bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB
Authors: Zhang Tinghao , Sun Shaohua , Wang Runzhou , Li Ting , Gan Bicheng , Zhang Yuezhou 
Published: January 2024

AbstractWithin the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/. Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists’ selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.
Graphical Abstract
The use of systematic reviews for conducting new studies in physiotherapy research: a meta-research study comparing author guidelines of physiotherapy-related journals
Authors: Rosen Diane , Reiter Nils L. , Vogel Barbara , Prill Robert 
Published: January 2024

Abstract
Background
Requiring authors to base their research on a systematic review of the existing literature prevents the generation of redundant scientific studies, thereby avoiding the deprivation of effective therapies for trial participants and the waste of research funds. Scientific medical journals could require this in their author guidelines. While this applies to all areas of research, it is also relevant to physiotherapy and rehabilitation research, which predominantly involve interventional trials in patients.

Objective
The aim of this study was to determine the extent to which the use of systematic reviews to justify a new trial is already being requested by physiotherapy-related scientific medical journals (PTJs). In addition, a comparison was made between PTJs and scientific medical journals with the highest impact factor in the Science Citation Index Extended (SCIE).

Methods
This meta-research study is based on a systematic examination of the author guidelines of 149 PTJs. The journals were identified and included based on the number of publications with physiotherapy as a keyword in the databases PEDro, and Medline (Pubmed). The included author guidelines were analysed for the extent to which they specified that a new trial should be justified by a systematic review of the literature. Additionally, they were compared with 14 scientific medical journals with the highest impact factor in the SCIE (LJs).

Results
In their author guidelines, none of the included PTJs required or recommended the use of a systematic review to justify a new trial. Among LJs, four journals (28.57%), all associated with the Lancet group, required the study justification through a systematic review of the literature.

Conclusion
Neither PTJs nor LJs require or recommend the use of a systematic review to justify a new trial in their author guidelines. This potentially leaves room for unethical scientific practices and should be critically considered in future research.
MSC-derived exosomes protect auditory hair cells from neomycin-induced damage via autophagy regulation
Authors: Liu Huan , Kuang Huijuan , Wang Yiru , Bao Lili , Cao Wanxin , Yu Lu , Qi Meihao , Wang Renfeng , Yang Xiaoshan , Ye Qingyuan , Ding Feng , Ren Lili , Liu Siying , Ma Furong , Liu Shiyu 
Published: January 2024

Abstract
Background
Sensorineural hearing loss (SNHL) poses a major threat to both physical and mental health; however, there is still a lack of effective drugs to treat the disease. Recently, novel biological therapies, such as mesenchymal stem cells (MSCs) and their products, namely, exosomes, are showing promising therapeutic potential due to their low immunogenicity, few ethical concerns, and easy accessibility. Nevertheless, the precise mechanisms underlying the therapeutic effects of MSC-derived exosomes remain unclear.

Results
Exosomes derived from MSCs reduced hearing and hair cell loss caused by neomycin-induced damage in models in vivo and in vitro. In addition, MSC-derived exosomes modulated autophagy in hair cells to exert a protective effect. Mechanistically, exogenously administered exosomes were internalized by hair cells and subsequently upregulated endocytic gene expression and endosome formation, ultimately leading to autophagy activation. This increased autophagic activity promoted cell survival, decreased the mitochondrial oxidative stress level and the apoptosis rate in hair cells, and ameliorated neomycin-induced ototoxicity.

Conclusions
In summary, our findings reveal the otoprotective capacity of exogenous exosome-mediated autophagy activation in hair cells in an endocytosis-dependent manner, suggesting possibilities for deafness treatment.
Model tests on ordinary and geosynthetic encased stone columns with recycled aggregates as filler material
Authors: Saxena Shivangi , Roy Lal Bahadur , Gupta Praveen Kumar , Kumar Virendra , Paramasivam Prabhu 
Published: January 2024

Abstract
Purpose
Sincethe availability of natural aggregates is very sparse, recycled industrial and construction waste provides a sustainable alternative to ground improvement using vibro replacement method. Utilizing recycled building waste caters the requirement for its disposal and offers an effective remedy for the scarcity of natural resources. The aim of this study was to give a sustainable alternative for the natural aggregates as the material for stone column.

Materials and methods
A good stone column material should be hard, dense, chemically inert and must comply with the size requirement. The utilization of construction debris and spent railway ballast as column material has been the subject of numerous researches. This work focuses on finding the suitability of railway ballast and concrete debris as alternatives for stone column material. A detailed laboratory testing of these materials has been carried to judge their strength requirements as the material for both Ordinary Stone Columns (OSCs) and Geosynthetic Encased Stone Columns (GESCs). The improvement in capacity of both OSCs and GESCs is evaluated by performing California Bearing Ratio (CBR) test in laboratory by creating unit cell stone column models of different recycled aggregates and comparing their load settlement behavior with natural aggregates.

