bluuebunny/crossref_metadata_2025 huggingface dataset:
Compensation of emulated atmospheric disturbance and tracking of a moving object by a real-time digital phase conjugate mirror using a liquid crystal spatial light modulator
Authors: Kawakami Kotomi , Nakagawa Tomoya , Tanaka Hiroto , Okamura Hideki
Published: May 2023

We developed a fast-response digital phase conjugate mirror using a 700 Hz high-speed liquid crystal spatial light modulator and a high-speed camera. The total delay from signal light acquisition to phase conjugate light generation was 9.7 ms at 1246 × 1024 and 5.9 ms at 640 × 512. The tracking experiment performed on a target moving at a constant distance perpendicular to the optical axis, produced an error of 2%. Furthermore, a heated soldering iron, used to compensate for artificially generated air disturbance, showed that beam wandering and intensity fluctuations were reduced by 86% and 55%, respectively, compared to a phase conjugate mirror with added delay. Phase conjugate light irradiation of a continuously moving target at a maximum speed of 0.9 mm s−1 was also performed. This study shows that real-time digital phase conjugate mirrors can correct wavefront distortion caused by air fluctuation, which is a major challenge in long-distance wireless optical transmission in the turbulent atmosphere, without complicated control, and prevent beam quality degradation in the presence of atmospheric disturbance.
Physical Work Demands of Maintenance Workers on Onshore Petroleum Facilities in Norway: An Observational Study Utilizing Wearable Sensor Technology
Authors: Tjøsvoll Svein O , Steiro Fimland Marius , Gonzalez Victor , Seeberg Trine M , Holtermann Andreas , Færevik Hilde , Wiggen Øystein
Published: May 2023

Objectives

High physical work demands can cause musculoskeletal disorders and sick leave in petroleum workers. However, our knowledge of their physical work demands is scarce and based on self-report. The objective of our study is to work towards closing this knowledge gap by assessing the physical work demands of onshore petroleum maintenance workers using body-worn sensors.

Methods

A total of 46 of 69 eligible maintenance workers (37 mechanics and 9 process technicians) from three onshore petroleum facilities in Norway filled in a questionnaire and diary and wore five accelerometers and a heart rate sensor for up to six consecutive workdays. Work-related physical activity and postures were classified using rule-based modelling in a modified version of the validated Acti4 software.

Results

The onshore maintenance petroleum workers were working an average of 10 h a day and spent on average this time with 48% (SD = 16.5) sitting, 1% (SD = 2.8) lying down, 39% (SD = 16.2) in light physical activity, and 9% (SD = 3.8) in moderate to vigorous physical activity. During work hours while at feet, we found arm elevation ≥60° to be 11% (SD = 7.1) (68 min), and forward bending of the trunk ≥60° to be 2% (SD = 2.2) (14 min). The workers spent 2% (SD = 2.5) (12 minu) of the workhours kneeling. We observed a high inter-individual variation for all these work exposures. Moreover, 26% (12) of the workers conducted static standing for >30% of the workday, and 17% (8) spent more than half of the work hours >33% of their estimated maximal cardiovascular capacity.

Conclusions

While onshore maintenance petroleum workers on average spend about half of the workday sitting or lying down, the remaining worktime is spent with a rather high duration of arm elevation and forward bending. Quite high fraction of the workers spends much of the workhours in static standing and kneeling. We see a substantial variation in these work exposures between the workers. The findings indicate a need for preventive measures in how work is organized and performed.
P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network
Authors: Wang Yan , Xuan Chenxu , Wu Hanwen , Zhang Bai , Ding Tao , Gao Jie
Published: May 2023

Although many single-cell computational methods proposed use gene expression as input, recent studies show that replacing ‘unstable’ gene expression with ‘stable’ gene–gene associations can greatly improve the performance of downstream analysis. To obtain accurate gene–gene associations, conditional cell-specific network method (c-CSN) filters out the indirect associations of cell-specific network method (CSN) based on the conditional independence of statistics. However, when there are strong connections in networks, the c-CSN suffers from false negative problem in network construction. To overcome this problem, a new partial cell-specific network method (p-CSN) based on the partial independence of statistics is proposed in this paper, which eliminates the singularity of the c-CSN by implicitly including direct associations among estimated variables. Based on the p-CSN, single-cell network entropy (scNEntropy) is further proposed to quantify cell state. The superiorities of our method are verified on several datasets. (i) Compared with traditional gene regulatory network construction methods, the p-CSN constructs partial cell-specific networks, namely, one cell to one network. (ii) When there are strong connections in networks, the p-CSN reduces the false negative probability of the c-CSN. (iii) The input of more accurate gene–gene associations further optimizes the performance of downstream analyses. (iv) The scNEntropy effectively quantifies cell state and reconstructs cell pseudo-time.
NanoPack2: population-scale evaluation of long-read sequencing data
Authors: De Coster Wouter , Rademakers Rosa
Published: May 2023

Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.

