bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mouse IgA modulates human gut microbiota with inflammatory bowel disease patients
Authors: Takahashi Keishu , Morita Naoki , Tamano Ryutaro , Gao Peng , Iida Noriho , Andoh Akira , Imaeda Hirotsugu , Kurokawa Ken , Tsuboi Mayo , Hayakawa Yoku , Fujishiro Mitsuhiro , Shinkura Reiko 
Published: June 2024

Abstract
Background
The imbalance of commensal bacteria is called dysbiosis in intestinal microflora. Secreted IgA in the intestinal lumen plays an important role in the regulation of microbiota. Although dysbiosis of gut bacteria is reported in IBD patients, it remains unclear what makes dysbiosis of their microflora. The intervention method for remedy of dysbiosis in IBD patients is not well established. In this study, we focused on the quality of human endogenous IgA and investigated whether mouse monoclonal IgA which binds to selectively colitogenic bacteria can modulate human gut microbiota with IBD patients.

Methods
IgA-bound and -unbound bacteria were sorted by MACS and cell sorter. Sorted bacteria were analyzed by 16S rRNA sequencing to investigate what kinds of bacteria endogenous IgA or mouse IgA recognized in human gut microbiota. To evaluate the effect of mouse IgA, gnotobiotic mice with IBD patient microbiota were orally administrated with mouse IgA and analyzed gut microbiota.

Results
We show that human endogenous IgA has abnormal binding activity to gut bacteria in IBD patients. Mouse IgA can bind to human microbiota and bind to selectively colitogenic bacteria. The rW27, especially, has a growth inhibitory activity to human colitogenic bacteria. Furthermore, oral administration of mouse IgA reduced an inflammation biomarker, fecal lipocalin 2, in mice colonized with IBD patient-derived microbiota, and improved dysbiosis of IBD patient sample.

Conclusion
Oral treatment of mouse IgA can treat gut dysbiosis in IBD patients by modulating gut microbiota.
Can instability variations warn developers when open-source projects boost?
Authors: Capilla Rafael , Salamanca Victor , Valdezate Alejandro , Robles Gregorio 
Published: June 2024

AbstractAlthough architecture instability has been studied and measured using a variety of metrics, a deeper analysis of which project parts are less stable and how such instability varies over time is still needed. While having more information on architecture instability is, in general, useful for any software development project, it is especially important in Open Source Software (OSS) projects where the supervision of the development process is more difficult to achieve. In particular, we are interested when OSS projects grow from a small controlled environment (i.e., the cathedral phase) to a community-driven project (i.e., the bazaar phase). In such a transition, the project often explodes in terms of software size and number of contributing developers. Hence, the complexity of the newly added features, and the frequency of the commits and files modified may cause significant variations of the instability of the structure of the classes and packages. Consequently, in this article we analyze the instability in OSS projects, especially during that sensitive phase where they become community-driven. Our results show that instability metrics can be easily obtained in such type of transitions. We also observed from our case studies that instability metrics can help finding out the balance between adding new functionality and performing refactoring. As a conclusions we state that instability metrics offer relevant information in the transition phase from the cathedral to the bazaar.
The NPGS Sudanese sorghum core collection encloses novel grain mold resistant germplasm
Authors: Cuevas Hugo E. , Prom Louis K. 
Published: June 2024

