bluuebunny/crossref_metadata_2025 huggingface dataset:
A Dynamic, D-dimer-based Thromboprophylaxis Strategy in Patients with COVID-19
Authors: Bhoopat Lantarima , Martynova Anastasia , Choi April , Pattharanitima Pattharawin , Han Semi , Du Senxi , Syed Ibrahim , Chan Catherine , Oh Esther E , Borok Zea , Liebler Janice , Wilson Melissa Lee , Tantiyavarong Pichaya , Connell Casey O
Published: August 2024

Background COVID-19 pandemics increases venous thromboembolism (VTE) risk during hospitalization, despite prophylactic anticoagulation. Limited radiological diagnosis in pandemic requires a guided protocol for anticoagulant adjustment. Methods This retrospective cohort study was conducted at a single center as part of a quality improvement program evaluating the efficacy and safety of anticoagulation protocols. The study focused on implementing a guideline for anticoagulant dosing protocol based on dynamic changes in D-dimer levels in COVID-19 hospitalized patients. The dosing guideline allowed for dose escalation from standard prophylactic levels to escalated prophylactic or therapeutic levels, depending on the patient's risk profile for VTE. The primary endpoints included in-hospital survival comparing between fix and dynamic adjustment treatment groups. Secondary endpoints encompassed major and clinically relevant non-major bleeding (CRNMB) events, incidence of breakthrough thrombosis, length of hospitalization and ICU stay, days of mechanical ventilator use, and survival duration. Findings Among the 260 COVID-19-infected patients hospitalized between March 15th and June 15th, 2020. The patients received fixed anticoagulant dosage in 188, 72.3%) patients, while 72 (27.7%) were up-titrated according to the protocol. In-hospital survival at 30 days demonstrated superiority among patients whose anticoagulation was up-titrated to either escalated prophylactic or therapeutic (80.2%) compared to receiving fixed anticoagulant dosage (51.3%) (p=0.01). Bleeding events were significantly higher in up-titrate group (12.5%) compared to fixed anticoagulant dosage group (2.13%). Most of them are CRNMB. Conclusion A dynamic, D-dimer-based dose escalation of anticoagulation for hospitalized patients with COVID-19 holds promise in improving in-hospital mortality rates without a significant increase in fatal bleeding events.
Building a digital supportive supervision system for improving health service delivery in Low- and Middle-Income countries through the collaborative requirements development methodology (CRDM): Experience from Tanzania
Authors: German Chrisogone Justine , Kengia James Tumaini , Mwanyika Henry , Makaranga Joseph T. , Werner Laurie , Benadotte Christina , Kisanga Auson , Macha Tumainiel , Weja Joel , Mugeta Stephano , Kinyenje Erick S. , Marandu Laura E. , Mwaisengela Syabo M , Ilomo Silvanus , Seiff Sultana , Kapologwe Ntuli , Hokororo Joseph C. , Eliakimu Eliudi S. , Sirili Nathanael , Settle Dykki , Rashid Seif
Published: August 2024

Background Supportive supervision is pivotal for both health service providers and managers to improve the quality of services and health outcomes. Tanzania's digital supportive supervision system is called Afya Supportive Supervision System (AfyaSS ®). The latter was designed and developed using a human-centered approach called Collaborative Requirements Development Methodology (CRDM). This paper describes the experiences of building the digital supportive supervision system through CRDM in Tanzania, a transition from the paper-based supportive supervision system. Methods In 2018, with the support of PATH, the government of Tanzania adopted a participatory human-centered design by carrying out desk reviews of existing guidelines and tools, field visits, stakeholder workshops, and user advisory groups to gather information for developing a digital supportive supervision system. The gathered information was analyzed with the lens of identifying the common challenges and system requirements. Results AfyaSS was successfully developed using CRDM and deployed in all regions across the country. It has consolidated multiple checklists for distinct health domains, and dashboard functionalities to track progress toward health system indicators, objectives, and action plans. As part of the deployment, several resources were developed to aid in the deployment process, such as a comprehensive user manual, facilitator's guide, training slides, and video tutorials. Health workers and managers can be empowered and motivated to implement comprehensive and coherent supportive supervision by using the lessons learned from this digitalization process to transform the current supervision processes to improve the quality of care by offering instruments that promote evidence-based actions. Conclusion A human-centered approach has been shown to be useful in developing digital tools for use in Tanzania’s health system. Tanzania's lessons can be applied in other low- and middle- income countries (LMICs) with similar contexts when considering implementing digital health interventions. While using the human-centered approach, it is crucial to establish a system development roadmap, conduct appropriate training, provide sustained information and communication technology, and management support for unforeseen issues, and ensure ongoing maintenance.
Natural sea water and artificial sea water are not equivalent in plastic leachate contamination studies
Authors: Ullmann Clemens Vinzenz , Arnone Maria Ina , Jimenez-Guri Eva
Published: August 2024

