Complete Analysis Research Articles

Implementation and engagement of the SMART Work & Life sitting reduction intervention: an exploratory analysis on intervention effectiveness

BackgroundTo enhance the impact of interventions, it is important to understand how intervention engagement relates to study outcomes. We report on the level of implementation and engagement with the SMART Work & Life (SWAL) programme (delivered with (SWAL plus desk) and without a height-adjustable desk (SWAL)) and explore the effects of different levels of this on change in daily sitting time in comparison to the control group.MethodsThe extent of intervention delivery by workplace champions and the extent of engagement by champions and participants (staff) with each intervention activity was assessed by training attendance logs, workplace champion withdrawal dates, intervention activities logs and questionnaires. These data were used to assess whether a cluster met defined criteria for low, medium, or high implementation and engagement or none of these. Mixed effects linear regression analyses tested whether change in sitting time varied by: (i) the number of intervention activities implemented and engaged with, and (ii) the percentage of implementation and engagement with all intervention strategies.ResultsWorkplace champions were recruited for all clusters, with 51/52 (98%) attending training. Overall, 12/27 (44.4%) SWAL and 9/25 (36.0%) SWAL plus desk clusters implemented all main intervention strategies. Across remaining clusters, the level of intervention implementation varied. Those in the SWAL (n = 8 (29.6%) clusters, 80 (32.1%) participants) and SWAL plus desk (n = 5 (20.0%) clusters, 41 (17.1%) participants) intervention groups who implemented and engaged with the most intervention strategies and had the highest percentage of cluster implementation and engagement with all intervention strategies sat for 30.9 (95% CI -53.9 to -7.9, p = 0.01) and 75.6 (95% CI -103.6 to -47.7, p < 0.001) fewer minutes/day respectively compared to the control group at 12 month follow up. These differences were larger than the complete case analysis. The differences in sitting time observed for the medium and low levels were similar to the complete case analysis.ConclusionsMost intervention strategies were delivered to some extent across the clusters although there was large variation. Superior effects for sitting reduction were seen for those intervention groups who implemented and engaged with the most intervention components and had the highest level of cluster implementation and engagement.Trial RegistrationISRCTN11618007. Registered on 24 January 2018. https://www.isrctn.com/ISRCTNISRCTN11618007.

Multi-MSIProcessor: Data Visualizing and Analysis Software for Spatial Metabolomics Research.

Mass spectrometry imaging (MSI) has emerged as a revolutionary analytical strategy in biomedical research for molecular visualization. By linking the characterization of functional metabolites with tissue architecture, it is now possible to reveal unknown biological functions of tissues. However, due to the complexity and high dimensionality of MSI data, mining bioinformatics-related peaks from batch MSI data sets and achieving complete spatially resolved metabolomics analysis remain a great challenge. Here, we propose novel MSI data processing software, Multi-MSIProcessor (MMP), which integrates the data read-in, MSI visualization, processed data preservation, and biomarker discovery functions. The MMP focuses on the AFADESI-MSI data platform but also supports mzXML and imzmL data input formats for compatibility with data generated by other MSI platforms such as MALDI/SIMS-MSI. MMP enables deep mining of batch MSI data and has flexible adaptability with the source code opened that welcomes new functions and personalized analysis strategies. Using multiple clinical biosamples with complex heterogeneity, we demonstrated that MMP can rapidly establish complete MSI analysis workflows, assess batch sample data quality, screen and annotate differential MS peaks, and obtain abnormal metabolic pathways. MMP provides a novel platform for spatial metabolomics analysis of multiple samples that could meet the diverse analysis requirements of scholars.

Novel Endophytic Pseudescherichia sp. GSE25 Strain Significantly Controls Fusarium graminearum and Reduces Deoxynivalenol in Wheat.

