bluuebunny/crossref_metadata_2025 huggingface dataset:
Joko Widodo’s speeches at the 42nd ASEAN Summit: A critical discourse analysis
Authors: Rahmasari Shafira , Roselani Ni Gusti Ayu
Published: October 2024

The 42nd ASEAN Summit was held in Indonesia, making Indonesia the chairman of the Summit. Joko Widodo, as the president, represented the country to welcome the ASEAN members and open the summit and the meetings by giving remarks and statements. This study attempted to examine how interpersonal metafunction is used in the opening remarks and press statements as well as to reveal the power strategy and ideology depicted in the opening remarks and press statements. Eight opening remarks and two press statements were analyzed utilizing Halliday’s Systemic Functional Linguistics. Fairclough’s Critical Discourse Analysis was employed to reveal the power relations and the ideology. The study found declarative, interrogative, and imperative were the mood types in which it utilized probability, obligation, and inclination modality. It showed that Joko Widodo acted as the initiator to promote collaboration to achieve ASEAN’s goals.
Employing keywords and lexical bundles within figure captions in earth science research articles
Authors: Tsaqifa Tsabita Intan , Roselani Ni Gusti Ayu
Published: October 2024

The presentation of data is considered an essential part of academic writing, especially in research articles, and it could not stand alone without a short text to describe the visual data, namely figure legends. This research aims to identify the keywords and lexical bundles frequently used in figure legends. In addition, this research also examines the functions conveyed by these linguistic features. Based on the identification of the corpus, there are 334 keywords found with the 20 highest frequencies belonging to the terminologies frequently used in earth science (fault, seismic, quartz, and formation) and words related to the visual representation of the figure legends (line/lines, map, area, figure and legend). Furthermore, noun-related bundles are found to be the greatest number for lexical bundles, with 165, followed by verb-related bundles with 79, clause-related bundles with 54, and preposition-related bundles with 17. These lexical bundles perform research-oriented, text-oriented, and participant-oriented functions. These findings suggest that lexical bundles play a role in explaining the research condition, connecting visual data and research results discussed in research articles, and displaying information about visual data or specific parts of research articles to readers.
Enhancing a multi-faceted verb-centered resource to help a language learner: the case of breton
Authors: Foret Annie , Hupel Erwan , Morvan Pˆer
Published: October 2024

This article builds on two recent resources for breton, a verb-centered database and a set of sentences in the universal dependencies (UD) format. Our focus is on breton, an endangered language in the celtic family. We provide an analysis of the verb resource and show how it can be connected and transformed to a multi-faceted system intended to help a learner in a flexible way. We discuss several scenarios.
Evaluating Automatic Pronunciation Scoring with Crowd-sourced Speech Corpus Annotations
Authors: Hjortnaes Nils , Dakota Daniel , Kübler Sandra , Tyers Francis
Published: October 2024

Pronunciation is an important, and difficult aspect of learning a language. Providing feedback to learners automatically can help train pronunciation, but training a model to do so requires corpora annotated for mispronunciation. Such corpora are rare. We investigate the potential of using the crowdsourced annotations included in Common Voice to indicate mispronunciation. We evaluate the quality of ASR generated goodness of pronunciation scores through the Common Voice corpus against a simple baseline. These scores allow us to see how the Common Voice annotations behave in a real use scenario. We also take a qualitative approach to analyzing the corpus and show that the crowdsourced annotations are a poor substitute for mispronunciation annotations as they typically reflect issues in audio quality or misreadings instead of mispronunciation.
Developing a Pedagogically Oriented Interactive Reading Tool with Teachers in the Loops
Authors: Lee Mihwa , Rudzewitz Björn , Chen Xiaobin
Published: October 2024

Reading is crucial for students' academic success and essential life skills. Particularly, the need for students to read in L2 English has grown due to its global significance. However, L2 readers often have limited opportunities for meaningful, interactive reading practice with immediate support. This paper introduces System A (Anonymized), a pedagogically oriented, web-based ICALL system designed to enhance L2 reading experiences, developed through an action research design involving teachers. System A offers a range of interactive features for students, including not only the autonomous identification of vocabulary and more than 650 grammar constructs, but making them interactively explorable in the text, providing detailed explanations and practical examples in contexts. To support effective teaching, System A employs a LLM for generating tailored reading comprehension questions and answer evaluation, with teachers actively involved. We present the development and application of the system from both technical and pedagogical perspectives to advance L2 learning research and refine educational tools.
Generating Contexts for ESP Vocabulary Exercises with LLMs
Authors: Nikolova-Stoupak Iglika , Bibauw Serge , Dumont Amandine , Stas Françoise , Watrin Patrick , François Thomas
Published: October 2024