Background Plastic contamination is one of the concerns of our age. With more than 150 million tons of plastic floating in the oceans, and a further 8 million tons arriving to the water each year, in recent times the scientific community has been studying the effects these plastics have on sea life both in the field and with experimental approaches. Laboratory based studies have been using both natural sea water and artificial sea water for testing various aspects of plastic contamination, including the study of chemicals leached from the plastic particles to the water. We set out to test this equivalence, looking at the leaching of heavy metals form plastic particles. Methods We obtained leachates of PVC plastic pre-production nurdles both in natural and artificial sea water and determined the elements in excess from untreated water by Inductively coupled plasma – optical emission spectrometry. We then used these different leachates to assess developmental success in the tunicate Ciona intestinalis by treating fertilised eggs through their development to hatched larvae. Results Here we report that chemical analysis of PVC plastic pre-production pellet leachates shows a different composition in natural and artificial sea water. We find that the Zn leaching from the plastic particles is reduced up to five times in artificial sea water, and this can have an effect in the toxicological studies derived. Indeed, we observe different effects in the development of C. intestinalis when using leachates in natural or artificial sea water. We also observe that not all artificial sea waters are suitable for studying the development of the tunicarte C. intestinalis. Conclusions Our results show that, at least in this case, both types of water are not equivalent to produce plastic leachaetes and suggest that precaution should be taken when conclusions are derived from results obtained in artificial sea water.
Impacts of obesity and obesogenic behaviours on climate change: a systematic review protocol
Authors: D'Agostino Francesco , Vliora Maria , Grillo Elisabetta , Corsini Michela , Ravelli Cosetta , Simonetto Anna , Gilioli Gianni , Mitola Stefania , Flouris Andreas D.
Published: August 2024

Background Unbalanced diet and sedentary habits, defined as obesogenic behaviours, are continuously rising in our society, posing serious threats to public health. Indeed, this lifestyle exacerbates pathological conditions, including obesity, metabolic syndrome, cardiovascular risk and cancer. Climate change, increasing temperatures and extreme weather exacerbate obesogenic behaviours. Climate and environment strongly influence lifestyles and can in some way promote obesogenic behaviour. However, little is known about the effects of obesogenic behaviours/obesity on climate change. To address this relation, we planned a systematic review with eventual meta-analysis. Methods Terms related to obesogenic behaviours and climate change will be used to develop the search algorithm which will be applied to four databases: PubMed, Scopus, Web of Science and EBSCO. Title and abstracts will be screened, and two reviewers will review article full-text. The risk of bias of the eligible publications will be assessed using the Office of Health Assessment and Translation (OHAT) tool. Results will be summarized narratively and if possible, meta-analysis will be performed. Discussion Obesogenic behaviours are recognized threats to public health. Instead, the effects that these habits could have on climate change are less recognized and, yet to date, no systematic review has addressed this relation. In this study we will consider the data currently available to deepen our knowledge about the role of human behaviours on greenhouse gases and climate change, and possibly identify strengths on which we can act. The identification of new strategies and guidelines could have a beneficial impact, on a short term, on public health and, on a long term, would mitigate climate changes, that in turn would reduce the incidence of obesity. Registration In accordance with PRISMA guidelines, our systematic review protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) on 29 October 2023 (registration number CRD42023473107).
Reframing the role of communication in consensual and/or ethical (non)monogamies: A proposal for a change in academic terminology
Authors: Cardoso Daniel
Published: August 2024

In this essay, I focus on the politics and impacts of naming, especially in the social and human sciences, and more specifically on studies that focus on subordinated or discriminated groups. Through this essay, I argue that naming conventions are some of the most important – and dangerous – tools and acts that researchers have at their disposal and, thus, should be employed with the utmost care. Considering the ongoing discussions – both inside and outside of academia – around the terms “consensual non-monogamies” and “ethical non-monogamies”, this essay proposes a novel solution to help create less morally-slanted, and overreaching, hypernyms, or umbrella terms. Here, I provide a rationale for using “explicitness” as a fundamental concept on which to build new classificatory hypernymic terminology. The terminology proposed is equally applicable (and applied) to both monogamies and non-monogamies, and is tripartite: Explicit, Implicit, and Covert. In addition to the terminological proposal, I include in this essay a series of intended limitations and constraints to its usage, its interoperability with other systems, objections to (and responses to) the usage of this system, and advantages of this novel classificatory system, as well as an outline of how this proposal might be improved upon.
Gestational Diabetes Mellitus: Unveiling Maternal Health Dynamics from Pregnancy Through Postpartum Perspectives
Authors: Mora-Ortiz Marina , Rivas-García Lorenzo
Published: August 2024

Gestational Diabetes Mellitus (GDM) is the most frequent pregnancy-related medical issue and presents significant risks to both maternal and foetal health, requiring monitoring and management during pregnancy. The prevalence of GDM has surged globally in recent years, mirroring the rise in diabetes and obesity rates. Estimated to affect from 5% to 25% of pregnancies, GDM impacts approximately 21 million live births annually, according to the International Diabetes Federation (IDF). However, consensus on diagnostic approaches remains elusive, with varying recommendations from international organizations, which makes the comparison between research complicated. Compounding concerns are the short-term and long-term complications stemming from GDM for mothers and offspring. Maternal outcomes include heightened cardiovascular risks and a notable 70% risk of developing Type 2 Diabetes Mellitus (T2DM) within a decade postpartum. Despite this, research into the metabolic profiles associated with a previous GDM predisposing women to T2D remains limited. While genetic biomarkers have been identified, indicating the multifaceted nature of GDM involving hormonal changes, insulin resistance, and impaired insulin secretion, there remains a dearth of exploration into the enduring health implications for both mothers and their children. Furthermore, offspring born to mothers with GDM have been shown to face an increased risk of obesity and metabolic syndrome during childhood and adolescence, with studies indicating a heightened risk ranging from 20% to 50%. This comprehensive review aims to critically assess the current landscape of Gestational Diabetes Mellitus (GDM) research, focusing on its prevalence, diagnostic challenges, and health impacts on mothers and offspring. By examining state-of-the-art knowledge and identifying key knowledge gaps in the scientific literature, this review aims to highlight the multifaceted factors that have hindered a deeper understanding of GDM and its long-term consequences. Ultimately, this scholarly exploration seeks to promote further investigation into this critical area, improving health outcomes for mothers and their children.
Pedagogical means of forming traditional Russian spiritual and moral values in children in the context of additional education
Authors: Bayborodova Lyudmila
Published: August 2024