Results and discussion
Railway ballast, natural aggregates, concrete debris and virgin soil were found to show decreasing order in CBR test results. Loading required for causing settlement in both OSCs and GESCsshowed remarkable increase as compared to that of virgin clay and the maximum load settlement improvement was observed for railway ballast in both the types of stone columns. The CBR values for GESC made from railway ballast, natural aggregates and concrete debris were 54, 49 and 38% respectively. On the other hand, CBR for OSC made from railway ballast, concrete debris and natural aggregates were found to be 25.5, 20.4 and 24% respectively and CBR of virgin clay was found to be just 11%.

Conclusion
The demonstrated application of sustainable sources in place of natural aggregates provides a crucial pathway for utilizing the recycled aggregates as stone column filler material. Up on encasing the OSC with geotextile the performance of stone columns has improved appreciably in terms of load capacity. Railway ballast and concrete debris can be adopted as an alternate for the natural stone column materials to improve the bearing capacity of site consisting mainly of soft clays.
A framework to improve churn prediction performance in retail banking
Authors: Brito João B. G. , Bucco Guilherme B. , Heldt Rodrigo , Becker João L. , Silveira Cleo S. , Luce Fernando B. , Anzanello Michel J. 
Published: January 2024

AbstractManaging customer retention is critical to a company’s profitability and firm value. However, predicting customer churn is challenging. The extant research on the topic mainly focuses on the type of model developed to predict churn, devoting little or no effort to data preparation methods. These methods directly impact the identification of patterns, increasing the model’s predictive performance. We addressed this problem by (1) employing feature engineering methods to generate a set of potential predictor features suitable for the banking industry and (2) preprocessing the majority and minority classes to improve the learning of the classification model pattern. The framework encompasses state-of-the-art data preprocessing methods: (1) feature engineering with recency, frequency, and monetary value concepts to address the imbalanced dataset issue, (2) oversampling using the adaptive synthetic sampling algorithm, and (3) undersampling using NEASMISS algorithm. After data preprocessing, we use XGBoost and elastic net methods for churn prediction. We validated the proposed framework with a dataset of more than 3 million customers and about 170 million transactions. The framework outperformed alternative methods reported in the literature in terms of precision-recall area under curve, accuracy, recall, and specificity. From a practical perspective, the framework provides managers with valuable information to predict customer churn and develop strategies for customer retention in the banking industry.
Exploring topological data analysis for information extraction: application to recognition of Arabic machine-printed numerals
Authors: Bouchaffra Djamel , Ykhlef Faycal 
Published: January 2024

AbstractThis manuscript explores the capability of topological data analysis (TDA) based on homology theory (HT: a subfield of algebraic topology) to extract relevant information for recognition of confusing Arabic machine-printed numerals. In fact, topological properties may significantly reduce the confusion between some numerals such as “1” and “4” in the context of small data sets. These two latter digits differ in the sense that digit 1 has no hole and digit 4 has one hole. Our contribution consists of evaluating the contribution of TDA with its invariant descriptors such as Betti numbers in machine-printed Arabic numerals recognition. Our investigation is driven by the following set of actions: (i) we extract Betti numbers invariant features of each numeral image and partition the ten numerals into three different clusters with respect to these features. (ii) We then perform a classification by assigning a test image to its corresponding cluster, and map this image to a numeral using dynamic-time warping as a metric defined in the Freemans’ chaincode space. We compared our proposed approach with major state-of-the-art methods depicting various ways of using TDA in character recognition. The advantages and limitations of TDA (including its pros and cons) are discussed further based on numeral recognition results.
Effects of Exogenous GIP and GLP-2 on Bone Turnover in Individuals With Type 2 Diabetes
Authors: Skov-Jeppesen Kirsa , Christiansen Charlotte B , Hansen Laura S , Windeløv Johanne A , Hedbäck Nora , Gasbjerg Lærke S , Hindsø Morten , Svane Maria S , Madsbad Sten , Holst Jens J , Rosenkilde Mette M , Hartmann Bolette 
Published: January 2024

Abstract

Context
Individuals with type 2 diabetes (T2D) have an increased risk of bone fractures despite normal or increased bone mineral density. The underlying causes are not well understood but may include disturbances in the gut-bone axis, in which both glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-2 (GLP-2) are regulators of bone turnover. Thus, in healthy fasting participants, both exogenous GIP and GLP-2 acutely reduce bone resorption.

Objective
The objective of this study was to investigate the acute effects of subcutaneously administered GIP and GLP-2 on bone turnover in individuals with T2D.