Availability and implementation

The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager.
Renal function is highly associated with podiatric risk in diabetic patients
Authors: Bonnet Jean-Baptiste , Szwarc Ilan , Avignon Antoine , Jugant Sébastien , Sultan Ariane
Published: May 2023

Background

Chronic kidney disease (CKD) is correlated with the incidence of diabetic foot ulcer (DFU). Furthermore, the International Working Group on the Diabetic Foot (IWGDF) has proposed a classification of the risk factors for DFU. The purpose of this study was to investigate the relationship between the IWGDF risk classification and the glomerular filtration rate level estimated by the CKD Epidemiology Collaboration formula (eGFR).

Methods

We conducted a prospective multicentric study. Patients were recruited from either diabetology or nephrology departments. The secondary objectives were to determine this relationship after excluding people on dialysis and to identify the factors associated with podiatric risk.

Results

Four hundred and eighty-six patients were included, with a mean age of 64.2 years (±15.7) and a mean diabetes duration of 15.7 years (±12.1). Based on the IWGDF classification, 53.5% of the population were in podiatric stage 0, 11.7% in stage 1 and 34.8% in stage 2 or 3. The mean eGFR level was significantly lower in patients with podiatric risk ≥2 (36.8 ± 33.9 mL/min/1.73 m2 vs 71.9 ± 35.3 mL/min/1.73 m2, P < .0001) and a significant association was found between the eGFR and the podiatric risk. This association remained significant after the exclusion of the hemodialysis patients. After receiver operating characteristic analysis, a cutoff of 45 ± 11 mL/min/1.73 m2 (area under the curve 0.76) was found discriminant to define a group of CKD patients at higher risk for podiatric stage ≥2.

Conclusion

eGFR levels are linked to podiatric stages in diabetes mellitus. Patients with eGFR <45 mL/min/1.73 m2 and dialysis patients should be carefully managed in collaboration with diabetic foot specialized centers.
Pulmonary embolism-related refractory out-of-hospital cardiac arrest and extracorporeal cardiopulmonary resuscitation: Prague OHCA study post hoc analysis
Authors: Pudil Jan , Rob Daniel , Smalcova Jan , Smid Ondrej , Huptych Michal , Vesela Michaela , Kovarnik Tomas , Belohlavek Jan
Published: May 2023

Aims

Refractory out-of-hospital cardiac arrest (r-OHCA) in patients with pulmonary embolism (PE) is associated with poor outcomes. The role of extracorporeal cardiopulmonary resuscitation (ECPR) in this patient group is uncertain. This study aims to analyse clinical course, outcomes, and the effect of an invasive procedure, including ECPR, in a randomized population.

Methods and results

A post hoc analysis of a randomized controlled trial (Prague OHCA study) was conducted to evaluate the effect of ECPR vs. a standard approach in r-OHCA. A subgroup of patients with PE-related r-OHCA was identified, and procedural and outcome characteristics, including favourable neurological survival, organ donation, and complications, were compared to patients without PE. Pulmonary embolism was identified as a cause of r-OHCA in 24 of 256 (9.4%) enrolled patients. Patients with PE were more likely to be women [12/24 (50%) vs. 32/232 (13.8%); P < 0.001] and presented more frequently with an initial non-shockable rhythm [23/24 (95.8%) vs. 77/232 (33.2%); P < 0.001], as well as more severe acidosis at admission [median pH (interquartile range); 6.83 (6.75–6.88) vs. 6.98 (6.82–7.14); P < 0.001]. Their favourable 180-day neurological survival was significantly lower [2/24 (8.3%) vs. 66/232 (28.4%); P = 0.049], but the proportion of accepted organ donors was higher (16.7 vs. 4.7%, P = 0.04).

Conclusion

Refractory out-of-hospital cardiac arrest due to PE has a different presentation and inferior outcomes compared to other causes but may represent an important source of organ donations. The ECPR method did not improve patient outcomes.
Trainability for cardiopulmonary fitness is low in patients with peripheral artery disease
Authors: Huang Shu-Chun , Yeh Chi-Hsiao , Hsu Chih-Chin , Lin Yu-Ching , Lee Chen-Hung , Hsiao Ching-Chung , Chiu Chien-Hung , Fu Tieh-Cheng
Published: May 2023

Aims

In patients with peripheral arterial disease (PAD), exercise therapy is recommended to relieve leg symptoms, as noted in the 2016 AHA/ACC and 2017 ESC/ESVS guidelines. We assessed the trainability for cardiopulmonary fitness (CPF) and quality of life (QOL); three distinct patient types, namely, PAD, heart failure (HF), and stroke, were compared.

Methods and results

This is a multicentre, retrospective analysis of prospectively collected data from three clinical studies. Data collected from 123 patients who completed 36 sessions of supervised aerobic training of moderate intensity were analysed, with 28 PAD, 55 HF, and 40 stroke patients totalling 123. Before and after training, cardiopulmonary exercise testing with non-invasive cardiac output monitoring and QOL evaluation using a 36-Item Short Form Survey (SF-36) were performed. Non-response was defined as a negative change in the post-training value compared with that in the pre-training value. The result showed an improvement in CPF in all three groups. However, cardiorespiratory fitness (CRF) increased by a lesser extent in the PAD group than in the HF and stroke groups; the physical and mental component scores (MCS) of SF-36 exhibited a similar pattern. Non-response rates of peak V˙O2, oxygen uptake efficiency slope, and MCS were higher in the PAD group. In the PAD group, non-responders regarding peak V˙O2 had a higher pulse wave velocity than responders.