The article substantiates the relevance of the formation of traditional Russian spiritual and moral values, characterizes the essence and stages of this process, names the approaches and principles of the formation of traditional values. Pedagogical means of forming values are considered, among Wich special attention is paid to subject-oriented technologies, project activities, self-government, and children-adult communities.
Effect of Swimming Training on Bone Tissue in Humans
Authors: Ragan Dagmara , Różańska-Smuszkiewicz Gabriela , Smuszkiewicz-Różański Paweł , Kmiotek Weronika , Oronowicz Radosław , Staszczak Paweł , Jaworska Barbara , Długosz Joanna , Bara Maciej , Miłkowski Paweł
Published: August 2024

Introduction and purpose: The skeletal system performs many important functions in the human body. It primarily bears the heavy loads associated with movement, protects internal organs, and participates in the regulation of mineral homeostasis. Through continuous processes of bone remodeling and modeling, optimal levels of calcium and phosphorus in the serum are achieved. The balanced removal of old bone tissue by osteoclasts and the formation of new bone by osteoblasts maintain the mechanical properties necessary for the proper functioning of the musculoskeletal system. Bone modeling has been shown to be activated in response to mechanical loading from physical activity. Conversely, the absence of significant loading (as in space travel, i.e., microgravity conditions) leads to increased bone resorption. Osteocytes, as the most numerous group of cells in the skeletal system, are mechanosensitive and are thought to respond to stimuli such as fluid flow, mechanical deformations, and hydrostatic pressure. In response, they regulate the work of osteoclasts and osteoblasts, translating into the regulation of processes occurring in the bone matrix.[1] It is suspected that the type, intensity, and nature of physical exercises can significantly influence these processes. The aim of this work is to gather information on the impact of swimming training (an example of physical exercise in conditions of partial gravity reduction) on the human skeletal system.
role of lactoferrin in the treatment of upper respiratory tract infections
Authors: Cąkała Marlena , Kozioł Magdalena , Błaszczak Karolina , Podgórniak Kamila , Piotrowska Julia , Skotnicka Joanna , Zajkowska Aleksandra , Witkowska Maria
Published: August 2024

Introduction
            Lactoferrin is a glycoprotein belonging to the group of transferrins found in most body fluids. It has been shown to possess antimicrobial, anti-inflammatory, immunomodulatory and anticancer properties. The increasing availability and widespread use of dietary supplements containing lactoferrin have been observed as supportive measures in managing various infections.
 
Aim of the study
            The objective of this study is to summarize the current knowledge regarding the anti-infective - mostly antiviral - effects of lactoferrin and the justification for its use in the treatment of upper respiratory tract infections.
 
Knowledge summary
            Scientific research has consistently confirmed the effectiveness of lactoferrin against pathogenic microorganisms. The antibacterial effect of this protein is based mainly on the management of available iron resources - an ingredient necessary for bacterial growth. On the other hand, the antiviral activity of this protein is based on the induction of interferon production.
 
 
Conclusion
            Dietary supplements containing lactoferrin are approved by the US Food and Drug Administration (FDA) for supportive use in infections. Lactoferrin exhibits antimicrobial activity supported by research in specific infections. It has a good tolerance and safety profile, therefore it seems that it can be used adjunctively in this indication.
Vitamin B12 (cobalamin) deficiency in gastroenterological diseases - review
Authors: Zatyka Piotr , Opala Dominika , Słomczyński Adam , Pawłowska Agata , Rabneda Michal , Osuch Dobromiła , Janik Piotr
Published: August 2024

Introduction: Vitamin B12 is a water-soluble vitamin found primarily in animal-derived products such as red meat, dairy, and eggs. An essential substance for its absorption is the intrinsic factor, produced by the parietal cells of the stomach. After absorption in the distal ileum, cobalamin acts as a coenzyme in DNA synthesis and the metabolism of fatty acids and homocysteine. In addition to its well-known influence on the nervous system, it has been associated with gastrointestinal diseases according to numerous authors.
Objective: The objective of this study is to gather and analyze literature regarding the associations between vitamin B12 deficiency and gastrointestinal diseases, including gastroesophageal reflux disease (GERD), gastritis, inflammatory bowel disease (IBD), small intestinal bacterial overgrowth (SIBO), and hepatitis C (HCV).
Materials and Methods: A literature review was conducted using the PubMed database with the following search terms: vitamin B12, cobalamin, deficiency, gastrointestinal diseases, GERD, IBD, SIBO, HCV.
Current Knowledge: Vitamin B12 deficiency can be caused by autoimmune factors, dietary insufficiencies, toxin exposure, and malabsorption disorders related to gastrointestinal diseases. Gastrointestinal conditions such as GERD and IBD can both lead to and be exacerbated by cobalamin deficiency. Furthermore, vitamin B12 deficiency may be worsened by prolonged use of proton pump inhibitors (PPIs) and Helicobacter pylori infection.
Conclusions: An adequate amount of vitamin B12 is crucial for gastrointestinal health. Deficiency can significantly impact the course and symptoms of many gastrointestinal diseases. Therefore, monitoring and supplementation of vitamin B12 should be an integral part of managing patients with gastrointestinal conditions.
Maximizing Engagement in Large-Scale Social Networks
Authors: Kroger Samuel , Validi Hamidreza , Hicks Illya V.
Published: August 2024

