bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complexity And Ergodicity In Chaos Game Representation Of Genomic Sequences
Authors: Mehrpooya Adel , Tavassoly Iman 
Published: December 2023

AbstractThe Chaos Game Representation (CGR) serves as a powerful graphical tool for transforming long one-dimensional sequences, such as genomic sequences, into visually insightful and complex graphical patterns. This algorithmic approach has revealed captivating fractal properties, providing a systems-level perspective on the underlying patterns inherent in specific genomic sequences. Each CGR image generated is distinctive and unique, capturing the individuality of different genomic sequences. We have investigated the nature of the fractal patterns discerned within CGR of genomic sequences, aiming to assess the ergodicity and identify potential ergodic patterns. Our findings present a mathematical proof establishing that CGRs are non-ergodic. This finding suggests that the distribution properties of nucleotide sequences play a pivotal role in shaping the emergent patterns within the CGR images.
Hypoxia impacts small intestinal organoid stemness and differentiation
Authors: Lan Xi , Qiu Ping , Mou Chunfeng 
Published: December 2023

SummaryComprised of several cell types functioning differently, the small intestinal epithelial cells perform their functions and synergistically maintain homeostasis in the first part of the mammalian intestine. Due to the uneven distribution of the vessel, the oxygen level exhibits a gradient decreasing pattern in the normal intestine and becomes aberrant in some intestinal diseases. In this work, we find certain levels of hypoxia simulated by cobaltous chloride (CoCl2) caused an increase in the secretive cell types and a decrease in the absorptive cell typesin vitrocultured mouse small intestinal organoids. Importantly, the intestinal stem cell amount is impacted which leads to attenuated epithelial regeneration. Our study highlights the cell-type-specific alterations under the hypoxia insult, which gives possible therapeutic hints for hypoxia-relevant gastrointestinal diseases.
Threshold of somatic mosaicism disrupting the brain function
Authors: Kim Jintae , Park Sang Min , Koh Hyun Yong , Ko Ara , Kang Hoon-Chul , Chang Won Seok , Kim Dong Seok , Lee Jeong Ho 
Published: December 2023

AbstractSomatic mosaicism in a fraction of brain cells causes neurodevelopmental disorders, including childhood intractable epilepsy. However, the threshold for somatic mosaicism leading to brain dysfunction is unknown. In this study, we induced various mosaic burdens in mice of focal cortical dysplasia type II (FCD II), featuring mTOR somatic mosaicism and spontaneous behavioral seizures. Mosaic burdens ranged from approximately 1,000 to 40,000 neurons expressing the mTOR mutant in the somatosensory (SSC) or medial prefrontal (PFC) cortex. Surprisingly, just ∼8,000-9,000 neurons expressing the MTOR mutant were sufficient to trigger epileptic seizures. Mutational burden correlated with seizure frequency and onset, with a higher tendency for electrographic inter-ictal spikes and beta- and gamma-frequency oscillations in FCD II mice exceeding the threshold. Moreover, mutation-negative FCD II patients in deep sequencing of their bulky brain tissues revealed somatic mosaicism of mTOR pathway genes as low as 0.07% in resected brain tissues through ultra-deep targeted sequencing (up to 20 million reads). Thus, our study suggests that extremely low levels of somatic mosaicism can contribute to brain dysfunction.
Gliogenesis from the subventricular zone modulates the extracellular matrix at the glial scar after brain ischemia
Authors: Ardaya Maria , Tiveron Marie-Catherine , Cremer Harold , Dehay Benjamin , Pérez-Cerdá Fernando , Matute Carlos , Soria Federico N. , Cavaliere Fabio 
Published: December 2023

