bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilot Introduction of long-lasting bednets and hammock nets in the Indigenous Comarca of Guna Yala, Panama
Authors: Gonzalez Oscar , Perez Carmen , Blanco Tania , Ayarza Cipriano , Chérigo Santiago , Ávila Mario , Montoya Lucía Fernández , Presley Nicholas , Espinosa Bernardo García , Mosquera Mariela 
Published: July 2024

Abstract

Background: After almost 70 years of using indoor residual spraying (IRS) as the primary intervention for malaria vector control, the Republic of Panama wanted to evaluate the operational feasibility, acceptability, and performance of distributing long-lasting insecticide-treated hammock nets (LLIHNs) and bed nets (LLIBNs) in the country.
Methods: A pilot study conducted in 2019 distributed LLIBNs and LLIHNs to cover all sleeping spaces in 15 high localities of the indigenous Comarca of Guna Yala and measured retention, coverage, use and physical deterioration, washing and drying practices, as well as people’s satisfaction with product characteristics post-distribution.
Results: Overall, 89.9% of enumerated sleeping spaces were covered during the campaign. Monitoring post-distribution showed that 82.7% of the population received messages about the campaign before it happened and 92.4% claimed to know the purpose of the net and how to care for and repair it. Adverse reactions to the LLINs were reported by 38.4% of the households. Two years after distribution, 86.3% of the LLINs were retained. Use was very high right after distribution (85%) but decreased to 57% six months after distribution and to 38% two years after distribution. The main reason for not using the LLINs was the reported absence of mosquitoes. Throughout the two years post-distribution, LLINs were preserved in good physical condition (4% torn), very few were washed with aggressive products (9%) or dried under the sun (15%), and LLINs were washed on average a bit less than once every two months. The average number of people per sleeping space was 1.34.
Conclusion: The LLIN distribution was operationally feasible. LLINs were initially well-accepted and cared for by these communities after distribution but use decreased drastically over the two years of follow-up. Further investigation into the reasons for low LLINs and corresponding tailored behavioral change efforts will be needed to ensure high LLIN use in these communities.
Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae
Authors: Rong Xianlin , Huang Lu , Shen Jianshuang 
Published: July 2024

Abstract

In this study, the codon usage patterns of the chloroplast genome of Rhododendron farrerae were analyzed to provide genetic information for the conservation and innovation of Rhododendron germplasm resources. Codon usage and preferences of 54 protein coding sequences (CDS) from R. farrerae were analyzed using software such as Codon, R package, and EMBOSS. The results showed that the average GC content of the 54 CDS in the chloroplast genome of R. farrerae was 38.10%, with GC1 (46.11%), GC2 (39.68%), and GC3 (28.51%) representing the GC contents at different positions, indicating that the third base of codons in the chloroplast genome of R. farrerae is predominantly composed of A and T. ENC-plot, PR2-plot, and neutral plotting analysis revealed that natural selection pressure was the most significant factor influencing the synonymous codon usage preference in the chloroplast genome of R. farrerae, leading to the identification of 16 optimal codons. This study provides genetic information for the chloroplast genome of R. farrerae and serves as a reference for genetic improvement and germplasm innovation.
Tumor-originated exosomal TREML1 is a novel predictive biomarker for tumorigenesis in lung cancer
Authors: Qiao Wenliang , Chen Juan , Yang Yongfeng , Hou Wang , Lei Kaixin , Wang Haibo , Zhu Guonian , Xian Jinghong , Wang Zhoufeng , Gan Jiadi , Liu Dan 
Published: July 2024