Motivated by the importance of user engagement as a crucial element in cascading leaving of users from a social network, we study identifying a largest relaxed variant of a degree-based cohesive subgraph: the maximum anchored k-core problem. Given graph [Formula: see text] and integers k and b, the maximum anchored k-core problem seeks to find a largest subset of vertices [Formula: see text] that induces a subgraph with at least [Formula: see text] vertices of degree at least k. We introduce a new integer programming (IP) formulation for the maximum anchored k-core problem and conduct a polyhedral study on the polytope of the problem. We show the linear programming relaxation of the proposed IP model is at least as strong as that of a naïve formulation. We also identify facet-defining inequalities of the IP formulation. Furthermore, we develop inequalities and fixing procedures to improve the computational performance of our IP model. We use benchmark instances to compare the computational performance of the IP model with (i) the naïve IP formulation and (ii) two existing heuristic algorithms. Our proposed IP model can optimally solve half of the benchmark instances that cannot be solved to optimality either by the naïve model or the existing heuristic approaches.

Funding: This work is funded by the National Science Foundation (NSF) [Grant DMS-2318790] titled AMPS: Novel Combinatorial Optimization Techniques for Smartgrids and Power Networks.

Supplemental Material: The online appendix is available at https://doi.org/10.1287/ijoo.2022.0024 .
Unveiling the Cost of Free: How an Ad-Sponsored Model Affects Serialized Digital Content Creation
Authors: Zhang Kaiyu , Wang Qili , Qiu Liangfei , Wang Nan
Published: August 2024

Within the field of serialized digital content, platforms have recently introduced the ad-sponsored model to provide free content and attract readers. Although this model potentially benefits readers by removing financial barriers, its impact on content creators remains unclear. Our study investigates the effects of the ad-sponsored model on the content creators’ productivity by leveraging a policy change on a leading web novel platform as a natural experiment. Our findings indicate a significant decline in content creators’ efforts in the ad-sponsored model, suggesting the potential adverse effects. Our results demonstrate that this decline is primarily due to reduced reader engagement, as readers may perceive lower “sunk costs” with free content compared with paid content. Our findings provide valuable insights for serialized digital content platforms adopting or considering the ad-sponsored model, emphasizing the importance of considering both creator and user dynamics when introducing new business models.
Exploring staff experiences of remote working in a new community rehabilitation team
Authors: Kidd Katherine , Czerwinski-Alley Natasha , Fenton Kelly
Published: August 2024

Background/Aims

Health services required significant adaptation during the COVID-19 pandemic. The remote community enhanced rehabilitation team was created during the pandemic in response to faster discharges. This service evaluation aimed to explore staff experiences of remote working when implementing this new community rehabilitation team.

Methods

Six members of the community enhanced rehabilitation team, including nursing and psychology staff, completed qualitative semi-structured interviews about staff experiences. The interviews explored experiences of delivering clinical care, providing and receiving team support and personal impacts of remote working. Data were analysed using thematic analysis via a critical-realist approach.

Results

Thematic analysis from the interview transcripts revealed five main themes: anxiety related to remote working practices during a global pandemic, work–life balance, developing relationships, limits to remote working and working towards a hybrid model.

Conclusions

Challenges and benefits of remote working were identified along with some mitigations. Moving forward, a hybrid working model would likely benefit both service users and staff.
Mental status examination
Authors: Loader Katie
Published: August 2024

The fundamentals series is a collection of articles that present key procedures and competencies, as outlined in the Nursing and Midwifery Council's Future nurse: standards of proficiency for registered nurses. In this article, Katie Loader provides an overview of the mental status examination and the skills needed to conduct this assessment.
Patient-friendly clinics: exotics
Authors: Valentine Adina
Published: August 2024

Patient-centric care is increasingly better represented across many veterinary practices, particularly in the most commonly kept domestic companion pets. With specialised accreditations such as the International Society of Feline Medicine ‘Cat Friendly Clinic’ award, the Rabbit Welfare Association and Fund ‘Rabbit Friendly Vets’ initiative and the Dogs Trust ‘Dog Friendly Vet Clinics’, veterinary practices and individuals are able to demonstrate their commitment to species-focused practice, incorporating up-to-date techniques and implementing species-specific adaptations to ultimately reduce stress to the patients and owners while simultaneously cementing a pledge to advocate for these patients when they are under veterinary care. Currently, there are fewer available resources or accreditations for the less commonly presented pets, which are often grouped as ‘exotics’ – a large category of animals from a variety of taxonomic groups including avian, reptilian, amphibian, invertebrate, rodent and small mammal species – though this does not mean that they should not be represented or advocated for, in the same way.
Managing Bowen's disease in primary care settings
Authors: Perry Margaret
Published: August 2024

Bowens disease is a rare condition, considered a precursor to squamous cell carcinoma. Because of its similarity to several other skin conditions, accurate diagnosis can be challenging. There are multiple risk factors and several treatment options. This article has hoped to give an overview of risk factors, signs and symptoms, treatment, and complications with the aim of giving nurses and non-medical prescribers increased confidence in recognising this disease.