Conclusion

In patients with PAD following exercise therapy, CRF and QOL improved to a lesser extent on average; their non-response rate was also higher compared with that of HF or stroke patients. Therefore, a higher dose of exercise might be needed to elicit adaptation in PAD patients, especially those with high pulse wave velocity.
Perceptions of patient-reported outcome data access and sharing among patients with heart failure: ethical implications for research
Authors: Mangal Sabrina , Niño de Rivera Stephanie , Reading Turchioe Meghan , Myers Annie , Benda Natalie , Goyal Parag , Dugdale Lydia , Masterson Creber Ruth
Published: May 2023

Aims

In the face of growing expectations for data transparency and patient engagement in care, we evaluated preferences for patient-reported outcome (PRO) data access and sharing among patients with heart failure (HF) using an ethical framework.

Methods and results

We conducted qualitative interviews with a purposive sample of patients with HF who participated in a larger 8-week study that involved the collection and return of PROs using a web-based interface. Guided by an ethical framework, patients were asked questions about their preferences for having PRO data returned to them and shared with other groups. Interview transcripts were coded by three study team members using directed content analysis. A total of 22 participants participated in semi-structured interviews. Participants were mostly male (73%), White (68%) with a mean age of 72. Themes were grouped into priorities, benefits, and barriers to data access and sharing. Priorities included ensuring anonymity when data are shared, transparency with intentions of data use, and having access to all collected data. Benefits included: using data as a communication prompt to discuss health with clinicians and using data to support self-management. Barriers included: challenges with interpreting returned results, and potential loss of benefits and anonymity when sharing data.

Conclusion

Our interviews with HF patients highlight opportunities for researchers to return and share data through an ethical lens, by ensuring privacy and transparency with intentions of data use, returning collected data in comprehensible formats, and meeting individual expectations for data sharing.
Achieved systolic blood pressure and cardiovascular outcomes in 60–80-year-old patients: the Strategy of Blood Pressure Intervention in the Elderly Hypertensive Patients (STEP) trial
Authors: Deng Yue , Bai Jingjing , Yang Xinchun , Liu Wei , Guo Zihong , Zhang Juyan , Huang Rongjie , Yang Xiaomin , Yu Chunli , Yu Jing , Guo Xiurong , Wu Hailei , Liu Peiyu , Zhang Weili , Cai Jun
Published: May 2023

Aims

Intensive systolic blood pressure (SBP) lowering has been increasingly used; however, data is missing on patients who had target-achieved (TA). This study aims to show the cardiovascular effect of maintaining SBP at intensive levels.

Methods

The Strategy of Blood Pressure Intervention in Elderly Hypertensive Patients (STEP) trial was a multicentre, randomized, controlled trial which enrolled 8511 young-older (60–80 years) hypertensive patients without prior stroke to compare the cardiovascular prognosis of the intensive treatment (SBP target, 110 to <130 mmHg) vs. the standard treatment (130 to <150 mmHg). This secondary analysis assessed data in patients who achieved a mean SBP within target values. The association of mean achieved SBP and cardiovascular events was examined using a cubic spline function.

Results

In total, 3053 patients (72.0%) in the intensive-treatment group and 3427 (80.3%) in the standard-treatment group had an SBP target achieved, with mean follow-up SBP values of 124.2 mmHg and 137.4 mmHg, respectively. Throughout the median 3.38-year follow-up, the cardiovascular risk was significantly lower in the TA intensive-treatment group than in the TA standard-treatment group [adjusted hazard ratio (HR) 0.61, 95% confidence interval (CI) 0.46–0.80; P < 0.001]. In the intensive-treatment group, patients failing to achieve SBP targets presented higher cardiovascular risk than those TA patients (HR 2.04, 95% CI 1.44–2.88; P < 0.001). A J-shaped relationship was observed between the mean achieved SBP and risk of cardiovascular events, with the lowest risk at an SBP of 126.9 mmHg.

Conclusions

Maintaining SBP at <130 mmHg offers additional cardiovascular benefits among young-older patients with hypertension.

Registration

ClinicalTrials.gov: NCT03015311.
Comprehensive characterization of non-cardiac comorbidities in acute heart failure: an analysis of ESC-HFA EURObservational Research Programme Heart Failure Long-Term Registry
Authors: Chioncel Ovidiu , Benson Lina , Crespo-Leiro Maria G , Anker Stefan D , Coats Andrew J S , Filippatos Gerasimos , McDonagh Theresa , Margineanu Cornelia , Mebazaa Alexandre , Metra Marco , Piepoli Massimo F , Adamo Marianna , Rosano Giuseppe M C , Ruschitzka Frank , Savarese Gianluigi , Seferovic Petar , Volterrani Maurizio , Ferrari Roberto , Maggioni Aldo P , Lund Lars H
Published: May 2023

Aims

To evaluate the prevalence and associations of non-cardiac comorbidities (NCCs) with in-hospital and post-discharge outcomes in acute heart failure (AHF) across the ejection fraction (EF) spectrum.

