bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Modification Detection using Nanopore Direct RNA Sequencing via improved Transformer
Authors: Xiong Yuanyan , Zhu Miaosong 
Published: May 2024

Abstract

RNA modifications are a common occurrence in transcriptome and play a crucial role in various biological processes. Nanopore direct RNA sequencing (DRS) provides raw current signal readings, which carry information of modifications. Supervised machine learning methods using DRS are advantageous for RNA modification detection. However, existing methods for RNA modification detection do not adequately capture sequential signal features within and between reads.Here, we represent NSWord, an improved transformer model with three types of self-attention blocks that integrates the transcript sequence and its signal reads to produce a comprehensive site-level prediction. NSWord outperforms existing deep learning methods, particularly in terms of precision of top-scoring predictions. Additionally, we investigate the impact of limiting the length or number of signal reads and explore the role of transcript sequence in modification prediction.
Psychological characteristics of environmental stakeholders and interactions in their social network
Authors: Przesdzink Felix , Sperling Nicol , Oswald Tom , Fiebelkorn Florian 
Published: May 2024

Abstract

This research explores the roles of Organizational Culture, Environmental Worldview, and Environmental Risk Perception in shaping the interactions between environmental stakeholders in Northwest Germany, with a particular focus on sustainable land use. By integrating a psychological Stakeholder Analysis and Social Network Analysis, the study examines the expression of these psychological constructs among key stakeholder groups—conservation associations, land use associations, research groups, and public authorities—and their correlation with the presence of collaboration and conflict. Our analysis reveals that Organizational Culture significantly affects stakeholder interactions, with Clan and Hierarchy cultures predominating and influencing the nature of stakeholder relationships. Moreover, the study highlights a generally pro-environmental orientation across stakeholders as captured by the New Environmental Paradigm (NEP), indicating a shared foundation for potential collaborative efforts. Analysis of Environmental Risk Perception, through the Cultural Theory's myths of physical nature, uncovers a widespread preference for the hierarchical myth, suggesting a common perception of environmental risks and resilience. This study emphasizes the importance of understanding psychological and social dimensions in environmental stakeholder management to enhance collaborative efforts towards sustainable development. It highlights the need for management approaches that acknowledge the complex interplay of diverse psychological constructs in driving effective and sustainable collaborations between stakeholders of regional land use and nature conservation. Through its insights into stakeholder interactions, this research contributes to the broader discourse on achieving sustainable development goals through informed, cooperative stakeholder engagement.
The impact of implementing a nursing care program based on Johnson's model on the behavioral systems of patients undergoing coronary artery bypass graft: a Randomized clinical trial
Authors: Rostami Sakineh , Molavynejad Shahram , Elahi Nasrin , Maraghi Elham 
Published: May 2024

Abstract

Introduction: Coronary artery bypass graft (CABG) is a very important intervention to relieve angina, improve quality of life, or increase life expectancy. This study aimed to determine the effect of implementing a nursing care program based on Johnson's model on the behavioral systems of patients undergoing CABG in Ahvaz teaching hospitals in 2022.
Materials and methods: The present study was a clinical trial on 128 patients undergoing CABG admitted to the cardiac ICU and cardiac surgery department of teaching hospitals in Ahvaz city. The patients were selected based on the inclusion criteria, and they were assigned into intervention and control groups using permutation blocks. In the intervention group, a nursing care program based on Johnson's model was implemented for three weeks. The data collection tool was a researcher-made questionnaire developed based on Johnson's theory.
Results: Before the intervention, the mean scores of the intervention group in terms of the seven subsystems of Johnson's model were as follows: achievement (-98.98 ± 75.77), affiliative (-87.34 ± 28.23), eliminative (-25.46 ± 33.27), ingestive (-135.67 ± 89.20), dependency (-122.26 ± 45.85), aggressive-protective (-62.18 ± 46.58), and restorative (-163.59 ± 62.03). After the intervention, the mean scores in the intervention group were as follows: achievement (-2.50 ± 71.55), affiliative (-66.33 ± 59.68), eliminative (19.29 ± 35.61), ingestive (152.75 ± 113.58, dependency (104.60 ± 53.42), aggressive-protective (52.18 ± 53.54), and restorative (198.43 ± 72.28), which shows the positive impact of the intervention (P > 0.05). No significant changes were observed in the sexual subsystem.
Conclusion: The implementation of a nursing care plan based on Johnson's model positively affected the behavioral systems of patients undergoing CABG. Therefore, this model is recommended to be used as a framework for nursing care.
Date of registration -05-12-2022
Trial registration number- IRCT20220831055838N1
Anthropogenic meadows provide foraging subsidies for white-tailed deer in fragmented forest ecosystems
Authors: Wuensch Matthew A , Eagar Andrew C , Ward David 
Published: May 2024

