bluuebunny/crossref_metadata_2025 huggingface dataset:
Harnessing Chlamydia trachomatis-Specific Immunity: Integrating Immunopeptidomics and Vaccination Strategies to Recruit and Enhance CD8+ T Cell Responses
Authors:   , Medfai Lobna
Published: October 2024

Chlamydia trachomatis (C. trachomatis), the leading cause of sexually transmitted bacterial infections globally, poses significant challenges in vaccine development due to its complex life cycle and interactions with the host. The bacterium forms a protective replication niche called an inclusion within host cells, evading immune defenses. Occasionally, "leakages" expose the bacterium or its antigens to the cytoplasm, aiding antigen processing. CD8+ T cells play a critical role in immune protection by inducing long-lasting memory during infection and vaccination, as outlined in Chapter I. Chapter II harnesses advanced mass spectrometry technology to investigate the immunopeptidome of human cells infected with C. trachomatis, revealing key features of the presented peptide library during infection and highlighting the pathogen-host immune system interactions. Chapters III and IV explore the potential of nucleic acid vaccines to stimulate efficient cellular immune responses through a prime-boost strategy, demonstrating the effectiveness of these vaccines in generating robust humoral and cellular immunity against intracellular pathogens. In Chapters V and VI, bacterial component-based vaccines, particularly outer membrane vesicles and particulate inclusion bodies, are examined for their ability to induce potent immune responses in mouse models. The novel particulate bodies platform showed significant promise in protecting against infection in challenge experiments, emphasizing its potential as a versatile and effective vaccination strategy. Overall, this thesis integrates various innovative vaccine platforms and an optimized antigen identification method, advancing our understanding of immune responses against C. trachomatis and paving the way for more effective vaccine development. The immunopeptidomics analysis using the inSPIRE-Select pipeline broadened the range of pathogen peptides identified, which could be critical for future vaccine design. By combining multiple antigens, optimizing delivery platforms, and balancing cellular and humoral responses, these approaches hold promise for developing a comprehensive and effective vaccine against C. trachomatis. Further research is needed to evaluate the long-term protection and clinical efficacy of these vaccines in human trials.
Newly sighted perceivers and the relation between sight and touch
Authors: Green E. J.
Published: October 2024

Molyneux’s question asks whether a person born blind who has learned to identify shapes by touch could, if suddenly granted sight, immediately identify shapes visually. This question has often been used to structure discussions of whether there is a “rational connection” between sight and touch—whether it is possible to rationally doubt whether the same shape properties are both seen and felt. I distinguish two questions under this general heading. The first concerns, roughly, whether the visual and haptic perception of shape is rationally connected in normally sighted perceivers. The second concerns, roughly, whether the visual and haptic perception of shape is rationally connected in all possible perceivers. I argue that real-world implementations of Molyneux’s question are irrelevant to the first question, but potentially relevant to the second. However, I also argue that the second question does not have the philosophical significance it is sometimes claimed to have. In particular, it cannot be used to adjudicate debates about whether the phenomenal character of perceptual experience is primarily determined “externally” by the worldly properties we perceive, or “internally” by physiological or functional properties of our brains.
On the Laurent Series Ring as a Loop Integral Constructed from Curvature Tensor Residues and Scalar Curvature Winding Numbers
Authors: CHEN WEN-XIANG
Published: October 2024

This paper establishes a profound connection between the Laurent Series Ring in complex analysis and the curvature tensors in differential geometry. By interpreting curvature tensors as residues and scalar curvature as winding numbers within loop integrals, we demonstrate that the Laurent Series Ring can be effectively constructed through these geometric constructs. This synthesis bridges complex analysis and differential geometry, offering new insights into the interplay between analytic and geometric structures.
Etnomedicine Tumbuhan Obat di Masyarakat Desa Belangian, Kalimantan Selatan
Authors: Syahfitri Laili Shinta Ayu , Nastiti Kunti , Kurniawati Darini , Rohama Rohama
Published: October 2024