Methods and results

The 9326 AHF patients from European Society of Cardiology (ESC)-Heart Failure Association (HFA)-EURObservational Research Programme Heart Failure Long-Term Registry had complete information for the following 12 NCCs: anaemia, chronic obstructive pulmonary disease (COPD), diabetes, depression, hepatic dysfunction, renal dysfunction, malignancy, Parkinson’s disease, peripheral vascular disease (PVD), rheumatoid arthritis, sleep apnoea, and stroke/transient ischaemic attack (TIA). Patients were classified by number of NCCs (0, 1, 2, 3, and ≥4). Of the AHF patients, 20.5% had no NCC, 28.5% had 1 NCC, 23.1% had 2 NCC, 15.4% had 3 NCC, and 12.5% had ≥4 NCC. In-hospital and post-discharge mortality increased with number of NCCs from 3.0% and 18.5% for 1 NCC to 12.5% and 36% for ≥4 NCCs.

Anaemia, COPD, PVD, sleep apnoea, rheumatoid arthritis, stroke/TIA, Parkinson, and depression were more prevalent in HF with preserved EF (HFpEF). The hazard ratio (95% confidence interval) for post-discharge death for each NCC was for anaemia 1.6 (1.4–1.8), diabetes 1.2 (1.1–1.4), kidney dysfunction 1.7 (1.5–1.9), COPD 1.4 (1.2–1.5), PVD 1.2 (1.1–1.4), stroke/TIA 1.3 (1.1–1.5), depression 1.2 (1.0–1.5), hepatic dysfunction 2.1 (1.8–2.5), malignancy 1.5 (1.2–1.8), sleep apnoea 1.2 (0.9–1.7), rheumatoid arthritis 1.5 (1.1–2.1), and Parkinson 1.4 (0.9–2.1). Anaemia, kidney dysfunction, COPD, and diabetes were associated with post-discharge mortality in all EF categories, PVD, stroke/TIA, and depression only in HF with reduced EF, and sleep apnoea and malignancy only in HFpEF.

Conclusion

Multiple NCCs conferred poor in-hospital and post-discharge outcomes. Ejection fraction categories had different prevalence and risk profile associated with individual NCCs.
Combining serum metabolomic profiles with traditional risk factors improves 10-year cardiovascular risk prediction in people with type 2 diabetes
Authors: Huang Zhe , Klaric Lucija , Krasauskaite Justina , Khalid Wardah , Strachan Mark W J , Wilson James F , Price Jackie F
Published: May 2023

Aims

To identify a group of metabolites associated with incident cardiovascular disease (CVD) in people with type 2 diabetes and assess its predictive performance over-and-above a current CVD risk score (QRISK3).

Methods and results

A panel of 228 serum metabolites was measured at baseline in 1066 individuals with type 2 diabetes (Edinburgh Type 2 Diabetes Study) who were then followed up for CVD over the subsequent 10 years. We applied 100 repeats of Cox least absolute shrinkage and selection operator to select metabolites with frequency >90% as components for a metabolites-based risk score (MRS). The predictive performance of the MRS was assessed in relation to a reference model that was based on QRISK3 plus prevalent CVD and statin use at baseline. Of 1021 available individuals, 255 (25.0%) developed CVD (median follow-up: 10.6 years). Twelve metabolites relating to fluid balance, ketone bodies, amino acids, fatty acids, glycolysis, and lipoproteins were selected to construct the MRS that showed positive association with 10-year cardiovascular risk following adjustment for traditional risk factors [hazard ratio (HR) 2.67; 95% confidence interval (CI) 1.96, 3.64]. The c-statistic was 0.709 (95%CI 0.679, 0.739) for the reference model alone, increasing slightly to 0.728 (95%CI 0.700, 0.757) following addition of the MRS. Compared with the reference model, the net reclassification index and integrated discrimination index for the reference model plus the MRS were 0.362 (95%CI 0.179, 0.506) and 0.041 (95%CI 0.020, 0.071), respectively.

Conclusion

Metabolomics data might improve predictive performance of current CVD risk scores based on traditional risk factors in people with type 2 diabetes. External validation is warranted to assess the generalizability of improved CVD risk prediction using the MRS.
Urban–rural differences in health literacy in the metropolitan area of Berlin, Germany, and its surroundings
Authors: Haeger Christine , Lech Sonia , Messer Melanie , Gellert Paul
Published: May 2023

Background

Health literacy is gaining importance as it concerns the ability of individuals to encounter the complex demands of health in modern societies. Little is known about the environmental associations of health literacy in high-income countries. This study aims to (i) analyse urban–rural differences in health literacy and further (ii) investigate the interrelations of associated factors.