Abstract

White-tailed deer (Odocoileus virginianus) populations persist at densities higher than historical estimates throughout much of their North American range. In forest ecosystems, heavy browsing by high-density deer populations can suppress the growth and regeneration of woody plants and promote the establishment and growth of non-preferred forage items, such as grasses and ferns. Additionally, as forests are altered by anthropogenic development, grasslands and meadows are becoming increasingly common in forest landscapes where deer occur. We used activity densities to measure the seasonal patch preference of white-tailed deer between forest patches and anthropogenically-introduced meadows in northeast Ohio, a region with high-density deer populations. We also quantified the plant communities that were present in each patch type to identify forage plants that were available to deer. We found that deer preferred meadow patches and avoided forests during spring and summer. Meadow patches primarily consisted of non-native forage plants that are nutritionally beneficial to deer, whereas forests possessed fewer nutritionally beneficial plants and contained an abundance of open ground. However, as plants senesced and forage availability on the landscape decreased during autumn and winter, deer did not prefer any patch type. Our results suggest that in anthropogenically fragmented forests, meadows can provide deer with a potentially overlooked foraging subsidy that should be considered when managing high-density deer populations.
Adaptive learning algorithms for CNN models incorporating meteorological data for precise environmental predictions
Authors: Ghorbani Mohammad Ali , Olusegun Christiana , Olusola Adeyemi Oludapo , Abdi Erfan 
Published: May 2024

Abstract

Weather forecasting through neural networks has increased and shown the potential for greater accuracy over recent years. Among numerous techniques, machine learning models provide more precise weather and climate prediction outcomes. The objective of this research was to analyze the highest and lowest monthly temperatures, as well as the highest wind speeds, in selected Nigerian cities, including Abuja, Lagos, Sokoto, Maiduguri, Calabar, and Port Harcourt through the use of cutting-edge machine learning technology such as deep learning (DL), and Convolution Neural Network (CNN). Our research approach involved compiling data on maximum and minimum temperatures and wind speeds from specific cities in Nigeria every month from 2000 to 2023. By successfully utilizing AMI, we pinpointed the optimal variables necessary for precisely evaluating the six cities as we built our model. The CNN algorithm stood out as a top-tier model in the test results due to its precise estimation of city temperature and wind speed values, highlighting exceptional generalization ability and minimal variance compared to the DL model.
A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids
Authors: Fernandez Rosa , Vargas-Chavez Carlos , Benitez-Alvarez Lisandra , Martinez-Redondo Gemma , Alvarez-Gonzalez Lucia , Salces-Ortiz Judit , Eleftheriadi Klara , Escudero Nuria , Guiglielmoni Nadege , Flot Jean-François , Novo Marta , Ruiz-Herrera Aurora , MacLysaght Aoife 
Published: May 2024

