bluuebunny/crossref_metadata_2025_split huggingface dataset:
Karyotype and LTR-RTs analysis provide insights into oak genomic evolution
Authors: CAO Rui-Bin , CHEN Ran , LIAO Ke-Xin , LI He , XU Gang-Biao , JIANG Xiao-Long 
Published: March 2024

Abstract
Background: Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.
Results: Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.
Conclusion: Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
Comparative transcriptomic analysis primarily explores the molecular mechanism of compound eye formation in Neocaridina denticulata sinensis
Authors: Yan Congcong , Wu Zixuan , Liu Yujie , Sun Yuying , Zhang Jiquan 
Published: March 2024

Abstract
Compound eyes formation in decapod crustaceans occurs after the nauplius stage. However, the key genes and regulatory mechanisms of compound eye development during crustacean embryonic development have not yet been clarified. In this study, RNA-seq was used to investigate the gene expression profiles of Neocaridina denticulata sinensis from nauplius to zoea stage. Based on RNA-seq data analysis, the phototransduction and insect hormone biosynthesis pathways were enriched, and molting-related neuropeptides were highly expressed. There was strong cell proliferation in the embryo prior to compound eye development. The formation of the visual system and the hormonal regulation of hatching were the dominant biological events during compound eye development. The functional analysis of DEGs across all four developmental stages showed that cuticle formation, muscle growth and the establishment of immune system occurred from nauplius to zoea stage. Key genes related to eye development were discovered, including those involved in the determination and differentiation of the eye field, eye-color formation, and visual signal transduction. In conclusion, the results increase the understanding of the molecular mechanism of eye formation in crustacean embryonic stage.
ClimResilience, a global climate resilience framework
Authors: BADOLO Mathieu 
Published: March 2024

Abstract
Baground: Climate change direct and indirect impacts on the main development sectors could induce social, economic, environmental, institutional or political regression dynamics in several regions of the world. The set of markers of such dynamics includes social inequalities and disparities accentuation, community conflicts over natural resources increase, climate migration amplification and humanitarian, social, institutional and political crises intensification. A significant and continuous improvement in knowledge, solutions, technologies and decision support tools for resilience is one of the levers to consider for efficient responses to climate change impacts.
Methods: In this article, we describe the Badolo ClimResilience framework, a global framework for innovating climate resilience governance models, plans, practices and solutions. It includes methodological tools, information and solutions vectors, information triangles, matrices and resilience schemes for improving climate resilience actions relevance, efficiency and performance
Results: The main results of this article are ClimResilience approach, information vectors, information triangles, resilience matrices and schemes. The resilience configurations and trajectories matrix is an innovative tool for planning, achieving and evaluating the desired progress in terms of resilience to climate change
Conclusion: Fundamentally, ClimResilience framework is a new scientific decision support tool for a significant improvement in the relevance, efficiency and performance of climate resilience actions.
Biomechanical control of vascular morphogenesis by the surrounding stiffness
Authors: Nishiyama Koichi , Hanada Yasuyuki , Halder Semanti , Haruta Misato , Ogura Shuntaro , Shiraki Yukihiko , Arima Yuichiro , Nakano Sota , Ozeki Yuka , Murohara Akiyoshi , MUROHARA TOYOAKI 
Published: March 2024