Methods

Based on secondary analyses using a population-based survey of individuals aged 35 years and older from Berlin, Germany, and the surrounding rural area. Health literacy, sociodemographic factors (gender, age, educational level, marital status, income), environmental factors (urban/rural) and health behaviour (physical activity) were assessed with questionnaires. T-tests, Analyses of Variance and multiple regression with interaction terms have been applied.

Results

In total, 1822 participants (51.2% female and 56.8% living in an urban region) took part in this study. Health literacy was significantly higher in rural regions (mean = 35.73, SD = 7.56) than in urban regions (mean = 34.10, SD = 8.07). Multiple multivariate regressions showed that living in urban regions, being older, having vocational or basic education, having mid or low income, being widowed, having moderate or low levels of physical activity were significantly negatively associated with health literacy. Incorporating interaction terms showed significance that being older is positively associated with urban regions.

Conclusion

We found higher levels of health literacy in rural regions and also demonstrated that multiple associated factors of health literacy work congruously. Thus, the environment, associated factors and their interplay must be considered in future urban–rural health literacy research.
Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff
Authors: Legierse Annabel , Struik Quinten , Smith Garrett , Echeveste Medrano Maider J , Weideveld Stefan , van Dijk Gijs , Smolders Alfons J P , Jetten Mike , Veraart Annelies J , Welte Cornelia U , Glodowska Martyna
Published: May 2023

Agricultural drainage ditches are subjected to high anthropogenic nitrogen input, leading to eutrophication and greenhouse gas emissions. Nitrate-dependent anaerobic methane oxidation (N-DAMO) could be a promising remediation strategy to remove methane (CH4) and nitrate (NO3−) simultaneously. Therefore, we aimed to evaluate the potential of N-DAMO to remove excess NO3− and decrease CH4 release from agricultural drainage ditches. Microcosm experiments were conducted using sediment and surface water collected from three different sites: a sandy-clay ditch (SCD), a freshwater-fed peatland ditch (FPD), and a brackish peatland ditch (BPD). The microcosms were inoculated with an N-DAMO enrichment culture dominated by Candidatus Methanoperedens and Candidatus Methylomirabilis and supplemented with 13CH4 and 15NO3−. A significant decrease in CH4 and NO3− concentration was only observed in the BPD sediment. In freshwater sediments (FPD and SCD), the effect of N-DAMO inoculation on CH4 and NO3− removal was negligible, likely because N-DAMO microorganisms were outcompeted by heterotrophic denitrifiers consuming NO3− much faster. Overall, our results suggest that bioaugmentation with N-DAMO might be a potential strategy for decreasing NO3− concentrations and CH4 emission in brackish ecosystems with increasing agricultural activities where the native microbial community is incapable of efficient denitrification.
Evolutionary genetics of the mitochondrial genome: insights from Drosophila
Authors: Dowling Damian K , Wolff Jonci N
Published: May 2023

Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.
Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep
Authors: Toner Tom M , Pancholi Rashi , Miller Paul , Forster Thorsten , Coleman Helen G , Overton Ian M
Published: May 2023

Background

Integration of data from multiple domains can greatly enhance the quality and applicability of knowledge generated in analysis workflows. However, working with health data is challenging, requiring careful preparation in order to support meaningful interpretation and robust results. Ontologies encapsulate relationships between variables that can enrich the semantic content of health datasets to enhance interpretability and inform downstream analyses.

Findings

We developed an R package for electronic health data preparation, “eHDPrep,” demonstrated upon a multimodal colorectal cancer dataset (661 patients, 155 variables; Colo-661); a further demonstrator is taken from The Cancer Genome Atlas (459 patients, 94 variables; TCGA-COAD). eHDPrep offers user-friendly methods for quality control, including internal consistency checking and redundancy removal with information-theoretic variable merging. Semantic enrichment functionality is provided, enabling generation of new informative “meta-variables” according to ontological common ancestry between variables, demonstrated with SNOMED CT and the Gene Ontology in the current study. eHDPrep also facilitates numerical encoding, variable extraction from free text, completeness analysis, and user review of modifications to the dataset.

Conclusions

eHDPrep provides effective tools to assess and enhance data quality, laying the foundation for robust performance and interpretability in downstream analyses. Application to multimodal colorectal cancer datasets resulted in improved data quality, structuring, and robust encoding, as well as enhanced semantic information. We make eHDPrep available as an R package from CRAN (https://cran.r-project.org/package=eHDPrep) and GitHub (https://github.com/overton-group/eHDPrep).
Genome assembly of an Australian native grass species reveals a recent whole-genome duplication and biased gene retention of genes involved in stress response
Authors: De Silva Nissanka P , Lee Christopher , Battlay Paul , Fournier-Level A , Moore Joslin L , Hodgins Kathryn A
Published: May 2023

Background

The adaptive significance of polyploidy has been extensively debated, and chromosome-level genome assemblies of polyploids can provide insight into this. The Australian grass Bothriochloa decipiens belongs to the BCD clade, a group with a complex history of hybridization and polyploid. This is the first genome assembly and annotation of a species that belongs to this fascinating yet complex group.