Bowen's disease is a rare condition thought to affect approximately 15 per 100,000 people in the UK each year. Because of the similarity with other skin conditions, diagnosis can be challenging for clinicians.
Dysphagia: causes, diagnosis and treatment – an update for practice nurses
Authors: Nazarko Linda
Published: August 2024

The number of people with dysphagia is rising in line with population ageing. It is now thought to affect around 5.2 million people in the UK, one adult in 8 ( Boaden et. al, 2019 ). It becomes more common as people age and is associated with neurological problems, frailty and poor outcomes ( Patel et. al, 2018 : Cohen et. al, 2021 ). This article aims to update practice nurses on the clinical features of dysphagia, how to identify it, when to refer and how it is managed.

As many as one adults in eight in the UK are affected by dysphagia. Linda Nazarko looks at what nurses need to know when managing this condition.
Diversity, composition, and role of woody Non-Timber Forest Products in Tawangmangu, Central Java, Indonesia
Authors: HAQQIN FAISYA , ARKAN FIKRI , IBRIZA NAILA MAULIDA , FADHILAH RIRIN NUR , SAFIRA RAISA NOOR , DEWANGGA ARU , KUSUMANINGRUM LIA , THENYA THUITA , SETYAWAN AHMAD DWI
Published: August 2024

Abstract. Haqqin F, Arkan F, Ibriza NM, Fadhilah RN, Safira RN, Dewangga A, Kusumaningrum L, Thenya T, Setyawan AD. 2024. Diversity, composition, and role of woody Non-Timber Forest Products in Tawangmangu, Central Java, Indonesia. Asian J Ethnobiol 7: 68-78. Forests have an important role in supporting biodiversity and providing various ecosystem services vital for human welfare; besides that, forests are also an important resource for Non-Timber Forest Products (NTFP), which are forest products other than timber used by local communities. NTFP can be categorized into fodder, firewood, food wrapping, medicinal plants, ornamental plants, spices, and food. The aim of this research was to analyze biodiversity and the use of NTFP in the villages of Plumbon, Nglebak, and Sepanjang, located in Tawangmangu Sub-district, Karanganyar District, Central Java, Indonesia. Data collection included interviews and field surveys. In the course of the interviews, a total of 62 respondents were engaged. The results showed that 83 plant species belonging to 41 families had been identified for many NTFPs such as (i) medicinal plant, (ii) food, (iii) ornamental plant, (iv) fodder, (v) spices; (vi) firewood; and (vii) food wrapping. The research findings indicate that Plumbon Village (Station A) exhibited the highest NTFP woody plant biodiversity value, with the highest values for each index component, i.e., 2.8 (H'), 5.9 (Dmg), and 0.765 (E). Each village is characterized by distinct dominant plant species: Melastoma malabatrichum dominates Plumbon Village (Station A), Manihot esculenta dominates Nglebak  Village (Station B), and Calliandra houstoniana dominates Sepanjang Village (Station C). Notably, the plant with the highest use value is Tectona grandis, which serves as a medicinal plant, firewood, and food wrapping material. This research provides a deeper understanding of the biodiversity and use of NTFPs in the region, which has important implications for natural resource management and the well-being of local communities.
Phylogenetic analysis of Dengue virus and insect-specific Flavivirus in Aedes aegypti from Gresik, Indonesia 2019
Authors: HAKIM RASYID NOOR , DAMAYANTI MAMIK , FAUZIYAH SHIFA , SUCIPTO TEGUH HARI
Published: August 2024

Abstract. Hakim RN, Damayanti M, Fauziyah S, Sucipto TH. 2024. Phylogenetic analysis of Dengue virus and insect-specific Flavivirus in Aedes aegypti from Gresik, Indonesia 2019. Biodiversitas 25: 2340-2347. The spread of several Flaviviruses, such as Dengue virus and insect-specific Flavivirus, is periodically detected in Indonesia, including Surabaya, which is an endemic area. Gresik, as one of Surabaya's satellite cities, has high traffic mobility between regions, increasing the possibility of viral transmission. In this study, we identified Flaviviruses from Aedes aegypti mosquito isolates from Gresik collected in 2019. We also revealed the possibility of virus transmission from Surabaya to Gresik. The mosquito samples were collected using mosquito trap method. The Flavivirus Partial Nonstructural Protein 5 (NS5) -encoding gene region was isolated via the nested reverse transcription-polymerase chain reaction method. Sequence alignment and phylogenetic analysis were carried out to determine the kinship of Gresik strain virus isolates with the GenBank database. The results revealed that six out of 29 isolated samples (Sample from Duduk Sampeyan (47 and 43), Mengare (212 and 31), Kedamean (58), and Manyar (38)) exhibited a 220 bp DNA band, which corresponds to the NS5 gene. Further analysis using basic local alignment search tool - nucleotide and phylogenetic methods revealed that two sample sequences (38 and 212) are closely related to DENV-1 genotype 1, while the other four (31, 43, 47, and 58) are associated with Insect-Spesific Flavivirus (ISF). The similarity in NS5 partial sequence and genotype classifications of the dengue virus suggests the potential transmission of the virus from Surabaya to Gresik. We hypothesize that this phenomenon is closely linked to the population mobility between the two areas.
The identification of yield components, genetic variability, and heritability to determine the superior cocoa trees in West Papua, Indonesia
Authors: SUPARNO ANTONIUS , ARBIANTO M. A. , PRABAWARDANI SARASWATI , CHADIKUN PAULUS , TATA HERMAN , LUHULIMA FIONA DJUNITA NATALIA
Published: August 2024