ABSTRACTActivation of the subventricular zone (SVZ) following cerebral ischemia is one of the brain’s early responses to counteract neuron loss and minimize tissue damage. Impaired brain regions communicate with the SVZ through various chemotactic signals that promote cell migration and differentiation, primarily involving neural stem cells (NSC), neuroblasts, or glioblasts. However, the activation of gliogenesis and the role of newly formed astrocytes in the post-ischemic scenario remain subjects of debate. We have previously demonstrated that adenosine release after brain ischemia prompts the SVZ to generate new astrocytes. Here, we used transient brain ischemia in mice to identify the cellular origin of these astrocytes within the SVZ neurogenic niche and to investigate their role in the pathological process. By combining immunofluorescence, BrdU-tracing, and genetic cell labeling, we tracked the migration of newborn astrocytes, positive for the proteoglycan marker Thbs4, from the dorsal and medial SVZ to the perilesional barrier surrounding the ischemic core, known as the “glial scar”. We found that these Thbs4-positive astrocytes modulate the dense extracellular matrix at the lesion border by both synthesizing and degrading hyaluronan. We also show that while the accumulation of hyaluronan at the lesion site is sufficient to recruit newborn astrocytes, its degradation at the SVZ correlates with gliogenesis. These findings suggest that newborn astrocytes could be a promising pharmacological target for modulating the glial scar after brain ischemia and facilitate tissue regeneration.
Plant breeding simulations with AlphaSimR
Authors: Bančič Jon , Greenspoon Philip , Gaynor Chris R. , Gorjanc Gregor 
Published: December 2023

AbstractPlant breeding plays a crucial role in the development of high-performing crop varieties that meet the demands of society. Emerging breeding techniques offer the potential to improve the precision and efficiency of plant breeding programs; however, their optimal implementation requires refinement of existing breeding programs or the design of new ones. Stochastic simulations are a cost-effective solution for testing and optimizing new breeding strategies. The aim of this paper is to provide an introduction to stochastic simulation with software AlphaSimR for plant breeding students, researchers, and experienced breeders. We present an overview of how to use the software and provide an introductory AlphaSimR vignette as well as complete AlphaSimR scripts of breeding programs for self-pollinated, clonal, and cross-pollinated plants, including relevant breeding techniques, such as backcrossing, speed breeding, genomic selection, index selection, and others. Our objective is to provide a foundation for understanding and utilizing simulation software, enabling readers to adapt the provided scripts for their own use or even develop completely new plant breeding programs. By incorporating simulation software into plant breeding education and practice, the next generation of plant breeders will have a valuable tool in their quest to provide sustainable and nutritious food sources for a growing population.
Exposure and resistance to lantibiotics impact microbiota composition and function
Authors: Zhang Zhenrun J. , Cole Cody , Lin Huaiying , Wu Chunyu , Haro Fidel , McSpadden Emma , van der Donk Wilfred A , Pamer Eric G. 
Published: December 2023

AbstractThe intestinal microbiota is composed of hundreds of distinct microbial species that interact with each other and their mammalian host. Antibiotic exposure dramatically impacts microbiota compositions and leads to acquisition of antibiotic-resistance genes. Lantibiotics are ribosomally synthesized and post-translationally modified peptides produced by some bacterial strains to inhibit the growth of competing bacteria. Nisin A is a lantibiotic produced byLactococcus lactisthat is commonly added to food products to reduce contamination with Gram-positive pathogens. Little is known, however, about lantibiotic-resistance of commensal bacteria inhabiting the human intestine. Herein, we demonstrate that Nisin A administration to mice alters fecal microbiome compositions and the concentration of taurine-conjugated primary bile acids. Lantibiotic Resistance System genes (LRS) are encoded by lantibiotic-producing bacterial strains but, we show, are also prevalent in microbiomes across human cohorts spanning vastly different lifestyles and 5 continents. Bacterial strains encoding LRS have enhancedin vivofitness upon dietary exposure to Nisin A but reduced fitness in the absence of lantibiotic pressure. Differential binding of host derived, secreted IgA contributes to fitness discordance between bacterial strains encoding or lacking LRS. Although LRS are associated with mobile genetic elements, sequence comparisons of LRS encoded by distinct bacterial species suggest they have been long-term components of their respective genomes. Our study reveals the prevalence, abundance and physiologic significance of an underappreciated subset of antimicrobial resistance genes encoded by commensal bacterial species constituting the human gut microbiome, and provides insights that will guide development of microbiome augmenting strategies.
Ex ante required rates of return and related factors in Indonesian PPP infrastructure projects
Authors: Wibowo Andreas 
Published: December 2023

