bluuebunny/crossref_metadata_2025_split huggingface dataset:
Residual efficacy of SumiShield™ 50WG for indoor residual spraying in Ethiopia
Authors: Yewhalaw Delenasaw , Simma Eba Alemayehu , Zemene Endalew , Zeleke Kassahun , Degefa Teshome 
Published: December 2022

Abstract
Background
The rate of decay of the biological efficacy of insecticides used for indoor residual spraying (IRS) is an important factor when making decisions on insecticide choice for national malaria control programmes. A key roadblock to IRS programme is insecticide resistance. If resistance is detected to most of the existing insecticides used for IRS (DDT, pyrethroids, organophosphates and carbamates), the logical next choice could be neonicotinoid insecticides, as pyrethroids are used to treat nets. SumiShield™ 50WG belongs to the neonicotinoid class of insecticides and has shown promising results in several phase I, II and III trials in different settings. The aim of this study was to assess the persistence of SumiShield™ 50WG by spraying on different wall surfaces and determine its decay rates over time in Ethiopia.

Methods
Five huts with different wall surface types (mud, dung, paint and cement) which represented the Ethiopian house wall surfaces were used to evaluate the residual efficacy of SumiShield™ 50WG. Actellic 300CS sprayed on similar wall surfaces of another five huts was used as a comparator insecticide and two huts sprayed with water were used as a control. All huts were sprayed uniformly by an experienced spray operator; non-stop starting from the door and moving clockwise to cover the entire wall surface of the hut. The treatments were assigned to huts randomly. The residual efficacy of the insecticide formulations was evaluated against a susceptible insectary-reared population of Anopheles arabiensis using WHO cone bioassays.

Results
SumiShield™ 50WG resulted in mortality rates of over 80% at 120 h post-exposure on all surface types for up to nine months post-spray, while Actellic 300CS yielded mortality rates of over 80% for eight months after spray.

Conclusions
The results of this trial demonstrated that the residual efficacy of SumiShield™ 50WG extends up to nine months on all treated wall surface types. The long-lasting residual efficacy and unique mode of action of the SemiShield™ 50WG shows that it could be an ideal product to be considered as a potential candidate insecticide formulation for IRS in malaria endemic countries such as Ethiopia or other sub-Saharan countries where the transmission season lasts up to four months or longer.
Factors influencing consistent use of bed nets for the control of malaria among children under 5 years in Soroti District, North Eastern Uganda
Authors: Akello Anne Ruth , Byagamy John Paul , Etajak Samuel , Okadhi Charles Stephen , Yeka Adoke 
Published: December 2022

Abstract
Background
The use of insecticide-treated bed nets has been proven to be effective in reducing malaria transmission in highly endemic areas. Use of long-lasting insecticidal nets (LLINs) has been embraced by many malaria endemic countries. LLINs are up to 95% effective in inhibiting blood feeding, when used consistently even after 7 years. The challenge, however, is enhancing their consistent use, especially by the most vulnerable groups (children under 5 years and pregnant women). The study established factors associated with consistent use of bed nets for malaria control among children under 5 years in Soroti district.

Methods
The study employed a cross-sectional design, with multi-stage sampling of households. A total of 400 households (HH) were sampled and the HH head in each household interviewed. Key informant interviews (KIIs) were conducted with 7 key informants who were knowledgeable on the subject matter. Data analysis was done using SPSS 17.0 at Univariate, Bivariate and Multivariable levels; after entry and cleaning. Key informants’ data were summarized manually; verbatim quotes and text used to reinforce quantitative data in line with objectives.

Results
Only 56.8% of the 690 children under 5 years used bed nets consistently. The factors affecting consistent bed net use were age of the child, their use of bed nets the previous night, occupation of caretaker, respondents’ perceived susceptibility, perceived risk of getting malaria, size and shape of the bed nets. Rectangular nets were difficult to hang daily in huts according to most key informants.

Conclusion
Consistent bed net use among under fives is still below the RBM target of 85% by 2015 and can be enhanced by providing conical bed nets and setting aside a health education programme to emphasize the effectiveness of even one mosquito in spreading malaria at night to the entire household and ability of bed nets to stop transmission better than other methods.
LncRNA ELF3-AS1 inhibits gastric cancer by forming a negative feedback loop with SNAI2 and regulates ELF3 mRNA stability via interacting with ILF2/ILF3 complex
Authors: Li Dandan , Shen Li , Zhang Xudong , Chen Zhen , Huang Pan , Huang Congcong , Qin Shanshan 
Published: December 2022

Abstract
Background
The biological function of lncRNA ELF3-AS1 remains largely unknown in cancers. The cause of SNAI2 overexpression in tumor metastasis remains largely unclear. The molecular mechanisms underlying the high co-expression of antisense lncRNAs and adjacent protein-coding genes remains unclear.

