Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled ...haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.
Better sensitivity of a biosensor could boost up the detection limit of analytes, thus a must in the fields of bio-sensing and bio-detection. To further enhance the sensitivity of a biosensor, in ...this work, we design an oblique-flat-sheet metamaterial perfect absorber (MPA) to concentrate the hot spots within air between the oblique flat sheet and the continuous ground metal, thus enabling fully interaction between analytes and hot spots. The corresponding field distributions in simulation corroborated our assumption and its sensitivity could be up to 1049 nm/RIU. Then, we fabricated the sample by e-beam lithography process for a seed layer and simply tilting the sample during deposition to obtain oblique flat sheets. When considering the stochastic nature of the deposited multiple oblique flat sheets, we modified the metallic upper resonator of the MPA from the single oblique-flat-sheet into randomly distributed oblique-wire-bundle (OWB) and in simulation, its sensitivity is boosted up to 3319 nm/RIU. In experiments, the measured sensitivity is 1329 nm/RIU under different concentrations of glucose solutions that is four times larger than the 330 nm/RIU of the planar MPA. The higher sensitivity was attributed to that the OWB MPA could provide hot spots within air not only between OWB and grounded metal but also among wires. Moreover, the OWB could also trap and concentrate the analytes locally.
Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical ...disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.
Abstract
In this work, we integrated a periodic seed layer and oblique deposition method to fabricate a stochastically-distributed oblique-flat-sheet metamaterial perfect absorber (MPA). Such design ...could increase its absorption bandwidth and tolerance to high angle-incidence due to the fact that various oblique flat sheets offer different resonance conditions while even a single oblique flat sheet could provide different optical paths for resonance. On the other hand, a seed layer could reduce uncertainty regarding to direct oblique deposition and provide abilities to manipulate the bandwidth of the MPA. We also setup a simulation model in the aids of Visual Basic Application and examined the absorption behavior of the MPA under TM and TE oblique incidence that could achieve high absorbance under 80° and 60° incidence, respectively. Finally, in measurement, the fabricated sample owns 65% absorbance within 80–250 THz and over 90% absorbance within 250–320 THz at x-polarization normal incidence; as for the y-polarization normal incidence, we could achieve overall 70% absorbance within 80–300 THz. The measured results reveal similar tendency compared to the simulated ones.
The objective of prehospital emergency medical services (EMSs) is to have a short response time. By increasing the operational efficiency, the survival rate of patients could potentially be ...increased. The geographic information system (GIS) is introduced in this study to manage and visualize the spatial distribution of demand data and forecasting results. A flexible model is implemented in GIS, through which training data are prepared with user-desired sizes for the spatial grid and discretized temporal steps. We applied moving average, artificial neural network, sinusoidal regression, and support vector regression for the forecasting of prehospital emergency medical demand. The results from these approaches, as a reference, could be used for the preallocation of ambulances. A case study is conducted for the EMS in New Taipei City, where prehospital EMS data have been collected for three years. The model selection process has chosen different models with different input features for the forecast of different areas. The best daily mean absolute percentage error during testing of the EMS demand forecast is 23.01%, which is a reasonable forecast based on Lewis' definition. With the acceptable prediction performance, the proposed approach has its potential to be applied to the current practice.
Background: Repetitive transcranial magnetic stimulation (rTMS) shows potential therapeutic effects for individuals with addiction, but few studies have examined individuals with opioid use disorder ...(OUD).
Objectives: We conducted an add-on double-blinded, sham-controlled rTMS feasibility pilot trial to examine OUD participants undergoing methadone maintenance therapy (MMT). The current report focused on the effects of rTMS on (1) craving and heroin use behavior and (2) depression, impulsivity, and attention.
Methods: Active or sham rTMS treatment was applied to the left dorsolateral prefrontal cortex (DLPFC) over a total of 11 sessions in 4 weeks (15-Hz frequency, 4 seconds per train, intertrain interval of 26 seconds, 40 trains per session) in OUD participants (ClinicalTrials.gov registration number: NCT03229642). Craving, heroin use severity, urine morphine tests, the Hamilton Depression Rating Scale (HDRS), the Barratt Impulsiveness Scale-11 (BIS-11), and the Continuous Performance Tests (CPTs) were measured.
Results: Twenty-two OUD participants were enrolled, of which eleven (8 males) were undergoing active rTMS and nine (8 males) were in the sham rTMS group. After 12 weeks of follow-up, the active rTMS group did not show significantly greater improvements than the sham group with respect to craving, heroin use, or urine morphine test results. However, HDRS scores, BIS-11 attentional subscales, and CPTs commission T-scores (C-TS) were significantly lower in the active rTMS group (P = .003, 0.04, and 0.02, respectively) than in the sham group.
Conclusion: Add-on rTMS did not appear to improve heroin use behavior but may have benefitted depressive symptoms, impulse control and attention in OUD participants undergoing MMT.