PurposeThis paper delves into the ex ante rates of return demanded by the private sector in Indonesian public–private partnership (PPP) infrastructure projects and the manifold factors emanating from project attributes that can influence these rates.Design/methodology/approachThis paper analyzes feasibility studies of 37 PPP projects across different sectors. The studies were carefully selected based on relevance, completeness and validity of data. The analysis uses statistical techniques, including Levene’s tests, t-tests, ANOVA tests, Cohen’s effect size and Pearson correlations, to explore differences in cost of capital and excess returns across various attributes.FindingsBased on the statistical analysis, no significant difference exists between the excess return of 200 basis points (bps) and the equity excess return of 0 bps. This suggests that the eligibility criteria for PPP projects require an internal rate of return (IRR) equal to the weighted average cost of capital plus 200 bps or an equity IRR equal to the cost of equity. The variations in the tested variables among diverse project attributes do not exhibit statistically significant disparities, even though specific attributes display moderate to high effect sizes.Originality/valueThis paper represents one of the first attempts to examine the rates of return demanded by the private sector in the context of Indonesian PPP projects. It comprehensively explores the factors that influence these rates, drawing on insights derived from feasibility studies.
Critical Success Factors for Affordable Housing Projects in Nigeria
Authors: Musa Mohammed Mukhtar , Nafiu Zadawa Abdullahi , Abubakar Muhammad Jamil , Adamu Dandajeh Mukhtar , Sani Shehu Auwalu 
Published: December 2023

Housing plays an important role in socio-economic development of any country. However, access to affordable housing is a challenge to many people in developing countries. The purpose of this study is to establish critical success factors for affordable private sector housing projects in Nigeria. Twenty-six (26) success attributes for affordable housing were identified from literature. A survey questionnaire was designed, and pre-tested, subsequently main survey was performed in which two hundred and eighty (280) questionnaires were administered to experienced researchers, senior managers in public housing agencies, developers and consultants with knowledge and experience in affordable housing. One hundred and seventy-six (176) completed questionnaires were returned completed representing 62.86% response rate. The data collected were analyzed using mean score, factor analysis and stepwise multiple regression analysis. The findings from this study produce four critical success factors for affordable housing projects namely, effective land policies for affordable housing, availability of effective financial institutions, good governance of housing systems, and political will. The results suggested that a well-functioning housing sector must satisfy these factors. It has been concluded that, government has an important role to play in the supply of affordable housing in Nigeria. Thus, government should be committed to supporting affordable housing development through the provision of policy solution and implementation. The study can assist policy makers to understand important factors that influence the success of affordable housing development, and thus include them in the formulation of housing policies in their countries.
Speciation by physiological selection of environmentally acquired traits
Authors: Noble Denis , Phillips Daniel 
Published: December 2023

AbstractA chance mutation affecting a single or extremely few individuals in a continuous population will be quickly diluted through interbreeding. Charles Darwin fully appreciated this difficulty with relying on natural selection alone, and suggested an enabling role for geographical isolation in the origin of species. However, Darwin also believed in evolution by the inheritance of acquired traits and in populations of interbreeding animals, both of which would need a different isolating mechanism to overcome dilution and play a role in animal evolution. Historically disputed, the inheritance of acquired characters is now increasingly accepted as a phenomenon, and Charles Darwin himself is acknowledged as closely pre‐empting the type of physiology necessary to mediate it in his hypothesis of ‘pangenesis’. In this article, we question how the inheritance of acquired traits might overcome the problem of dilution by interbreeding and contribute to evolution. Specifically, we describe how Darwin's young protégé, George Romanes, developed ideas he discussed with Darwin and extended pangenesis to include a conceivable solution published after Darwin's death: physiological selection of fertility. In light of the ‘rediscovery’ of pangenesis, here we recount physiological selection as a testable hypothesis to explain how environmentally acquired characteristics could become coupled to the generation of species.image
Principles of Ritual Prayer: An 18th Century Catechism in Bahdini Kurdish
Authors: Öpengin Ergin 
Published: December 2023