Abstract

Background
Lung cancer is a major contributor to cancer rates and deaths worldwide. Due to its complexity and variability, lung cancer progresses quickly and has a grim outlook, making early and precise diagnosis imperative. Despite numerous clinical methods available to aid doctors in detecting lung cancer, there is still a need for a non-invasive biomarker for cancer development.
Methods
We examine the levels of TREML1 mRNA and protein expression in exosomes derived from tumors in both normal and cancerous lung tissues of humans, utilizing information from TCGA, GTEx, HPA databases, as well as samples obtained from clinical settings. Validation experiments were performed on tissue microarrays obtained from lung cancer samples. We examined targeted next-generation sequencing data from the TCGA database to gain insight into the frequency of TREML1 mutations and the collection of genes that are co-altered in tumors with TREML1 mutations.
Results
Our findings reveal that TREML1 is highly expressed in lung cancer, and could be one valueable predictor which may be applied in clinic in the future. Analysis of survival data from the TCGA and GTEx database suggests that high levels of TREML1 expression are associated with poor clinical prognosis in lung cancer. Analysis of gene mutations revealed that TTN (53.7%) is the most frequent alteration associated with TREML1 overexpression in LUAD, while APOB is the most common alteration in LUSC.
Conclusions
It can be concluded that TREML1 is a suitable target for prognosis and treatment markers. Additional research is required to comprehensively grasp how TREML1 interacts with these signaling pathways, which will be the primary focus of our upcoming studies.
Water Quality Assessment and Modelling Using Machine Learning
Authors: Mishra Km Shashi Prabha , Patel Prabhat Kumar , Singh Asit 
Published: July 2024

Abstract

One of the most essential sources of water for people to drink is groundwater. Several studies on groundwater have been carried out in India. However, the characteristics of groundwater have not been investigated through machine learning (ML tools). There is a need for a defined strategy which would concentrate on a specific part of groundwater management, which means the protection of groundwater from contamination. This study makes use of 97 groundwater samples that were taken from tube wells and dug wells in various places within Ayodhya, Uttar Pradesh, India from the year 2000–2018 groundwater data yearbook. Seven hydro-chemical parameters from each sample were ascertained and compared to the standard values recommended for drinking purposes by the Bureau of Indian Standards (BIS) 10,500:2012. Anticipating the Water Quality Index (WQI) and Water Quality Classification (WQC) so that WQI is a crucial indication for water validity is the difficulty this research aims to solve. Parameter adjustment and optimization are used in this work to increase the accuracy of multiple machine learning ARIMA model, in which the process of forecasting WQI and WQC is performed. The analysis of the proposed algorithms will assist the relevant government agencies in identifying substitute water for consumption in the affected regions.
Design and development of a spectrophotometric cyanide assay based on a cascade reaction catalyzed by cyanide hydratase, formamidase and formate dehydrogenase
Authors: Šťastná Katarína , Martínková Ludmila , Rucká Lenka , Křístková Barbora , Bojarová Pavla , Pátek Miroslav 
Published: July 2024

Abstract

Cyanide assays are required for the analyses of industrial, environmental, food and clinical samples. Enzymatic methods are not widely used in this field despite their selectivity and other promising properties. Therefore, we present here a proof of concept for a new enzymatic assay of free cyanide (fCN) which consists of HCN and CN- at a pH dependent ratio. The assay is based on the transformation of HCN into the readily detectable NADH. The reaction is catalyzed by a multienzyme cascade consisting of cyanide hydratase, formamidase and formate dehydrogenase. The last step is a spectrophometric quantification of NADH with a tetrazolium salt, WST-8. The new assay offers selectivity (with the exception of formic acid interference) and mild operational conditions; in addition, fCN is detoxified during the reaction. The assay has been miniaturized to a microtiter plate format, making consumption of enzymes and chemicals very low. The limit of detection (LOD) and the limit of quantification (LOQ) were calculated to be 9.1 µM fCN and 27.6 µM fCN, respectively. An analogous assay without CynH can be used for the determination of formamide with LOD and LOQ of 7.0 µM and 21.4 µM, respectively. Further measures to improve sensitivity are possible.
Enhancing Organic Photodetector Performance Based on PBDB-T/ITIC and GO: A SCAPS-1D Simulation Study
Authors: Alali Ahmet Sait , Oduncuoglu Murat 
Published: July 2024