The current paper addresses the need for language students and teachers to have access to a large number of pedagogically sound contexts for vocabulary acquisition and testing. We investigate the automatic derivation of contexts for a vocabulary list of English for Specific Purposes (ESP). The contexts are generated by contemporary Large Language Models (namely, Mistral-7B-Instruct and Gemini 1.0 Pro) in zero-shot and few-shot settings, or retrieved from a web-crawled repository of domain-relevant websites. The resulting contexts are compared to a professionally crafted reference corpus based on their textual characteristics (length, morphosyntactic, lexico-semantic, and discourse-related). In addition, we annotated the automatically derived contexts regarding their direct applicability, comprehensibility, and domain relevance. The 'Gemini, zero-shot' contexts are rated most highly by human annotators in terms of pedagogical usability, while the 'Mistral, few-shot' contexts are globally closest to the reference based on textual characteristics.
Automatic Text Simplification: A Comparative Study in Italian for Children with Language Disorders
Authors: Padovani Francesca , Marchesi Caterina , Pasqua Eleonora , Galletti Martina , Nardi Daniele
Published: October 2024

Text simplification aims to improve the readability of a text while maintaining its original meaning. Despite significant advancements in Automatic Text Simplification, particularly in English, other languages like Italian have received less attention due to limited high-quality data. Moreover, most Automatic Text Simplification systems produce a unique output, overlooking the potential benefits of customizing text to meet specific cognitive and linguistic requirements. These challenges hinder the integration of current Automatic Text Simplification systems into Computer-Assisted Language Learning environments or classrooms. This article presents a multifaceted output that highlights the potential of Automatic Text Simplification for Computer-Assisted Language Learning. First, we curated an enriched corpus of parallel complex-simple sentences in Italian. Second, we fine-tuned a transformer-based encoder-decoder model for sentences simplification. Third, we parameterized grammatical text features to facilitate adaptive simplifications tailored to specific target populations, achieving state-of-the-art results, with a SARI score of 60.12. Lastly, we conducted automatic and manual qualitative and quantitative evaluations to compare the performance of ChatGPT-3.5, and our fine-tuned transformer model. By demonstrating enhanced adaptability and performance through tailored simplifications in Italian, our findings underscore the pivotal role of ATS in Computer-Assisted Language Learning methodologies.
A Conversational Intelligent Tutoring System for Improving English Proficiency of Non-Native Speakers via Debriefing of Online Meeting Transcriptions
Authors: Pérez-Ortiz Juan Antonio , Esplà-Gomis Miquel , Sánchez-Cartagena Víctor M. , Sánchez-Martínez Felipe , Chernysh Roman , Mora-Rodríguez Gabriel , Berezhnoy Lev
Published: October 2024

This paper presents work-in-progress on developing a conversational system designed to enhance non-native English speakers' language skills through post-meeting analysis of the transcriptions of video conferences in which they have participated. Following recent advances in chatbots and agents based on large language models (LLMs), our tutoring system leverages pre-trained LLMs within an ecosystem that integrates different techniques, including in-context learning, external non-parametric memory retrieval, efficient parameter fine-tuning, grammatical error correction models, and error-preserving speech synthesis. A detailed analysis of the different technologies employed in each of these aspects is provided, along with a description of the datasets used. The system is currently in development, with a planned pilot study to evaluate its effectiveness among students of L2-English.
Evaluating the Generalisation of an Artificial Learner
Authors: Stearns Bernardo , Ballier Nicolas , Gaillat Thomas , Simpkin Andrew , McCrae John P.
Published: October 2024

This paper focuses on the creation of LLM-based artificial learners. Motivated by the capability of language models to encode language representation, we evaluate such models in predicting masked tokens in learner corpora. We pre-trained two learner models, one in a training set of the EFCAMDAT (natural learner model) and another in the C4200m dataset (syntehtic learner model), evaluating them against a native model using an external corpora of English for Specific purposes corpus of French undergraduates (CELVA) as test set. We measured metrics related to accuracy, consistency and divergence. While the native model performs reasonably well, the natural learner pre-trained model show improvements token in recall at k. We complement the accuracy metric showing that the native language model make "over-confident" mistakes where our artificial learners make mistakes where probabilities are uniform. Finally we show that the general tokens choices from the native model diverges from the natural learner model and that this divergence is higher on lower proficiency levels.
Semantic Error Prediction: Estimating Word Production Complexity
Authors: Strohmaier David , Buttery Paula
Published: October 2024

Estimating word complexity is a well-established task in computer-assisted language learning. So far, however, complexity estimation has been largely limited to comprehension. This neglects words that are easy to comprehend, but hard to produce. We introduce semantic error prediction (SEP) as a novel task that assesses the production complexity of content words. Given the corrected version of a learner-produced text, a system has to predict which content words replace tokens from the original text. We present and analyse one example of such a semantic error prediction dataset, which we generate from an error correction dataset. As neural baselines, we use BERT, RoBERTa, and LLAMA2 embeddings for SEP. We show that our models can already improve downstream applications, such as predicting essay vocabulary scores.
GRAMEX: Generating Controlled Grammar Exercises from Various Sources
Authors: Toussaint Guillaume , Parmentier Yannick
Published: October 2024

This paper presents Gramex, an application designed to assist teachers in the creation of learning materials, namely grammar exercises. More precisely Gramex leverages state-of-the-art parsing techniques to morpho-syntactically annotate texts and turn these into grammar exercises while aligning these with official curricula. Allowing teachers to freely select excerpts of texts from which to generate specific grammar exercises aims to increase learners' engagement in educational activities. Gramex currently supports 4 types of exercises (Fill-in-the-Blanks, Mark-the-Words, Single and Mutliple Choice questionnaires) and 3 output formats (JSON objects, printable workbooks, H5P interactive content). Gramex is under active development and has been experimentally used with teachers of L1-learners in elementary and middle French schools.
LLM chatbots as a language practice tool: a user study
Authors: Tyen Gladys , Caines Andrew , Buttery Paula
Published: October 2024