Fusarium heading blight (FHB) is a devastating disease in wheat, primarily caused by field invasion of Fusarium graminearum. Due to the scarcity of resistant wheat varieties, the agricultural sector resorts to chemical fungicides to control FHB incidence. On the other hand, biocontrol represents a promising, eco-friendly approach aligned with sustainable and green agriculture concepts. In the present study, a bacterial endophyte, Pseudescherichia sp. (GSE25), was isolated from wheat seeds and identified through complete genome sequencing and phylogenetic analysis. In vitro testing of this endophytic strain demonstrated strong antifungal activity against F. graminearum PH-1 by inhibiting spore germination, suppressing germ tube growth, and causing cell membrane damage. Under field conditions, the strain GSE25 significantly reduced the FHB incidence and the associated deoxynivalenol mycotoxin accumulation by over 60% and 80%, respectively. These findings highlight the potential of the isolated bacterial endophyte Pseudescherichia sp. GSE25 strain as a biocontrol agent in protecting wheat from FHB-caused F. graminearum. This is the first report showing a biocontrol effect of Pseudescherichia sp. a strain against phytopathogens.

Usefulness of Combined Ultrasound Assessment of E/e' Ratio, Pulmonary Pressure, and Cava Vein Status in Patients With Acute Heart Failure

Congestion is poorly investigated by ultrasound scans during acute heart failure (AHF) and systematic studies evaluating ultrasound indexes of cardiac pulmonary and systemic congestion during early hospital admission are lacking. We aimed to investigate the prevalence of ultrasound cardiac pulmonary and systemic congestion in a consecutive cohort of hospitalized patients with AHF, analyzing the relevance of each ultrasound congestion component (cardiac, pulmonary, and systemic) in predicting the risk of death and rehospitalization. This is a prospective research study of a single center that evaluates patients with an AHF diagnosis who are divided according to the left ventricular ejection fraction in patients with heart failure with preserved ejection fraction or reduced ejection fraction. We performed a complete bedside echocardiography and lung ultrasound analyses within the first 24hours of hospital admission. The ultrasound congestion score was preliminarily established by measuring the following parameters: cardiac congestion, which was defined as the contemporary presence of E/e' >15 and pulmonary systolic pressure >35mm Hg and the pulmonary congestion, defined as the total B-line number >25 at the lung ultrasound performed in 8 chest sites; moreover, the systemic congestion was defined if the inferior vena cava (IVC) was >21mm and if it was associated with a reduced inspiratory collapse >50%. We thoroughly assessed 230 patients and evaluated their results. Of these patients, 135 had heart failure with reduced ejection fraction and there were 95 patients with heart failure with preserved ejection fraction; 122 patients experienced adverse events during the 180-day follow-up. The receiver operating characteristic curve analysis showed that the tricuspid annular peak systolic excursion (TAPSE) (area under the curve [AUC] 0.34 [0.26 to 0.41], p <0.001), E/e' (AUC 0.62 [0.54 to 0.69], p=0.003), and IVC (AUC 0.70 [0.63 to 0.77], p <0.001) were all significantly related to poor prognosis detection. The univariate Cox regression analysis revealed that cardiac congestion in terms of E/e' and pulmonary systolic pressure (hazard ratio [HR] 1.49 [1.02 to 2.17], p=0.037), TAPSE (HR 0.90 [0.85 to 0.94], p <0.001), and systemic congestion (HR 2.64 [1.53 to 4.56], p <0.001) were all significantly related to the 180-day outcome. After adjustment for potential confounders, only TAPSE (HR 0.92 [0.88 to 0.98], p=0.005) and IVC (HR 1.92 [1.07 to 3.46], p=0.029) confirmed their prognostic role. The multivariable analysis of multiple congestion levels in terms of systemic plus cardiac (HR 1.54 [1.05 to 2.25], p=0.03), systemic plus pulmonary (HR 2.26 [1.47 to 3.47], p <0.001), and all 3 congestion features (HR 1.53 [1.06 to 2.23], p=0.02) revealed an incremental prognostic role for each additional determinant. In conclusion, among the ultrasound indexes of congestion, IVC and TAPSE are related to adverse prognosis, and the addition of pulmonary and cardiac congestion indexes increases the risk prediction accuracy. Our data confirmed that right ventricular dysfunction and systemic congestion are the most powerful predictive factors in AHF.