Methods
RNA-seq, CHIP and dual-luciferase reporter assay were performed to identify lncRNAs regulated by SNAI2. MicroRNA-seq and RNA-seq studies were conducted to reveal the biological function of ELF3-AS1 in GC. RNA pulldown and CHIRP assays were conducted to identify the protein that interacts with ELF3-AS1.

Results
A total of 123 lncRNAs were identified to be regulated by SNAI2 in GC by RNA sequencing. The ELF3 gene and antisense lncRNA ELF3-AS1 were both transcriptionally repressed by SNAI2 or SNAI1. Down-regulation of ELF3-AS1 and ELF3 predicted poor prognosis in GC. Nuclear localized lncRNA ELF3-AS1 negatively regulated GC cell cycle progression via suppressing G1/S transition and histone synthesis. ELF3-AS1 mainly inhibited GC metastasis by repressing SNAI2 signaling. Additionally, ELF3-AS1 modulated ELF3 mRNA stability by RNA-RNA interaction. The RNA duplexes formed by ELF3 mRNA and lncRNA ELF3-AS1 directly interacted with the double-stranded RNA (dsRNA) binding protein complex ILF2/ILF3 (NF45/NF90). In turn, the ILF2/ILF3 complex dynamically regulated the expression of ELF3-AS1 and ELF3 by affecting the dsRNA stability.

Conclusions
The SNAI2-ELF3-AS1 feedback loop regulates ELF3 expression at transcriptional and post-transcriptional levels and drives gastric cancer metastasis by maintaining SNAI2 overexpression. The ILF2/ILF3 complex plays a critical role in regulating dsRNA stability. In addition, our work provides a direct evidence that head-to-head antisense lncRNAs can share promoters with neighboring coding genes, which make their expression subject to similar transcriptional regulation, leading to high co-expression.
Increased copy number of imprinted genes in the chromosomal region 20q11-q13.32 is associated with resistance to antitumor agents in cancer cell lines
Authors: Krushkal Julia , Vural Suleyman , Jensen Travis L. , Wright George , Zhao Yingdong 
Published: December 2022

Abstract
Background
Parent of origin-specific allelic expression of imprinted genes is epigenetically controlled. In cancer, imprinted genes undergo both genomic and epigenomic alterations, including frequent copy number changes. We investigated whether copy number loss or gain of imprinted genes in cancer cell lines is associated with response to chemotherapy treatment.

Results
We analyzed 198 human imprinted genes including protein-coding genes and noncoding RNA genes using data from tumor cell lines from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We examined whether copy number of the imprinted genes in 35 different genome locations was associated with response to cancer drug treatment. We also analyzed associations of pretreatment expression and DNA methylation of imprinted genes with drug response. Higher copy number of BLCAP, GNAS, NNAT, GNAS-AS1, HM13, MIR296, MIR298, and PSIMCT-1 in the chromosomal region 20q11-q13.32 was associated with resistance to multiple antitumor agents. Increased expression of BLCAP and HM13 was also associated with drug resistance, whereas higher methylation of gene regions of BLCAP, NNAT, SGK2, and GNAS was associated with drug sensitivity. While expression and methylation of imprinted genes in several other chromosomal regions was also associated with drug response and many imprinted genes in different chromosomal locations showed a considerable copy number variation, only imprinted genes at 20q11-q13.32 had a consistent association of their copy number with drug response. Copy number values among the imprinted genes in the 20q11-q13.32 region were strongly correlated. They were also correlated with the copy number of cancer-related non-imprinted genes MYBL2, AURKA, and ZNF217 in that chromosomal region. Expression of genes at 20q11-q13.32 was associated with ex vivo drug response in primary tumor samples from the Beat AML 1.0 acute myeloid leukemia patient cohort. Association of the increased copy number of the 20q11-q13.32 region with drug resistance may be complex and could involve multiple genes.