Abstract. Suparno A, Arbianto MA, Prabawardani S, Chadikun P, Tata H, Luhulima FDN. 2024. The identification of yield components, genetic variability, and heritability to determine the superior cocoa trees in West Papua, Indonesia. Biodiversitas 25: 2363-2373. One of the obstacles to increasing the productivity of cocoa is the existence of superior cocoa clones. This research, therefore, was carried out to select the superior cocoa tree candidates from the existing cocoa plantation populations over 30 years old, using a descriptive method on the yield components of superior cocoa candidates in PT. Cokran Cocoa Plantation, South Manokwari. This research was conducted from May 2020 to May 2022. The initial information on 32 superior cocoa trees was obtained from the farmers who were involved and worked at the PT. Cokran Cocoa Plantation for 30 years. Cocoa was planted on an area of 1,680 ha with a spacing of 2 x 4 m. Data on the 13 quantitative characters of the cocoa pod and cocoa beans were analyzed using ANOVA (SAS V.9 For Window). These 13 quantitative data, including 11 qualitative data of leaves and fruit were used to analyze the relationship of kinship pattern among the accessions using NTSys ver. 2.1. Results of the research show that 8 cocoa accessions had a high production potential of more than 6,000 g per tree annually, namely CKR-02, CKR-03, CKR-04, CKR-09, CKR-12, CKR-26, CKR-28, and CKR-41 accessions. Accessions that produced 1,000 g of dry cocoa beans in less than 20 pods were CKR-03, CKR-04, CKR-07, CKR-09, CKR-12, CKR-15, CKR-22, CKR-26, CKR-40, and CKR-41. Candidate cocoa clones that have the potency to produce dry cocoa beans with grade AA quality were CKR-03, CKR-04, CKR-12, CKR-26, CKR-40, and CKR-41. Wide phenotypic and genotypic coefficients of variations were found among the 32 accessions. High heritability was produced by pod length, pod girth, pod fresh mass, seed number/pod, seed fresh mass, and seed dry mass. The cluster analysis showed a wide morphological diversity of the 32 cocoa accession candidates based on the yield component characters.
Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken
Authors: INDRIJANI HENI , HILMIA NENA , ANANG ASEP , PANGESTU MUHAMAD SYAHID PANJI
Published: August 2024

Abstract. Indrijani H, Hilmia N, Anang A, Pangestu MSP. 2024. Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken. Biodiversitas 25: 2434-2441. TLR1A is a candidate gene related to the immune system in chickens, which contributes to disease resilience, which could impact their productivity. This study aimed to determine mutations in the TLR1A gene in three indigenous Indonesian chickens namely, Pelung, Black Kedu and Sentul. A total of 127 DNA samples were used and consisted of 38, 41 and 48 respectively for Pelung, Black Kedu and Sentul chickens. DNA was isolated from white blood cells and amplification of TLR1A gene was conducted in part of exon 4 using PCR with specific primer. The sequencing results for the TLR1A gene were analyzed to identify mutations using the BioEdit and MEGA X programs. The results showed genetic polymorphisms in the TLR1A gene in Indonesian indigenous chicken. One synonymous mutation, g.710C>T, in which amino acid coded leusine at 207th, and four non-synonymous mutation, i.e., g.822A>G, altered amino acids coding from threonine to alanine (T245A), g.835C>T, which altered amino acids coding 249th from threonine to methionine (T249M), g.1015G>A that altered amino acids coding 309th from serine to aspargine (S309N) and g.1165T>G that changed amino acid from arginine to proline R359P. All mutation frequencies for the alleles are lower than those for the non-mutation alleles. The non-synonymous mutation of the TLR1A gene might alter the metabolism of this hormone related to the immune system in chickens.
Identification and differentiation of rice ferritin gene in two different chromosomes in several local Indonesian rice varieties
Authors: PERMATASARI SHELA EMILIA , SALAMAH ANDI
Published: August 2024

Abstract. Permatasari SE, Salamah A. 2024. Identification and differentiation of rice ferritin gene in two different chromosomes in several local Indonesian rice varieties. Biodiversitas 25: 2547-2555. The presence of ferritin protein in rice plants indicates a regulatory response to environmental iron stress. It prevents the destructive effects of the chain reaction resulting from Fe2+ accumulation in the cell. This study aimed to detect and identify the location of the ferritin gene (OsFER) in eight local rice varieties in Indonesia. OsFER2, as the target gene was amplified using PCR, visualized by electrophoresis, and then sequenced. The sequencing results were analyzed using DNA Baser, BioEdit, and ClustalX2. The predicted proteins were visualized using the SWISS-MODEL server, Rice Genome Annotation Project Database, and chromosome map tools. The results show that all rice varieties studied have 100% alignment similarity and OsFER characteristics on chromosome 11 at LOC_Os11g01530 and chromosome 12 at LOC_Os12g01530, which have striking differences. The complete protein structure of the complex is found on chromosome 12, while only a portion of alpha-helix ferritin is found on chromosome 11. Differences in the position of the ferritin gene at different chromosomes impact the functional changes in the ferritin protein as an iron homeostasis key role. The two genes show different characteristics and are located at different genomic positions, suggesting a potential regulatory impact on the level of iron stress resistance in Indonesian rice varieties.
Isolation and characterization of plant growth-promoting bacteria from medicinal plants Java cardamom (Amomum compactum) and bitter ginger (Zingiber zerumbet)
Authors: GERALDI ALMANDO , CLEMENT CHRISTOPHER , PERTIWI MAYA DEWI , LESTARI YESYI , PARINNATA DHAMMARUCI HEMADHIRA , ARSAD RIFAID NUR , SADIKIN RAMA ALI , LUQMAN ARIF , SANTOSO HERI , KRISTANTI ALFINDA NOVI , MANUHARA YOSEPHINE SRI WULAN , WIBOWO ANJAR TRI
Published: August 2024