Abstract

This study investigates the optimization of organic photodetectors (OPDs) using SCAPS-1D simulation, focusing on the effects of layer thickness, doping density, temperature, external quantum efficiency (EQE), and responsivity on key performance metrics. The device structure includes PBDB-T/ITIC as the active layer and graphene oxide (GO) as the hole transport layer (HTL). By systematically varying the thickness of the PBDB-T/ITIC active layer and the GO hole transport layer, as well as adjusting the donor and acceptor densities, we analyze their impact on open-circuit voltage (Voc), short-circuit current density (Jsc), fill factor (FF), power conversion efficiency (η), EQE, and responsivity. The simulation results reveal that an optimal active layer thickness of 800 nm for PBDB-T/ITIC and a GO layer thickness of 50 nm maximize device performance. Additionally, a donor density of \({9\times 10}^{19}{cm}^{-3}\) for PFN and an acceptor density of \({10}^{20}{cm}^{-3}\) for GO significantly enhance efficiency. The photodetector demonstrates a high current under illumination, peaking responsivity around 920 nm, and excellent performance in the visible spectrum. Temperature variations show optimal performance around 330 K. These findings highlight the critical role of precise material and structural optimization in achieving high-efficiency OPDs, providing valuable insights for future research and development in this field.
Nemabiome metabarcoding to assess the diversity of trichostrongyle nematodes in plains bison from the mid-western USA
Authors: Chelladurai Jeba R. J. Jesudoss , Johnson William L. , Quintana Theresa A. , Nilaweera Guwin Weerawarna , Wolfe Hayden , Wehus-Tow Bradly , Brennan Jameson , Krus Catherine B. , Buttke Danielle , Herrin Brian H. , Martin Jeff M. 
Published: July 2024

Abstract

Background
Parasitic gastrointestinal nematode (GIN) infections in North American plains bison, predominated by trichostrongyles of Clade V, are a major cause of health and production losses, even death. The diversity and distribution of trichostrongyles in bison in the USA remains poorly understood. The aim of this study was to assess the diversity of GIN in plains bison and to identify key species to target for parasite control strategies in bison herds.
Methods
We used the “nemabiome” deep amplicon sequencing technique to amplify the ITS2 region from DNA derived from trichostrongyle third-stage larvae obtained by coproculture of the feces of 134 individual bison belonging to 16 herds from 8 mid-western states in the USA. ITS2 amplicons were library prepped and sequenced on an Illumina MiSeq. Anthelmintic usage history in the herds was unknown. Sequencing data was analysed using the DADA2 pipeline and diversity metrics were calculated.
Results
Analysis revealed 269 amplified sequence variants (ASVs), belonging to 5 genera and 9 species. A significant proportion of individual bison and herds had multiple infections with ≥ 2 trichostrongyle infections. Cooperia oncophora, Ostertagia ostertagi and Haemonchus placei were the most abundant species. Individual bison harbored an average of three trichostrongyle species, while herds harbored an average of 4.5 species. In a majority of individuals and herds, Shannon alpha diversity index was < 1, indicating lower species abundance and richness, while inverse Simpson index was between 1–3 indicating moderate species diversity.
Conclusion
There was variation in parasite diversity within and between individual bison and herds. This is the first study to utilize the “nemabiome” technique in plains bison herds living in the USA and results of this investigation reveal the importance of understanding key species to target for parasite control strategies.
Enhancing Cloud Network Security with Innovative Time Series Analysis
Authors: Al-Musawi Bahaa , ALMAZRAWE AMER 
Published: July 2024