Comparative Analysis of Plant Cover of Plain and Mountain Shirvan (Azerbaijan)

A complete comparative analysis of the plain and mountainous parts of the Shirvan region of Azerbaijan has been shown in the paper. Basis the ecological and phytocenological principles widely used in modern geobotany have been taken in classifying the vegetation of the Shirvan territory. The species composition of edificators and subedificators (life forms) was taken as the main criterion when grouping and systematizing plants. Comparative analysis was carried out and for the first time, a map of the vegetation cover of Shirvan was compiled with botanical and geographical zoning on a scale of 1:100,000 based on ecological and phytocenological principles.

Near Real-Time Detection and Moment Tensor Inversion of the 11 May 2022, Dharchula Earthquake

On 11 May 2022, an earthquake of Mw 5.2 occurred in the Dharchula region of Uttarakhand Himalayas, India. The Uttarakhand State Earthquake Early Warning System (UEEWS) detected and transmitted the warning within 11.61 s from the origin time, taking only 4.26 s for processing, location, and magnitude estimation and warning dissemination. The complete analysis was performed using three seconds of waveforms. Using the initial earthquake parameters provided by the UEEWS, moment tensor inversion was performed using the broadband seismometers network installed in northern India. The moment tensor (MT) inversion was performed for the event using both the body waves and the surface waves. The first motion polarity was used along with waveform data to enhance the solution’s stability. This paper discusses the importance of real-time event detection and efforts towards real-time MT source inversion of earthquakes in the Uttarakhand Himalayas. Relocation of two past earthquakes near Dharchula is also undertaken in this study. The outcome of this study provides insights into mitigating seismic hazards, understanding earthquake source mechanisms, and enhancing knowledge of local fault structures.

Development of a Digital Module with an Ethnomathematic Nuance with the Problem Based Learning Model to Improve Solving Capability Primary School Student Problems

Problem solving skills for primary school students are very important. Because problem solving ability is an understanding of how to solve problems in everyday life. One of the learning models that can improve problem solving skills is the Problem Based Learning model. Ethnomathematics is a learning approach that is carried out by teaching mathematics by linking mathematics to a person's cultural work. This research aims to develop a digital module with ethnomathematics nuances with a problem-based learning model to improve elementary school students' problem-solving abilities. This research uses a research and development (R&amp;D) design with the ADDIE model. The subjects in this research were 33 class V students at SDN Pudak Payung 02. Data collection techniques in this research were observation, interviews, questionnaires and tests. The data analysis techniques for this research include analysis of media validation results, analysis of media practicality data, analysis of classical completeness, and analysis of student test results. The results of this research include: 1) A digital module with ethnomathematics nuances with a problem based learning model; 2) The digital module with an ethnomathematics nuance with a problem based learning model is very valid with an overall average score of the media validation test of 0.87 and the digital module developed is of very practical quality with an overall average score of the media practicality test of 93%; 3) The classical completeness value of testing the potential effects of digital media with an ethnomathematics nuance using the problem based learning model obtained high effectiveness results with a percentage of 88%; 4) The digital module with an ethnomathematics nuance with a problem based learning model was declared effective with the difference between the pretest and posttest scores, as well as the results of the n-gain test with an average of 0.55 classified as medium. The conclusion of this research is that digital modules with ethnomathematics nuances with problem-based learning models are effectively used to improve elementary school students' problem-solving abilities. Keywords: digital module, ethnomathematics, problem-based learning and problem-solving abilities.