Abstract
Sprouting angiogenesis is a form of morphogenesis which expands vascular networks from the preexisting ones in both developmental and postnatal settings. During this process, endothelial cells (ECs) collectively elongate new branches via their directional movement. Almost simultaneously, the vessel lumen develops internally with blood flowing into it. Our recent study has suggested lumen expansion induced by blood inflow to be an inhibitory factor for branch elongation. However, the precise mechanism governing efficient angiogenic branch elongation during lumen development under the influence of blood inflow remains unknown. Herein, we show perivascular stiffening to be a major factor that integrates branch elongation and lumen development during angiogenic morphogenesis. We found that the circumferential expansion seen during lumen development inhibits directional EC movement driving angiogenic branch elongation, as clarified by an approach combining in vitro on-chip reconstitutions and in vivo validation experiments. This process was counter-regulated by perivascular stiffening that prevents excessive lumen expansion. We also found that appropriate collagen-IV (Col-IV) deposition on the vascular basement membrane (VBM) from ECs driven by pericytes accounts for spatiotemporal perivascular stiffening. Our results demonstrate how ECs elongate branches while developing the lumen by properly building the surrounding physical environment in coordination with pericytes during angiogenesis. These findings provide insights enhancing our understanding of principles biomechanically integrating different morphogenetic processes not only in angiogenesis but also other forms of tissue development, and may in addition provide insights that open avenues to novel applications in clinical management as well as regenerative medicine.
Mothers’ perceptions regarding the implementation of skin-to-skin contact for their preterm infants in intensive care units of the North West Province: A qualitative study
Authors: Denge Takalani , Bam Nokwanda Edith , Lubbe Welma , Rakhudu Mahlasela 
Published: March 2024

Abstract

Background
Approximately 15 million preterm infants are born globally and require hospital care. The health consequences are significant, with complications from preterm birth representing the leading cause of death for children under 5 years of age globally. Fortunately, the majority of these deaths can be prevented with proper care, such as skin-to-skin contact (SSC). SSC is one of the four components of kangaroo care (KC) and is also a valued alternative to incubators in low-income countries. SSC enhances infant and maternal wellbeing and requires an educational programme for implementation. Therefore, mothers' perceptions regarding the implementation of SSC in intensive care units (ICUs) can be influenced by their understanding of its benefits, as well as the support and education provided by healthcare professionals. The purpose of this study was to explore and describe mothers’ perceptions regarding the implementation of SSC for preterm infants in ICUs in Northwest Province (NWP).
Methods
We conducted a qualitative descriptive and exploratory study to describe and explore mothers' perceptions regarding the implementation of SSC for preterm infants in intensive care units of Level 2 hospitals in the NWP from September to November 2023. A total of 24 mothers who had preterm infants admitted to ICUs practicing SSC were included in the Focus Group Discussions (FGDs). Four FGDs consisting of six participants were conducted until data saturation was reached. The data were analyzed thematically using the steps proposed by Creswell and Creswell 2017.
Results
Four main themes were identified, namely, knowledge of SSC, perceived benefits of SSC, challenges experienced by mothers during the implementation of SSC, and support needs for mothers regarding the implementation of SSC, and nine subthemes emerged.
Conclusions
SSC for preterm infants in intensive care units has been found to have positive effects on both mothers and neonates. Mothers perceive SSC as a method of warmth that facilitates bonding and promoting breastfeeding. The findings can inform the programme and preparedness strategies needed to support the implementation of SSC in ICUs.
An efficient topology optimization algorithm for large-scale three-dimensional structures
Authors: Vitorino Alfredo , Gomes Francisco 
Published: March 2024

Abstract
Designing the topology of three-dimensional structures is a challenging problem due to its memory and time consumption. In this paper, we present a robust and efficient algorithm for solving large-scale 3D topology optimization problems. The robustness of the algorithm is ensured by adopting a globally convergent sequen- tial linear programming method with a stopping criterion based on the first-order op- timality conditions of the nonlinear problem. To increase the algorithm’s efficiency, it is combined with a multiresolution scheme that employs different discretizations to deal with displacement, design, and density variables. In addition, the time spent solving the linear equilibrium systems is substantially reduced using multigrid as a preconditioner for the conjugate gradient method. Since multiresolution can lead to the appearance of unwanted artefacts in the structure, we propose an adaptive strategy for increasing the degree of the displacement elements, with a technique for suppress- ing unnecessary variables that provides accurate solutions with a moderate impact on the algorithm’s performance. We also propose a new thresholding strategy, based on gradient information, to obtain structures composed only by solid or void regions. Computational experiments carried out in Matlab prove that the new algorithm effec- tively generates high-resolution structures at a low computational cost.
Shed teeth from Portezuelo Formation at Sierra del Portezuelo reveal a higher diversity of predator theropods during Turonian-Coniacian times in northern Patagonia
Authors: Meso Jorge Gustavo , Gianechini Federico , Gomez Kevin , Muci Luciana , Baiano Mattia Antonio , Pol Diego , Kaluza Jonatan , Garrido Alberto , Pittman Michael 
Published: March 2024