Abstract
This article presents an edition and linguistic analysis of a verse catechism in the Bahdini dialect of Kurdish. The manuscript of the text is dated to late 18th century and is held among the Oriental manuscripts collections of the Berlin State Library. The text is a didactic verse on the principles and rules of the Islamic ritual prayer (ṣalāt), belonging thus to the catechism or in its Turkish-Arabic term ʿilm -i ḥāl genre. It is the oldest example of the catechism genre, different from creeds, in Kurdish literature that started in the late 16th century. The text is edited here within the context of religious treatises in Kurdish and analysed for its historical-linguistic and dialectological aspects that illustrate Early Modern Kurdish.
“Denomination Doesn’t Matter”? A Proposal for a Receptive Ecumenical Missiology from a Theological Action Research Project on Methodists and Catholics Engaging Together in Social Action
Authors: Butler James 
Published: December 2023

Abstract
In ecumenical social action and mission it is common to hear phrases like, ‘denomination doesn’t matter’, and ‘we are all just Christians’. This reflects a wider tension with modern ecumenism between doctrinal and practice-based approaches to ecumenism. In this theological action research project on Methodists and Catholics engaging together in social action many espoused this pragmatic approach to action over ecclesial tradition. However, in practice they engaged with the complexities of ecumenical life and ecclesial tradition, many in significant ways. Drawing on the themes of receptivity, identity and practical wisdom seen in their practice and their understanding of ecumenism as something which is ‘lived’ rather than ‘done’, I offer a receptive ecumenical missiology. This ecumenical missiology, based in a pneumatological receptivity, offers an integrated way forward, overcoming many of the tensions between practice, mission and doctrine felt within modern ecumenism.
Effects of electroacupuncture on intestinal microflora and plasma metabolites in an insulin-resistant mouse model of type 2 diabetes mellitus
Authors: Cao Linhui , Zhou Sheng , Li Jianjun , Chen Kefang , Xue Xiaojin , Yi Wei 
Published: December 2023

Objective: To investigate the effects of electroacupuncture (EA) at ST36 on intestinal microflora and plasma metabolites in a mouse model of type 2 diabetes mellitus (T2DM), to provide a theoretical basis and guidance for the clinical treatment of T2DM by traditional Chinese medicine (TCM). Methods: Sixteen T2DM db/db mice were randomly divided into treatment (T, n = 8) and model (M, n = 8) groups, and a further eight normal db/m+ mice reared under the same conditions served as a non-diabetic control group (C, n = 8). The general conditions of mice were observed weekly. After obtaining blood and stool samples, the mice were euthanized. Fasting blood glucose (FBG) was measured using a glucometer and fasting insulin (FINS) was measured in plasma by enzyme-linked immunosorbent assay (ELISA). Liver and colon tissues were embedded in paraffin and subjected to hematoxylin–eosin (HE) staining to observe pathological changes in these tissues. In addition, 16S ribosomal RNA (rRNA) sequencing was performed to analyze changes in the intestinal flora and metabolomics was employed to assess changes in metabolites in the blood. Results: EA significantly reduced FBG and FINS levels and alleviated pathological damage to the liver and colon. Furthermore, EA increased intestinal community richness and diversity by decreasing the relative abundance of Clostridium and incresasing the relative abundance of Lactobacillus. EA also reduced D-fructose levels in T2DM mice according to plasma metabolomics. Conclusion: EA has a positive regulatory effect on the intestinal flora and can regulate blood glucose and improve insulin resistance in T2DM model mice.
One size fits all? The role of task complexity in L2 production via the audio chat
Authors: Qian Li , Shamsudin Sarimah 
Published: December 2023