Abstract. Geraldi A, Clement C, Pertiwi MD, Lestari Y, Parinnata DH, Arsad RN, Sadikin RA, Luqman A, Santoso H, Kristanti AN, Manuhara YSW, Wibowo AT. 2024. Isolation and characterization of plant growth-promoting bacteria from medicinal plants Java cardamom (Amomum compactum) and bitter ginger (Zingiber zerumbet). Biodiversitas 25: 2556-2564. Java cardamom (Amomum compactum) and bitter ginger (Zingiber zerumbet) are valuable medicinal plants native to Indonesia with significant economic and pharmacological importance. While their pharmacological properties have been extensively studied, little is known about the role of their endophytic bacterial communities in influencing plant growth and development. Understanding the interactions between these plants and their associated bacteria could provide insights into novel strategies to enhance their cultivation. This study investigates the potential of endophytic bacteria associated with A. compactum and Z. zerumbet in promoting plant growth. Samples were collected from leaf, rhizome, and rhizosphere soil, followed by isolation and characterization of bacterial strains. Molecular identification revealed the presence of Methylobacterium aquaticum, Paenibacillus tyrfis, Priestia megaterium strain 1, Priestia aryabhattai, and Microbacterium arthrosphaerae among the isolated strains from A. compactum, while strains isolated from Z. zerumbet included Enterobacter mori, Pr. megaterium strain 2, and Pr. megaterium strain 3. Those results demonstrated that Pr. megaterium strains exhibited strong phosphate solubilization, nitrogen fixation, and cellulolytic activity, while Pr. aryabhattai and Pa. tyrfis showed significant nitrogen fixation and cellulolytic potential. Additionally, M. aquaticum, Pa. tyrfis, and Pr. aryabhattai exhibited anti-phytopathogenic activity against Xanthomonas campestris. These findings not only highlight the diverse beneficial attributes of the isolated bacterial strains but also suggest their potential application as biofertilizers and biocontrol agents in agriculture, offering a promising avenue for sustainable farming practices.
Morphology characteristic and tuber content of yard cultivated Canna indica (ganyong) in Cibinong, West Java, Indonesia
Authors: NORIKO NITA , SASAERILA YORIANTA HIDAYAT , ANISAH SITI
Published: August 2024

Abstract. Noriko N, Sasaerila YH, Anisah S. 2024. Morphology characteristic and tuber content of yard cultivated Canna indica (ganyong) in Cibinong, West Java, Indonesia. Biodiversitas 25: 2586-2593. Canna indica L. (ganyong) tubers have the potential to be an alternative food and functional food. This study aims to obtain morphology characteristics, including the content of white tubers of C. indica planted in yards in the Cibinong; research methodology by conducting surveys and laboratory analysis. The results showed C. indica can grow in the yard without special treatment. At the age of 8 months, the average 59.8 cm of plant height, 10.8 numbers of leaves, 0.80 mm leaf thickness, 9.14 cm stem diameter, 24.51 cm2 leaf area, 112.64 g dry weight of tuber, 6.9 g dry weight of stem, 6.81 g dry weight of leaves at 34.3°C temperature, 59% humidity, 20086 lux light intensity, 4.85 soil pH, 2.3% organic C, 0.62% total N, 32.13% P2O5, 6.08% K2O, 0.51 me Ca, 0.36 me Mg, 0.31 me K, 0.5 me Na, 5.44 me/100 gr CEC, 3.71 (mg FDA g-¹soil d.w. h-¹) soil enzyme activity and 1.66 (g/cm³) bulk density. The flour from tubers contains 0.58% ash, 0.15% lipid, 1.01% protein, 1.11% crude fiber, 12.78% carbohydrates, 56.51 kcal calories, alkaloid, saponin, flavonoid, triterpenoid, and low antioxidant. Planting in the yard is recommended in the shade of sunlight. Watering and fertilizing including microelements are also required.
Species diversity and ecological roles of macrofungi in Lentang Forest Reserve, Pahang, Malaysia
Authors: MD NOORDIN NOOR AISYAH , ZAINUDIN NUR AIN IZZATI MOHD , KHAIRUDDIN NURUL HASMILA , YUSOF MOHD TERMIZI
Published: August 2024