Failure Forensics of Shaped PDC Cutters Using Image Analysis and Deep Learning

Summary One of the major advances in polycrystalline diamond compact (PDC) bits in the last 10 years is the global adoption of 3D-shaped PDC cutters. By manipulating the cutter shape based on the understandings of cutter–rock interaction mechanisms, the cutting efficiency and mechanical properties of PDC cutters have been greatly improved. Ongoing innovations in 3D-shaped PDC cutter technology are critical to overcoming the more and more challenging formations in ultradeep wells, such as the 10 000-m-deep wells being drilled in China. Such an important role for 3D-shaped PDC cutters in oil and gas drilling applications necessitates a complete and effective failure analysis method. However, the current International Association of Drilling Contractors (IADC) dull grading cannot fulfill this objective. It is out of date in judging the damages to PDC bits and exhibits more limitations in addressing the unique challenges presented by complicated cutter shapes. To address this issue, an intelligent recognition model for PDC bit damage identification was developed based on the image analysis technology and the YOLOv7 algorithm. More than 10,000 dull bit images were used to train and validate this intelligent recognition model, which were collected from 363 PDC bits that suffered different degrees of damage after being used to drill 185 wells in the Sinopec Shengli Oilfield. Compared to the existing models, the developed intelligent recognition model has several notable contributions. First, the developed model is capable of recognizing the damages of various shaped PDC cutters commonly used by the global bit manufacturers, enabling a more accurate assessment of the failure behaviors of shaped cutters and their bits. The detection accuracy of the developed model exceeds 80% based on the confusion matrix. The recognition results by the developed artificial intelligence (AI) model are consistent with the actual failure modes judged by experienced drilling engineers. Second, the developed AI model provides direct qualitative identification of the failure modes and failure reasons for both cutters and PDC bits rather than the quantitative evaluation of the missing diamond layer used by IADC dull grading. Furthermore, the developed model eliminates the effect of reclaimed cutters on the AI detection results based on the implicit use of spatial cues in the YOLOv7 algorithm. The intelligent recognition model developed in this work can provide reliable and valuable guidance for the post-run evaluation, the bit selection for the next run, and the iterative optimization of bit design.

A complete analysis of the link uncertainty budget for pulsed laser time transfer on China space station

High-precision Time-Frequency Rack (HTFR) mission, a part of experiment module II of the China Space Station (CSS), was equipped with a Sr optical clock, H-maser, and laser-cooled microwave clock. To compare time and frequency across widely separated clocks, a microwave link, and a pulsed laser link were both established, which probably enables new possibilities for fundamental science, geodesy, and metrology. Based on the existing relativistic theory for time and frequency transfer, we derive a relativistic model of satellite-ground laser time transfer on CSS (CLT), which can be of direct use in CLT data processing. In addition to first and second-order Sagnac effects, it also includes relativistic rate shifts, atmospheric refraction, and turbulence, laser retroreflector array (LRA) range correction, and position correction between detector and reflector, satisfying the stability evaluation of CSS atomic clocks with fractional frequency stability of 3 × 10−17/10000 s. Additionally, we numerically investigate the link error magnitude and use Monte Carlo simulations to assess the impact of correcting for link errors on the stability of the CLT, taking into account the CSS orbit and attitude determinations as well as the CLT payload calibration parameters. It is shown that the CLT link can be considered to reach a TDEV of approximately 0.1 ps/300 s while meeting the CSS design objectives. The primary factors that influence the stability of the CLT are the position correction between detector and reflector, LRA range correction, and the coupling relation of these two error distributions.

Investigation of intermolecular interactions of l-Valine and l-Phenylalanine with muscle relaxant drug mephenesin molecule prevalent in aqueous solution by various physico-chemical methods at T=298.15K–313.15K