Abstract

The genomic basis of cladogenesis and adaptive evolutionary change has intrigued biologists for decades. The unique insights from a genome-level perspective have revealed a striking pattern of conserved macrosynteny across huge evolutionary distances in animals, yet progress in many lineages has been hampered by the absence of genome-level data. Here, we show that the origin of Clitellata, a clade composed of most freshwater and all terrestrial species of the phylum Annelida, coincided with an unprecedented genome-wide scrambling event that resulted in massive loss of macrosynteny between marine annelids and clitellates. This complete breakdown of chromosome-level relationships on just one short branch is unlike any other known pattern of evolutionary genome rearrangement, and instead resembles chromosome shattering and reassembly seen in chromoanagenesis. These massive punctuated rearrangements included the formation of neocentromeres with newly-acquired transposable elements, and preceded a further period of genome-wide reshaping events including whole genome duplications and massive macrosyntenic reshuffling between clitellate lineages, potentially triggered by the loss of genes involved in genome stability or homeostasis of cell division. Notably, while these rearrangements broke short-range interactions observed between genes in marine annelids (including Hox), they were reformed as long-range interactions in clitellates. Our study provides evidence of punctuated genomic change via chromoanagenesis leading not only to the origin of a new animal lineage - a ‘hopeful monster’ - but also to adaptive genomic changes facilitating the colonisation of new habitats.
Comparison of semi-solid, liquid, and temporary immersion bioreactor systems for efficient plant regeneration of Gerbera jamesonii cv. ‘Shy Pink’
Authors: Lim Myeong-Jin , Han Jong-Eun , Hosakatte Niranjana Murthy , Song Hyun-Young , Lee Su-Young , Ho Thanh-Tam , Park So-Young 
Published: May 2024

Abstract

Temporary immersion system (TIS) cultures are reported to be superior when compared to semi-solid (SS) and liquid cultures for in vitro plant regeneration of many plant species. In the present study, we used the TIS system for plant regeneration of Gerbera jemesonii cv. ‘Shy Pink’ and compared the results with that of SS and liquid cultures. The shoots regenerated with SS and liquid cultures demonstrated 3.33 and 4.22% hyperhydricity, whereas the shoots regenerated with TIS were healthy even though the number of shoots regenerated was less in number. The plantlets regenerated with TIS demonstrated higher values with the number of roots, root length, biomass of plantlets, leaf length/width, and area compared to SS and liquid cultures. The photosynthetic pigments were highest in Gerbera jemesonii cv. ‘Shy Pink’ plants were regenerated with TIS. The number of stomata on the abaxial surface of leaves was 11.40 and the frequency of closed stomata was 59% with plants regenerated with TIS. Furthermore, Gerbera jemesonii cv. ‘Shy Pink’ showed the highest survival of plants that were regenerated in TIS compared to SS and liquid cultures. TIS was found as the most suitable culture system for the micropropagation of Gerbera jemesonii cv. ‘Shy Pink’ compared to SS and liquid cultures.
Health worker perspectives on barriers and facilitators of tuberculosis investigation coverage among index case contacts in rural southwestern Uganda: a qualitative study
Authors: Tukamuhebwa Paddy Mutungi , Munyewende Pascalia , Tumwesigye Nazarius Mbona , Nabirye Juliet , Ndlovu Ntombizodwa 
Published: May 2024

Abstract

Background
In 2012, the World Health Organization recommended screening and investigation of contacts of index tuberculosis patients as a strategy to accelerate detection of tuberculosis (TB) cases. Nine years after the adoption of this recommendation, coverage of TB contact investigations in Uganda remains low. The objective of this study was to examine health care providers' perceptions of factors influencing coverage of TB contact investigations in three selected rural health facilities in Mbarara district, southwestern Uganda.
Methods
Using an exploratory qualitative study design, semi-structured interviews with 19 health workers involved in the TB program at district, health facility and community levels were conducted from April 2020 and July 2020. Analysis was inductively using reflexive thematic analysis in six iterative steps: familiarizing with the data, creating initial codes, searching for themes, reviewing themes, developing theme definitions, and writing the report.
Results
Nineteen health care workers participated in this study which translates to a 100% response rate. These included two district TB and leprosy supervisors, five nurses, five clinical officers, six village health team members and one laboratory technician. The three themes the emerged from the analysis were intervention-related, health system and contextual factors. Health system-related barriers included inadequate or delayed government funding for the TB program, shortage of human resources, insufficient personal protective equipment, and a stock-out of supplies such as Xpert MTB cartridges. Contextual barriers included steep terrain, poverty or low income, and the stigma associated with TB and COVID-19. Facilitators comprised increased knowledge and understanding of the intervention, performance review and on-the-job training of health workers.
Conclusions
This study identified provider opinions on the barriers and facilitators to implementation of TB contact investigation using the Consolidated Framework for Implementation Research. This study found that the bulk of the hinderances limiting TB contact investigations in rural communities are related to health system constraints such as inadequate or delayed funding and human resource shortages. The Ministry of Health in Uganda must strengthen the foundational elements of the health system—health financing and human resources to establish a comprehensive TB control program that will enable the efficient identification of missing TB patients.
Impact of the shape of the ampulla of Vater and biliary tree pathology on access technique and post-ERCP complications
Authors: Andrzej Jamry 
Published: May 2024