AbstractThe pervasive use of information and computer technology in second or foreign language learning has led researchers to explore the ideal tasks for technological environments to facilitate second language (L2) learning. This study intended to contribute new knowledge to this area by examining the effects of the task complexity manipulated along the variable +-few elements in Robinson’s Cognition Hypothesis on L2 production of 42 lower intermediate Chinese EFL (English as a Foreign Language) learners who completed two interactive tasks (simple versus complex) in dyads via audio chat of the video-conferencing platform WeMeet in a laboratory setting. Participants were also instructed to measure the difficulty of the tasks by responding to a self-rating questionnaire immediately after they completed each task. Their L2 output in the two tasks were recorded, transcribed and coded in three dimensions namely, syntactic complexity, lexical complexity and accuracy. SPSS 26 was used for statistical analyses. The results revealed that increasing task complexity induced significantly more lexically complex language. However, it did not result in significant changes in terms of syntactic complexity or accuracy of learners’ L2 output via audio chat. These results contradicted the predictions of the Cognition Hypothesis, suggesting the inapplicability of Cognition Hypothesis in audio chat.
Historia stall zachodnich w kościele Wniebowzięcia Najświętszej Marii Panny w Toruniu w świetle ostatnich prac badawczych i konserwatorskich
Authors: Raczkowski Juliusz 
Published: December 2023

Autor dokonuje próby wstępnego rozwarstwienia zespołu stall chórowych w kościele pofranciszkańskim WNMP w Toruniu, korzystając z metod analizy strukturalnej wspartej badaniami nieniszczącymi (NIR) i dendrochronologią. Wywód jest skoncentrowany na jednym ich fragmencie – siedziskach, przeniesionych prawdopodobnie w XVII wieku z prezbiterium do ostatniego przęsła nawy głównej, w strefę portalu zachodniego. Meble te (dawniej zapewne jeden element należący do kompletu stall w chórze) zostały tu rozbudowane o przedpiersia i przystosowane technicznie do wymogów nowego miejsca, a także wizualnie zharmonizowane z wzniesioną w tym czasie emporą zachodnią. W okresie bernardyńskim ich estetykę dopasowano znów do zmian w obrębie empory (zostały ozdobione – dziś już niewidocznym – ornamentem rocaille’owym). Na nowym miejscu stalle zyskały „nowe życie” i rejestrują przemiany konfesyjnie i funkcjonalne kościoła. Osobną uwagę autor poświęca dwóm wątkom ideowym: treściom ikonograficznym gotyckiego policzka z scenami z bajek Ezopa i historii lisa Reynarta, które zostały odsłonięte po niemal stu latach w 2021 roku, oraz – uczytelnionym dzięki podczerwieni – bernardyńskim sentencjom medytacyjnym na przedpiersiach, później zamalowanym. Odkrycia te były możliwe dzięki badaniom w projekcie „Inwentarz sztuki Torunia” i sondażowej konserwacji-restauracji policzka i przedpiersi północnych w 2022 roku. Prace konserwatorskie przy stallach zachodnich są kontynuowane, a niniejszy tekst jest propozycją rekonstrukcji historii tego zabytku, która być może zostanie w przyszłości uzupełniona lub odmiennie zinterpretowana.
Effects of Drying Techniques and Different Solvents on Phytochemical Composition and Antioxidant Activity of Carica papaya Seed Extracts: Implications for Industrial Use and Medicinal Benefits
Authors: Olatunya Ayomadewa Mercy 
Published: December 2023

Plant has always been of immense health benefits to humanity because, plant contains different parts that have been found to have various medicinal and industrial values. Therefore, plants play a crucial role in obtaining their most effective extracts for medical and industrial applications. The primary components of these preparations involve the extraction and drying methods. Carica papaya is a plant that is known to have different parts with numerous and unexplored medicinal and industrial benefits. Thus, this study investigated the effects of drying techniques and different extracting solvents on the phytochemical composition and antioxidant activity of Carica papaya seeds extract using standard analytical procedures. The results showed that drying technique has significant effect (p < 0.05) on the phytochemical composition of the C. papaya seeds with air-drying at room temperature having the highest amount of total phenolic compounds, flavonoids, saponin content and antioxidant activity when compared to other techniques. Hexane extracted the highest amount of total phenolic compounds (121.08 mg/GAE/100 g). Diethyl ether extracted the highest amount of total flavonoid and saponin content while polar solvents (aqueous and ethanol) extracts have the highest amount of antioxidant activity. This study showed that air drying at room temperature is a good method of preservation of the phytochemicals present in medicinal plants and that stereochemistry and structural diversity of compounds determine the efficiency of their extraction in any solvent. Furthermore, the highlighted phytochemicals and antioxidant activity of C. papaya seed extracts could be of immense benefits in various industries and for medicinal purposes.