Second language learners often experience language anxiety when speaking with others in their target language. As the generative capabilities of Large Language Models (LLMs) continue to improve, we investigate the possibility of using an LLM as a conversation practice tool. We conduct a user study with 160 English language learners, where an LLM chatbot is used to simulate real-world conversations. We present our findings on 1) how an interactive session with a chatbot might impact performance in real-world conversations; 2) whether the learning experience differs for learners of different proficiency levels; 4) how changes in difficulty affects the learner's experience; and 3) how online, synchronous conversation provided by an LLM compares with a purely receptive experience. Additionally, we propose a simple yet effective way to detect linguistic complexity on-the-fly: clicking on words to reveal dictionary definitions. We demonstrate that clicks correlate well with linguistic complexity and indicate which words learners find difficult to understand.
Sailing through multiword expression identiﬁcation with Wiktionary and Linguse: A case study of language learning
Authors: Überrück-Fries Till , Savary Agata , Dryja´nska Agnieszka
Published: October 2024

Multiword expressions (MWEs), due to their idiomatic nature, pose particular challenges in comprehension tasks and vocabulary acquisition for language learners. Current NLP tools fall short off comprehensively aiding language learners when encountering MWEs. While proficient in identifying MWEs seen during training, current systems are constrained by limited training data. To address the specific needs of language learners, this research integrates expansive MWE lexicons and NLP methodologies as championed by Savary et al. (2019a). Outcomes encompass a specialized MWE corpus from Wiktionary, the enhancement of Linguse, a reading application for language learners, with MWE annotations, and empirical validation with French language students. The culmination is an MWE identifier optimally designed for language learner requirements.
Non-Surgical Treatment of Residual Cyst in Maxillary Anterior Region of an 11-year-old Patient: A Case Report
Authors: Mathur Jyoti , Patel Hinal , Patel Chirag , Pansheriya Ekta
Published: October 2024

We aim to report a case of residual cyst in an 11-year-old male patient, which was treated by marsupialization as a conservative alternative to surgical enucleation.
An 11-year-old male patient reported to our department with a painless swelling of approximately 1.5x1 cm in size intraorally, both in the maxillary right buccal and palatal region for about 1 month. On fine needle aspiration, a yellow-coloured highly viscous fluid was observed which on histopathological examination revealed an infected cyst. This along with the clinical examination and history confirmed the diagnosis of a residual cyst. Marsupialization was chosen as a conservative treatment due to the size of the cyst and the age of the patient. Weekly follow-up and dressing change were carried out for 6 months which lead to a complete resolution of the cyst with continuous normal development of the occlusion. No adverse effects such as fever, infection, or pus discharge were seen at any time during treatment.
We have been able to design a treatment protocol which has provided us with a nonsurgical solution for large cystic lesions in growing patients without adverse effects for the complete duration of treatment.
Marsupialization should be considered as a treatment option for large residual cysts, especially in pediatric patients.

Key Words - Marsupialization, Maxilla, Mixed dentition, Residual cyst
Acute and long-term SARS-CoV-2 infection and neurodegeneration processes—circulus vitiosus
Authors: Krahel Weronika Daria , Bartak Michalina , Cymerys Joanna
Published: October 2024

The global pandemic of COVID-19 caused by SARS-CoV-2 has had a devastating impact. Although many survived the acute effects of the pandemic, a significant number of survivors, including those with only mild symptoms, are now experiencing a prolonged and debilitating post-viral syndrome known as LC/PASC (long COVID/post-acute sequelae of SARS-CoV-2). Typical symptoms of LC/PASC include fatigue, breathlessness, chest pain, impaired cognition, difficulty sleeping, fever and gastrointestinal symptoms. Anxiety and depression can also last for weeks to months and range from mild to disabling. The association between neuropsychiatric symptoms and SARS-CoV-2 infection raises questions about the possible routes of SARS-CoV-2 entry to the central nervous system (CNS) and long-term effects of the virus on the CNS, their molecular basis, and the potential risk of neuronal damage associated with the subsequent development of neurodegenerative diseases.
Causal association between gastrointestinal diseases and coronary artery disease: a bidirectional Mendelian randomization study
Authors: Wang Zhuoxi , Ban Jifang , Zhou Yabin , Qie Rui
Published: October 2024

Background

Coronary artery disease (CAD) has been a dominating reason of mortality globally due to its complexity of etiology. A variety of gastrointestinal disorders (GDs) have been accounted to be related to CAD. Thus, this study aims to determine their causal relationship by two-sample Mendelian randomization (MR) analysis.

Methods

Single-nucleotide polymorphisms (SNPs) relevant to 22 GDs were employed as instrumental variables from the genome-wide association summary (GWAS) datasets. Genetic associations with CAD and HF were acquired from UK Biobank, FinnGen, and other GWAS studies. We conducted a univariable MR (UVMR) analysis followed by a meta-analysis. A multivariable MR (MVMR) analysis was then performed with smoking and body mass index (BMI) as justifications. Also, a bi-directional MR analysis was leveraged to verify the reverse causal correlations.