Latar Belakang: Keanekaragaman suku dan budaya di Indonesia menjadikanadanya perbedaan budaya dan pengetahuan tradisional salah satunya dalammemanfaatkan tumbuhan untuk pengobatan suatu penyakit. Salah satu suku yangtersebar luas di Pulau Kalimantan yang kental dengan pengobatan tradisionalnyaadalah Suku Banjar yang berada di Desa Belangian, Kalimantan Selatan.Etnomedisin merupakan pengobatan oleh etnis tertentu yang didasarkan atas tradisiturun temurun dalam pengobatan tradisionalnya dalam hal ini adalah penggunaantumbuhan berkhasiat obat.Tujuan: Tujuan dari penelitian ini adalah untuk mengetahui etnomedicinetumbuhan obat yang digunakan oleh Suku Banjar Desa Belangian, KecamatanAranio, Provinsi Kalimantan Selatan.Metode: Penelitian ini bersifat deskriptif dengan menggunakan metode kualitatifdan kuantitatif. Analisis kuantitatif dengan perhitungan Fidelity Level (FL) untukmasing-masing jenis tumbuhan obat.Hasil: Berdasarkan hasil penelitian dari 38 informan diperoleh 58 spesies denganjumlah family sebanyak 36. Terdapat 50 penyakit yang dapat diobati dari 58 jenistumbuhan obat. Metode yang paling digemari pada pengolahan adalah direbus56,89 kemudian diminum 72,41%. Bagian tumbuhan obat paling banyak digunakanadalah bagian daun 41,73%. Lima jenis tanaman dengan nilai FL tertinggi yangmenyatakan efektivitas untuk pengobatan yaitu Cymbopogon citratus 86,84%,Zingiber officinale 78,94%, Jatropha multifida L 73,64%, Peronema canescensjack 68,42%, Syzygium polyanthum 65,78%. Tradisi pengobatan dengan tumbuhanobat oleh Suku Banjar ini secara turun temurun dengan nilai kearifan lokal dalampemanfaatannya.Simpulan: Terdapat 58 jenis tumbuhan obat yang dapat dimanfaatkan sebagai obatatau pereda untuk sesuatu penyakit tertentu oleh masyarakat Suku Banjar, DesaBelangian. Dengan nilai FL lima tertinggi ialah terdapat pada tanamanCymbopogon citratus 86,84%, Zingiber officinale 78,94%, Jatropha multifida L73,64%, Peronema canescens jack 68,42%, Syzygium polyanthum 65,78%.
Navigating biosafety regulatory frameworks for genetic engineering in Africa: a focus on genome editing and gene drive technologies
Authors: Rabuma Tilahun , Moronta-Barrios Felix , Craig Wendy
Published: October 2024

Genome editing and gene drive technologies are increasingly gaining attraction in Africa, with researchers exploring their potential applications in agriculture, health and the environment. Acknowledging that robust regulatory frameworks are crucial in facilitating the development and utilization of these technologies, informed decision-making is, however, being impeded by the fragmented information availability and readiness of regulatory authorities on the continent.

Objectives

This study investigates the regulatory frameworks governing genome editing and gene drive technologies in African countries, identifies common regulatory challenges and proposes actionable solutions.

Methods

Primary data were collected through questionnaires and complemented by analysing existing biosafety regulations from online databases and scientific literature.

Results

Our findings suggest that while a few African countries have recently updated their regulatory frameworks, many are still under discussion. Challenges to development and implementation include limited resources, expertise, awareness, and public resistance.

Conclusion

The findings underscore the urgent need for further development in regulatory capacities. By shedding light on these challenges, our study could provide African regulators with valuable insights to guide the formulation of effective regulatory frameworks. Such frameworks are essential for harnessing the potential of genome editing and gene drive technologies while safeguarding human health and the environment in Africa.
Antimicrobial peptide GL13K-Modified titanium in the epigenetic regulation of osteoclast differentiation via H3K27me3
Authors: Gao Yuerong , Lai Yingzhen , Wang Hong , Su Jingjing , Chen Yan , Mao ShunJie , Guan Xin , Cai Yihuang , Chen Jiang
Published: October 2024

Implant surface designs have advanced to address challenges in oral rehabilitation for healthy and compromised bone. Several studies have analyzed the effects of altering material surfaces on osteogenic differentiation. However, the crucial role of osteoclasts in osseointegration has often been overlooked. Overactive osteoclasts can compromise implant stability. In this study, we employed a silanization method to alter pure titanium to produce a surface loaded with the antimicrobial peptide GL13K that enhanced biocompatibility. Pure titanium (Ti), silanization-modified titanium, and GL13K-modified titanium (GL13K-Ti) were co-cultured with macrophages. Our findings indicated that GL13K-Ti partially inhibited osteoclastogenesis and expression of osteoclast-related genes and proteins by limiting the formation of the actin ring, an important structure for osteoclast bone resorption. Our subsequent experiments confirmed the epigenetic role in regulating this process. GL13K-Ti was found to impact the degree of methylation modifications of H3K27 in the NFATc1 promoter region following RANKL-induced osteoclastic differentiation. In conclusion, our study unveils the potential mechanism of methylation modifications, a type of epigenetic regulatory modality, on osteoclastogenesis and activity on the surface of a material. This presents novel concepts and ideas for further broadening the clinical indications of oral implants and targeting the design of implant surfaces.
Cyclic behaviours of soft silty clay with long-term traffic loading considering drainage conditions
Authors: Jiang Yexiang , Li Ruofei , Su Fengyang , Chen Guanyu , Xia Chaobo , Tong Junhao , Wu Tingyu
Published: October 2024

The traffic loading is a typical cyclic loading with variable confining pressure and always lasts long, and is believed to have a significant effect on the subgrade soil, especially for the subgrade filled with soft clay. However, the mechanics have yet to be fully understood. Given that the duration of traffic loading lasts long enough, the partially drained conditions should be considered for the soft clay under the long-term cyclic loading, rather than the undrained conditions adopted commonly by most previous researches. In this study, 28 cyclic tests were conducted on the remolded saturated soft clay, utilizing both constant confining pressure and variable confining pressure under partially drained and undrained conditions. The effect of cyclic confining pressure and different drainage conditions is analyzed in relation to the evolution of pore pressure and deformation behaviors. Incorporating both the cyclic confining pressure and cyclic stress ratio, a concise pre-diction model of permanent strain is proposed and validated by the experimental results.
Whole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates
Authors: Podbielski Andreas , Köller Thomas , Warnke Philipp , Barrantes Israel , Kreikemeyer Bernd
Published: October 2024

Introduction

Cutibacterium acnes can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are C. acnes strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results.

