Miracle-dz/UniFAR-FTUs huggingface dataset:
Composite genotypes of progestogen-associated endometrial protein gene and their association with composition and quality of dairy cattle milk

Objective The progestogen-associated endometrial protein (PAEP) gene encodes the main whey protein in milk, β-lactoglobulin. The aim of the study was to investigate polymorphism in the PAEP gene and its association with milk yield, composition, and quality. Methods Test-day records for 782 dairy cows were analysed. A total of 10 single nucleotide polymorphisms (SNP) within the PAEP gene were investigated. The following parameters were recorded: milk yield (MY, kg/d), percent milk fat (%), protein (PP, %), dry matter (DMP, %) and lactose (LP, %), urea content (UC, mg/L) as well as natural logarithm for somatic cell count (LnSCC, ln). Effect on genomic estimated breeding values accuracy was evaluated with pedigree and single step model. Results Results show that only three SNPs were polymorphic, creating 5 composite genotypes: P1 to P5. Differences in MY between composite genotypes were noted in the two tested herds. Cows with P5 composite genotypes were characterised by the highest PP and LnSCC and the lowest LP and UC (p<0.05). P4 was linked to an increased DMP and UC, while P3 to an increase in LP and decrease in PP and LnSCC. Both factors are important markers in herd management and have high influences on the herds economics. For 5 out of 7 traits the accuracy of prediction was improved by including the haplotype as a fixed effect. Conclusion Presented results may suggest a new way to optimise breeding programmes and demonstrate the impact of using genomic data during that process.
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing

Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen.
Task-Dependent Functional and Effective Connectivity during Conceptual Processing

Abstract Conceptual knowledge is central to cognition. Previous neuroimaging research indicates that conceptual processing involves both modality-specific perceptual-motor areas and multimodal convergence zones. For example, our previous functional magnetic resonance imaging (fMRI) study revealed that both modality-specific and multimodal regions respond to sound and action features of concepts in a task-dependent fashion (Kuhnke P, Kiefer M, Hartwigsen G. 2020b. Task-dependent recruitment of modality-specific and multimodal regions during conceptual processing. Cereb Cortex. 30:3938–3959.). However, it remains unknown whether and how modality-specific and multimodal areas interact during conceptual tasks. Here, we asked 1) whether multimodal and modality-specific areas are functionally coupled during conceptual processing, 2) whether their coupling depends on the task, 3) whether information flows top-down, bottom-up or both, and 4) whether their coupling is behaviorally relevant. We combined psychophysiological interaction analyses with dynamic causal modeling on the fMRI data of our previous study. We found that functional coupling between multimodal and modality-specific areas strongly depended on the task, involved both top-down and bottom-up information flow, and predicted conceptually guided behavior. Notably, we also found coupling between different modality-specific areas and between different multimodal areas. These results suggest that functional coupling in the conceptual system is extensive, reciprocal, task-dependent, and behaviorally relevant. We propose a new model of the conceptual system that incorporates task-dependent functional interactions between modality-specific and multimodal areas.
A Novel Time-Incremental End-to-End Shared Neural Network with Attention-Based Feature Fusion for Multiclass Motor Imagery Recognition

In the research of motor imagery brain-computer interface (MI-BCI), traditional electroencephalogram (EEG) signal recognition algorithms appear to be inefficient in extracting EEG signal features and improving classification accuracy. In this paper, we discuss a solution to this problem based on a novel step-by-step method of feature extraction and pattern classification for multiclass MI-EEG signals. First, the training data from all subjects is merged and enlarged through autoencoder to meet the need for massive amounts of data while reducing the bad effect on signal recognition because of randomness, instability, and individual variability of EEG data. Second, an end-to-end sharing structure with attention-based time-incremental shallow convolution neural network is proposed. Shallow convolution neural network (SCNN) and bidirectional long short-term memory (BiLSTM) network are used to extract frequency-spatial domain features and time-series features of EEG signals, respectively. Then, the attention model is introduced into the feature fusion layer to dynamically weight these extracted temporal-frequency-spatial domain features, which greatly contributes to the reduction of feature redundancy and the improvement of classification accuracy. At last, validation tests using BCI Competition IV 2a data sets show that classification accuracy and kappa coefficient have reached 82.7 ± 5.57% and 0.78 ± 0.074, which can strongly prove its advantages in improving classification accuracy and reducing individual difference among different subjects from the same network.
MEASUREMENT OF CONCENTRATIONS OF POLYCYCLIC AROMATIC HYDROCARBONS AND DIOXIN COMPOUNDS IN CANINE LUNGS