A complete chemical analysis of significant intermolecular interactions of l-Valine (L-Val) and l-Phenylalanine (L-Phe) with Mephenesin (MEPN) molecules in aqueous solution has been studied by different physicochemical methodologies at various temperatures (T = 298.15 K–313.15 K at an interval of 5 K) and concentrations (0.001 mol kg−1, 0.003 mol kg−1, 0.005 mol kg−1) of aqueous MEPN solution. The limiting apparent molar volume (φV0) and experimental slope (SV*) values are found from the equation of Masson, viscosity A and B-coefficient determined using the equation of Jones-Doles, molar refraction (RM) and limiting molar refraction (RM0) derived by the Lorentz-Lorenz equation, express that in our experimental solution of amino acids (AAs) in aqueous MEPN, the solute-solvent interaction predominates over the solute-solute and solvent-solvent interactions for these ternary solutions. These are also justified by the measurement of various thermodynamic parameters, free energy of activation of viscous flow per mole of solvent(Δμ1°#) and solute (Δμ2°#), activation of viscous flow of enthalpies (ΔH°#) and entropies (ΔS°#). The characteristics of structure-breaking of solutes in the aqueous drug solution have been identified by Hepler's method and dB/dT value. The spectroscopic methods like UV–visible and proton-NMR studies help to explicate the strong AA-MEPN interactions in the solution phase and obtain a good correlation with theoretical studies. Theoretical investigations are checked to authenticate the experimental observations and according to both studies, L-Phe-MEPN interaction is greater than L-Val-MEPN interaction. The experimental and correlated research data are useful for the development of model combinations of AAs with drug molecules in pharmaceutical and medicinal chemistry.

Influence of COVID-19 Lockdown on Noise Level Reduction: A Scoping Review With Stakeholders’ Consultation

EIn light of the COVID-19 pandemic, empirical evidence suggests that the global community has commenced a recuperation process and witnessed a notable positive influence. Despite several published research on the topic, a complete analysis examining the effects of lockdown measures implemented during the COVID-19 pandemic on environmental noise has yet to be conducted. Thus, this scoping review with stakeholders’ consultation was conducted to systematically identify literature related to noise level reduction. An electronic search was conducted up to August 8, 2020, on four databases (Science Direct, SCOPUS, CINAHL, and PubMed). Eight articles met our criteria for further review where G20 countries conducted most studies. Three were reviewed, two were experimental, two were case reports, and the other was protocol. Although the current literature is minimal, it is evident that global noise levels are decreasing significantly. However, our review revealed that none of the included studies addressed the effect of noise level reduction on human health, and we view the decrease not necessarily as an outcome of the COVID-19 pandemic outbreak but rather because of the transition from outdoor to indoor environments. As this subject matter has received a lack of attention and is often overlooked, more innovative research to look for state-of-the-art stagnant initiatives is needed to control the issue of noise pollution and to provide a basis for government policies.

An Eulerian finite element method for tangential Navier-Stokes equations on evolving surfaces

The paper introduces a geometrically unfitted finite element method for the numerical solution of the tangential Navier–Stokes equations posed on a passively evolving smooth closed surface embedded in R 3 \mathbb {R}^3 . The discrete formulation employs finite difference and finite elements methods to handle evolution in time and variation in space, respectively. A complete numerical analysis of the method is presented, including stability, optimal order convergence, and quantification of the geometric errors. Results of numerical experiments are also provided.

Complete genome sequence analysis and genome organization of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1) from Turkey.

The economically important pale tussock moth Dasychira pudibunda L. (Lepidoptera: Lymantriidae), known as a beech pest in Europe, primarily inflicts damage on beech leaves. In the present study, we aim to reveal the genome characteristics of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1), which was detected for the first time in Turkey and compare it with the reference genome and other baculovirus genomes. The DapuNPV-T1 genome was determined to be a circular, double-stranded DNA molecule with 136,920bp and a nucleotide distribution of 54.4% G + C. Bioinformatics analysis showed that the DapuNPV-T1 genome contains 163 open reading frames with more than 150 nucleotides. Fifty-four ORFs of unknown function, 6 homologous regions (hrs), 1 AC-rich region, and 3 bro genes (bro-a, bro-b, and bro-c) were determined in the genome sequence. Comparative analysis with other baculovirus strains revealed distinctions in the DapuNPV-T1 genome based on ORF. The gene parity plot and phylogenetic analysis confirmed that DapuNPV-T1 belongs to the alphabaculovirus group Ib. In addition, the DapuNPV-T1 isolate was found to be close to the nucleopolyhedrovirus Poland isolate in Dasychira pudibunda and Orgyia pseudotsugata multiple nucleopolyhedrovirus. With this study, the first genome analysis of DapuNPV from Turkey became the second in the world to enter the literature. Comprehensive information on a wide range of isolates will provide a more detailed overview of baculoviruses and help overcome their shortcomings as biocontrol agents.