Methods

In the present study, we prospectively collected C. acnes strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality.

Results

Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups.

Discussion

Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits
A use case of ChatGPT: summary of an expert panel discussion on electronic health records and implementation science
Authors: Rinne Seppo T. , Brunner Julian , Hogan Timothy P. , Ferguson Jacqueline M. , Helmer Drew A. , Hysong Sylvia J. , McKee Grace , Midboe Amanda , Shepherd-Banigan Megan E. , Elwy A. Rani
Published: October 2024

Objective

Artificial intelligence (AI) is revolutionizing healthcare, but less is known about how it may facilitate methodological innovations in research settings. In this manuscript, we describe a novel use of AI in summarizing and reporting qualitative data generated from an expert panel discussion about the role of electronic health records (EHRs) in implementation science.

Materials and methods

15 implementation scientists participated in an hour-long expert panel discussion addressing how EHRs can support implementation strategies, measure implementation outcomes, and influence implementation science. Notes from the discussion were synthesized by ChatGPT (a large language model—LLM) to generate a manuscript summarizing the discussion, which was later revised by participants. We also surveyed participants on their experience with the process.

Results

Panelists identified implementation strategies and outcome measures that can be readily supported by EHRs and noted that implementation science will need to evolve to assess future EHR advancements. The ChatGPT-generated summary of the panel discussion was generally regarded as an efficient means to offer a high-level overview of the discussion, although participants felt it lacked nuance and context. Extensive editing was required to contextualize the LLM-generated text and situate it in relevant literature.

Discussion and conclusions

Our qualitative findings highlight the central role EHRs can play in supporting implementation science, which may require additional informatics and implementation expertise and a different way to think about the combined fields. Our experience using ChatGPT as a research methods innovation was mixed and underscores the need for close supervision and attentive human involvement.
How schoolchildren use digital media in class and outside of school over several weeks: a quantitative case study with media diaries
Authors: Meier Jennifer Virginie , Kaspar Kai
Published: October 2024

Introduction

Digital media play a central role in the lives of today’s schoolchildren, immersed in an increasingly digital world. Modern technologies blur the lines between formal school settings and informal settings outside of school. Although formats like bring-your-own-device align the use in the formal setting with informal usage, a disjunction exists between children’s interactions with digital technologies in their home environments and those within the educational setting. For bridging the gap between school learning and children’s lives outside of school, it is essential to explore the differences and similarities in media usage in both settings.

Methods

In our case study, we examined schoolchildren’s motives and evaluations of digital media usage in both settings, addressing individual needs. Additionally, we explored several dimensions of digital literacy through self-assessment, identified associated learning opportunities within and outside the school environment, and captured self-reported learning gains. We collected this data over the course of several weeks in a longitudinal design with media diaries, aiming to estimate the extent of the fluctuation.

Results

Eighty-four German schoolchildren aged between 10 and 16 years participated over a six-week period. We found differences but also similarities between media usage outside of school and in class. Digital media were less frequently used in class for entertainment, communication, and learning compared to outside of school, but no differences were reported regarding information search. Schoolchildren expressed above-average satisfaction with their media usage in both settings, but they perceived the usage of digital media outside of school as significantly more important than in class. Regarding their digital competencies, the schoolchildren displayed high self-confidence in most areas. Only in the areas of algorithms and programming, schoolchildren rated themselves as below average. While learning opportunities were identified in class and outside of school, the frequency of these opportunities varied across different digital skills. The self-reported learning gain in digital media usage remained consistently low in both settings. Across all analyses, there was no substantial temporal fluctuation in media usage over the study period.