Polycyclic aromatic hydrocarbons (PAHs) and dioxin compounds remaining in canine lungs were measured with an alkaline decomposition method employing KOH/ethanol. PAHs extracted from the lungs of 31 dogs were between 0.07 and 0.47 ng/wet-g (mean: 0.19 ng/wet-g) for BaA; 0.03 and 0.16 ng/wet-g (mean: 0.08 ng/wet-g) for BkF; 0.05 and 0.29 ng/wet-g (mean: 0.13 ng/wet-g) for BaP; and 0.05 and 0.35 ng/wet-g (mean: 0.17 ng/wet-g) for BghiP. Dioxin concentrations were between 0.047 and 0.870 pg-TEQ/wet-g (mean: 0.179 pg-TEQ/wet-g). There were big differences between the PAH concentrations and dioxin concentrations in the canine lungs. Strong relationships were observed between individual PAHs (r = 0.73–0.95). In this study, we detected PAHs and dioxins in all samples, confirming that canine lungs were contaminated by those pollutants.
Differences between diabetic and non-diabetic nephropathy patients in cardiac structure and function at the beginning of hemodialysis and their impact on the prediction of mortality

Objectives To characterize differences in cardiac structure and function in hemodialysis (HD) patients with diabetic nephropathy (DN) and in those without using echocardiography and to determine their impact on the prediction of mortality using echocardiographic parameters. Methods Clinical, laboratory, and echocardiographic data were collected from patients commencing HD. Results Compared with those without DN, patients with DN had lower peak velocity of the early diastolic wave (e′), larger left atria, and higher peak early diastolic velocity (E)/e′ and peak velocity of tricuspid regurgitation (TR). In addition, a larger proportion of DN patients had a combination of left ventricular (LV) diastolic dysfunction, cardiac valve calcification, moderate-to-severe cardiac valve regurgitation (CVR), and at least moderate pericardial effusion (PE). After accounting for age, sex, smoking, hypertension, hemoglobin, and albumin, DN was responsible for e′ < 10 cm/s, E/e′ >13 m/s, TR >2.8 m/s, LV diastolic dysfunction, CVR, and PE. LV diastolic dysfunction and E/e′ >13 were the most useful predictors of mortality in patients with DN. Conclusions Patients with DN who undergo HD tend to have worse LV diastolic function and are more likely to have heart valve problems. LV diastolic dysfunction and E/e′ are predictors of death in DN patients.
Does the beta regularization parameter of bayesian penalized likelihood reconstruction always affect the quantification accuracy and image quality of positron emission tomography computed tomography?

Abstract Purpose This study aims to provide a detailed investigation on the noise penalization factor in Bayesian penalized likelihood (BPL)‐based algorithm, with the utilization of partial volume effect correction (PVC), so as to offer the suitable beta value and optimum standardized uptake value (SUV) parameters in clinical practice for small pulmonary nodules. Methods A National Electrical Manufacturers Association (NEMA) image‐quality phantom was scanned and images were reconstructed using BPL with beta values ranged from 100 to 1000. The recovery coefficient (RC), contrast recovery (CR), and background variability (BV) were measured to assess the quantification accuracy and image quality. In the clinical assessment, lesions were categorized into sub‐centimeter (<10 mm, n = 7) group and medium size (10–30 mm, n = 16) group. Signal‐to‐noise ratio (SNR) and contrast‐to‐noise ratio (CNR) were measured to evaluate the image quality and lesion detectability. With PVC was performed, the impact of beta values on SUVs (SUVmax, SUVmean, SUVpeak) of small pulmonary nodules was evaluated. Subjective image analysis was performed by two experienced readers. Results With the increasing of beta values, RC, CR, and BV decreased gradually in the phantom work. In the clinical study, SNR and CNR of both groups increased with the beta values (P < 0.001), although the sub‐centimeter group showed increases after the beta value reached over 700. In addition, highly significant negative correlations were observed between SUVs and beta values for both lesion‐size groups before the PVC (P < 0.001 for all). After the PVC, SUVpeak measured from the sub‐centimeter group was no significantly different among different beta values (P = 0.830). Conclusion Our study suggests using SUVpeak as the quantification parameter with PVC performed to mitigate the effects of beta regularization. Beta values between 300 and 400 were preferred for pulmonary nodules smaller than 30 mm.
Use of Nanopore Sequencing to Characterize African Horse Sickness Virus (AHSV) from the African Horse Sickness Outbreak in Thailand in 2020.