Unraveling the Gender Gap: A Comparative Analysis of School Enrollment and Secondary Education Completion in Pakistan's Provinces

This study examines the gender gap in school enrollment and secondary school completion in Pakistan using secondary data from the Pakistan Social and Living Standards Measurement Survey (PSLM) and Pakistan Education Statistics reports. A comparative analysis of the four provinces and their districts is conducted to identify regional dynamics contributing to gender disparities in education. The research investigates the relationship between students who ever attended school, those who passed secondary school, and the gender gap in enrollment. Descriptive statistics analyze school enrollment rates and dropouts across different regions. Data from the official governmental reports, including the Pakistan Bureau of Statistics and PSLM (2019-20), and education statistics reports from 2017 for Punjab, Sindh, Khyber Pakhtunkhwa, and Balochistan, serve as the foundation for this analysis. The study offers valuable insights into the complex web of causality and influence shaping the persistence of gender disparities in education in Pakistan.

A Large Recurrent Retroperitoneal Lymphangioma in a Previously Healthy Adolescent Male: A Case Report

Lymphangiomas are uncommon benign lymphatic vessel tumors that can affect any area of the body served with the lymphatic system. Intra-abdominal lymphangiomas are considered rare, accounting for less than 5 percent of all lymphangioma cases. In this case report, we present a recurrent large retroperitoneal lymphangioma in a previously healthy 15-year-old boy. The patient presented to the Emergency Department with abdominal pain lasting for one week. The pain, described as diffuse, crampy, and non-radiating, gradually increased with time and was aggravated by movement. A large retroperitoneal fluid collection was found on the Computed Tomography (CT) scan. Subsequently, the patient underwent CT-guided drainage, at which 700ml of bloody fluid was extracted. After three months, the patient was readmitted to the hospital for a similar presentation of abdominal fullness and pain. Complete blood count analysis indicated an unremarkable profile, except for a left shift of 82.2% neutrophils and a white blood cell count of 11,300/mcl. A CT scan of the abdomen reported a large, thin-walled cystic lesion in the right hemi-abdomen with minimal thin internal septations, resulting in moderate right hydronephrosis/hydroureter.

Transcriptomic Changes in Response to Form of Selenium on the Interferon-Tau Signaling Mechanism in the Caruncular Tissue of Beef Heifers at Maternal Recognition of Pregnancy.

We have reported that selenium (Se) provided to grazing beef cattle in an inorganic (ISe) form versus a 1:1 mixture (MIX) of inorganic and organic (OSe) forms affects cholesterol biosynthesis in the corpus luteum (CL), the abundance of interferon tau (IFNτ) and progesterone (P4)-induced mRNAs in the caruncular (CAR) tissue of the endometrium, and conceptus length at maternal recognition of pregnancy (MRP). In this study, beef heifers were supplemented with a vitamin-mineral mix containing 35 ppm Se as ISe or MIX to achieve a Se-adequate status. Inseminated heifers were killed at MRP (d 17, n = 6 per treatment) for tissue collection. In CAR samples from MIX versus ISe heifers, qPCR revealed that mRNA encoding the thyroid regulating DIO2 and DIO3 was decreased (p < 0.05) and a complete transcriptomic analysis revealed effects on the interferon JAK-STAT1/2 pathway, including decreased expression of mRNAs encoding the classical interferon stimulated genes IFIT1, IFIT2, IFIT3, IRF1, IRF9, ISG15, OAS2, and RSAD2 (p < 0.05). Treatment also affected the abundance of mRNAs contributing to the immunotolerant environment (p < 0.05). In combination, these findings suggest more advanced preparation of the CAR and developing conceptus for implantation and to evade immune rejection by the maternal system in MIX- vs. ISe-treated heifers.