Discussion

The findings raise crucial considerations regarding the integration of digital media in the classroom, fostering a discussion on their implications for both research and educational practices.
Is synchronous online learning more beneficial than asynchronous online learning in a Saudi EFL setting: teachers’ perspectives
Authors: Alfares Nurah
Published: October 2024

This research investigates the English as a foreign language (EFL) teachers’ perception of the pros and cons of synchronous and asynchronous online learning for EFL students in Saudi Arabia. 121 EFL teachers from public schools in different regions participated in this study. A questionnaire has been used to collect this study’s main data and distributed it online to all EFL teachers in Saudi Arabia. After the statistical analysis of data, the study’s main findings revealed that the advantages of synchronous learning are helping learners reduce space barriers and saving time for learners. However, the main disadvantages of synchronous learning are the disruption of the internet: slow speed, the miscommunication of learners and getting bored through learning. The main findings for the advantages of asynchronous learning are the chances for learners to replay the lesson many times, the opportunities for learners to have more time for thinking, and the opportunities for learners to enhance autonomy and self-regulated learning. However, the disadvantages perceived by the participants were that asynchronous learning requires more responsibilities from learners in self-controlling, self-motivation, and autonomous learning skills. This study is one of the few studies investigating and comparing EFL teachers’ perceptions of synchronous and asynchronous online learning. Therefore, this research could serve the Ministry of Education by exploring the challenges that instructors face in teaching and highlighting the advantages of online teaching to increase awareness among Saudi teachers of its essential role in EFL learning.
A method of determining the carbon emission reduction contribution of regional distribution networks based on spherical fuzzy sets
Authors: Du Puliang , Yang Miaoheng , Hu Wei , Wang Pengfei , Xing Qiang
Published: October 2024

Introduction

An innovative methodology is proposed to delve into the pivotal role of regional distribution networks (RDNs) in fostering low-carbon development.

Methods

The methodology first constructs an evaluation framework encompassing various dimensions and then integrates spherical fuzzy sets (SFSs) with the best-worst method (BWM), enabling the precise calculation of indicator weight parameters. Subsequently, we employ the measurement of alternatives and ranking according to compromise solution (MARCOS) with SFSs to process and synthesize decision making information.

Results

Take the Shanghai region as an example, results show that C4 has the highest performance and C10 has the lowest.

Discussion

In conclusion, this research presents a significant step forward in understanding the importance of RDNs in promoting low-carbon development and offers a practical approach for decision-makers to assess and enhance the performance of RDNs.
The effect of firewood combustion cookstove types on indoor air pollution and deforestation in selected rural houses of Ethiopia
Authors: Fekadu Miftah , Molla Moges , Hailu Birhanu
Published: October 2024

Introduction

Indoor air pollution occurs in a microenvironment such as residential homes, closed working places, or industries in which people spend a large part of their time. Cooking or baking food in traditional or open three-stone cookstoves by using firewood is the cause for kitchen-related smoke indoor air pollution and deforestation. Modifying traditional firewood cookstoves could reduce the emissions of indoor air pollutants. The objective of the present study was to determine the effect of firewood cookstove types on indoor air pollution, emission reduction, and deforestation in selected rural houses of Bure, Ameya, and Dalocha woredas (districts) of Ethiopia.

Methods

Indoor air pollutants such as carbonmonoxide (CO), carbon dioxide (CO2), sulfurdioxide (SO2), and particulate matters (PMs) were measured in three replicates for 3 min. within an average cooking time of 1 h using an automatic gas sensor. The amount of wood was separately measured by using graduated weight balance (0.1 gm).

Results and discussion

The cooking place was mostly the same room as the sleeping place without a separate kitchen. The improved cookstoves were installed without a chimney (smokeoutlet) and with wider spaces left for a firewood inlet. In improved Injera baking cookstoves, the mean emission of CO was 1004.80 mg/m3, 33.00 mg/m3, and 53.85 mg/m3 in Bure, Ameya, and Dalocha woredas, respectively, which were lower than the emissions from open cookstoves. The mean concentration of PM2.5 in open cookstoves in Bure, Ameya, and Dalocha woredaswas 124.50 mg/m3, 0.53 mg/m3, and 0.04 mg/m3, respectively, which are higher than the emission from improved stoves. In Bure woreda households, the CO exposure was above 26 times the permissible limit of WHO standards. Biomass consumption was positively correlated with the moisture content of wood (p < 0.05). Improved cookstoves reduced indoor air pollution by 13%–81% and carbon emission and deforestation by 20%–41% when compared with the open three-stone cookstoves. Indoor air pollutants are risks to health and cause climate change problems. Therefore, awareness should be created on the health effects of firewood smoke indoor air pollution, ventilation of cooking places, and installation of chimneys with improved cookstoves.
Borealization impacts shelf ecosystems across the Arctic
Authors: Husson Bérengère , Bluhm Bodil A. , Cyr Frédéric , Danielson Seth L. , Eriksen Elena , Fossheim Maria , Geoffroy Maxime , Hopcroft Russell R. , Ingvaldsen Randi B. , Jørgensen Lis L. , Lovejoy Connie , Meire Lorenz , Mueter Franz , Primicerio Raul , Winding Mie
Published: October 2024