Abstract
Grain mold is one of the most devasting diseases in sorghum [Sorghum bicolor L. (Moench)] that affects the endosperm and deteriorates the pericarp tissue, reducing the quality of the grain. Today, sorghum breeding programs have a limited number of sources of resistance for the development of resistant cultivars. Therefore, the USDA-Agriculture Research Service, National Plant Germplasm System Sudan core collection was assessed to identify new sources of grain mold resistance based on seed emergence and deterioration. A total of 246 accessions were evaluated for two years and a subset of 46 accessions with grain mold resistance were subsequently evaluated for two additional years together with 11 breeding resistant lines from the sorghum association panel. The analysis identified 39 grain mold resistance accessions including seven that showed both high seedling emergence (> 82%) and low seed deterioration (< 2.15). Phylogenetic analysis revealed that five accessions (PI 570382, PI 570776, PI 570330, PI 570702, and PI 570348) that clustered distantly from reference sets and showed both high seedling emergence and low seed deterioration can be classified as new resistance sources. Genome-wide association analysis using 147,069 SNPs identified two genomic regions in chromosome 2 and 3 associated with seedling emergence rate and seed deterioration, respectively. The analysis of both genomic regions found two genes of interest associated with phenylpropanoid metabolic process and phosphorylase kinase. These Sudanese grain mold resistance accessions provide new genetically diverse germplasm for breeding programs and insights in the defense resistance responses.
Genetic diversity analysis and DNA fingerprinting of primary Qingke (Hordeum vulgare L. var. nudum Hook. f.) cultivars
Authors: Hu Qian , Yao Youhua , Cui Yongmei , Li Xin , An Likun , Bai Yixiong , Ding Baojun , Yao Xiaohua , Wu Kunlun 
Published: June 2024

Abstract
To assess the genetic diversity of the primary Qingke cultivars and establish their unique genetic profiles, 837 barley simple sequence repeat (SSR) primers were screened across 12 cultivars. The selection process involved the utilization of polyacrylamide gel electrophoresis and capillary electrophoresis technology, to identify primers exhibiting desirable characteristics, such as polymorphism, stability, and reproducibility. Subsequently, we analyzed the genetic diversity of the primary Qingke cultivars to for DNA fingerprints. A total of 18 pairs of SSR markers were selected as the optimal markers for constructing fingerprints of major Qingke cultivars. These included 83 observed alleles (Na), ranging from there to 11, with an average of 4.61 per pair. Notably, Bmag0496 and Scssr04163 exhibited higher allelic diversity, with 11 and 8 loci, respectively. The polymorphism information content (PIC) ranged from 0.36 to 0.74, with an average of 0.52. The expected heterozygosity (He) ranged from 0.4031 to 0.7682, with an average of 0.59, and the observed heterozygosity (Ho) varied between 0.13 and 0.67, with an average of 0.32. The outcomes obtained through phylogenetic tree analysis, population structure assessment and principal component analysis demonstrated that the primary Qingke cultivars could be classified into three distinct groups: group I primarily originated from Xizang and Qinghai provinces; group II mainly consisted of cultivars from Yunnan and Heilongjiang provinces; and group III predominantly comprised cultivars originating from Qinghai and Gansu provinces. Interestingly, the Sichuan cultivars were distributed across all three groups without any clear tendency toward a specific cluster or subgroup. These findings indicated that the genetic distance among Qingke cultivars was significantly correlated with geographic location but not exclusively determined by it. The construction of DNA fingerprints for the primary Qingke cultivars used these identified sets of SSR primers (18 pairs) laid a solid foundation for cultivar identification, conservation and utilization efforts related to this crop.
Residual profit splitting: a theory-based approach to tax multinationals
Authors: Richter Wolfram F. 
Published: June 2024

AbstractAbout 140 countries have agreed to reallocate the rights to tax international corporate profits and to introduce minimum tax rates. The agreed plan is the product of pragmatism and a search for consensus, but ambitious. It requires far-reaching system changes such as a move towards unitary profit taxation, better known as formula apportionment. The formulary apportionment of profit earned by a multinational enterprise (MNE) assumes international agreement on common rules for the determination of taxable profit. This is a critical departure from the well-established tradition of separate entity accounting (SEA) and may still turn out to be a serious design flaw of the reform. This paper argues for a reform that retains SEA and addresses the flaws in the current system of corporate taxation at their root rather than merely fixing symptoms. To this end, a reform aimed specifically at the rules governing the taxation of intangible assets is recommended. The proposed system can be interpreted as a theory-based generalization of the withholding tax solution of Article 12B of the UN Model Tax Convention to cases where an MNE maintains a physical presence in the source country or intra-group supplies of goods and services entail allocable costs.
Objective Linguistic Markers Associated with Callous-Unemotional Traits in Early Childhood
Authors: Waller R. , Flum M. , Paz Y. , Perkins E. R. , Rodriguez Y. , Knox A. , Pelella M.R. , Jones C. , Sun S. , Denham S.A. , Herrington J. , Parish-Morris J. 
Published: June 2024