Results

Generally, UVMR analyses separately observed the causal effects of GDs on CAD and HF. Genetic liability to gastroesophageal reflux disease displayed a positive association with both CAD (OR=1.19; 95%CI: 1.01-1.41) and HF (OR=1.22; 95%CI: 1.00-1.49) risk; genetic liability to celiac disease separately attributed to CAD (OR=1.02; 95%CI: 1.01-1.03) and HF (OR=1.01; 95%CI: 1.00-1.02), which also maintained after MVMR analysis. Besides, we observed mutually causal associations between CAD and celiac disease.

Conclusion

Our work suggested that genetic susceptibility to some GDs might causally increase the risk of CAD and HF, emphasizing the importance of preventing CAD in patients with GDs.
Riverine macroplastic survey along the segments of Tullahan River in Metro Manila, Philippines
Authors: Talavera Allyza L. , Dalida Lorrayne Faye M. , Diola Ma. Brida Lea D.
Published: October 2024

The Philippines is one of the world’s main contributors to global marine plastic pollution. However, field data remains scarce, so model estimates of riverine plastic pollution may be inaccurate. This paper aims to characterize the macrolitter observed along the Tullahan River, with focus on plastics, passing through the barangays of Quezon City and Valenzuela City in Metro Manila. The impact of solid waste management and land use activities on plastic flux were also investigated. For the floating litter, visual counting and float method were used to determine the plastic flux and river velocity, respectively. Riverbank litter was collected manually to characterize it based on plastic product and polymer type. Results show that the macroplastic flux was lowest on the site where residential houses are farthest from the stream. Waste characterization revealed that riverbank litter was primarily plastic – 30%–41% were residuals, and 5%–21% were recyclables. Both methods revealed that wrappers and thin PE plastics are the top contributors to riverine macroplastic pollution. Therefore, the entry of macroplastics into the river may be due to land use activities and weak enforcement of existing solid waste management (SWM) policies. The points discussed in the study can help in improving SWM and land use planning. The results can also increase the accuracy of model estimates.
Forest certification and economic insights: a European perspective
Authors: Corticeiro Sofia , Brás Gonçalo , Tomé Margarida , Lillebø Ana , Vieira Helena
Published: October 2024

In recent years, there has been an increasing demand for forest certification and certified forest products in Europe. This trend is related to major worldwide challenges, such as the need to decarbonize the economy and mitigate climate change but also social and consumer demands for wider fair trade. However, whether forest certification influences economic valorization in forestry remains a question. The aim of this study is to analyze forest certification levels across Europe and identify potential relationships between the level of certification in forest areas and relevant economic indicators at country level. This study collected openly available data on total and certified forest areas, economic indicators, and environmental indicators for 28 European countries and explored the correlation between certified forest areas and economic performance in the forestry sector. Findings show that forest certification can significantly improve the economic performance of European forests. It has a more pronounced positive effect on economic incomes than on costs’ reduction. While certification costs do rise with the extent of forest area, they tend to stabilize at larger scales, suggesting that the certification process is economically sustainable and scale is relevant. Czechia and the Netherlands stand out for having the highest net values added related to forest certification, reflecting an effective economic exploration of forest resources. This study offers new perspectives to natural and social scientists, as well as to industry and policy makers, by proving contextualized data to support decision making. Additionally, it provides hints for further studies and policy guidelines on sustainable development and the impact of forest certification schemes.
ONT sequencing identifies a high prevalence of crt sensitive, triple mutant dhfr and single mutant dhps parasites within an ANC population in Nigeria
Authors: Adegbola Adebanjo Jonathan , Ndwiga Leonard , Wamae Kevin , Osoti Victor , Bolaji Oluseye Oladotun , Bejon Philip , Ochola-Oyier Lynette Isabella
Published: October 2024

Background

Malaria in pregnancy is a major public health issue, particularly among vulnerable populations in malaria-endemic sub-Saharan African countries. To mitigate its risks, WHO recommends sulphadoxine-pyrimethamine (SP) for chemoprevention and artemisinin-based combination therapy (ACT) to treat uncomplicated Plasmodium falciparum malaria. These interventions have helped to alleviate the risk associated with malaria in pregnancy; however, in the context of the emergence of SP- and ACT-resistant P. falciparum, maintained efficacy is under threat. Molecular surveillance is a reliable tool to monitor the emergence of resistance where molecular markers are known. Thus, the objective of the study was to use a multiplexed amplicon Oxford Nanopore sequencing approach to assess the molecular markers for antimalarial resistance among pregnant women in Nigeria.

Methods

Dried blood spots (DBS) were collected from pregnant women who received IPTp-SP at the enrollment and follow-up visits. P. falciparum genomic DNA was extracted by the Chelex® method and Pf18S qPCR was used to detect parasite DNA in each sample. With nested PCR assays, fragments of Pfdhps, Pfdhfr, Pfmdr1, Pfcrt, Pfk13 and Pfama1 genes were amplified and multiplexed amplicon-based sequencing was conducted on the minION Oxford Nanopore Technology.