Climate change is rapidly modifying biodiversity across the Arctic, driving a shift from Arctic to more boreal ecosystem characteristics. This phenomenon, known as borealization, is mainly described for certain functional groups along sub-Arctic inflow shelves (Barents and Chukchi Seas). In this review, we evaluate the spatial extent of such alterations across the Arctic, as well as their effects on ecosystem-level processes and risks. Along the inflow shelves, borealization is driven by long-term strengthened inflow of increasingly warm waters from the south and punctuated by advection and low sea ice extreme events. A growing body of literature also points to an emerging borealization of the other Arctic shelf ecosystems, through a “spillover” effect, as local changes in environmental conditions enable movement or transport of new species from inflow shelves. These modifications are leading to changes across functional groups, although many uncertainties remain regarding under-sampled groups, such as microbes, and technical challenges of consistent, regular monitoring across regions. There is also clear consensus that borealization is affecting phenology, species composition, community traits, population structure and essential habitats, species interactions, and ecosystem resilience. Non-dynamic environmental factors, such as depth and photoperiod, are thought to limit the complete borealization of the system, and may lead to intermediate, “hybrid” ecosystems in the future. We expect current borders of Arctic and boreal ecosystems to progress further northward and ultimately reach an equilibrium state with seasonal borealization. Risks to the system are difficult to estimate, as adaptive capacities of species are poorly understood. However, ice-associated species are clearly most at risk, although some might find temporary refuge in areas with a slower rate of change. We discuss the likely character of future Arctic ecosystems and highlight the uncertainties. Those changes have implications for local communities and the potential to support Blue Growth in the Arctic. Addressing these issues is necessary to assess the full scale of Arctic climate impacts and support human mitigation and adaptation strategies.
Multi-scenario evolutionary simulation of land cover-based carbon stock during rapid urbanization: a case of shijiazhuang city
Authors: Li Qiang , Kong Lingran
Published: October 2024

China is undergoing rapid urbanization, which brings about drastic land cover changes and thus has an important impact on land carbon stocks. Therefore, it is of great significance to study the driving factors of land cover changes in typical cities and simulate their carbon stocks in multiple scenarios, in order to promote the development of sustainable use of land resources and to achieve the goal of “dual-carbon.” In this study, based on the synergistic relationship between land cover and carbon stock (CS), a coupled modeling framework based on MOP-FLUS-InVEST (MFI) is proposed, which integrates the advantages of three models: targeted optimization of the land cover (LC) structure, patch-level simulation of the layout, and rapid probing of spatial and temporal evolutions of CS. In addition, based on the 30 m resolution surface cover data, we analyzed the land cover change characteristics of Shijiazhuang, a city undergoing rapid urbanization in China, from 2000 to 2020 using a dynamic attitude model. The results show that the rate of surface cover change in Shijiazhuang City is relatively fast, but the rate of surface cover change gradually slows down during the 20-year period. The LC change is mainly manifested in the mutual transfer of cropland, woodland and grassland. In the future, the area of cropland, water bodies and bare land decreases, the business-as-usual development (BAU) scenario has the most drastic increase in construction land, and the changes in woodland and grassland are weak, with an increase in economic benefits. In the Ecological Priority Development (EDP) scenario, woodland and grassland expand significantly while construction land growth stagnates, and ecological functions are restored. In the Ecologically and Economically Balanced Development (EEB) scenario, ecological land increases and the growth of built-up land slows down, realizing both economic and ecological benefits. The continuous shrinkage of water bodies is a pressing issue. The coupled model can provide scientific references for the simulation of spatial and temporal changes of LC and CS, the early warning of ecological risks, and the development of land cover planning.
Bibliometric analysis of genomic selection in breeding of animal from 1993 to 2024: global trends and advancements
Authors: Çelik Şenol
Published: October 2024

Animal breeding became a difficult science when numerous genes influenced economically significant features. The major source of genetic improvement is selection, and as such, the large generation intervals in these strategies lead to reduced rates of improvement. Therefore, breeding control, genetic improvement research, and selection processes are accelerated by genomic selection. This article regarding global research interest trends in genomic selection in animal breeding themes was examined using bibliometric analysis, which employed papers from 1993 to 2024 from the SCI-Expanded, SSCI, AHCI, and E-SCI indexes. Over the period of 31 years, the first 3,181 published articles on genomic selection in animal breeding were gathered. Additionally, the study displays trends in co-authorships according to nations and academic institutions as well as co-occurrences of author keywords. There have been more articles since 2010 about the use of genomic selection in animal breeding, building up a sizable library of work that will last until 2024. Among the top academics in the field are Calus MPL, Li J, and Wang Y. The most productive institutions were The United Kingdom’s University of Edinburgh, Aarhus University (Denmark) and China Agricultural University. The current hotspots in this field of study include “selection,” and “association,” according to keyword co-occurrence and frequency analysis. China, the United States, Brazil, Canada, and United Kingdom are the top five countries that produced the most papers with the highest levels of international collaboration and networking. The main topics of current study include prediction, accuracy, association, traits, and selection. New techniques for selection, prediction, accuracy, traits, and association were developed as the discipline matured. Research collaborations across countries, institutions, and writers promote knowledge sharing, effective issue resolution, and superior outcomes.
Metabolomics combined with transcriptomics and physiology reveals the regulatory responses of soybean plants to drought stress
Authors: Wang Liwei , He Peijin , Hui Mengmeng , Li Hainan , Sun Anni , Yin Hong , Gao Xining
Published: October 2024

