bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the robustness and stability of a machine learning model for breast cancer prognosis through the use of multi-modal classifiers
Authors: Arya Nikhilanand , Saha Sriparna , Mathur Archana , Saha Snehanshu 
Published: March 2023

AbstractBreast cancer is a deadly disease with a high mortality rate among PAN cancers. The advancements in biomedical information retrieval techniques have been beneficial in developing early prognosis and diagnosis systems for cancer patients. These systems provide the oncologist with plenty of information from several modalities to make the correct and feasible treatment plan for breast cancer patients and protect them from unnecessary therapies and their toxic side effects. The cancer patient’s related information can be collected using various modalities like clinical, copy number variation, DNA-methylation, microRNA sequencing, gene expression, and histopathological whole slide images. High dimensionality and heterogeneity in these modalities demand the development of some intelligent systems to understand related features to the prognosis and diagnosis of diseases and make correct predictions. In this work, we have studied some end-to-end systems having two main components : (a) dimensionality reduction techniques applied to original features from different modalities and (b) classification techniques applied to the fusion of reduced feature vectors from different modalities for automatic predictions of breast cancer patients into two categories: short-time and long-time survivors. Principal component analysis (PCA) and variational auto-encoders (VAEs) are used as the dimensionality reduction techniques, followed by support vector machines (SVM) or random forest as the machine learning classifiers. The study utilizes raw, PCA, and VAE extracted features of the TCGA-BRCA dataset from six different modalities as input to the machine learning classifiers. We conclude this study by suggesting that adding more modalities to the classifiers provides complementary information to the classifier and increases the stability and robustness of the classifiers. In this study, the multimodal classifiers have not been validated on primary data prospectively.
Top-down and bottom-up effects modulate species co-existence in a context of top predator restoration
Authors: Burgos Tamara , Salesa Javier , Fedriani Jose María , Escribano-Ávila Gema , Jiménez José , Krofel Miha , Cancio Inmaculada , Hernández-Hernández Javier , Rodríguez-Siles Javier , Virgós Emilio 
Published: March 2023

AbstractMesopredators abundance is often limited by top-order predators and also by key food resources. However, the contribution of these bidirectional forces to structure carnivore community is still unclear. Here, we studied how the presence and absence of an apex predator which is currently recovering its former distribution range, the Iberian lynx (Lynx pardinus), determined the absolute abundance and fine-scale spatiotemporal avoidance mechanisms of two sympatric mesocarnivores (stone marten Martes foina and common genet Genetta genetta) with different dietary plasticity. We hypothesized that the lynx causes a mesopredator suppression and subordinate predators develop segregation strategies in respect to their trophic niche breadth. We placed 120 camera-traps in Southern Spain for 8 months in two consecutive years to estimate mesocarnivore abundances by using SCR Bayesian models, prey availability and assess spatio-temporal patterns. We found that the lynx reduced mesocarnivore abundance up to 10 times. Stone marten, a mesopredator with a broad food resources spectrum, showed a total spatial exclusion with the apex predator. Meanwhile, fine-scale avoidance mechanisms allowed the genet to persist in low density inside lynx territories, probably taking advantage of high availability of its preferred prey. Thus, the strength of these top-down and bottom-up effects was rather species-specific. Given the recent recovery of large carnivore populations worldwide, variation in suppression levels on different mesopredator species could modify ecosystem functions provided by the carnivore community in contrasting ways.
Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity
Authors: Kim Ryeong-Hui , Tagele Setu Bazie , Jeong Minsoo , Jung Da-Ryung , Lee Dokyung , Park TaeHyung , Tino Bashizi Flory , Lim Kyeongmo , Kim Min A. , Park Yeong-Jun , Shin Jae-Ho 
Published: March 2023

AbstractSpinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot −1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4+, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.
High-performance glass filters for capturing and culturing circulating tumor cells and cancer-associated fibroblasts
Authors: Tanaka Hiromasa , Iwata Daijiro , Shibata Yuki , Hase Tetsunari , Onoshima Daisuke , Yogo Naoyuki , Shibata Hirofumi , Sato Mitsuo , Ishikawa Kenji , Nagasawa Ikuo , Hasegawa Yoshinori , Ishii Makoto , Baba Yoshinobu , Hori Masaru 
Published: March 2023