AbstractBackground. Callous-unemotional (CU) traits are associated with interpersonal difficulties and risk for severe conduct problems (CP). The ability to communicate thoughts and feelings is critical to social success, with language a promising treatment target. However, no prior studies have examined objective linguistic correlates of childhood CU traits in early childhood, which could give insight into underlying risk mechanisms and novel target treatments. Methods. We computed lexical (positive emotion, sad, and anger words) and conversational (interruptions and speech rate) markers produced by 131 children aged 5–6 years (M = 5.98; SD = 0.54, 58.8% female) and their parents while narrating wordless storybooks during two online visits separated by 6–8 weeks (M = 6.56, SD = 1.11; two books, order counterbalanced). Audio recordings were diarized, time-aligned, and orthographically transcribed using WebTrans. Conversational markers were calculated using R and word frequencies were calculated using Linguistic Inquiry and Word Count (LIWC) software. We examined links between child CU traits and linguistic markers, and explored whether relationships were moderated by child sex. Results. Higher CU traits were associated with fewer positive emotion words produced by parents and children. Higher CU traits were also associated with greater concordance in the degree of interruptions and expression of anger emotion words by parents and children. Conclusions. Results suggest that objective linguistic correlates of CU traits are detectable during early childhood, which could inform adjunctive treatment modules that improve outcomes by precisely tracking and targeting subtle communication patterns.
ASYMPTOTIC NORMALITY OF THE COEFFICIENTS OF THE MORGAN-VOYCE POLYNOMIALS
Authors: Benoumhani Moussa , Heim Bernhard , Neuhauser Markus 
Published: June 2024

AbstractWe study arithmetic and asymptotic properties of polynomials provided by $$Q_n(x):= x \sum _{k=1}^n k \, Q_{n-k}(x)$$

Q
n

(
x
)

:
=
x

∑

k
=
1

n

k

Q

n
-
k

(
x
)

with initial value $$Q_0(x)=1$$

Q
0

(
x
)

=
1

. The coefficients satisfy a central limit theorem and a local limit theorem involving Fibonacci numbers. We apply the methods of Berry and Esseen, Harper, Bender, and Canfield.
Effects of a human amniotic membrane extract on ARPE-19 cells
Authors: Lulli Matteo , Tartaro Ruggero , Papucci Laura , Magnelli Lucia , Kaur Indu Pal , Caporossi Tomaso , Rizzo Stanislao , Mannini Antonella , Giansanti Fabrizio , Schiavone Nicola 
Published: June 2024

Abstract

Background
Human Amniotic Membrane (hAM) is endowed with several biological activities and might be considered an optimal tool in surgical treatment for different ophthalmic pathologies. We pioneered the surgical use of hAM to treat retinal pathologies such as macular holes, tears, and retinal detachments, and to overcome photoreceptor damage in age-related macular degeneration. Although hAM contributed to improved outcomes, the mechanisms of its effects are not yet fully understood. The characterization and explanation of the effects of hAM would allow the adoption of this new natural product in different retinal pathologies, operative contexts, and hAM formulations. At this end, we studied the properties of a hAM extract (hAME) on the ARPE-19 cells.

Methods and results
A non-denaturing sonication-based technique was developed to obtain a suitable hAME. Viability, proliferation, apoptosis, oxidative stress, and epithelial-mesenchymal transition (EMT) were studied in hAME-treated ARPE-19 cells. The hAME was able to increase ARPE-19 cell viability even in the presence of oxidative stress (H2O2, TBHP). Moreover, hAME prevented the expression of EMT features, such as EMT-related proteins, fibrotic foci formation, and migration induced by different cytokines.