Drought, a prevalent environmental stressor, has had significant consequences on soybean (Glycine max L.), notably impeding its growth and production. Therefore, it is crucial to gain insight into the regulatory responses of soybean plants exposed to drought stress during soybean flowering in the field. In this study, the cultivar ‘Liaodou 15’ was performed light drought (LD, 24.3% soil moisture content), moderate drought (MD, 20.6% soil moisture content) and severe drought (SD, 16.9% soil moisture content) treatments at flowering stages of soybean and then rehydrated (30% soil moisture content) until harvest. The yield-related indicators were measured and revealed that MD and SD treatments significantly reduced 6.3% and 10.8% of the 100-grain weight. Soybean plants subjected to three drought stresses showed that net photosynthetic rates were 20.8%, 51.5% and 71.8% lower in LD, MD and SD than that of CK. The WUE increased by 31.8%, 31.5% and 18.8% under three drought stress treatments compared to CK. In addition, proline content was 25.94%, 41.01% and 65.43% greater than that of CK under three drought stress treatments. The trend of the MDA content was consistent with that of the proline content. SOD activity was significantly increasing by 10.86%, 46.73% and 14.54% under three drought stress treatments. The activity of CAT in the SD treatment increased by 49.28%. All the indices recovered after rehydration. Furthermore, 54,78 and 51 different expressed metabolomics (DEMs) were identified in the LDCK/LD, MDCK/MD and SDCK/SD groups, respectively. There were 1,211, 1,265 and 1,288 different expressed genes (DEGs) were upregulated and 1,003, 1,819 and 1,747 DEGs were downregulated. Finally, combined transcriptomic and metabolomic analysis suggested that 437 DEGs and 24 DEMs of LDCK/LD group, 741 DEGs and 35 DEMs of MDCK/MD group, 633 DEGs and 23 DEMs of SDCK/SD group, were highly positively correlated in soybean plants under drought stress. Drought stress induced the expression of the PAO1, PAO4, PAO5 and P5CS genes to promote the accumulation of spermidine and proline. Our study elucidates the responses of drought-stressed soybean plants in the field and provides a genetic basis for the breeding of drought-tolerant soybean plants.
Genome-wide association and functional genomic analyses for body conformation traits in North American Holstein cattle
Authors: Sousa Junior Luis Paulo B. , Pinto Luis Fernando B. , Cruz Valdecy A. R. , Oliveira Junior Gerson A. , Oliveira Hinayah R. , Chud Tatiane S. , Pedrosa Victor B. , Miglior Filippo , Schenkel Flávio S. , Brito Luiz F.
Published: October 2024

Body conformation traits are directly associated with longevity, fertility, health, and workability in dairy cows and have been under direct genetic selection for many decades in various countries worldwide. The main objectives of this study were to perform genome-wide association studies and functional enrichment analyses for fourteen body conformation traits using imputed high-density single nucleotide polymorphism (SNP) genotypes. The traits analyzed include body condition score (BCS), body depth (BD), bone quality (BQ), chest width (CW), dairy capacity (DC), foot angle (FAN), front legs view (FLV), heel depth (HDe), height at front end (HFE), locomotion (LOC), rear legs rear view (RLRV), rear legs side view (RLSV), stature (ST), and a composite feet and legs score index (FL) of Holstein cows scored in Canada. De-regressed estimated breeding values from a dataset of 39,135 North American Holstein animals were used as pseudo-phenotypes in the genome-wide association analyses. A mixed linear model was used to estimate the SNP effects, which ranged from 239,533 to 242,747 markers depending on the trait analyzed. Genes and quantitative trait loci (QTL) located up to 100 Kb upstream or downstream of the significant SNPs previously cited in the Animal QTLdb were detected, and functional enrichment analyses were performed for the candidate genes identified for each trait. A total of 20, 60, 13, 17, 27, 8, 7, 19, 4, 10, 13, 15, 7, and 13 genome-wide statistically significant SNPs for Bonferroni correction based on independent chromosomal segments were identified for BCS, BD, BQ, CW, DC, FAN, FLV, HDe, HFE, LOC, RLRV, RLSV, ST, and FL, respectively. The significant SNPs were located across the whole genome, except on chromosomes BTA24, BTA27, and BTA29. Four markers (for BCS, BD, HDe, and RLRV) were statistically significant when considering a much stricter threshold for the Bonferroni correction for multiple tests. Moreover, the genomic regions identified overlap with various QTL previously reported for the trait groups of exterior, health, meat and carcass, milk, production, and reproduction. The functional enrichment analyses revealed 27 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously reported as linked to bone development, metabolism, as well as infectious and immunological diseases.
Genetically modified and unmodified cellular approaches to enhance graft versus leukemia effect, without increasing graft versus host disease: the use of allogeneic cytokine-induced killer cells
Authors: Rambaldi Benedetta , Rizzuto Giuliana , Rambaldi Alessandro , Introna Martino
Published: October 2024