10031-GGE-2 GENOMIC ANALYSIS OF MENINGIOMA USING GENE PANEL TESTING

Abstract Recently, cancer gene panel tests have been covered by insurance and their usefulness has been reported. In addition to the cancer gene panel tests covered by insurance, we are conducting the PleSSision-Rapid test, a cancer gene panel test that can measure 143 genes, as a clinical research project. The former has been used for 14 cases brain tumors, and the latter has been used for brain tumors in about 100 cases, respectively. The PleSSision-Rapid test has now completed analysis of 87 cases, with gliomas accounting for 33, meningiomas for 29, and metastatic brain tumors for 14 cases. Tumor mutation burden (TMB) was high in 18 cases, and microsatellite instability was high in none. NTRK gene fusion was observed in 1 case. Of the 29 meningiomas, 9 were male and 20 female, ranging in age from 31 to 79 years (mean 57). Twenty of the cases were located at the skull base. Twenty four were primary cases, whereas 5 were recurrent cases. WHO grade 1, 2, and 3 were 23, 4, and 2, respectively. There was no difference in TMB among grades, and Ki-67 values increased with increasing grade. Comparing grade 1 and grade 2/3, NF2 and KDM6A were found to be significantly different in the rate of gene mutations. Grade 2/3 patients had a significantly higher frequency of copy number aberrations such as genes related to DNA repair, histone modification, and chromatin remodeling, than grade 1 patients,

Molecular characteristics and pathogenicity of a novel chicken astrovirus variant

It is well-established that the genetic diversity, regional prevalence, and broad host range of astroviruses significantly impact the poultry industry. In July 2022, a small-scale commercial broiler farm in China reported cases of growth retardation and a 3% mortality rate. From chickens displaying proventriculitis and pancreatitis, three chicken astroviruses (CAstV) isolates were obtained and named SDAU2022-1-3. Complete genomic sequencing and analysis revealed the unique characteristics of these isolates from known CAstV strains in ORF1a, ORF1b, and ORF2 genes, characterized by an unusually high variability. Analysis of amino acid mutations in ORF1a, ORF1b, and ORF2 indicated that the accumulation of these mutations played a pivotal role in the emergence of the variant strain. Inoculation experiments demonstrated that affected chickens exhibited liver and kidney enlargement, localized proventricular hemorrhage, and a dark reddish-brown appearance in about two-thirds of the pancreas. Histopathological examination unveiled hepatic lymphocytic infiltration, renal tubular epithelial cell swelling, along with lymphocytic proventriculitis and pancreatitis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated viremia and viral shedding at 3 days post-infection (dpi). The proventriculus displayed the highest viral loads, followed by the liver, kidney, duodenum, and pancreas. Liver parameters (AST and ALT) and kidney parameters (UA and UN) demonstrated mild damage consistent with earlier findings. While the possibility of new mutations in the ORF2 gene of CAstV causing proventriculitis and pancreatitis warrants further investigation, these findings deepen our comprehension of CAstV’s pathogenicity in chickens. Additionally, they serve as valuable references for subsequent research endeavors.

Dealing with missing observations in the outcome and covariates in randomized controlled trials

This article compares different missing data methods in randomized controlled trials, specifically addressing cases involving joint missingness in the outcome and covariates. In the existing literature, it is still unclear how advanced methods like linear mixed model (LMM) and multiple imputation (MI) perform in comparison to simpler methods regarding the estimation of treatment effects and their standard errors. We therefore evaluates the performance of LMM and MI against simple alternatives across a wide range of simulation scenarios for various realistic missingness mechanisms. The results show that no single method universally outperforms the others. However, LMM followed by MI demonstrates superior performance across most missingness scenarios. Interestingly, a simple method that combines complete case analysis for the missing outcome and mean imputation for the missing covariate (CCAME) performs similarly to LMM and MI. All methods are furthermore compared in the context of a randomized controlled trial on chronic obstructive pulmonary disease.

In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.

We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.