Conclusions
Copy number of imprinted and non-imprinted genes in the chromosomal region 20q11-q13.32 was associated with cancer drug resistance. The genes in this chromosomal region may have a modulating effect on tumor response to chemotherapy.
Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients
Authors: Janke Florian , Angeles Arlou Kristina , Riediger Anja Lisa , Bauer Simone , Reck Martin , Stenzinger Albrecht , Schneider Marc A. , Muley Thomas , Thomas Michael , Christopoulos Petros , Sültmann Holger 
Published: December 2022

AbstractBackgroundDNA methylation (5-mC) signals in cell-free DNA (cfDNA) of cancer patients represent promising biomarkers for minimally invasive tumor detection. The high abundance of cancer-associated 5-mC alterations permits parallel and highly sensitive assessment of multiple 5-mC biomarkers. Here, we performed genome-wide 5-mC profiling in the plasma of metastaticALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy. We established a strategy to identifyALK-specific 5-mC changes from cfDNA and demonstrated the suitability of the identified markers for cancer detection, prognosis, and therapy monitoring.MethodsLongitudinal plasma samples (n = 79) of 21ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Information on genomic alterations (i.e., somatic mutations/fusions and copy number alterations) determined in matched plasma samples was available from previous studies.ResultsWe devised a strategy that identified tumor-specific 5-mC biomarkers by reducing 5-mC background signals derived from hematopoietic cells. This was followed by differential methylation analysis (cases vs. controls) and biomarker validation using 5-mC profiles ofALK-positive tumor tissues. The resulting 245 differentially methylated regions were enriched for lung adenocarcinoma-specific 5-mC patterns in TCGA data and indicated transcriptional repression of several genes described to be silenced in NSCLC (e.g.,PCDH10,TBX2,CDO1, andHOXA9). Additionally, 5-mC-based tumor DNA (5-mC score) was highly correlated with other genomic alterations in cell-free DNA (Spearman,ρ > 0.6), while samples with high 5-mC scores showed significantly shorter overall survival (log-rankp = 0.025). Longitudinal 5-mC scores reflected radiologic disease assessments and were significantly elevated at disease progression compared to the therapy start (p = 0.0023). In 7 out of 8 instances, rising 5-mC scores preceded imaging-based evaluation of disease progression.ConclusionWe demonstrated a strategy to identify 5-mC biomarkers from the plasma of cancer patients and integrated them into a quantitative measure of cancer-associated 5-mC alterations. Using longitudinal plasma samples of ALK-positive NSCLC patients, we highlighted the suitability of cfDNA methylation for prognosis and therapy monitoring.
Regulation of muscle stem cell fate
Authors: Fu Xin , Zhuang Cheng-le , Hu Ping 
Published: December 2022

AbstractSkeletal muscle plays a critical role in human health. Muscle stem cells (MuSCs) serve as the major cell type contributing to muscle regeneration by directly differentiating to mature muscle cells. MuSCs usually remain quiescent with occasionally self-renewal and are activated to enter cell cycle for proliferation followed by differentiation upon muscle injury or under pathological conditions. The quiescence maintenance, activation, proliferation, and differentiation of MuSCs are tightly regulated. The MuSC cell-intrinsic regulatory network and the microenvironments work coordinately to orchestrate the fate transition of MuSCs. The heterogeneity of MuSCs further complicates the regulation of MuSCs. This review briefly summarizes the current progress on the heterogeneity of MuSCs and the microenvironments, epigenetic, and transcription regulations of MuSCs.
Fish species classification using a collaborative technique of firefly algorithm and neural network
Authors: Prasenan Pooja , Suriyakala Chethamangalathu Damodharaprabhu 
Published: December 2022

AbstractMonitoring various Fish Species and its distribution of the species obtains a primary significance in receiving the insights to marine ecological-system. After this, visual classification of those species would aid in tracing out the movement and yield the patterns and trends in fish activities, which provides in depth knowledge of the species. Unconstrained under-water images pose highly variations because of the fish orientation changes, Light-intensities, similarity in fish patterns and fish shapes. This would create the greater challenge for Image-processing techniques in accurate classification of Fish species or the Fish classes. Hence, for this reason, Underwater Image Enhancement is implemented in combination of Morphological-operations in pre-processing method. The pre-processed image is then subjected to feature extraction process by using Speed-up Robust Feature algorithm. This is followed by Firefly Algorithm, applied for optimization of Region of interest selection in the selected-features. For the categorization of Fish-species, PatternNet is a technique which is employed, in classifying 10,000 marine fish-images to five categories (Dascyllus reticulatus, Plectroglyphidodon dickii, Chromis chrysura, Amphiprion clarkii, and Chaetodon lunulatus). The Efficiency of the proposed-framework is performed in terms of Classification accuracy, execution time, precision value, F-measure and recall factors with respect to various categories of fish species. The comparison of the proposed-framework is also assessed with the other existing methods. 98% of accuracy rate in classification was produced by the evaluation results of the proposed framework with a lesser average computation time of 3.64 s upon different tested images. Thus, the higher efficiency of the proposed framework is proved by the outcomes of the study.
Do task and item difficulty affect overestimation of one’s hand hygiene compliance? A cross-sectional survey of physicians and nurses in surgical clinics of six hospitals in Germany
Authors: Lamping Jonas , Tomsic Ivonne , Stolz Maike , Krauth Christian , Chaberny Iris F. , von Lengerke Thomas 
Published: December 2022