Although allogeneic hematopoietic cell transplantation (HCT) represents a curative approach for many patients with hematological diseases, post-transplantation relapse occurs in 20-50% of cases, representing the primary cause of treatment failure and mortality. Alloreactive donor T cells are responsible for the graft versus leukemia (GvL) effect, which represents the key mechanism for the long-term curative effect of HCT. However, the downside is represented by graft versus host disease (GvHD), largely contributing to transplant-related mortality (TRM). Multiple factors play a role in regulating the delicate balance between GvL and GvHD, such as the optimization of the donor HLA and KIR match, the type of graft source, and the adaptive use of post-transplant cellular therapy. In addition to the standard donor lymphocyte infusion (DLI), several attempts were made to favor the GvL effect without increasing the GvHD risk. Selected DLI, NK DLI, activated DLI and more sophisticated genetically engineered cells can be employed. In this scenario, cytokine-induced killer (CIK) cells represent a suitable tool to boost GvL while minimizing GvHD. CIK cells are T lymphocytes activated in culture in the presence of monoclonal antibodies against CD3 (OKT3), interferon-gamma (IFN-g), and interleukin-2 (IL-2), characterized by the expression of markers typical of NK cells and T cells (CD3+, CD56+, with a prevalent CD8+ phenotype). CIK cells can mediate cytotoxicity through both MHC and non-MHC restricted recognition, which is the so‐called “dual‐functional capability” and display minimum alloreactivity. Allogeneic CIK cells showed a favorable rate of response, especially in the setting of minimal residual disease, with a rate of GvHD not exceeding 25%. Finally, the CIK cell platform can be adapted for chimeric antigen receptor (CAR) cell strategy, showing promising results in both preclinical and clinical settings. In this review, we describe the main immunological basis for the development of the GvL and the possible cellular therapy approaches used to boost it, with a particular focus on the use of CIK cells.
Analysis of the treatment efficacy and prognostic factors of PD-1/PD-L1 inhibitors for advanced gastric or gastroesophageal junction cancer: a multicenter, retrospective clinical study
Authors: Yang Yuanyuan , Wang Zhe , Xin Dao , Guan Lulu , Yue Bingtong , Zhang Qifan , Wang Feng
Published: October 2024

Introduction

Immune checkpoint inhibitors (ICIs) have transformed advanced gastric cancer treatment, yet patient responses vary, highlighting the need for effective biomarkers. Common markers, such as programmed cell death ligand-1 (PD-L1), microsatellite instability/mismatch repair (MSI/MMR), tumor mutational burden, tumor-infiltrating lymphocytes, and Epstein–Barr virus, face sampling challenges and high costs. This study seeks practical, minimally invasive biomarkers to enhance patient selection and improve outcomes.

Methods

This multicenter retrospective study analyzed 617 patients with advanced gastric or gastroesophageal junction cancer treated with programmed cell death protein-1 (PD-1)/PD-L1 inhibitors from January 2019 to March 2023. Clinical data and peripheral blood marker data were collected before and after treatment. The primary endpoints were overall survival (OS) and progression-free survival (PFS); the secondary endpoints included the objective response rate (ORR) and disease control rate (DCR). Least absolute shrinkage and selection operator (LASSO)-Cox and LASSO logistic regression analyses identified independent factors for OS, PFS, and ORR. Predictive nomograms were validated using receiver operating characteristic (ROC) curves, areas under the curve (AUCs), C-indices, and calibration curves, with clinical utility assessed via decision curve analysis (DCA), net reclassification improvement (NRI), and integrated discrimination improvement (IDI).

Results

OS-related factors included treatment line, T stage, ascites, pretreatment indirect bilirubin (pre-IBIL), posttreatment CA125, CA199, CA724, and the PLR. PFS-related factors included treatment lines, T stage, metastatic sites, pre-IBIL, posttreatment globulin (GLOB), CA125, and CA199 changes. ORR-related factors included treatment line, T stage, N stage, liver metastasis, pretreatment red cell distribution width-to-platelet ratio (RPR), CA125, and CA724 changes. The nomograms showed strong predictive performance and clinical utility.

Conclusions

Early treatment, lower T stage, the absence of ascites, and lower pre-IBIL, post-CA125, CA199, CA724, and PLR correlate with better OS. Factors for improved PFS include early treatment, lower T stage, fewer metastatic sites, and lower pre-IBIL, post-GLOB, and post-CA125 levels. Nomogram models can help identify patients who may benefit from immunotherapy, providing valuable clinical guidance.
Long-term follow up of fecundability after ectopic pregnancy in Taiwan: a nationwide population-based study
Authors: Yin Chih-Hsiang , Lee Yi-Liang , Chang Chia-Ching , Chien Wu-Chien , Wu Gwo-Jang
Published: October 2024

Background

Ectopic pregnancy (EP) occurs when a fertilized ovum is implanted outside the uterine cavity. Its incidence is 2% of all pregnancies and is known to decrease fertility. This study aimed to measure pregnancy rates after EP, identify the various parameters influencing pregnancy, and compare these variables in women with and without a history of EP, as well as determine in which medical facilities women with EP seek medical help.