Methods
We included 10 men with T2D. Participants met fasting in the morning on 3 separate test days and were injected subcutaneously with GIP, GLP-2, or placebo in a randomized crossover design. Blood samples were drawn at baseline and regularly after injections. Bone turnover was estimated by circulating levels of collagen type 1 C-terminal telopeptide (CTX), procollagen type 1 N-terminal propeptide (P1NP), sclerostin, and PTH.

Results
GIP and GLP-2 significantly reduced CTX to (mean ± SEM) 66 ± 7.8% and 74 ± 5.9% of baseline, respectively, compared with after placebo (P = .001). In addition, P1NP and sclerostin increased acutely after GIP whereas a decrease in P1NP was seen after GLP-2. PTH levels decreased to 67 ± 2.5% of baseline after GLP-2 and to only 86 ± 3.4% after GIP.

Conclusion
Subcutaneous GIP and GLP-2 affect CTX and P1NP in individuals with T2D to the same extent as previously demonstrated in healthy individuals.
Expanding the evo-devo toolkit: generation of 3D mammary tissue from diverse mammals
Authors: Kim Hahyung Y. , Sinha Ishani , Sears Karen E. , Kuperwasser Charlotte , Rauner Gat 
Published: January 2024

ABSTRACT
The varying pathways of mammary gland development across species and evolutionary history are underexplored, largely due to a lack of model systems. Recent progress in organoid technology holds the promise of enabling in-depth studies of the developmental adaptations that have occurred throughout the evolution of different species, fostering beneficial phenotypes. The practical application of this technology for mammary glands has been mostly confined to rodents and humans. In the current study, we have successfully created next-generation 3D mammary gland organoids from eight eutherian mammals and the first branched organoid of a marsupial mammary gland. Using mammary organoids, we identified a role for ROCK protein in regulating branching morphogenesis, a role that manifests differently in organoids from different mammals. This finding demonstrates the utility of the 3D organoid model for understanding the evolution and adaptations of signaling pathways. These achievements highlight the potential for organoid models to expand our understanding of mammary gland biology and evolution, and their potential utility in studies of lactation or breast cancer.
Caracterização ambiental em condomínios e loteamentos na região oeste da cidade de São Carlos – SP
Authors: Oliveira Keithy Juliane de , Rios Leonardo , Ribeiro Maria Lúcia 
Published: January 2024

Um fenômeno cada vez mais presente em muitas cidades ao redor do mundo é a expansão urbana, sendo que os condomínios e os loteamentos são uma das principais formas de desenvolvimento urbano. Deste modo, esta pesquisa procurou esclarecer algumas indagações observadas na produção do espaço urbano pelos loteamentos e condomínios e sua rápida expansão na cidade de São Carlos-SP, em especial a região Oeste, buscando responder a seguinte questão: qual modelo ou padrão de condomínio ou de loteamento, localizado na região Oeste da cidade de São Carlos-SP, tem maior impacto na produção do espaço urbano à luz das questões ambientais? Sendo assim, este trabalho tem como objetivo caracterizar os impactos ambientais nas diversas modalidades e padrões de condomínios e loteamentos na zona oeste da cidade de São Carlos - SP. Foi utilizando o SIG ferramentas do geoprocessamento, QGIS 3.16, para digitalizar a topografia, hidrografia, contorno dos loteamentos e condomínios bem como, gerar as áreas de preservação permanentes e gerar o mapa de declividade. Os parâmetros de caracterização ambiental utilizados foram consumo de água, geração de efluente sanitário, áreas permeáveis e respeito as áreas de preservação permanentes. Os resultados demonstram que dos empreendimentos analisados, os de padrão popular foram os que apresentaram menor consumo de água e geração de efluentes sanitários e os de maior padrão socioeconômicos foram os que apresentaram os maiores consumos e geração. Todos os empreendimentos respeitaram as áreas de APPs e possuem áreas permeáveis. Apesar de não constar documentação dos Estudos de Impacto Ambiental em sua implantação, todos cumprem a legislação ambiental de acordo com as variáveis analisadas.
Carl Stumpf and the Curious Incident of Music in Wittgenstein’s
Tractatus
Authors: Guter Eran 
Published: January 2024