Abstract

The study of thirty-two shed crowns from the Portezuelo Formation (middle Turonian-late Coniacian) at the Sierra del Portezuelo locality, reveals six distinct tooth morphotypes identified through cladistic, discriminant, and cluster analyses. Two morphotypes were identified as belonging to Megaraptoridae, three to Abelisauridae, one to Abelisauroidea, and one to Alvarezsauridae. Additionally, two of the morphotypes exhibit a combination of dental features typically found in megaraptorid and abelisauridtheropods. These results suggest a greater diversity of theropods in the original ecosystem than previously thought, including the presence of a second morphotype of megaraptorid and alvarezsaurid previously undocumented in this formation. Furthermore, the existence of Morphotype 6 indicates the potential coexistence of medium-sized abelisauroids alongside larger abelisaurids in the same ecosystem. These findings underscore the importance of future expeditions to the Sierra del Portezuelo locality to further our understanding of these previously unknown theropod species.
SKSR1 identified as key virulence factor in Cryptosporidium by genetic crossing
Authors: Xiao Lihua , He Wei , Sun Lianbei , Hou Tianyi , Yang Zuiwei , Yang Fuxian , Zhang Shengchen , Wang Tianpeng , Li Na , Guo Yaqiong , Sibley L. , Feng Yaoyu 
Published: March 2024

Abstract
Cryptosporidium is a major cause of severe diarrhea. Although Cryptosporidium isolates exhibit significant differences in infectivity and virulence, the genetic determinants for these traits are not clear. In this study, we used classical genetics to cross two Cryptosporidium parvum isolates of different virulence and used bulked segregant analysis of whole-genome sequence data from the progeny to identify quantitative trait loci (QTL) associated with Cryptosporidium infectivity and virulence. Of the 26 genes in three QTL, two had loss-of-function mutations in the low-virulence isolates. Deletion of the SKSR1 gene or expression of the frame-shift mutant sequence reduced the pathogenicity of infection in vivo. SKSR1 is a polymorphic secretory protein expressed in small granules, secreted into the parasite-host interface, and may cooperate with other secretory proteins in pathogenesis. These results demonstrate that SKSR1 is an important virulence factor in Cryptosporidium, and suggest that the extended SKSR protein family, encoded by variant subtelomeric genes, may contribute to pathogenesis.
In silico investigations of triazole -trimethoxyphenyl hybrids as anti-proliferative agents against adenocarcinomic human alveolar basal epithelial cells (A549): DFT, QSAR and Molecular Docking Approaches
Authors: Sunday Ameh Ojima , Abdullahi Shehu , Gabriel Obiyenwa Kehinde , Moses Osang Ekuli , Banjo Semire 
Published: March 2024

Abstract
Twenty-eight sets of synthesized triazole-trimethoxyphenyl hybrids (TPD) were considered as anti-proliferative drugs against human alveolar basal epithelial (A549) cancer cell lines using DFT, QSAR, ADMET profile and molecular docking methods. The considered compounds were used to develop a robust QSAR model, which was used to design new triazole-trimethoxyphenyl compounds that could serve as anti-proliferative drug candidate against human alveolar basal epithelial (A549) cancer. The parameters obtained from DFT calculations such as the HOMO, LUMO, Dipole moment, chemical hardness and softness favoured TPD-11 and TPD-25 over etopoxide as strong inhibitors against human alveolar basal epithelialcancer cell (A549), which agreed with the experimental data. The QSAR modeling and validation indicated the major influence of MATS4p, minHBint3, and ATSC7c descriptors on the reported anticancer activity of the drugs in the A549- MLR-GFA QSAR (R2 = 0.8632, adjusted R2 = 0.7951, Q2Loo = 0.6023 and R2 - Q2Loo = 0.2609). By leveraging data from the model, four new triazole-trimethoxyphenyl hybrids were proposed (NTPD-3, NTPD-4, NTPD-6 and NTPD-9). The DFT and molecular docking analysis showed these four compounds could be good inhibitors against adenocarcinomic human alveolar basal epithelial cells (A549) than etopoxide. However, ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties revealed NTPD-6 showed excellent pharmacokinetic and toxicological profiles and might serve as a road map for new and more effective anticancer agents.
Assessment of Physico-chemical and Microbiological Characteristics of Water from Lake Dapao, Lanao del Sur, Philippines
Authors: Caneos Warren G. , Macapando Solaiman , Clavano Chelmarie Joy , Abragan Dulce Fe 
Published: March 2024