Methods

The data was extracted from the National Health Insurance Research Database during 2000–2013. The study group included of women with a history of one EP (study group) and women without EP (control group). The chi-square/Fisher exact test was performed for categorical variables, and t-tests were used for continuous variables.

Results

The EP group had a higher cumulative pregnancy rate (41.55%) than the control group (37.14 %), and a 1.16 times higher rate in developing pregnancy (p < 0.001). While the pregnancy rate in the EP group was initially lower than in the control group during the first 5 years, it surpassed the control group’s rate between the 10th and 14th years.

Conclusions

Fecundability after EP was lower at the beginning but increased at long-term follow-up.
Treatment intensification with radium-223 plus enzalutamide in patients with metastatic castration-resistant prostate cancer
Authors: Shore Neal , Carles Joan , McDermott Ray , Agarwal Neeraj , Tombal Bertrand
Published: October 2024

Several life-prolonging therapies with diverse mechanisms of action (MoA) are available for the treatment of metastatic hormone-sensitive/castration-resistant prostate cancer, with many patients requiring multiple lines of therapy. Nevertheless, treatment optimization to further delay disease progression and improve overall survival remains an unmet need. Despite the number of agents with differing MoAs approved for advanced prostate cancer, many patients receive only one or two life-prolonging therapies. One strategy for enhancing the benefit of treatment for this aggressive disease is combining therapies with different MoAs (treatment intensification) early in the disease course, which may be more effective than administering therapies sequentially, yet still allow for subsequent sequential use of individual therapies to optimize patient outcomes. In this narrative review we discuss the rationale for combining 223radium dichloride (223Ra; an alpha-emitting radionuclide) with enzalutamide (an androgen receptor inhibitor) for treatment intensification, including their differing MoAs, their individual efficacy in this setting, and their largely non-overlapping tolerability profiles. We also summarize the preclinical and clinical data available for this combination to date, including interim safety data from the phase 3 EORTC 1333/PEACE III study which highlight the low fracture risk of 223Ra plus enzalutamide when administered concomitantly with bone health agents. Relevant data were sourced from clinical studies published by the authors and via searches of PubMed, clinical trial registries and congress abstracts.
A semantic segmentation method to analyze retinal vascular parameters of diabetic nephropathy
Authors: Lu Youlv , Fang Ruolin , Xu Bolun , Feng Chunyun , Zhu Zhentao , Yu Meiting , Tong Yuhua
Published: October 2024

Introduction

By using spectral domain optical coherence tomography (SD-OCT) to measure retinal blood vessels. The correlation between the changes of retinal vascular structure and the degree of diabetic nephropathy is analyzed with a full-pixel Semantic segmentation method.

Methods

A total of 120 patients with diabetic nephropathy who were treated in the nephrology department of Quzhou People’s Hospital from March 2023 to March 2024 were selected and divided into three groups according to the urinary albumin creatinine ratio (UACR). The groups included simple diabetes group (UACR < 30 mg/g), microalbuminuria group (30 mg/g ≤ UACR <300 mg/g) and macroalbuminuria group (UACR ≥300 mg/g). SD-OCT was used to scan the arteries and veins in the superior temporal area B of the retina. The semantic segmentation method built into the SD-eye software was used to automatically identify the morphology and structure of the vessels and calculate the parameters of arteriovenous vessels. The parameters of arteriovenous vessels are as follows: outer diameter of the retinal artery (RAOD); inner diameter of the retinal artery (RALD); arterial wall thickness (AWT); arterial wall to lumen ratio (AWLR); cross sectional area of arterial wall (AWCSA); retinal vein outer diameter (RVOD); retinal vein inner diameter (RVLD); vein wall thickness (VWT); vein wall to lumen ratio (VWLR); cross sectional area of vein wall (VWCSA). Statistical analysis software was used to compare and analyze the parameters of retinal arteriovenous vessels of the three groups.

Results

The study revealed statistically significant differences in RAOD and RALD among the three groups (p < 0.05) with the RAOD and RALD of the macroalbuminuria group and microalbuminuria group being lower than those of the simple diabetes group. Conversely, there were no significant differences in AWT, AWLR and AWCSA among the three groups (p > 0.05). Additionally, the differences in RVOD and RVLD among the three groups were found to be statistically significant (p < 0.05) with the RVOD and RVLD of the simple diabetes group being lower than those of the microalbuminuria group and macroalbuminuria group. No significant differences were observed in VWT and VWL among the groups. Additionally, RVOD and RVLD were weakly associated with UACR (R = 0.247, p = 0.007; R = 0.210, p = 0.021). Full-pixel semantic segmentation method combined with OCT images is a new retinal vascular scanning technology, which can be used as a new method for early diagnosis of diabetic nephropathy. The structural changes of retinal vessels can be used to predict the severity of diabetic nephropathy during the development of diabetic nephropathy.