Abstract
For fresh foods, the purpose and benefits of modified atmosphere packaging (MAP) generally include the preservation of antioxidants, the extension of shelf life, deferral of microbial ...spoilage, and retention of product color. Commercial MAP products frequently involve a mixture of nitrogen, oxygen, and carbon dioxide, affecting consumer acceptability, cost‐effectiveness, and hygienic food safety issues. This study investigated a novel active MAP formulation for strawberries in retail packaging which ensures changes in quality‐related physicochemical characteristics including hardness, moisture, vitamin C, total soluble solids (TSS), titratable acid, and appearance during low‐temperature storage, whereas samples of different storage times were assessed for shelf life by sensory evaluation. The innovative active MAP formulation of 0.8 g of sodium ascorbate, 2.6 g of sodium carbonate, and 1.6 g of ferrous sulfate achieved atmosphere equilibrium in packaged strawberries in <48 h, compared to 5–6 days in the control group. Strawberries treated with active MAP maintained their moisture, firmness, vitamin C, TSS, and titratable acid contents better than the control group (
p
< 0.05). The strawberries showed softening and waterlogging of tissue and 50% moldiness by the 14th day, while the control group lost commercial value by the 8th. New applications of similar commodities in food are unavailable based on current knowledge. Therefore, the scope of fresh food applications covered in this study and the refinement of other functions will be helpful directions for future research.
Understanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up ∼3% of the human genome but are often excluded ...from association analysis owing to poor read mappability or divergent repeat content. Although methods exist to estimate VNTR length from short-read data, it is known that VNTRs vary in both length and repeat (motif) composition. Here, we use a repeat-pangenome graph (RPGG) constructed on 35 haplotype-resolved assemblies to detect variation in both VNTR length and repeat composition. We align population-scale data from the Genotype-Tissue Expression (GTEx) Consortium to examine how variations in sequence composition may be linked to expression, including cases independent of overall VNTR length. We find that 9422 out of 39,125 VNTRs are associated with nearby gene expression through motif variations, of which only 23.4% are accessible from length. Fine-mapping identifies 174 genes to be likely driven by variation in certain VNTR motifs and not overall length. We highlight two genes,
and
, that have expression associated with motif variation, showing the utility of RPGG analysis as a new approach for trait association in multiallelic and highly variable loci.
Objective To date, the association between sleep duration or sleep quality and hyperuricemia has remained unclear. In addition, sleep duration and quality were not considered concomitantly in ...previous studies. Thus, this study was aimed toward an examination of the association of sleep duration and quality with uric acid level in a Taiwanese population. Methods A total of 4,555 patients aged greater than or equal to18 years were enrolled in this study. The sleep duration was classified into three groups: short (5. Results Poor sleepers were younger and had lower body mass index, blood pressure, uric acid, blood sugar, cholesterol, creatinine level, shorter sleep duration, and engaged in less exercise but had a higher white blood cell count and prevalence of smoking as compared to good sleepers. There were also differences in body mass index, blood pressure, uric acid, blood sugar, lipid profiles, and sleep quality among subjects with different sleep durations. After adjusting for other variables, poor sleep quality was associated with lower uric acid levels. In addition, short sleep duration was positively associated with higher uric acid levels. Conclusions Poor sleep quality was related to lower uric acid levels, whereas short sleep duration was associated with higher uric acid levels.
Objectives/Hypothesis
To examine the pathogenic bacterial spectra and prognosis of deep neck infection (DNI) in end‐stage renal disease (ESRD) patients.
Study Design
Retrospective study.
Methods
...Patients diagnosed with DNI between 2004 and 2015 in Chang Gung Memorial Hospital were enrolled and divided into three groups, namely ESRD‐DNI, chronic kidney disease (CKD)‐DNI, and non‐CKD‐DNI. Differences in pathogenic bacteria, treatment, and prognosis were compared across the three groups.
Results
The bacterial spectra differed among the three groups. The main three facultative anaerobic or aerobic bacteria causing ESRD‐DNIs were methicillin‐resistant Staphylococcus aureus (MRSA; 25.4%), methicillin‐susceptible S. aureus (MSSA; 14.1%), and Klebsiella pneumoniae (KP; 12.7%). For CKD‐DNIs, they were KP (23.5%), Viridans streptococci (VS; 23.5%), and MSSA (14.7%). For non‐CKD‐DNIs, they were VS (31.7%), KP (17.2%), and coagulase‐negative staphylococci (8.0%). Compared with the other groups, the ESRD‐DNI group had higher white blood cell and C‐reactive protein levels, longer hospital stays, more frequent admissions to the intensive care unit, more mediastinal complications, and a significantly higher mortality rate.
Conclusions
The ESRD‐DNI group exhibited more severe disease activity and higher mortality compared with those of the CKD‐DNI and non‐CKD‐DNI groups. MRSA was the leading pathogen for patients with ESRD‐DNI. Physicians must implement strategies for the early detection of MRSA to accurately prescribe antibiotics and prevent nosocomial transmission.
Level of Evidence
4 Laryngoscope, 132:1403–1409, 2022
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