Abstract
Physico-chemical and microbiological characteristics of water from Lake Dapao, Lanao del Sur, Philippines, were assessed. Water samples were randomly collected from the four established sampling stations in the lake and replicated thrice. In situmeasurements of physico-chemical parameters such as dissolved oxygen, temperature, pH, total dissolved solids (TDS), and water turbidity were done. Water samples were sent to the First Analytical Services and Technical (FAST) Laboratories, Inc., Cagayan de Oro City, for microbiological analysis such as total coliform count, thermotolerant (fecal) coliform count and E. colicount. Results revealed that dissolved oxygen, pH and temperature showed no significant differences between stations, while total dissolved solids and water turbidity showed significant differences between stations. The results of the physico-chemical parameters are considered suitable for fish production, as stated in DAO 2016–08. However, the results of the microbiological tests appeared to have failed to conform to the given water standards as stated in DAO 2017-0010 (PNSDW); thus, the lake waters are not suitable for drinking.
The impact of feeding varied dietary quantities of zinc and copper on turkey poult performance, immunological response and skeletal health
Authors: Agashe Jayanti , Deo Chandra , Biswas Avishek , Sharma Divya , Nampalle Mukesh T , Tiwari Ashok Kumar 
Published: March 2024

Abstract
In this study, the impact of varying dietary zinc (Zn) and copper (Cu) levels on the growth, immunological response, and skeletal health of developing turkey poults was investigated. For 0–4 and 5–8 weeks of age, respectively, three Zn levels of 50, 70, and 90 mg/kg and 45, 65, and 85 mg/kg were employed. Three Cu levels, namely 8, 12, and 16 mg/kg for 0–8 weeks of age, were also utilized. There were 288 (9×4×8) day old turkey poults with equal body weight that were randomly assigned to 9 treatments, each consisting of 4 replicates and 8 poults per replicate. In comparison to other dietary combinations, there was a significant (P ≤ 0.05) increase in body weight gain observed in the 90 and 85 mg Zn/kg with 16 mg Cu/kg diet during 0–4 and 0–8 weeks of age, respectively, and the 70 and 65 mg Zn with 16 mg Cu /kg diet during 0–4 and 0–8 weeks of age, respectively. When compared to low levels of zinc in the diet at 5–8 and 0–8 weeks of age, respectively, feed conversion ratio was shown to be considerably (P ≤ 0.01) lower and better at 90 and 85 mg Zn/kg diet. In a similar pattern, feed utilisation efficiency was considerably (P ≤ 0.01) higher at 16 mg Cu/kg diet than it was at lower Cu levels in the diets given to the animals over the 0–4 week period. Compared to other dietary combinations, there was a substantial (P ≤ 0.01) improvement in cell mediated immune response (foot web index to PHAP) and humoral immune response (HA titer to SRBC) when an 85 mg zinc and 16 mg copper/kg diet was consumed at 0–4 and 5–8 weeks of age, respectively. At greater dietary Zn and Cu levels than its lower values, the weight of the spleen and thymus was considerably higher. In a dietary combination of 90 mg Zn with 16 mg Cu/kg meal during 0–4 and 85 mg Zn with 16 mg Cu/kg diet during 5–8 weeks of age, respectively, there were significantly (P ≤ 0.05) greater bone width (proximal and distal), tibia bone ash, calcium, and phosphorus detected respectively. Significantly (P ≤ 0.01) greater Zn and Fe contents were found in the tibia bone at 90 and 85 mg Zn/kg diet, respectively, compared to values obtained at other Zn levels in the diet throughout 0–4 and 5–8 weeks of age. During the first eight weeks of life, a diet containing 12 mg of copper per kilogramme was shown to have a significantly (P ≤ 0.05) increased Zn and Fe content in the tibia bone compared to other levels. It is possible to draw the conclusion from the data that, for growing turkey poults, dietary combinations of 90 mg Zn/kg with 16 mg Cu/kg diet and 85 mg Zn with 16 mg Cu/kg diet between 0–4 and 5–8 weeks of age, respectively, were sufficient for optimum development, immunity, and skeletal health indices.
Silencing the Shore: The Effects of Onshore Anthropogenic Noise on Marine Mammal Abundances Informed by Mixed Methods
Authors: O'Connor Ryan , Ardoin Nicole , De Leo Giulio 
Published: March 2024