Abstract

Background and aim: Difficulties and complications during endoscopic retrograde cholangiopancreatography (ERCP) can depend on the anatomy of the papillae, the pathology of the biliary tree, and proper selection of the endoscopic technique. However, knowledge about these relationships is limited.
Methods: This single-center retrospective study included 1002 patients who underwent ERCP. The analyses included the impact of the existing anatomy (shape of the papillae [modified Haraldsson classification], periampullary diverticulum [PAD], common bile duct [CBD] diameter ≤9 mm, outflow obstruction level and choledocholithiasis]) on cannulation difficulty, access technique (classic sphincterotomy [CS], classic precut [CPC], needle precut [NPC], two-step access, unintended Wirsung duct cannulation) and complications (bleeding, hyperamylasemia, pancreatic pain and postendoscopic pancreatitis [PEP]). Results: According to the modified Haraldsson classification,47.4% of the papillae were type 1, 31.3% were type 2; 11.1% were type 3, and 10.2% were type 4. Cannulation was considered difficult in 56.9% (58/102; p=0.0014) of type 4 papillae and 46.4% (162/349; p= 0.001) and 49.5% (46/93; p=0.039) of patients with distal and medial CBD obstruction, respectively. CPC was used for 42.2% (43/102; p=0.017) of patients with type 4 papillae. NPC was used 38.7% (43/111; p<0.0001) of patients with type 3 papillae, and 26.0% (34/131; p=0.008) of patients with a CBD diameter ≤9 mm. Two-step access was used for 28.4% (29/102; p<0.0001) of type 4 papilla patients, 17.8% (53/315; (p= 0.002)) of type 2 papilla patients and 18.9% (66/349; p=0.002)of patients with distal CBD obstruction. Bleeding occurred for 21.9% (104/475; p=0.003) of type 1papilla patients. A total of 19.0% (85/448,p<0.0001) of patients with CBD diameters ≤9 mm had hyperamylasemia; 6.2% (28/449,p=0.025); had pancreatic pain and 4% (18/449; p=0.021)had PEP .
Conclusion: The existing anatomy of the papillae and biliary tree affected the difficulty of cannulation, the selection of access technique, and the occurrence of side effects.
Hourglass pattern matching for deep aware neural network text recommendation model
Authors: Gao Li , Li Hongjun , Chen Qingkui , Peng Dunlu 
Published: May 2024

Abstract

In recent years, with the rapid development of deep learning, big data mining, and natural language processing (NLP) technologies, the application of NLP in the field of recommendation systems has attracted significant attention. However, current text recommendation systems still face challenges in handling word distribution assumptions, preprocessing design, network inference models, and text perception technologies. Traditional RNN neural network layers often encounter issues such as gradient explosion or vanishing gradients, which hinder their ability to effectively handle long-term dependencies and reverse text inference among long texts. Therefore, this paper proposes a new type of depth-aware neural network recommendation model (Hourglass Deep-aware neural network Recommendation Model, HDARM), whose structure presents an hourglass shape. This model consists of three parts: The top of the hourglass uses Word Embedding for input through Finetune-Bert to process text embeddings as word distribution assumptions, followed by utilizing bidirectional LSTM to integrate Transformer models for learning critical information. The middle of the hourglass retains key features of network outputs through CNN layers, combined with pooling layers to extract and enhance critical information from user text. The bottom of the hourglass avoids a decline in generalization performance through deep neural network layers. Finally, the model performs pattern matching between text vectors and word embeddings, recommending texts based on their relevance. In experiments, this model improved metrics like MSE and NDCG@10 by 8.74% and 10.89% respectively compared to the optimal baseline model.
Assessment of vaccine wastage and associated factors in Rukungiri District, Southwestern Uganda, 2018–2019: a mixed-methods study
Authors: Kemigisha Miriah , Migisha Richard , Kyamwanga Imelda. T. 
Published: May 2024