Result

In total, 251 pregnant women were enrolled in the study and 457 DBS samples were collected. P. falciparum genomic DNA was detected in 12% (56/457) of the samples, 31 at baseline and the remaining during the follow-up visits. Pfama1, pfk13, Pfdhps, Pfdhfr, Pfmdr1 and Pfcrt were successfully sequenced in a single run. Notably, k13 artemisinin resistance mutations were absent, the frequencies of Pfdhfr and Pfdhps SP resistance haplotypes, IRN for pyrimethamine resistance and ISGKA/IAGKA associated with sulphadoxine resistance were 82% (36/44) and 64% (27/42), respectively, and the Pfcrt CVIET resistant haplotype was at approximately 22% (7/32).

Conclusion and recommendations

Here a multiplexed amplicon-based ONT assay established that triple mutant Pfdfhr-IRN, double mutant Pfdhps-SG haplotypes and the chloroquine sensitive strain were prevalent among pregnant women in Nigeria.
Prenatal diagnosis and postnatal follow-up of 15 fetuses with 16p13.11 microduplication syndrome
Authors: Zhao Yan , Song Lina , Zhang Shuxia , Hou Fei , Shan Shan , Jin Hua
Published: October 2024

Background

The clinical phenotypes of 16p13.11 microduplication syndrome have been extensively reported in previous studies, mostly about adults and children, with limited information available on fetal cases. This study aims to explore the genotype-phenotype correlation of fetuses with 16p13.11 microduplication syndrome and analyze the characteristics of prenatal diagnosis indications and provide clinical information for prenatal and postnatal genetic counseling.

Methods

We conducted a retrospective analysis of 3,451 pregnant women who underwent invasive prenatal diagnosis for SNP array between January 2018 and December 2022 at the Jinan Maternal and Child Health Hospital. Descriptive statistical analysis was performed on the prenatal diagnosis indications, pedigree analysis, pregnancy outcomes and postnatal follow-up of 15 fetuses with 16p13.11 microduplication syndrome.

Results

SNP array revealed that 15 fetuses had duplications in the 16p13.11 region with varying prenatal diagnosis indications. Among the cases, 6/15 exhibited ultrasound abnormalities, 5/15 had abnormal chromosomal copy number variations as indicated by non-invasive prenatal testing (NIPT), one case involved advanced maternal age, and 3/15 had other abnormalities. 16p13.11 microduplication syndrome was closely related to ultrasound abnormalities, especially structural abnormalities and soft marker anomalies (abnormal ultrasonic soft indicators), while the indication of NIPT could improve the detection rate of copy number variations (CNVs) in this region. Only 7/15 fetuses underwent pedigree verification, with one case of de novo 16p13.11 microduplication, and the others inherited from one parent. Pregnancy was terminated in 2/15 cases and the outcome of one case is unknown due to loss to follow-up. Among the remaining cases, only one case exhibited a ventricular septal defect, while another presented with omphalocele. No other obvious abnormalities were reported postnatally.

Conclusion

The prenatal phenotypes of fetuses with 16p13.11 microduplication were highly associated with ultrasound abnormalities but lacked specificity. Comprehensive genetic tracing, outcome analysis, and follow-up are essential for providing accurate prenatal and postnatal genetic counseling.
Contribution of tryptophan and its metabolites to transplant outcome: a mini-review
Authors: Donoso-Meneses Darío , Padilla Cristina , Moya-Guzmán María José , Alegre Maria-Luisa , Pino-Lagos Karina
Published: October 2024

Long-term tolerance in the absence of immunosuppressive drugs is a major goal in the transplantation field, not yet attained. Recent research on the role of commensal microbiota in the control of immunity has opened new avenues for the search of novel clinical interventions. Indeed, products of intestinal metabolism generated by both host cells and the microbiota have been identified as modulators of the immune response. Among these, tryptophan (Trp) and its derivatives are being investigated to understand their impact on alloimmunity and their potential usefulness as therapeutic targets to improve allograft survival. Here, we reviewed the latest findings on the contribution of Trp metabolic pathways to transplant outcomes.
Functional genomic analysis of the 68-1 RhCMV-Mycobacteria tuberculosis vaccine reveals an IL-15 response signature that is conserved with vector attenuation
Authors: Sung Cheng-Jung , Whitmore Leanne S. , Smith Elise , Chang Jean , Tisoncik-Go Jennifer , Barber-Axthelm Aaron , Selseth Andrea , Feltham Shana , Ojha Sohita , Hansen Scott G. , Picker Louis J. , Gale Michael
Published: October 2024

