, and metabolic diseases.

IMPORTANCE
Gut microbiota can regulate many physiological processes within gastrointestinal tract and other distal sites. Dysbiosis may not only influence chronic diseases like inflammatory bowel disease (IBD), metabolic disease, tumor and its therapeutic efficacy, but also deteriorate acute injuries. While the application of bibliometrics in the field of gut microbiota and immune microenvironment still remains blank, which focused more on the regulation of the gut microbiota on the immune microenvironment of different kinds of diseases. Here, we intended to review and summarize the presented documents in gut microbiota and immune microenvironment field by bibliometrics. And we revealed researches on gut microbiota and immune microenvironment were growing. More attention should be given to the latest hotspots like gut microbiota, inflammation, IBD, cancer and immunotherapy, acute traumas, and metabolic diseases.
HutZ is required for efficient heme utilization and contributes to the pathogenicity of
Avibacterium paragallinarum
Authors: Huo Caiyun , Jiao Lijiao , Li Guiping , Li Donghai , Lin Wutong , Sun Yingjian , Sun Huiling 
Published: September 2023

ABSTRACT

Avibacterium paragallinarum
is the pathogen that causes infectious coryza, a highly contagious respiratory disease that brings a serious threat to chickens. Heme utilization systems play an important role in bacterial adversity adaptation and pathogenicity, and our previous report found the presence of heme utilization (HutZ) in
Av. paragallinarum
. However, little is known about the function of HutZ in
Av. paragallinarum
. In this study, the HutZ mutant strain of
Av. paragallinarum
was successfully developed and identified by PCR and western blot analysis. Mutation of HutZ significantly retards bacterial growth under reduced iron conditions, indicating the regulatory role of HutZ on growth and iron acquisition. Notably, the HutZ mutant strain had slower growth than the wild-type strain when heme was provided as the sole source of iron; thus, HutZ is crucial for heme utilization in
Av. paragallinarum
. Moreover, the HutZ mutant strain exhibited a markedly compromised tolerance to acid stress compared to the wild-type strain. Pathogenicity analysis showed that mutation of HutZ significantly weakened the ability of bacteria to invade and reproduce in host macrophage cells
in vitro
. Furthermore, the HutZ mutation could significantly decrease the bacterial virulence in chickens, which displayed lower morbidity and milder clinical symptoms. Hence, this is the first study to demonstrate in-depth the essential roles of HutZ on iron homeostasis and pathogenesis of
Av. paragallinarum
, which provides novel insight into advances of new prophylactic vaccines against this kind of bacteria.

Importance

Heme utilization (HutZ) protein has been characterized as an important heme-degrading enzyme that is critical for the cleavage of heme to biliverdin
via
verdoheme and can release iron to be used by bacteria. The interaction between HutZ and
Av. paragallinarum
is still unknown. Here, we unraveled the role of HutZ on the growth, iron acquisition, heme utilization, and resistance to acidic stress in
Av. paragallinarum
. We also uncovered the importance of HutZ for the success of
Av. paragallinarum
infection and provided new clues to the pathogenesis strategies of this organism. This work constitutes a relevant step toward an understanding of the role of HutZ protein as a master virulence factor. Therefore, this study is of great importance for understanding the mechanisms underlying
Av. paragallinarum
virulence and may contribute to therapeutic applications.
Investigating weathering signatures in terrestrial muds: Can climatic signatures be separated from provenance?
Authors: Demirel-Floyd Cansu , Soreghan Gerilyn S. , Webb Nina D.S. , Roche Autumn , Joo Young Ji , Hall Brenda , Levy Joseph S. , Elwood Madden Andrew S. , Elwood Madden Megan E. 
Published: September 2023