African horse sickness (AHS) is a highly infectious and deadly disease despite availability of vaccines. Molecular characterization of African horse sickness virus (AHSV) detected from the March 2020 Thailand outbreak was carried out by whole genome sequencing using Nanopore with a Sequence Independent Single Primer Amplification (SISPA) approach. Nucleotide sequence of the whole genome was compared with closest matching AHSV strains using phylogenetic analyses and the AHSV-1 virus shared high sequence identity with isolates from the same outbreak. Substitution analysis revealed non-synonymous and synonymous substitutions in the VP2 gene as compared to circulating South African strains. The use of sequencing technologies, such as Nanopore with SISPA, has enabled rapid detection, identification, and detailed genetic characterization of the AHS virus for informed decision making and implementation of disease control measures. Active genetic information sharing has also allowed emergence of AHSV to be better monitored on a global basis.
Participation and autonomy in the first 10 months after diagnosis of ALS: a longitudinal study

Abstract Introduction: More insight is needed into participation in daily activities and autonomy among patients with amyotrophic lateral sclerosis (ALS). Aims of this study were (1) to describe the course of participation restrictions and autonomy in participation during the first 10 months after diagnosis; (2) to study the influence of the rate of ALS progression on the course of participation. Methods: Secondary analysis of data from the longitudinal multicenter FACTS-2-ALS study. Self-report questionnaires were administered at inclusion (T0; n = 71), at 4 months (T1), 7 months (T2), 10 months (T3) after inclusion. Median duration of follow-up was 10.0 months. Participation restrictions were assessed using the sum of the Mobility Range and Social Behavior subscales of the Sickness Impact profile-68 (SIPSOC). Autonomy in participation was assessed using the Impact on Participation and Autonomy (IPA) Questionnaire. Fast disease progression was defined as an increase of 1.1 points per month or more on the ALS Functional Rating Scale. Results: Patients reported participation restrictions in all subscales while having mild physical limitations. There was a decrease of participation over time (restrictions and autonomy). This decrease was greatest in patients with fast disease progression. Disease progression negatively influenced movement-related participation more than social interaction domains. Rate of disease progression was more strongly related to SIPSOC scores compared to IPA scores. Discussion: Preserving participation may be an important determinant of quality of care for patients with ALS. Rate of progression of the disease should be taken into account as it was found to be significantly associated with the level of participation.
In situ preparation of hetero-polymers/clay nanocomposites by CUAAC click chemistry

A series of polymer/clay nanocomposites containing mechanistically two different polymers, poly(ethylene glycol) (PEG) and poly(epsilon caprolactone) (PCL), were prepared by simultaneous copper(I)-catalyzed alkyne-azide cycloaddition click reactions. Both clickable polymers, PEG-Alkyne and PCL-Alkyne, were simultaneously clicked on to azide-functional montmorillonite (MMT-N3) nanoclay to get corresponding PEG-PCL/MMT nanocomposites. The chemical structures of the resulting nanocomposites were verified by following azide and silicone-oxygen bands using FT-IR and characteristic bands of PEG and PCL segments using 1H-NMR spectroscopy. The combined XRD and TEM analysis confirmed that all PEG-PCL/MMT nanocomposites had partially exfoliated/intercalated morphologies. In addition, the increase of MMT-N3 loading not only improved the onset and maximum degradation temperatures of the nanocomposites but also their char yields. Furthermore, the incorporation of MMT-N3 in the polymer matrix did not significantly influence the crystallization behavior of both PEG and PCL segments.
The use of the plasma chemistry unit as an aid to the scanning electron microscope study of avian egg‐shell structure

1. In order to study the mammillary layer of the avian egg shell by scanning electron microscopy, it is necessary to separate the outer shell membrane from the calcified shell. 2. Chemical methods of effecting membrane removal are difficult to standardise due to variations in the strength of the membrane‐shell bond. 3. The use of reactive gas plasma provides an alternative, more efficient method for removing membranes without the risk of damage to underlying crystalline structures.
Automated Signal Quality Assessment for Heart Sound Signal by Novel Features and Evaluation in Open Public Datasets

Automated heart sound signal quality assessment is a necessary step for reliable analysis of heart sound signal. An unavoidable processing step for this objective is the heart sound segmentation, which is still a challenging task from a technical viewpoint. In this study, ten features are defined to evaluate the quality of heart sound signal without segmentation. The ten features come from kurtosis, energy ratio, frequency-smoothed envelope, and degree of sound periodicity, where five of them are novel in signal quality assessment. We have collected a total of 7893 recordings from open public heart sound databases and performed manual annotation for each recording as gold standard quality label. The signal quality is classified based on two schemes: binary classification (“unacceptable” and “acceptable”) and triple classification (“unacceptable”, “good,” and “excellent”). Sequential forward feature selection shows that the feature “the degree of periodicity” gives an accuracy rate of 73.1% in binary SVM classification. The top five features dominate the classification performance and give an accuracy rate of 92%. The binary classifier has excellent generalization ability since the accuracy rate reaches to (90.4 ± 0.5) % even if 10% of the data is used to train the classifier. The rate increases to (94.3 ± 0.7) % in 10-fold validation. The triple classification has an accuracy rate of (85.7 ± 0.6) % in 10-fold validation. The results verify the effectiveness of the signal quality assessment, which could serve as a potential candidate as a preprocessing in future automatic heart sound analysis in clinical application.
Amide-to-Amide Hydrogen Bonds in the Presence of a Pyridine Functionality: Crystal Structures of Bis(pyridinecarboxamido)alkanes