Abstract. Md Noordin NA, Zainudin NAIM, Khairuddin NH, Yusof MT. 2024. Species diversity and ecological roles of macrofungi in Lentang Forest Reserve, Pahang, Malaysia. Biodiversitas 25: 2615-2622. Macrofungi are high-value forest components with functionally significant roles in the forest ecosystem, however, fungi and their functions remain among the least studied. Therefore, this study aims to unravel the current diversity of macrofungi in Lentang Forest Reserve, located in Pahang, Malaysia to provide data for comparison with other ecosystems. Macrofungal sporocarps were collected from selected sites using convenience sampling. A total of 332 sporocarps were identified based on morphological and Internal Transcribed Spacer (ITS) sequence analysis. Ascomycota and Basidiomycota predominated in the Lentang Forest Reserve, with 28 genera representing 8 families were successfully identified. A Shannon diversity index of 0.454 indicated high fungal diversity in the sampling location. Microclimatic changes do not significantly affect fungal orders and substrates across the studied sites, suggesting random chance rather than systematic influences. The samples of Polyporales had the highest amounts, which showed that microclimate factors affected the make-up of the fungal fruiting community. In harsh microclimates, tough-fleshed fruit bodies were more common. The Agaricomycetes class exhibited the highest species presence, accounting for 89.09% of the identified species. The findings of this study can serve as a valuable checklist for future research on fungal distribution in tropical regions and will significantly contribute to biodiversity conservation efforts.
Identification and validation of reference genes for gene expression study using Quantitative Real-Time PCR in shallot (Allium cepa L. Aggregatum group) based on bulb development phase
Authors: SULISTYANINGSIH ENDANG , SAWITRI WIDHI DYAH , HANDAYANI VALENTINA DWI SUCI , WICAKSONO ADDIN WAHYU , SILALAHI CLARENCIA MARGARETH , MURTI RUDI HARI
Published: August 2024

Abstract. Sulistyaningsih E, Sawitri WD, Handayani VDS, Wicaksono AW, Silalahi CM, Murti RH. 2024. Identification and validation of reference genes for gene expression study using Quantitative Real-Time PCR in shallot (Allium cepa L. Aggregatum group) based on bulb development phase. Biodiversitas 25: 2645-2651. Shallot (Allium cepa L. Aggregatum group) is cultivated vegetatively using bulbs (produce many bulbs) and generatively using TSS (True Seed of Shallot) which tends to produce single bulbs. Bulb aggregation is influenced by activity of genes and the gene expression could be analyzed using quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). The qRT-PCR analysis requires reference gene data (housekeeping gene) as a comparison gene against our target gene. This study aimed to select and validate three housekeeping genes in shallot as an initial study for qRT-PCR analysis. The research flow began with the preparation of shallot 'TukTuk' leaves and bulb samples in bulb formation from bulb initial phase to mature phase. Furthermore, a specific primer design based on actin, tubulin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences were obtained from gene bank data. The results showed that the actin, tubulin, and GAPDH genes were successfully amplified and the products were 142 bp, 116 bp, and 136 bp in size, respectively and the genes were expressed almost constantly in leaves and bulbs in all phases of bulb formation. The tubulin gene had the potential as a reference gene for qRT-PCR analysis in shallot with the most consistently expressed.
Exploring the biocontrol and plant growth-promoting potential of Streptomyces kronopolitis isolate SA18 against durian foliar blight and dieback disease
Authors: KRAIVUTTINUN PARINYA , PIRAPAK KUNCHIT , PINNAK PATTACHAI , PIRAPAK WANWISA
Published: August 2024

Abstract. Kraivuttinun P, Pirapak K, Pinnak P, Pirapak W. 2024. Exploring the biocontrol and plant growth-promoting potential of Streptomyces kronopolitis isolate SA18 against durian foliar blight and dieback disease. Biodiversitas 25: 2661-2669. Actinomycetes have been extensively studied for their potential as plant growth promoters and biocontrol agents against fungal plant pathogens. In Thailand, durian is a highly valuable fruit crop, celebrated for its delectable fleshy arils. Rhizoctonia solani destruction causes foliar blight and dieback, a severe disease on durian plantations. Our investigation objective was to isolate, select, and identify actinomycetes that exhibit antagonistic properties and could improve the growth of durian. This study revealed that 37 actinomycete isolates were obtained, comprising 14 endophytic isolates and 23 soil-derived actinomycete isolates from durian plantations in Thailand's Uttaradit and Sukhothai Provinces. All actinomycete isolates demonstrated the ability to inhibit pathogen growth through in vitro antagonistic bioassay. Isolate SA18 exhibited the highest percentage inhibition of radial growth against R. solani isolate 01, achieving an impressive 92% inhibition. Furthermore, isolate SA18 demonstrated the capacity to produce 5.91 ?g/mL of indole acetic acid after seven days of culture, increasing to 45.72 ?g/mL after 14 days. This isolate also exhibited phosphate solubilization ability. In the detached leaf bioassay, isolate SA18 effectively controlled the spread of fungal pathogens, reducing disease severity significantly from 93.75% in the control treatment to 53.75% with a concentration of 108 spores/mL of isolate SA18. Morphological examination and 16S rRNA gene sequencing revealed that isolate SA18 formed smooth-surfaced spores in chains and showed a close relationship with Streptomyces kronopolitis based on the 16S rDNA sequence. This study is the first to report the presence of S. kronopolitis in soil samples collected from durian orchards in Thailand. This isolate can improve plant growth and control R. solani in bioassays. S. kronopolitis isolate SA18 can potentially be a biocontrol agent for durian plantations.