Conclusions
Our results demonstrate that the hAME retains most of the properties observed in the whole tissue by others. The hAME, other than providing a manageable research tool, could represent a cost-effective and abundant drug to treat retinal pathologies in the future.
Unmasking early colorectal cancer clues: in silico and in vitro investigation of downregulated IGF2, SOCS1, MLH1, and CACNA1G in SSA polyps
Authors: Mirbahari Seyedeh Nasim , Fatemi Nayeralsadat , Savabkar Sanaz , Chaleshi Vahid , Zali Neda , Taleghani Mohammad Yaghoob , Mirzaei Ebrahim , Rejali Leili , Moghadam Pardis Ketabi , Mojarad Ehsan Nazemalhosseini 
Published: June 2024

Abstract

Background and aim
Colorectal cancer (CRC) originates from pre-existing polyps in the colon. The development of different subtypes of CRC is influenced by various genetic and epigenetic characteristics. CpG island methylator phenotype (CIMP) is found in about 15–20% of sporadic CRCs and is associated with hypermethylation of certain gene promoters. This study aims to find prognostic genes and compare their expression and methylation status as potential biomarkers in patients with serrated sessile adenomas/polyps (SSAP) and CRC, in order to evaluate which, one is a better predictor of disease.

Method
This study employed a multi-phase approach to investigate genes associated with CRC and SSAP. Initially, two gene expression datasets were analyzed using R and Limma package to identify differentially expressed genes (DEGs). Venn diagram analysis further refined the selection, revealing four genes from the Weissenberg panel with significant changes. These genes, underwent thorough in silico evaluations. Once confirmed, they proceeded to wet lab experimentation, focusing on expression and methylation status. This comprehensive methodology ensured a robust examination of the genes involved in CRC and SSAP.

Result
This study identified cancer-specific genes, with 8,351 and 1,769 genes specifically down-regulated in SSAP and CRC tissues, respectively. The down-regulated genes were associated with cell adhesion, negative regulation of cell proliferation, and drug response. Four highly downregulated genes in the Weissenberg panel, including CACNA1G, IGF2, MLH1, and SOCS1. In vitro analysis showed that they are hypermethylated in both SSAP and CRC samples while their expressions decreased only in CRC samples.

Conclusion
This suggests that the decrease in gene expression could help determine whether a polyp will become cancerous. Using both methylation status and gene expression status of genes in the Weissenberg panel in prognostic tests may lead to better prognoses for patients.
A cytosol-tethered YHB variant of phytochrome B retains photomorphogenic signaling activity
Authors: Hu Wei , Lagarias J. Clark 
Published: June 2024

AbstractThe red and far-red light photoreceptor phytochrome B (phyB) transmits light signals following cytosol-to-nuclear translocation to regulate transcriptional networks therein. This necessitates changes in protein–protein interactions of phyB in the cytosol, about which little is presently known. Via introduction of a nucleus-excluding G767R mutation into the dominant, constitutively active phyBY276H (YHB) allele, we explore the functional consequences of expressing a cytosol-localized YHBG767R variant in transgenic Arabidopsis seedlings. We show that YHBG767R elicits selective constitutive photomorphogenic phenotypes in dark-grown phyABCDE null mutants, wild type and other phy-deficient genotypes. These responses include light-independent apical hook opening, cotyledon unfolding, seed germination and agravitropic hypocotyl growth with minimal suppression of hypocotyl elongation. Such phenotypes correlate with reduced PIF3 levels, which implicates cytosolic targeting of PIF3 turnover or PIF3 translational inhibition by YHBG767R. However, as expected for a cytoplasm-tethered phyB, YHBG767R elicits reduced light-mediated signaling activity compared with similarly expressed wild-type phyB in phyABCDE mutant backgrounds. YHBG767R also interferes with wild-type phyB light signaling, presumably by formation of cytosol-retained and/or otherwise inactivated heterodimers. Our results suggest that cytosolic interactions with PIFs play an important role in phyB signaling even under physiological conditions.
A review on the work of German urban biodiversity networks – from national to international activities
Authors: Müller Norbert , Werner Peter 
Published: June 2024