Crystal structures of bis(4-pyridinecarboxamido)alkane and bis(3-pyridinecarboxamido)alkane derivatives were determined and analyzed in terms of hydrogen bond networks. Seven crystal structures out of the eight structures studied exhibited amide-to-amide hydrogen bonds. Out of these seven, five form the anticipated β-sheet network whereas two structures form a doubly interpenetrated (4,4)-network. In only one structure does the pyridyl group interfere in the amide-to-amide hydrogen bond, leading to the formation of an N−H···N hydrogen bond network. The analyses and rationalization of these structures and also related derivatives in the Cambridge Structural Database suggested that amide-to-amide hydrogen bond formation depends on the interplanar angle between amide and pyridine groups.
Assessment of a Potential Synergistic Effect of Souvenaid® in Mild Alzheimer’s Disease Patients on Treatment with Acetylcholinesterase Inhibitors: An Observational, Non-Interventional Study

We evaluated the efficacy and safety of Souvenaid (a multinutrient supplement) in patients with mild Alzheimer’s disease (AD) in real clinical practice and assessed a potential synergistic effect of acetylcholinesterase (AChE) inhibitors. Clinical Dementia Rating (CDR) scale was evaluated after six months follow-up. Patients were divided into 4 groups according to the treatment they received: Souvenaid + AChE inhibitors (n = 23); only Souvenaid (n = 8); only AChE inhibitors (n = 7); no treatment (n = 16). The Souvenaid + AChE inhibitors and Souvenaid alone groups were associated with significantly lower increases in CDR per month than the AChE inhibitors or no treatment ones. The efficacy of Souvenaid + AChE inhibitors tended to be higher than Souvenaid alone.
Impact of socioeconomic deprivation on incidence and outcomes of acute type A aortic dissection repair in New Zealand

Socioeconomic deprivation (SED) has been associated with increased 30‐day mortality and reduced long‐term survival after surgical repair of acute type A aortic dissection (ATAAD). The study aimed to determine the incidence rate ratio of ATAAD in New Zealand population with higher and lower SED indices and to evaluate any association between SED and outcomes after ATAAD repair.
Human-centered development of an electronic health record-embedded, interactive information visualization in the emergency department using fast healthcare interoperability resources

OBJECTIVE Develop and evaluate an interactive information visualization embedded within the electronic health record (EHR) by following human-centered design (HCD) processes and leveraging modern health information exchange standards. MATERIALS AND METHODS We applied an HCD process to develop a Fast Healthcare Interoperability Resources (FHIR) application that displays a patient's asthma history to clinicians in a pediatric emergency department. We performed a preimplementation comparative system evaluation to measure time on task, number of screens, information retrieval accuracy, cognitive load, user satisfaction, and perceived utility and usefulness. Application usage and system functionality were assessed using application logs and a postimplementation survey of end users. RESULTS Usability testing of the Asthma Timeline Application demonstrated a statistically significant reduction in time on task (P < .001), number of screens (P < .001), and cognitive load (P < .001) for clinicians when compared to base EHR functionality. Postimplementation evaluation demonstrated reliable functionality and high user satisfaction. DISCUSSION Following HCD processes to develop an application in the context of clinical operations/quality improvement is feasible. Our work also highlights the potential benefits and challenges associated with using internationally recognized data exchange standards as currently implemented. CONCLUSION Compared to standard EHR functionality, our visualization increased clinician efficiency when reviewing the charts of pediatric asthma patients. Application development efforts in an operational context should leverage existing health information exchange standards, such as FHIR, and evidence-based mixed methods approaches.
Magnitude of blood pressure change and clinical outcomes after thrombectomy in stroke caused by large artery occlusion

Extremes of both high and low systolic blood pressure (SBP) after mechanical thrombectomy (MT) in large artery occlusion stroke are known predictors of unfavorable outcome. However, the effect of SBP change (∆SBP) during the first 24 h on thrombectomy outcomes remains unclear. We aimed to investigate the association between ∆SBP at different time intervals and thrombectomy outcomes.