Siliciclastic muds (clay- and silt-sized sediment) concentrate physical and chemical weathering products. However, both rock composition and climate can affect the mineralogy and geochemistry of these sediments. We quantitatively assessed the influence of provenance and climate on muds collected from end-member climates to test, which, if any, of these potential weathering signatures are indicative of climate in fine-grained, fluvial sediments. Granulometry, mineralogy, and geochemistry of the studied muds indicated that provenance and mineral sorting hinder interpretation of (paleo)climate signals. These issues also affect chemical index of alteration (CIA) values, as well as mafic-felsic-weathering (MFW), Al2O3−(CaO* + Na2O)−K2O (A-CN-K), and Al2O3−(CaO* + Na2O + K2O)−(FeOT + MgO) (A-CNK-FM) ternary plots, decreasing their utility as paleoclimate proxies. CaO content is heavily weighted within the calculations, resulting in even felsic-sourced sediment commonly plotting as mafic owing to the relative enrichment in CaO from preferential sorting of Ca-rich minerals into the mud-sized fraction during transport. These results cast doubt on the indiscriminate use of CIA values and ternary plots for interpreting chemical weathering and paleoclimate within muds, particularly from glacial systems.
Most notably, the positive correlations between CIA and climatic parameters (mean annual temperature and mean annual precipitation) diminished when sediments that had formed in nonglacial settings were filtered out from the data sets. This implies that CIA may only be applicable when used in nonglacial systems in which the composition of the primary source material is well constrained—such as soil/paleosol profiles. Within this end-member climate data set, CIA was only useful in discriminating hot-humid climates.
A New Species of Hapalodectes (Hapalodectidae, Mesonychia) from the Paleocene of Mongolia
Authors: Lopatin A. V. 
Published: September 2023

Abstract
Hapalodectes paradux sp. nov. (Hapalodectidae, Mesonychia) is described on the base of the dentary fragment with M2–M3 from the Tsagan-Khushu locality in Mongolia (Upper Paleocene, Naran Bulak Formation, Zhigden Member). The M2 and M3 are approximately the same size, with a high protoconid, anteriorly displaced reduced metaconid, anterolingually directed protocristid, very deep posterior notch, narrow talonid, and distinct hypoconid, entoconid and hypoconulid. Based on dental characters, the new species is presumably related to the base of the lineage of Hapalodectes that dispersed to North America at the beginning of the Eocene. Tsagan-Khushu is the only known locality where two species of Hapalodectes co-occur (larger H. dux Lopatin, 2001 and smaller H. paradux sp. nov.).
Infrared subtleties and chiral vertices at NLO: an implicit regularization analysis
Authors: Rosado Ricardo J. C. , Cherchiglia Adriano , Sampaio Marcos , Hiller Brigitte 
Published: September 2023

AbstractWe employ implicit regularization (IReg) in quark-antiquark decays of the Z, or of a scalar (CP-even or odd) boson at NLO, and compare with dimensional schemes to reveal subtleties involving infrared divergence cancellation and $$\gamma _5$$

γ
5

-matrix issues. Besides the absence of evanescent fields in IReg, such as $$\epsilon $$
ϵ
-scalars required in certain schemes that operate partially in the physical dimension, we verify that our procedure preserves gauge invariance in the presence of the $$\gamma _5$$

γ
5

matrix without requiring symmetry preserving counterterms while the amplitude is infrared finite as stated by the KLN theorem.
Exploring the Explainable Aspects and Performance of a Learnable Evolutionary Multiobjective Optimization Method
Authors: Misitano Giovanni 
Published: September 2023

Multiobjective optimization problems have multiple conflicting objective functions to be optimized simultaneously. The solutions to these problems are known as Pareto optimal solutions, which are mathematically incomparable. Thus, a decision maker must be employed to provide preferences to find the most preferred solution. However, decision makers often lack support in providing preferences and insights in exploring the solutions available.
We explore the combination of learnable evolutionary models with interactive indicator-based evolutionary multiobjective optimization to create a learnable evolutionary multiobjective optimization method. Furthermore, we leverage interpretable machine learning to provide decision makers with potential insights about the problem being solved in the form of rule-based explanations. In fact, we show that a learnable evolutionary multiobjective optimization method can offer advantages in the search for solutions to a multiobjective optimization problem. We also provide an open source software framework for other researchers to implement and explore our ideas in their own works.

Our work is a step toward establishing a new paradigm in the field on multiobjective optimization:
explainable and learnable multiobjective optimization
. We take the first steps toward this new research direction and provide other researchers and practitioners with necessary tools and ideas to further contribute to this field.