AbstractThis review analyses the development of three urban biodiversity networks in Germany since 1970. The first network “Biotope Mapping in Populated Areas” (BMPA) was founded by Herbert Sukopp (Berlin) and the Federal Agency for Nature Conservation in connection with the development of the first comprehensive urban ecology studies in Berlin. The aim was to establish standardized methods for the investigation of urban biodiversity, obtain comparable results on the national level, and exchange information for sustainable development and management in urban areas. From 1979 to 2005 this network held 21 meetings in different German cities and one meeting in Vienna. In 2005, the network merged with the “Competence Network Urban Ecology” (CONTUREC) aiming to link local research and activities both on urban biodiversity and urban ecology. From 2006 to 2011 CONTUREC organized several national conferences, published their results in its own book series, and sent out a newsletter with information to local projects and current international research. With financial support by the German Ministry of the Environment CONTUREC organized in 2008 in Erfurt the first international conference “Urban Biodiversity and Design”. The results were brought to the following up 9th Conference of the Parties (COP) within the Convention on Biological Diversity (CBD), which was held in Bonn (Germany) and underlined the urgent need to create an own Major Group for “Cities and Biodiversity”. On this occasion, the “International Network Urban Biodiversity and Design” (URBIO) was founded to promote urban biodiversity and design through a continuing dialogue with the CBD and their partners. This network was following CONTUREC and is organizing international conferences prior to the COP meetings and is exchanging over a newsletter and the website the state on urban biodiversity research and its application. To date, eight URBIO conferences and three URBIO workshops were held, and the results were published in a book and in special issues in international journals.This article describes the development and challenges to run the three different urban biodiversity networks. It gives suggestions for the future based on the experiences done so far.
Dewatering and valorizing lake sediments by electroosmotic dewatering for lakes restoration
Authors: Li Huilin , Ottosen Lisbeth M. 
Published: June 2024

AbstractDredging eutrophic lake sediments can improve water quality, but it also requires dewatering and valorizing the dredged material to avoid wasting resources like phosphorus. This study experimentally investigated the basic mechanism and performance of electroosmotic dewatering of 1-L dredged sediments using different electric currents (20 mA, 40 mA, and 60 mA) after gravity filtration. The dewatering performance, moisture content and distribution, effect of electrochemical reaction on dewaterability, energy consumption, and changes in metals and phosphorus (P) distribution and pH values were analyzed. The results indicated that electroosmotic dewatering effectively decreased sediment mass by predominantly eliminating free and a portion of interstitial water, with reductions ranging from 7 to 20%. The optimal duration and current should, however, be considered to balance water removal and energy consumption. Higher moisture removal occurred with 40 mA for 24 h and 60 mA for 6 h, while the energy consumption obtained with 60 mA (0.201 kWh/kg water removed) was significantly lower than that of applying 40 mA for 24 h (0.473 kWh/kg water removed), with the assistance of ohmic heating, resulting in reduced viscosity and water release from capillaries. The tested conditions did not significantly extract heavy metals or P from the sediments, which may facilitate the disposal of the removed water back into the lake and the utilization of the treated sediments for different purposes. This technology is easy to operate and suitable for the treatment of dredged sediments, and the dewatering result is comparable to low pressurized filtration but at low energy consumption.
Evolutionary Invasion Analysis of Modern Epidemics Highlights the Context-Dependence of Virulence Evolution
Authors: Surasinghe Sudam , Kabengele Ketty , Turner Paul E. , Ogbunugafor C. Brandon 
Published: June 2024

AbstractModels are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict how the relationship between virulence (the harm to hosts caused by an infection) and transmission will evolve in certain virus-host contexts. In this study, we invoke evolutionary invasion analysis—a method used to identify the evolution of uninvadable strategies in dynamical systems—to examine how the virulence-transmission dichotomy can evolve in models of virus infections defined by different natural histories. We reveal peculiar patterns of virulence evolution between epidemics with different disease natural histories (SARS-CoV-2 and hepatitis C virus). We discuss the findings with regards to the public health implications of predicting virus evolution, and in broader theoretical canon involving virulence evolution in host-parasite systems.