Abstract
This essay explores Wittgenstein’s encounter with Stumpf’s work in Tone Psychology during a rarely studied period in Wittgenstein’s early career when he worked as a researcher in Myers’s laboratory for experimental psychology in Cambridge. I argue that Stumpf’s emphasis on the notion of musicality as the ability to characterize what is ‘musical’ about music troubled Wittgenstein’s initial formulation of his career-long adherence to the comparison between language and music. In the Tractatus the importance of internal projective relations far exceeds that of arbitrariness in language. This results in the curious elision of musicality in the Tractatus, as shown in his gramophone analogy. The acknowledgment of the enormous complexity pertaining to the facts of human life remained underdeveloped in Wittgenstein’s philosophy until the anthropological turn in his middle-period. Only then do we see the blooming of the language-as-music simile and its eventual impact on Wittgenstein’s later philosophy.
Mechanical properties and microstructure of roller compacted concrete incorporating brick powder, glass powder, and steel slag
Authors: Yaseen Mohammed Hazim , Hashim Syed Fuad Saiyid , Dawood Eethar Thanon , Johari Megat Azmi Megat 
Published: January 2024

Abstract
The objective of this study is to explore the feasibility of developing environmentally friendly green roller-compacted concrete (RCC) by utilizing locally available materials. The research investigates the behavior of RCC properties when different amounts of solid waste materials (brick powder, glass powder, and steel slag) are added as substitutes for cement content. To accomplish this, four laboratory tests were conducted: compressive strength, flexural strength, X-ray diffraction analysis, and scanning electron microscope imaging. These tests aimed to identify the changes in concrete properties resulting from the inclusion of waste construction materials as cement replacements. The study employed an approach that involved adding waste materials to the concrete mixture, with replacement percentages ranging from 10.0 to 40.0% in increments of 10.0%. Consequently, 12 concrete mixtures were prepared to examine the effects of adding waste materials (10.0–40.0%) as substitutes for cement content. In addition, one reference mixture was designed without any inclusion of waste materials for comparison purposes. In general, the results indicate that as the percentage of waste construction materials increases in the mixtures, there is a corresponding decrease in compressive strength. However, it is noteworthy that the strength activity index (SAI) exceeded 75% according to ASTM C618 standards. This indicates that the waste construction materials possess pozzolanic properties, making them suitable for use as cement replacements in RCC mixtures.
Exploring plasmonic gradient metasurfaces for enhanced optical sensing in the visible spectrum
Authors: Huang Shih-Hsiu , Wu Pin Chieh 
Published: January 2024

Abstract
While conventional optical sensors hold historical significance, they face inherent limitations in sensitivity, operational intricacies, and bulky size. A breakthrough in this realm comes from the advent of metasurface sensors, which leverage nanoscale optical effects, thereby expanding the horizons of optical sensing applications. However, past methods employed in metasurface sensors predominantly rely on wavelength shifts or intensity changes with high-Q resonances, thereby significantly restricting the detection bandwidth. In response to these challenges, this study introduces a plasmonic gradient metasurface-based sensor (PGMS) designed for refractive index detection across a wide wavelength spectrum. Through the utilization of the Pancharatnam–Berry phase method, the PGMS achieves a distinctive 2π phase shift, facilitating the simultaneous generation of specular and deflected beams. The introduction of a far-field intensity ratio (I* = I
+1/I
0) amplifies the change in optical response by maximizing the deflected beam’s intensity while minimizing specular reflection. Experimental validation attests to the PGMS’s consistent performance across diverse media and wavelengths, successfully overcoming challenges associated with oxidation issues. Furthermore, the incorporation of a normalization factor enhances the PGMS’s sensing performance and versatility for broadband optical sensing, accommodating variations in the refractive index. Particularly sensitive in green wavelengths, the PGMS demonstrates its potential in visible spectrum applications, such as biomedical diagnostics and environmental monitoring. This research not only addresses challenges posed by conventional sensors but also propels optical sensing technologies into a realm of heightened sensitivity and adaptability.
Developing the Framework for a Green Constitution: Strengthening Environmental Protection Initiatives in Indonesia
Authors: Hakim Rianta Muhammad , Imron Pradnya Kayla Ali 
Published: January 2024

The current global environmental crisis occurs due to various factors, such as failed policies, destructive technologies, and lack of political commitment. To address these issues, the green constitution approach has emerged as an effective solution. However, Indonesia has not fully implemented the concept of a green constitution. This research uses a normative legal research method with comparative, conceptual, and statutory approaches. Data is obtained from a literature study of national and international regulations, books, articles, and scientific journals. Through a comparative study with Ecuador and France, the results show that Indonesia has the potential to integrate environmental principles that have been integrated into the constitutions of these countries. Ecuador, often referred to as "The Real Green Constitution," explicitly recognizes the rights of nature and regulates preventive measures against environmental damage. In France, the Environmental Charter has been integrated into the constitution, affirming the need for wise management of the environment and a balance between protection and utilization of natural resources. Indonesia can learn from these two countries in applying the concept of a green constitution and integrating environmental principles into its constitution in order to strengthen environmental protection, promote sustainable development, and help address the impacts of climate change. The resulting recommendation is an amendment to the constitution to further incorporate environmental principles as part of the main elements in the constitution.