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is a deadly infectious disease having a major impact on global health. Using the CMV vector for development of novel vaccines is a promising new strategy that elicits strong and durable, high frequency memory T cell responses against heterologous immunogens. We conducted functional transcriptomic analysis of whole blood samples collected from cohorts of rhesus (Rh) macaques that were administered RhCMV/TB vector using a prime-boost strategy. Two modified CMV vectors were used in this study, including 68-1 RhCMV/TB-6Ag (encoding 6 Mtb protein immunogens, including Ag85A, ESAT-6, Rv3407, Rv2626, Rpf A, and Rpf D) and its attenuated variant, 68-1 RhCMV/Δpp71-TB-6Ag (a cell-to-cell spread-deficient vaccine vector lacking the Rh110 gene encoding the pp71 tegument protein). Bulk mRNA sequencing, differential gene expression, and functional enrichment analyses showed that these RhCMV/TB vaccines induce the innate and adaptive immune responses with specific transcriptomic signatures, including the IL-15-induced protective gene signature previously defined to be linked with protection against simian immunodeficiency virus (SIV) by the 68-1 RhCMV/SIV vaccine. While both vectors exhibited a transcriptomic response of the IL-15 protective signature in whole blood, we show that lack of pp71 does not maintain induction of the protective signature for the full duration of the study compared to the parental non-attenuated vector. Our observations indicate that RhCMV vector vaccines induce a transcriptomic response in whole blood that include a conserved IL-15 signature of which vector-encoded pp71 is an important component of response durability that upon future Mtb challenge may define specific vaccine protection outcomes against Mtb infection.
Advances of natural hydrogel-based vascularization strategies for soft tissue repair
Authors: Xia Zhuoheng , Guo Bin , Wu Danni , Yang Fan , Ding Yude
Published: October 2024

Regeneration of soft tissues, especially those requiring complex vascularization, is a major challenge in the field of tissue engineering. The current types of tissue engineering scaffolds include sponges, electric spinning silk, hydrogels, and 3D printed biomaterials. Among them, hydrogels have the unique property of mimicking extracellular matrix (ECM), which can provide a relatively stable microenvironment for cellular activities and facilitate cell adhesion, proliferation, and differentiation; thus, have become a promising scaffold. In this paper, we present a review of the commonly used types of natural hydrogels and their applications as scaffolds in tissue vascularization. First, we enumerate the importance and advantages of several types of commonly used hydrogels of natural origin in terms of fabricating vascularized tissues or organs. Second, we discuss two different formation modalities of blood vessels, as well as natural hydrogel-based vascularization strategies, including carrying growth factors, stem cell delivery, special scaffold structures and pharmaceutical-enhanced strategy. In addition, we describe the crosslinking strategies of hydrogels as scaffolds for regeneration of vascularized soft tissues, as well as the factors affecting it. Finally, new insights are provided for the development of natural hydrogel-based vascularized soft tissue regeneration research.
Isolated melanoma metastasis in a patient with large congenital nevus without detectable primary melanoma: a case report and review of literature
Authors: Pabianek Marta , Jatczak-Grochala Ilona , Lesiak Aleksandra , Narbutt Joanna , Siekierko Aleksandra , Stasikowska-Kanicka Olga , Ciążyńska Magdalena
Published: October 2024

Giant congenital pigmented nevi constitute an extremely diverse group of skin lesions with varying morphologies. These nevi are often associated with many clinical implications, such as increased risk of melanoma and the presence of neurocutaneous melanosis, with melanoma being the primary concern. We present a rare case of a 62-year-old patient with a giant congenital birthmark who reported to the oncology department due to a tumor in the lower abdomen detected during an ultrasound examination. A biopsy of the lesion showed the presence of melanoma metastasis. Four independent dermatologists performed a dermoscopic examination of the patient’s skin and mucous membranes. In the PET/CT examination, apart from the previously described change in the lower abdomen, no metabolically active foci with features of malignant growth were found. The patient underwent surgical removal of the lesion in the lower abdomen. The postoperative histopathological examination confirmed the presence of metastasis of melanoma in the subcutaneous tissue of the abdomen with no connection to the epidermis. The BRAFV600 mutation was not found in the molecular test. For stage IV R0 melanoma with distant metastasis, with stage T0N0M1a, the only adjuvant treatment option following radical resection is nivolumab. After a rheumatological consultation, the patient was qualified for adjuvant treatment with nivolumab.
Regenerative topical skincare: stem cells and exosomes
Authors: Taub Amy Forman
Published: October 2024

Regenerative medicine and its offshoot, regenerative aesthetics, have been hot topics over the past 15 years. Studies with heterochronic parabiosis and others pointed to a circulating factor that could rejuvenate aging tissues. Stem cells are known to have regenerative powers, but they are difficult to extract, grow in culture or maintain. Exosomes (EVs), extracellular vesicles from 30 to 150 nm, have been discovered to be a primary form of communication between tissues. Using stem cell supernatants to generate desirable EVs has become a heralded treatment for aesthetic treatments. Preclinical studies with EVs show many benefits including improving the function of fibroblasts and healing wounds more rapidly. Clinical studies with EVs in aesthetics are very few. Thus, the excitement generated by EVs should be tempered with realism about the lack of available treatment products as well as the lack of scientific proof.
Constrictive bronchiolitis and paraneoplastic pemphigus caused by unicentric Castleman disease in a young woman: a case report
Authors: Chen Ruxuan , Teng Yaqun , Xiao Yinbo , Zhang Lu , Han Xianlin , Wang Weibin , Lu Zhaohui , Tian Xinlun
Published: October 2024

Introduction

Constrictive bronchiolitis is a rare and severe condition characterized by progressive and irreversible obstruction of small airways. Constrictive bronchiolitis could be part of paraneoplastic autoimmune multiorgan syndrome secondary to Castleman disease.