Abstract

Cloud computing has revolutionized computing infrastructure abstraction and utilisation, characterized by its cost-effective and high-quality services. However, the challenge of securing cloud networks persists, primarily due to the extensive exchange of data and the inherent complexity of these systems. Anomaly detection emerges as a promising solution to enhance cloud network security, offering insights into system behaviour and alerting operators for further actions. This paper presents a novel time series analysis technique for detecting anomalies in cloud networks. Our approach utilises a multi-dimensional matrix profile, an innovative time series analysis method, to highlight anomalous patterns within multiple features extracted from network traffic streams. Additionally, we employ the Kneedle algorithm to pinpoint the highlighted patterns that identify anomalies. To evaluate the effectiveness of our method, we implemented timestamp-based and index-based methods to two distinct datasets: the most widely used UNSW-NB15 and the recently introduced CICIoT2023 datasets. The results highlight the efficacy of our proposed method in identifying cloud network anomalies. It achieved an impressive accuracy of 99.6% and an F1-score of 99.8% using the timestamp-based analysis method. For the index-based analysis method, the accuracy reached 98%, accompanied by an outstanding F1-score of 99.9%.
Targeted delivery of TGF-β mRNA to lung parenchyma using one-component ionizable amphiphilic Janus Dendrimers.
Authors: Atochina-Vasserman Elena , Meshanni Jaclynn , Stevenson Emily , Zhang Dapeng , Sun Rachel , Ona Nathan , Reagan Erin , Abramova Elena , Guo Chang-Jiang , Wilkinson Melissa , Baboo Ishana , Yang Yuzi , Pan Liuyan , Maurya Devendra , Percec Virgil , Li Yongsheng , Gow Andrew , Weissman Drew 
Published: July 2024

Abstract

Current clinical strategies for the delivery of pulmonary therapeutics to the lung are primarily targeted to the upper portions of the airways. However, targeted delivery to the lower regions of the lung is necessary for the treatment of parenchymal lung injury and disease. Here, we have developed an mRNA therapeutic for the lower lung using one-component Ionizable Amphiphilic Janus Dendrimers (IAJDs) as a delivery vehicle. We deliver an anti-inflammatory cytokine mRNA, transforming growth factor-beta (TGF-β), to produce transient protein expression in the lower regions of the lung. This study highlights IAJD’s potential for precise, effective, and safe delivery of TGF-β mRNA to the lung. This delivery system offers a promising approach for targeting therapeutics to the specific tissues, a strategy necessary to fill the current clinical gap in treating parenchymal lung injury and disease.
Oral management is positively associated with reduced antibiotic and narcotic use and in-hospital mortality in patients undergoing allogeneic HSCT: a retrospective observational study at a Japanese acute hospital
Authors: Moriwaki Mutsuko , Toba Mikayo , Takizawa Makiko , Shimizu Hiroaki , Tanaka Haruna , Takahashi Chihiro , Imai Shinobu , Kakehashi Msayuki , Fushimi Kiyohide 
Published: July 2024

Abstract

Background: Oral bacteria play a significant role in the development of bloodstream infections in patients undergoing hematopoietic stem cell transplantation (HSCT). Therefore, recommendations are being made to manage oral function before and after transplantation. This study aimed to elucidate the short-term effects and assess the influence of a medical care delivery system on oral management.
Methods:This study focused on patients aged 16 years or older who underwent HSCT and were discharged from acute care hospitals in Japan between April 2018 and March 2022. The patients were categorized into autologous and allogeneic HSCT groups for analysis. Multivariate analysis was conducted to determine the impact of oral management on the use of antibiotics and narcotics injections within 14- and 30-days post-transplantation and mortality rates. Additionally, we investigated the association between the implementation of oral management at each hospital and the underlying medical care delivery systems.
Results:The analysis encompassed 14,031 patients, with the final cohort comprising 5,936 autologous and 6,312 allogeneic HSCT patients across 298 hospitals. The total amount of antibiotics utilized within 14 days post-transplant demonstrated a coefficient of Β=-2.66, whereas it demonstrated a coefficient of Β=-6.74 within 30 days post-transplantation. Moreover, the number of broad-spectrum antibiotics administered within 30 days post-transplantation exhibited a coefficient of Β=-2.79, and within 14 days post-transplantation displayed a coefficient of Β=-0.34. The use of narcotics within 30 days post-transplantation yielded a coefficient of B=-0.70. Oral management also affected in-hospital mortality. Conversely, no significant outcomes were observed after autologous HSCT. The medical care delivery system that influenced the management implementation rate in hospitals was the certification standard for performing unrelated HSCT.
Conclusion:Maintaining optimal oral hygiene in patients undergoing HSCT, pre- and post-transplantation, is crucial for preventing infections, improving prognosis, and alleviating discomfort. Establishing a collaborative medical care delivery system, wherein dental and medical teams work together, is imperative to ensure that patients undergoing HSCT receive safe, tailored, and superior medical care.
Ex vivo T-lymphopoiesis assays assisting corrective treatment choice for genetically undefined T- lymphocytopaenia
Authors: Golwala Zainab M. , Goncalves Helena Spiridou , Moirangthem Ranjita Devi , Evans Grace , Lizot Sabrina , Koning Coco , Garrigue Alexandrine , Corredera Marta Martin , Howley Evey , Kricke Susanne , Awuah Arnold , Obiri-Yeboa Irene , Rai Rajeev , Sebire Neil , Bernard Fanette , Braem Victoria Bordon Cueto , Boztug Kaan , Cole Theresa , Gennery Andrew R. , Hackett Scott , Holm Mette , Kusters Maaike A. , Klocperk Adam , Marzollo Antonio , Marcus Nufar , Schmid Jana Pachlopnik , Pichler Herbert , Sellmer Anna , Soler-Palacin Pere , Soomann Maarja , Montfrans Joris , Nierkens Stefan , Adams Stuart , Buckland Matthew , Gilmour Kimberly , Worth Austen , Thrasher Adrian J. , Davies E. Graham , André Isabelle , Kreins Alexandra Y. 
Published: July 2024