Abstract

Background
Vaccine wastage undermines the cost-effectiveness of immunization programs, especially in resource-constrained settings. However, data on vaccine wastage in Uganda are limited. We assessed the magnitude of vaccine wastage, its causes, and associated factors in Rukungiri District, South-western Uganda.
Methods
In a cross-sectional mixed-methods study, we analyzed data from the District Health Information Systems database and immunization program records at health facilities in Rukungiri District for July 2018–June 2019. Wastage rates were calculated as the proportion of vaccine doses wasted after an immunization session, expressed as a percentage of the total doses opened. Chi-square or Fischer’s exact tests were used to examine the association between wastage and various factors. Qualitative data were collected through in-depth interviews with health workers involved in immunization activities and analyzed thematically.
Results
Vaccine wastage rates varied across different vaccines, with BCG at 81.1%, OPV at 31.6%, IPV at 31.3%, DPT-HepB-Hib at 20.0%, PCV-10 at 10.2%, MCV at 57.7%, and Rota virus vaccine at 2.1%. The main cause of wastage was discarding leftover doses. For BCG, larger health facilities had significantly lower wastage than smaller ones (Hospital 66.0%, HCIV 74.3%, HCIII 80.6%,HCII 87.0%, p = 0.005), facilities with predominantly small session sizes had higher wastage rates than those with mixed or large session sizes (84.4%vs64.3%vs62.0%p < 0.01) and fewer static sessions per month were associated with higher wastage (82.1%vs 66.0%p = 0.013). Good coverage was linked to lower wastage for DPT-HepB-Hib and PCV-10 (DPT-HepB-Hib 16.8% vs 31.2%p = 0.033 PCV-10 9.1%vs13.7%p = 0.001). Freeze-dried vaccines had a substantially higher wastage rate of 75.0% compared to liquid vaccines at 20.2% (p < 0.01). Injectable vaccines had a higher wastage rate (47.1%) than oral vaccines (22.6%, p < 0.01). Larger vial sizes were also associated with higher wastage rates. Knowledge and skills gaps were identified in stock and cold chain management practices.
Conclusion
Wastage rates for several vaccines exceeded national limits, primarily due to discarding leftover doses. Factors like vaccine type, administration method, vial size, and facility size influenced wastage. Targeted strategies, including stock management improvements and health worker training, could enhance immunization program cost-effectiveness and sustainability in the region
The effects of substitution degree in the carboxymethylation of jackfruit seed starch on starch digestibility
Authors: Pham Thu Ha , Nguyen Trung Duc , Pham Ngoc Anh , Le Hong Thuy , Nguyen Ngoc Tuan , Nguyen Thanh Tung 
Published: May 2024

Abstract

Starch from jackfruit seeds shows potential for use in food production processes with high starch content. Modification of jackfruit seed starch to increase the resistant starch content makes it a promising candidate for prebiotics in the food industry. This study chemically denatures starch through carboxymethylation at different concentrations of sodium hydroxide to investigate the effect of carboxymethyl substitution on digestible properties of the starch. Carboxymethylation exhibited a high degree of substitution from 0.28–0.57% as a function of the concentration of sodium hydroxide (5–10 wt%). The treatment enhanced the improvement of swelling, water solubility, and water/oil absorption. The resistant starch content increased from ~ 21 to ~ 39.67%. The degree of carboxymethyl group substitution was increased by increasing the NaOH concentration. However, the high degree of substitution showed structural deformation of the starch granules with a decrease in crystallinity from about 35 to 1% by SEM and XRD. The degree of carboxymethyl substitution increased resistant starch content, reduced rapidly digestible starch, and negligible impact to SDS. The results showed that jackfruit seed starch treated with 10% by weight of NaOH was the optimal value that increased carboxymethyl substitution to 0.57% and resistant starch content to ~ 40%. This concentration was also optimal for the functional properties of starch with the highest values of swelling degree (~ 27 g/g), water solubility (~ 50%), freeze-thaw stability (~ 20% of syneresis after 4 freeze-thaw cycles), and oil and water absorption (150% of oil absorption and 180% of water absorption).