Case description

A 20-year-old female presented with progressive exertional dyspnea and severe obstructive ventilatory dysfunction. She also experienced recurrent and painful oral mucosal erosions. Upon investigation for underlying conditions, contrast-enhanced CT imaging revealed a pelvic mass exhibiting marked enhancement and hypertrophied vessels. A diagnosis of Castleman disease was confirmed via ultrasound-guided percutaneous biopsy of the pelvic tumor. Autoantibodies indicative of paraneoplastic pemphigus were detected using indirect immunofluorescence on rat bladder tissue. Complete surgical resection of the pelvic mass was undertaken with the collaborative efforts of a multidisciplinary team. Despite resolution of mucocutaneous lesions, symptoms of constrictive bronchiolitis persisted after the surgery. Subsequently, the patient underwent lung transplantation and demonstrated significant improvement in lung function.

Conclusion

Timely diagnosis and comprehensive multidisciplinary management of this rare and life-threatening syndrome are crucial for enhancing patient outcomes.
Comparing ovarian reserve parameters after laparoscopic endometrioma resection in the follicular vs. luteal phase: a prospective cohort study
Authors: Takmaz Ozguc , Asoglu Mehmet Resit , Ceyhan Mehmet , Unsal Gozde , Gungor Mete
Published: October 2024

Objective

To evaluate whether performing laparoscopic endometrioma surgery in the follicular or luteal phase affects changes in ovarian reserve.

Methods

This prospective cohort study was conducted in a university-affiliated hospital. A total of 55 women who underwent unilateral laparoscopic endometrioma removal were included in the study. Of these, 28 were in the follicular phase of the menstrual cycle (follicular group), and 27 were in the luteal phase (luteal group). The primary outcomes were the rates of decreased anti-Mullerian hormone (AMH) levels and antral follicle counts (AFC) 6 months after the surgery, which were compared between the groups.

Results

The groups were similar in patient characteristics and endometrioma sizes. AMH levels and AFCs were significantly lower in the post-operative 6th month compared with their pre-operative values (p < 0.05 for both groups). The rate of decrease in AMH levels 6 months after the surgery was not significantly different between the follicular and luteal groups (24.5 and 19.5%, respectively, p > 0.05). Similarly, the rate of decrease in AFCs 6 months after the surgery did not differ between the groups (13.4 and 14.3%, respectively, p > 0.05).

Conclusion

Performing laparoscopic endometrioma surgery, whether in the follicular or luteal phase, does not seem to affect the changes in the ovarian reserve.

Clinical trial registration

https://clinicaltrials.gov/study/NCT03484546, identifier NCT034845.
Detection of cardiac neuroendocrine tumour metastases by somatostatin receptor PET/CT: a systematic review and meta-analysis
Authors: Campanale Daniela , Imperiale Alessio , Albano Domenico , Rizzo Alessio , Piccardo Arnoldo , Treglia Giorgio
Published: October 2024

Background

Cardiac neuroendocrine tumour metastases (CNTM) are rare, but advancements in molecular imaging including somatostatin receptor PET/CT (SSTR-PET/CT) could lead to a more frequent identification. The aim of this article is to perform a systematic review and meta-analysis on the detection of CNTM by SSTR-PET/CT.

Methods

A comprehensive literature search of studies on CNTM detected by SSTR-PET/CT was carried out. Three different bibliographic databases were screened (Cochrane library, PubMed/MEDLINE, EMBASE) until 20 August 2024. Two review authors independently selected the eligible original articles and performed the quality assessment and the data extraction. Main findings of eligible studies were summarized and a proportion meta-analysis on the prevalence of patients with CNTM among those with neuroendocrine neoplasm (NEN) performing SSTR-PET/CT was carried out using a random-effects model.

Results

Ten articles reporting data on 163 patients with CNTM were included in the systematic review. SSTR was able to detect CNTM earlier compared to other radiological imaging techniques. Most patients with CNTM had other metastatic sites and CNTM were often asymptomatic. The meta-analysis of seven articles demonstrated a pooled prevalence of 1.5% (95% confidence interval: 1.0–1.9%) of patients with CNTM (n = 119) among those performing SSTR-PET/CT for NEN (n = 9,300). Moderate statistical heterogeneity was found (I2 test: 62%).

Conclusion

Evidence-based data demonstrate that SSTR-PET/CT enables early and better detection of CNTM compared to other radiological imaging methods. CNTM are encountered with a pooled prevalence of 1.5% of NEN patients performing SSTR-PET/CT. Prospective and multicentric studies are warranted to better clarify the impact of CNTM detection by SSTR-PET/CT on overall survival and clinical decision-making in NEN patients.
Effect of conservation agriculture on soil fungal diversity in rice-wheat-greengram cropping system in eastern Indo-Gangetic plains of South Asia
Authors: Kumar Rakesh , Choudhary Jaipal Singh , Naik Sushanta Kumar , Mishra Janki Sharan , Banra Sushmita , Poonia Shish Pal , Mondal Surajit , Das Anup , Rao Karnena Koteswara , Kumar Virender , Bhatt Bhagwati Prasad , Chaudhari Suresh Kumar , Malik Ram Kanwar , McDonald Andrew
Published: October 2024

Introduction

Conservation agriculture (CA) is emerging as an eco-friendly and sustainable approach to food production in South Asia. CA, characterized by reduced tillage, soil surface cover through retaining crop residue or raising cover crops, and crop diversification, enhances crop production and soil fertility. Fungal communities in the soil play a crucial role in nutrient recycling, crop growth, and agro-ecosystem stability, particularly in agricultural crop fields.