Abstract
Background
One barrier to hand hygiene compliance is overestimation of one’s own performance. Overconfidence research shows that overestimation tends to be higher for difficult tasks, which suggests that the magnitude of overestimation also depends on how it is assessed. Thus, we tested the hypothesis that overestimation was stronger for hand hygiene indications with low compliance (i.e., high difficulty), and the hypothesis that self-reported overall compliance based on a single item is higher than based on “5 Moments of Hand Hygiene” (WHO-5) items, since the single item implies an aggregation across indications.

Methods
In the WACH trial (German Clinical Trials Register [DRKS] ID: DRKS00015502), a questionnaire survey was conducted among physicians and nurses in nine surgical clinics (general/visceral surgery or orthopedics/trauma surgery) of six German hospitals. Self-reported compliance was assessed both by a single item and the WHO-5-items using percentage scales. These were compared with each other and with direct observations. Relative frequencies of the WHO-5 indications used to calculate the WHO-5-based self-reported overall compliance rate were estimated by a systematized review of the literature (see appendix). In analysis, t-tests, Chi2-tests and multiple linear regressions were used.

Results
Ninety-three physicians (response rate: 28.4%) and 225 nurses (30.4%) participated. Significant compliance differences between physicians and nurses were found for direct observations and were in favor of nurses, while no such differences were found for self-reports. Across the WHO-5, overestimation showed inverse correlations with observed compliance (physicians: r = −0.88, p = 0.049; nurses: r = −0.81, p = 0.093). Support for the hypothesis that the self-reported overall compliance based on one item is higher than that based on WHO-5 items was found for physicians (M = 87.2 vs. 84.1%, p = 0.041; nurses: 84.4 vs. 85.5%, p = 0.296). Exploratory analyses showed that this effect was confined to orthopedic/trauma surgeons (89.9 vs. 81.7%, p = 0.006).

Conclusion
Among physicians, results indicate stronger hand hygiene overestimation for low-compliance indications, and when measurements are based on a single item versus the five WHO-5 items. For practice, results contribute to infection prevention and control’s understanding of overestimation as a psychological mechanism that is relevant to professional hand hygiene.
Prevalence of anti-leptospiral IgM and detection of pathogenic Leptospira species DNA in neonates presenting with clinical sepsis in Southwestern Uganda
Authors: Hope Derick , Businge Stephen , Kyoyagala Stella , Bazira Joel 
Published: December 2022

AbstractBackgroundLeptospirosis is an emerging neglected zoonotic disease that presents with nonspecific signs/symptoms and it can be mistaken for other diseases. Owing to limited diagnostic capacity and unawareness, the data on human leptospirosis particularly in neonates are scarce in many sub-Saharan countries. It has been underreported hindering preventive and control measures in place. The study aimed at determining prevalence of leptospirosis as a cause of febrile illness in neonates using IgM ELISA and a quantitative real-time PCR (qPCR).MethodsThis was a descriptive cross-sectional study that included 103 neonatal sepsis cases whose parents/legal guardians gave informed consent. The data on demographic and clinical characteristics were collected using structured data collection form. EDTA whole blood sample was collected from the neonates by trained study nurses. From the samples, IgM ELISA was done using automated analyzers, DNA extracted and qPCR was performed using primers for LipL32, specific for the pathogenic leptospires.ResultsThe prevalence of anti-leptospiral IgM among the neonates as determined by ELISA was 4.3%, where all of them presented with lethargy and poor feeding. No pathogenicLeptospiraspecies DNA was amplified by qPCR.ConclusionsEvidence of leptospirosis was demonstrated in neonatal sepsis cases in this study. The findings suggest considerations of leptospirosis in the differential diagnosis of neonates with sepsis. More data are needed on the real epidemiology, clinical features, and burden of leptospirosis in neonates. There is need to include intermediate pathogenic species ofLeptospirain the diagnostic qPCR assays.
An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics
Authors: Shen Jiaxian , McFarland Alexander G. , Blaustein Ryan A. , Rose Laura J. , Perry-Dow K. Allison , Moghadam Anahid A. , Hayden Mary K. , Young Vincent B. , Hartmann Erica M. 
Published: December 2022

AbstractBackgroundEffective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources.ResultsThe workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes.ConclusionsThis workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.