Findings

Using Illumina short reads, 10X Genomics linked reads, and Hi-C sequencing data, we assembled a highly contiguous genome of B. decipiens, with a total length of 1,218.22 Mb and scaffold N50 of 42.637 Mb. Comparative analysis revealed that the species experienced a relatively recent whole-genome duplication. We clustered the 20 major scaffolds, representing the 20 chromosomes, into the 2 subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation and differences in the activity of transposable elements between the subgenomes prior to hybridization. Duplicates were enriched for genes involved in transcription and response to external stimuli, supporting a biased retention of duplicated genes following whole-genome duplication.

Conclusions

Our results support the hypotheses of a biased retention of duplicated genes following polyploidy and point to differences in repeat activity associated with subgenome dominance. B. decipiens is a widespread species with the ability to establish across many soil types, making it a prime candidate for climate change– resilient ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research on Australian grasses.
Spatiotemporal profiles of gene activity in stamen delineate nucleo-cytoplasmic interaction in a male-sterile somatic cybrid citrus
Authors: Jiang Nan , Feng Meng-Qi , Cheng Lai-Chao , Kuang Li-Hua , Li Chao-Chao , Yin Zhao-Ping , Wang Rong , Xie Kai-Dong , Guo Wen-Wu , Wu Xiao-Meng
Published: May 2023

Cytoplasmic male sterility (CMS) has long been used to produce seedless fruits in perennial woody crops like citrus. A male-sterile somatic cybrid citrus (G1 + HBP) was generated by protoplast fusion between a CMS callus parent ‘Guoqing No. 1’ Satsuma mandarin (Citrus unshiu, G1) and a fertile mesophyll parent Hirado Buntan pummelo (Citrus grandis, HBP). To uncover the male-sterile mechanism of G1 + HBP, we compared the transcriptome profiles of stamen organ and cell types at five stages between G1 + HBP and HBP, including the initial stamen primordia, enlarged stamen primordia, pollen mother cells, tetrads, and microspores captured by laser microdissection. The stamen organ and cell types showed distinct gene expression profiles. A majority of genes involved in stamen development were differentially expressed, especially CgAP3.2, which was downregulated in enlarged stamen primordia and upregulated in tetrads of G1 + HBP compared with HBP. Jasmonic acid- and auxin-related biological processes were enriched among the differentially expressed genes of stamen primordia, and the content of jasmonic acid biosynthesis metabolites was higher in flower buds and anthers of G1 + HBP. In contrast, the content of auxin biosynthesis metabolites was lower in G1 + HBP. The mitochondrial tricarboxylic acid cycle and oxidative phosphorylation processes were enriched among the differentially expressed genes in stamen primordia, meiocytes, and microspores, indicating the dysfunction of mitochondria in stamen organ and cell types of G1 + HBP. Taken together, the results indicate that malfunction of mitochondria-nuclear interaction might cause disorder in stamen development, and thus lead to male sterility in the citrus cybrid.
From Peace Talks to Pandemics: The Continuum of Feminist Peace Activism
Authors: Anderson Miriam J , Eskandari Madeline F
Published: May 2023

Feminist scholarship has convincingly shown that violence is more accurately conceptualized as a continuum rather than a war/peace binary. While recent scholarship has elucidated women's peace activism during armed conflict, peace negotiations, and post-peace agreement transitions, we know little about the work of self-identified women peace activists beyond those highly visible moments. We examine the activities of a Burundian women's peace organization in exile, Mouvement Inamahoro, during COVID-19. Our data are derived from thirty-six semi-structured interviews with individual members of the organization and reviewing hundreds of primary-source documents. We find that from Inamahoro’s standpoint, the intersection of COVID-19 and exile constituted security threats, relevant to its mandate to build peace. Accordingly, it responded with humanitarian assistance, advocacy, and awareness-raising among its own members as well as with Burundians both inside and outside the country. Inamahoro also continued its regular activities to promote longer-term peace and security in Burundi through media programming, training women and girls for political leadership, and liaising with Burundian civil society and international non-governmental organizations (INGOs). Based on the continuum of violence concept and building inductively from the Inamahoro case, we propose a multidimensional continuum of activism that occurs before, during, and following conflict (dimension 1, time); is conducted in multiple arenas (dimension 2, space); deals with issues of insecurity at multiple levels (dimension 3, scale); and is concerned with threats that are structural, direct, and cultural/symbolic (dimension 4, type). In so doing, we offer a preliminary framework with which to examine the everyday activities of women peace activists, which constitute often overlooked interventions in global politics.
Validation of the AnticFast® Beta-Lactams Rapid Test Kit for Detection of Beta-Lactams (Penicillins and Cephalosporins) in Raw Cow’s Milk: AOAC Performance Tested MethodSM 032303
Authors: Broekaert Katrien , Ooghe Sigrid , Yang Meng , Tian Xiumei , Reybroeck Wim
Published: May 2023

Background

AnticFast® Beta-Lactams Rapid Test Kit is a qualitative two-step (2 min + 5 min) rapid lateral flow assay to detect β-lactam (penicillins and cephalosporins) antibiotic residues in raw commingled cow’s milk.