Methods

This study investigates the impact of seven combinations of tillage and crop residue management practices of agricultural production systems, including various tillage and crop residue management practices, on soil fungal diversity. Using the Illumina MiSeq platform, fungal diversity associated with soil was analysed.

Results and discussion

The results show that the partial CA-based (pCA) production systems had the highest number of unique operational taxonomic units (OTUs) (948 OTUs) while the conventional production system had the lowest number (665 OTUs). The major fungal phyla identified in the topsoil (0–15 cm) were Ascomycota, Basidiomycota, and Mortierellomycota, with their abundance varying across different tillage-cum-crop establishment (TCE) methods. Phylum Ascomycota was dominant in CA-based management treatments (94.9±0.62), followed by the partial CA (pCA)-based treatments (91.0 ± 0.37). Therefore, CA-based production systems play a crucial role in shaping soil fungal diversity, highlighting their significance for sustainable agricultural production.
Characterization of the emerging recombinant infectious bronchitis virus in China
Authors: Wang Suchun , Pan Junhui , Zhou Kaiyutai , Chu Dianfeng , Li Jinji , Chen Yiping , Qi Qian , Wei Shimeng , Li Chao , Sui Jinyu , Wu Faxing , Li Jinping , Hou Guangyu , Liu Hualei , Wang Kaicheng
Published: October 2024

Infectious bronchitis virus (IBV) can cause serious harm to poultry industry. It is belong to Coronaviridae which is highly variable. A kind of emerging recombinant IBV (ahysx-1) has been detected in chicken from China in 2016. To understand the epidemiology and characterization of the emerging recombinant IBV, 35,455 samples of chickens from the 15 provinces in China were collected and detected. One hundred and ninety-six out of the 537 flocks (positive rate, 36.49%), and 908 out of 35,455 samples (positive rate, 2.56%) were positive in the detection. The results showed that the emerging recombinant IBV was pandemic in China. Thirteen emerging recombinant IBV isolates were selected and continuous subcultured to the fourth generation and analyzed by Next-generation sequencing. Compared with the reported sequence of ahysx-1, the genomic analysis showed that multiple position insertions and deletions were in 1a gene, 3b gene, M gene and N gene. The identity of the S gene nucleotide sequence between all the 13 emerging recombinant IBV isolates and reference stain ahysx-1 were 98.1–99.1%, while the identity of amino acid sequence were 98.0–99.8%. To better understand the recombination mechanism of the emerging recombinant IBV, the genomic sequence of the 13 isolates were compared with turkey coronavirus or guinea fowl coronavirus. The results suggest that all the 13 emerging recombinant IBV isolates were likely to be the recombination of turkey coronavirus or guinea fowl coronavirus with IBV. Turkey coronavirus or guinea fowl coronavirus as minor parents are the donors of S gene. The major parents donors of the genome backone of these recombination events were lineages GI-19 or GVI-1 of IBV. One isolate (IBV/chicken/Henan/H1173/2021) was selected for pathogenicity analysis. The results showed that IBV/chicken/Henan/H1173/2021 was avirulent to SPF embryonated eggs, but could cause intestinal symptoms in of chicks. This study provides a foundation for understanding the epidemic situation and characterization of the emerging recombinant IBV. It is of great significance for the prevention and control of avian coronavirus infection.
Design and synthesis of quorum-sensing agonist for improving biofilm formation and the application of Acidithiobacillus thiooxidans in bioleaching
Authors: Tang Deping , Xi Yanpeng , Song Wentao , Li Mengjiao , Liu Yali , Lin Yanyan , Zhang Ran , Mao Aihong
Published: October 2024

Introduction

Currently, there are few investigations on the effect of a synthetic exogenous quorum sensing (QS) agonist on the bioleaching rate of Acidithiobacillus thiooxidans (A. thiooxidans).

Methods

We created AHL (N-acyl-homoserine lactone) analogues and investigated their effects on A. thiooxidans biofilm formation, adsorption kinetics, bioleaching, and mechanism.

Results

The findings revealed that N-(3-thiolactone)- dodecylamine (Y3) significantly increased the biofilm formation of A. thiooxidans in 96-well plates and sulfur sheets. Adsorption tests revealed that Y3 increased the adhesion rate, adsorption constant, and adsorption efficiency. Bioleaching tests indicated that Y3 boosted bioleaching efficiency, with Ni2+ and Cu2+ bioleaching rates increasing by 49.13% and 33.03%, respectively. Transcriptomic analysis revealed that Y3 increased genes associated with QS pathways and biofilm formation, particularly afeI, which was dramatically elevated 42 times.

Discussion

The study laid the groundwork for a better understanding of the mechanics of A. thiooxidans biofilm formation, which could help improve the potential application of A. thiooxidans in bioleaching.