AbstractVarious liquid biopsy methods have been developed for the non-invasive and early detection of diseases. In particular, the detection of circulating tumor cells (CTCs) and cancer-associated fibroblasts (CAFs) in blood has been receiving a great deal of attention. We have been developing systems and materials to facilitate such liquid biopsies. In this study, we further developed glass filters (with various patterns of holes, pitches, and non-adhesive coating) that can capture CTCs, but not white blood cells. We optimized the glass filters to capture CTCs, and demonstrated that they could be used to detect CTCs from lung cancer patients. We also used the optimized glass filters for detecting CAFs. Additionally, we further developed a system for visualizing the captured cells on the glass filters. Finally, we demonstrated that we could directly culture the captured cells on the glass filters. Based on these results, our high-performance glass filters appear to be useful for capturing and culturing CTCs and CAFs for further examinations.
CSF tau phosphorylation occupancies at T217 and T205 represent improved biomarkers of amyloid and tau pathology in Alzheimer’s disease
Authors: Barthélemy Nicolas R. , Saef Benjamin , Li Yan , Gordon Brian A. , He Yingxin , Horie Kanta , Stomrud Erik , Salvadó Gemma , Janelidze Shorena , Sato Chihiro , Ovod Vitaliy , Henson Rachel L. , Fagan Anne M. , Benzinger Tammie L. S. , Xiong Chengjie , Morris John C. , Hansson Oskar , Bateman Randall J. , Schindler Suzanne E. 
Published: March 2023

AbstractCerebrospinal fluid (CSF) amyloid-β peptide (Aβ)42/Aβ40 and the concentration of tau phosphorylated at site 181 (p-tau181) are well-established biomarkers of Alzheimer’s disease (AD). The present study used mass spectrometry to measure concentrations of nine phosphorylated and five nonphosphorylated tau species and phosphorylation occupancies (percentage phosphorylated/nonphosphorylated) at ten sites. In the present study we show that, in 750 individuals with a median age of 71.2 years, CSF pT217/T217 predicted the presence of brain amyloid by positron emission tomography (PET) slightly better than Aβ42/Aβ40 (P = 0.02). Furthermore, for individuals with positive brain amyloid by PET (n = 263), CSF pT217/T217 was more strongly correlated with the amount of amyloid (Spearman’sρ = 0.69) than Aβ42/Aβ40 (ρ = −0.42,P < 0.0001). In two independent cohorts of participants with symptoms of AD dementia (n = 55 andn = 90), CSF pT217/T217 and pT205/T205 were better correlated with tau PET measures than CSF p-tau181 concentration. These findings suggest that CSF pT217/T217 and pT205/T205 represent improved CSF biomarkers of amyloid and tau pathology in AD.
Characterization of a bloom-associated alphaproteobacterial lineage, ‘Candidatus Phycosocius’: insights into freshwater algal-bacterial interactions
Authors: Tanabe Yuuhiko , Yamaguchi Haruyo , Yoshida Masaki , Kai Atsushi , Okazaki Yusuke 
Published: March 2023

Abstract
Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage ‘Candidatus Phycosocius’ (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: ‘Ca. Phycosocius spiralis.’ Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5–3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in ‘Ca. P. spiralis’ that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.
O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases
Authors: Labourel Aurore , Parrou Jean-Luc , Deraison Céline , Mercier-Bonin Muriel , Lajus Sophie , Potocki-Veronese Gabrielle 
Published: March 2023

Abstract
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.
Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota
Authors: La Rosa Sabina Leanti , Lindstad Lars J. , Westereng Bjørge 
Published: March 2023

Abstract
Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid–base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.
Accounting for component condition and preventive retirement in power system reliability analyses
Authors: Toftaker Håkon , Foros Jørn , Sperstad Iver Bakken 
Published: March 2023

AbstractDeteriorated power system components have a higher probability of failure than new components. Still, the reliability of supply analyses traditionally models all components of the same type with the same probability of failure, and thus neglects the effect of deteriorated components. This paper presents a methodology to integrate a condition‐dependent component probability of failure model into a power system reliability analysis. The component state is described by a semi‐Markov process, and the paper shows how this, under reasonable assumptions, can be approximated by a Markov process. The Markov assumption simplifies the analysis and allows the model to include preventive retirement and be calibrated to statistical data. A case study using statistical data for Norwegian power transformers shows that, in the Norwegian power system, the proportion of failures that are due to the poor condition is small, partly due to the common strategy of preventive retirement. However, if the condition of the transformers were worse, the impact of poor conditions can be considerable. The methodology further enables the identification of the transformers that contribute most to the risk to the reliability of supply. The paper thus highlights the importance of accounting for the component condition in strategic decisions such as long‐term renewal planning
Recent trends in nanocomposite packaging films utilising waste generated biopolymers: Industrial symbiosis and its implication in sustainability
Authors: Tabassum Zeba , Mohan Anand , Mamidi Narsimha , Khosla Ajit , Kumar Anil , Solanki Pratima R. , Malik Tabarak , Girdhar Madhuri 
Published: March 2023