Objective

The method performance was evaluated according to Commission Decision 2002/657/EC, Commission Implementing Regulation 2021/808, and Community Reference Laboratories Residues Guidelines for the Validation of Screening Methods for Residues of Veterinary Medicines.

Methods

The AnticFast Beta-Lactams Rapid Test Kit was evaluated for detection capability, selectivity, false-positive results, repeatability, robustness, suitability for various milk types and milk compositions, milks from various species, and test kit consistency and stability. Samples included milks spiked at concentrations bracketing the EU maximum residue limits (MRLs) for β-lactams as well as bulk farm and tanker milks.

Results

The AnticFast Beta-Lactams Rapid Test Kit is specific for the detection of β-lactams in milk and does not detect compounds from other antibiotic families. Interference was seen with clavulanic acid, a β-lactamase inhibitor, which was expected. The test can detect all residues of β-lactams (penicillins and cephalosporins) present on the EU-MRL list for milk at their respective MRL except for desfuroylceftiofur and cephalexin, which were above the MRL. No false positives were detected in the 602 (300 blank farm and 302 tanker load) samples tested. Robustness testing indicated that the detection in heat-treated milk types may be slightly hampered. For substances with a detection capability well below the MRL, this interference does not cause problems since detection at MRL remains guaranteed, but care should be taken for substances with a CCβ at or near their MRL. Diminished sample flow was seen with reconstituted milk powder and blank ewes’ milk, so sample flow should always be verified for these milk types.

Conclusions

Results of this validation show that the AnticFast Beta-Lactams Rapid Test Kit is a reliable test for rapid screening of raw cows’ milk for residues of β-lactam antibiotics.

Highlights

AnticFast Beta-Lactams Rapid Test Kit is an easy, realiable, robust and highly specific test for screening of raw cows' milk for residues of penicillins and cephalosporins.
Sensitive Instrumental Method for Quantitative Determination of High-Brominated Flame Retardants in Human Serum Samples
Authors: Grande Cristina , Castaño Argelia , Ramos Juan José
Published: May 2023

Background

High-brominated flame retardants (BFRs) can be released into the environment from consumer products, such as electric and electronic equipment, and enter the human body by different pathways. Because of their toxicity and the regulations, it is very relevant to know their levels and trends in human samples. However, chromatographic serum analysis of some of these compounds represents nowadays a challenge in the general population.

Objective

To optimize and validate an instrumental method based on gas chromatography coupled to mass spectrometry, which, together with a simple sample preparation procedure, allows the analysis of decabromodiphenyl ether (BDE-209), decabromodiphenyl ethane (DBDPE), and tetrabromobisphenol A-bis(2,3-dibromopropyl ether) (TBBPA-DBPE) in human serum samples from the general population.

Method

To minimize the high degradation during instrumental analysis, GC parameters such as injection volumes, carrier flow rates, and column lengths were assessed and optimized. This instrumental approach in combination with solid-phase extraction (SPE) followed by multilayer silica gel column purification allowed satisfactory analysis using only 1 mL of serum.

Results

The performance of the complete method was evaluated at three spiking levels, 0.01, 0.05, and 0.2 ng/mL. Recoveries in the range 87–108% were obtained whereas the relative standard deviation in interday measurements, were, in general, lower than 19%. Limits of detection were in the range of 0.0045–0.0070 ng/mL. The optimized procedure was successfully applied to the determination of the investigated pollutants in real human samples of general population.

Conclusions

The proposed method could contribute to the inclusion of these environmental pollutants in human biomonitoring (HBM) studies, increasing the knowledge of levels and trends in the general population.

Highlights

GC-MS parameters optimization to minimize instrumental analytes degradation. Successful application to human serum samples from the general population. Tetrabromobisphenol A bis(2,3-dibromopropyl ether) human serum levels are reported for the first time.
Application of Rapid Identification and Determination of Moisture Content of Coptidis Rhizoma From Different Species Based on Data Fusion
Authors: Tian Mengyin , Ma Xiaobo , Liang Mengying , Zang Hengchang
Published: May 2023

Background

For thousands of years, traditional Chinese medicine (TCM) has been clinically proven, and doctors have highly valued the differences in utility between different species.

Objective

This study aims to replace the complex methods traditionally used for empirical identification by compensating for the information loss of a single sensor through data fusion. The research object of the study is Coptidis rhizoma (CR).

Method

Using spectral optimization and data fusion technology, near infrared (NIR) and mid-infrared (MIR) spectra were collected for CR. PLS-DA (n = 134) and PLSR (n = 63) models were established to identify the medicinal materials and to determine the moisture content in the medicinal materials.

Results

For the identification of the three species of CR, the mid-level fusion model performed better than the single-spectrum model. The sensitivity and specificity of the prediction set coefficients for NIR, MIR, and data fusion qualitative models were all higher than 0.95, with an AUC value of 1. The NIR data model was superior to the MIR data model. The results of low-level fusion were similar to those of the NIR optimization model. The RPD of the test set of NIR and low-level fusion model was 3.6420 and 3.4216, respectively, indicating good prediction ability of the model.