Abstract

Newborn screening for severe combined immunodeficiency promotes early diagnosis and timely treatment, improving clinical outcomes. Selective T-lymphocytopaenia is found both in haematopoietic cell-intrinsic and thymic stromal cell-intrinsic defects, including congenital athymia which is associated with a T-B + NK + immunophenotype. Without a molecular diagnosis, it is challenging to determine whether haematopoietic cell transplantation (HCT) or thymus transplantation ought to be performed. Ex vivo T-lymphocyte differentiation assays have been proposed to assist clinical decision-making for genetically undefined T-lymphocytopaenic patients by assessing the intrinsic potential of their haematopoietic progenitors to differentiate into mature T-lymphocytes. We investigated 18 T-lymphocytopaenic patients, including 12 patients awaiting first-line treatment and 6 patients with failed immune reconstitution after previous HCT or thymus transplantation. Whilst early developmental blocks in ex vivo T-lymphopoiesis indicated haematopoietic cell-intrinsic defects, successful differentiation of mature T-lymphocytes required careful interpretation, in conjugation with clinical status and presentation, immunophenotyping, and available genetic investigations. 5 patients were referred for HCT and 12 for thymus transplantation. 12/18 patients proceeded to treatment with successful immune reconstitution in 4/5 patients after HCT and 4/7 after thymus transplantation, the latter including two patients previously treated with HCT. Two treated patients died, either after HCT or after thymus transplantation, due to pre-existing complications, and two patients have yet to show immune reconstitution seven months and one year after thymus transplantation respectively. Overall, we conclude that including ex vivo T-lymphocyte differentiation assays in the diagnostic pathway for genetically undefined T-lymphocytopaenia improves patient outcomes by facilitating corrective treatment choice between HCT and thymus transplantation.
Effects of High-Order Nonlinearities on Phononic Frequency Combs
Authors: Ganesan Adarsh , Tiwari Priya 
Published: July 2024

Abstract

Phononic frequency combs (PFC) hold promise for bringing the utility of celebrated optical frequency combs into the domain of phonons. The interactions of multiple phonon modes in a nonlinear medium result in the generation of PFC. Previous work established the existence conditions of PFC for two-modal interactions via quadratic nonlinearity. However, in real situations, higher-order nonlinearities could also play a role in comb generation. To this end, this work derives multiple analytical expressions to quantify the effects of high-order nonlinearities on PFC and their existence boundaries. The odd-order nonlinearities affect the amplitude parameters of existence boundary curve and the even-order nonlinearities modulate the frequency parameters. The frequency and amplitude parameters of existence boundary curve are analytically derived and the effects of high-order nonlinearities on the existence boundaries of PFC are quantified for a published experimental case.