AbstractUncontrolled waste generation and management difficulties are causing chaos in the ecosystem. Although it is vital to ease environmental pressures, right now there is no such practical strategy available for the treatment or utilisation of waste material. Because the Earth's resources are limited, a long‐term, sustainable, and sensible solution is necessary. Currently waste material has drawn a lot of attention as a renewable resource. Utilisation of residual biomass leftovers appears as a green and sustainable approach to lessen the waste burden on Earth while meeting the demand for bio‐based goods. Several biopolymers are available from renewable waste sources that have the potential to be used in a variety of industries for a wide range of applications. Natural and synthetic biopolymers have significant advantages over petroleum‐based polymers in terms of cost‐effectiveness, environmental friendliness, and user‐friendliness. Using waste as a raw material through industrial symbiosis should be taken into account as one of the strategies to achieve more economic and environmental value through inter‐firm collaboration on the path to a near‐zero waste society. This review extensively explores the different biopolymers which can be extracted from several waste material sources and that further have potential applications in food packaging industries to enhance the shelf life of perishables. This review‐based study also provides key insights into the different strategies and techniques that have been developed recently to extract biopolymers from different waste byproducts and their feasibility in practical applications for the food packaging business.
Visualised genotyping assay with oral swabs in a closed tube by nested invasive reaction assisted with gold nanoparticle probes
Authors: Li Yijun , Wei Wei , Ma Yi , Shan Jingwen , Chu Yanan , Zhang LiKun , Liu Danni , Ma Xueping , Zhou Guohua , Wu Haiping 
Published: March 2023

AbstractSingle nucleotide polymorphism (SNP) typing is crucial for drug dosage and disease progression. Therefore, a simple and convenient genotyping assay is essential for personalised medicine. Herein, we developed a non‐invasive, closed‐tube, and visualised method for genotyping. In this method, oral swabs were lysed to directly perform PCR coupled with nested invasive reaction and visualisation based on gold nanoparticle probes in a closed tube. The strategy for genotyping assay depends on the single base recognition property of invasive reaction. This assay allowed quick and simple sample preparation and the detection of 25 copies/μL of CYP2C19*2 and 100 copies/μL of CYP2C19*3 within 90 min. Further, 20 oral swab samples for CYP2C19*2 and CYP2C19*3 were correctly typed, which agreed with pyrosequencing, indicating that this method has great potential for SNP typing in source‐limited regions to guide personalised medicine.
Analysis of the retention of women in higher education STEM programs
Authors: Ortiz-Martínez Gabriela , Vázquez-Villegas Patricia , Ruiz-Cantisani María Ileana , Delgado-Fabián Mónica , Conejo-Márquez Danna A. , Membrillo-Hernández Jorge 
Published: March 2023

AbstractGender equity and quality education are Sustainable Development Goals that are present when a culture of equity and inclusion is pursued in society, companies, and institutions. Particularly in undergraduate programs in Science, Technology, Engineering, and Mathematics (STEM), there is a noticeable gender gap between men and women. The objective of this study was to find out the causes of permanence in STEM careers of women, as well as the possible causes of career abandonment towards another STEM or non-STEM career. This was done by analyzing historical data for admission to STEM careers and using an instrument (survey) for data collection carried out in a private university in Mexico. Historical data indicates that only 17% of the total population were women choosing a STEM career. A survey was carried out for 3 months to obtain information on the factors that affect the decision to opt for a STEM career or to remain in it. It was found that men and women prefer inspiring Faculty who motivate them to continue their careers. Factors such as the competitive environment and the difficulty of teaching with less empathetic Faculty were negative and decisive aspects of decision-making. School achievement did not influence the dropout rate of women in STEM careers. The factors of choice and desertion of women in STEM careers were determined, and actions of educational innovation such as mentoring and timely monitoring of already enrolled female students, digital platforms for students and Faculty, awareness workshops for Faculty, and talks with successful women in STEM areas were proposed.
Electromagnetoelastic transport through a piezoelectric slab: Selective parity interplay of electromagnetic and acoustic resonances
Authors: Konovalenko A. , Makarov N. M. , Pérez-Rodríguez F. 
Published: March 2023

We present the complete solution concerning to transport properties of coupled transverse electromagnetic and shear acoustic waves propagating via a piezoelectric slab embedded into a homogeneous dielectric medium. Since the electroacoustics of our setup is governed by four electromagnetoelastic eigenmodes, we had to succeed in developing a 4 × 4 transfer matrix method to analytically resolve the problem. As a result, the exact frequency spectra of the transmission, reflection, and transformation transport coefficients were obtained and analyzed in detail for two basic cases where the piezoelectric slab subjected by electromagnetic/acoustic perturbation generates acoustic/electromagnetic response. We establish that wave transformation is effectively realized in vicinities of electromagnetic and acoustic Fabry–Pérot resonances. Surprisingly, as a consequence of the problem geometry and accepted 4 mm symmetry of the piezoelectric medium, the phenomenon of the resonant parity selection arises: in the vicinity of an electromagnetic Fabry–Pérot resonance of the given (odd/even) parity, only acoustic Fabry–Pérot resonances with opposite (even/odd) parity are excited in the coefficient of generation. The piezoelectric coupling vanishes when the parities of both resonances coincide. The changes in transmission and reflection spectra turn out to be more sophisticated. The phenomenon is observed due to quite great distinction between electromagnetic and acoustic wave numbers provided by the fundamental difference between light and sound velocities. In our analysis, particular attention is also paid to the ability of increasing the mutual transformation of electromagnetic and acoustic fluxes.