Conclusions

Data fusion technology using NIR and MIR can be applied to identify CR species and to determine the moisture content of CR. It provides technical support for the rapid determination of moisture content, with a fast analysis speed and without the need for complex pretreatment methods.

Highlights

This study is the first to introduce spectral data fusion technology to identify CR species. Data fusion technology is feasible for multivariable calibration model performance and reduces the cost of manual identification. The moisture content of CR can be quickly evaluated, reducing the difficulty of traditional methods.
Virtual reality-based assembly-level design for additive manufacturing decision framework involving human aspects of design
Authors: Auyeskhan Ulanbek , Steed Clint Alex , Park Soohyung , Kim Dong-Hyun , Jung Im Doo , Kim Namhun
Published: May 2023

There is a combinatorial explosion of alternative variants of an assembly design owing to the design freedom provided by additive manufacturing (AM). In this regard, a novel virtual reality-based decision-support framework is presented herein for extracting the superior assembly design to be fabricated by AM route. It specifically addresses the intersection between human assembly and AM hence combining design for assembly, and design for additive manufacturing using axiomatic design theory. Several virtual reality experiments were carried out to achieve this with human subjects assembling parts. At first, a two-dimensional table is assembled, and the data are used to confirm the independence of non-functional requirements such as assembly time and assembly displacement error according to independence axiom. Then this approach is demonstrated on an industrial lifeboat hook with three assembly design variations. The data from these experiments are utilized to evaluate the possible combinations of the assembly in terms of probability density based on the information axiom. The technique effectively identifies the assembly design most likely to fulfill the non-functional requirements. To the authors’ best knowledge, this is the first study that numerically extracts the human aspect of design at an early design stage in the decision process and considers the selection of the superior assembly design in a detailed design stage. Finally, this process is automated using a graphical user interface, which embraces the practicality of the currently integrated framework and enables manufacturers to choose the best assembly design.
The Non-Triliteral Theory of Verbal Morphology of the Karaite Joseph IBN Nūḥ
Authors: Dachman Joshua
Published: May 2023

This study examines the morphological theory of Joseph (Yūsuf) Ibn Nūḥ, a tenth-century Hebraist with a non-triliteral theory of Hebrew. Ibn Nūḥ’s approach is first outlined using the previously-developed framework for non-triliteral Hebrew verbal morphology. Ibn Nūḥ’s morphological model is then explored and it is determined that Ibn Nūḥ has an Item-and-Process model of morphology. With that insight it is suggested that Ibn Nūḥ recognizes roots only ‘abstractively’, with word-forms being constructed from ‘bases’ rather than ‘roots’. Example passages are presented to demonstrate the contrast between Ibn Nūḥ’s and Dunash Ibn Labraṭ’s respective models of morphology.
Estimation of Covid-19 Prevalence Dynamics from Pooled Data
Authors: Scherting Braden , Peel Alison J , Plowright Raina , Hoegh Andrew
Published: May 2023

Estimating the prevalence of a disease, such as COVID-19, is necessary for evaluating and mitigating risks of its transmission. Estimates that consider how prevalence changes with time provide more information about these risks but are difficult to obtain due to the necessary survey intensity and commensurate testing costs. Motivated by a dataset on COVID-19, from the University of Notre Dame, we propose pooling and jointly testing multiple samples to reduce testing costs. A nonparametric, hierarchical Bayesian model is used to infer population prevalence from the pooled test results without needing to retest individuals from pools that test positive. This approach is shown to reduce uncertainty compared to individual testing at the same budget and to produce similar estimates compared to individual testing at a much higher budget through simulation studies and an analysis of COVID-19 infections at Notre Dame.
The extended predicative Mahlo universe in Martin-Löf type theory
Authors: Dybjer Peter , Setzer Anton
Published: May 2023

This paper addresses the long-standing question of the predicativity of the Mahlo universe. A solution, called the extended predicative Mahlo universe, has been proposed by Kahle and Setzer in the context of explicit mathematics. It makes use of the collection of untyped terms (denoting partial functions) which are directly available in explicit mathematics but not in Martin-Löf type theory. In this paper, we overcome the obstacle of not having direct access to untyped terms in Martin-Löf type theory by formalizing explicit mathematics with an extended predicative Mahlo universe in Martin-Löf type theory with certain indexed inductive-recursive definitions. In this way, we can relate the predicativity question to the fundamental semantics of Martin-Löf type theory in terms of computation to canonical form. As a result, we get the first extended predicative definition of a Mahlo universe in Martin-Löf type theory. To this end, we first define an external variant of Kahle and Setzer’s internal extended predicative universe in explicit mathematics. This is then formalized in Martin-Löf type theory, where it becomes an internal extended predicative Mahlo universe. Although we make use of indexed inductive-recursive definitions that go beyond the type theory $\mathbf {IIRD}$ of indexed inductive-recursive definitions defined in previous work by the authors, we argue that they are constructive and predicative in Martin-Löf’s sense. The model construction has been type-checked in the proof assistant Agda.