Abstract
We undertook a mixed-methods study to investigate the recent decline in abundance of a colony of Harbor Seals (Phoca vitulina) carefully documented by a community science group in Pacific Grove, California, USA. Combining a generalized additive modeling (GAM) analysis with qualitative analysis of data collected through semi-structured interviews, we analyzed abundance trends between 2003 and 2023, documented Local Ecological Knowledge (LEK) about noisy anthropogenic disturbances and their impact on Harbor Seal behavior and reproductive success, and investigated hypotheses about Harbor Seal abundance trends at the study site. We found that LEK identified a range of potential anthropogenic disturbances whose cumulative effect might explain the decline of the Harbor Seal abundance in recent years. We also found that, in 2022 and 2023, Harbor Seal abundance was 29.81% lower than predicted given the probability of occurrence of forage fish, an important ecological determinant of Harbor Seal abundance. Roadwork construction that occurred in 2022 near the harbor seal colony during the early pupping season may have had significant adverse effects on reproductive success and, consequently, on Harbor Seal abundance at the study site as the “final straw” in an environment of increasing disturbance. This study demonstrates (1) the potential demographic effects of anthropogenic disturbance on marine mammals, (2) the value of mixed-methods design, qualitative interview methods, and community-based science in understanding ecological dynamics in complex social-ecological coastal systems, and (3) the important of mitigating anthropogenic disturbance to sensitive marine mammal colonies.
Selenium level and parameters of diabetes and insulin resistance in middle-aged women
Authors: Schneider-Matyka Daria , Cybulska Anna Maria , Rachubińska Kamila , Pilarczyk Bogumiła , Panczyk Mariusz , Grochans Elżbieta , Ćwiek Dorota , Barczak Katarzyna 
Published: March 2024

Abstract
(1) Background: Selenium is a trace element essential for selenoprotein synthesis. Selenoproteins are known for their antioxidant and cytoprotective properties. The mechanisms underlying insulin resistance and diabetes have not so far been fully elu-cidated. A certain role in the development and progression of type 2 diabetes is attributed to oxidative stress, which became the basis for studying the association between the level of selenium and type 2 diabetes. The aim of the study was to investigate the selenium level in the context of diabetes and insulin resistance parameters in middle-aged women.
(2) Methods: The study included 387 middle-aged women. It consisted of three stages: questionnaire-based survey, anthropometric measurements, and analysis of the biological material (blood) for the levels of glycemia, insulin, HbA1c (%), HOMA-IR, and selenium.
(3) Results:The mean level of selenium was 99.33 ± 19.79 µg/l, glucose—85.60 ± 12.43 mg/dl, insulin―9.79 ± 5.60 µIU/ml, and HbA1c―5.41 ± 0.45%. (4) Conclusions: In the study group of women, selenium levels and parameters of diabetes and insulin resistance were within the normal range.