A BCI Based Alerting System for Attention Recovery of UAV Operators.

As unmanned aerial vehicles have become popular, the number of accidents caused by an operator's inattention have increased. To prevent such accidents, the operator should maintain an attention status. However, limited research has been conducted on the brain-computer interface (BCI)-based system with an alerting module for the operator's attention recovery of unmanned aerial vehicles. Therefore, we introduce a detection and alerting system that prevents an unmanned aerial vehicle operator from falling into inattention status by using the operator's electroencephalogram signal. The proposed system consists of the following three components: a signal processing module, which collects and preprocesses an electroencephalogram signal of an operator, an inattention detection module, which determines whether an inattention status occurred based on the preprocessed signal, and, lastly, an alert providing module that presents stimulus to an operator when inattention is detected. As a result of evaluating the performance with a real-world dataset, it was shown that the proposed system successfully contributed to the recovery of operator attention in the evaluating dataset, although statistical significance could not be established due to the small number of subjects.

Refolding, characterization, and dye decolorization ability of a highly thermostable laccase from Geobacillus sp. JS12.

A putative laccase gene (lacG) from Geobacillus sp. JS12 was cloned and expressed as a fusion protein with six histidine residues in Escherichia coli BL21 (DE3) cells, and the protein was primarily found in inclusion bodies. The resulting insoluble proteins were solubilized with 6 M guanidine HCl and refolded using an on-column refolding procedure. Ni-chelation affinity chromatography found the laccase to be a 30 kDa monomeric protein. Spectrophotometry and electron paramagnetic resonance (EPR) analysis indicated LacG as a multi-copper oxidase, with the usual laccase copper sites, Type 1, 2, and 3 Cu(II). The optimum pH for enzymatic activity was 3.0, 6.0, and 6.5 with 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), guaiacol and 2,6-dimethoxyphenol (2,6-DMP) as the substrate, respectively. The recombinant protein displayed high thermostability, with a heat inactivation half-life of approximately 2 h at 95 °C, and an optimum temperature of 80 °C with 2,6-DMP. Catalytic efficiency (kcat/Km) showed that guaiacol and 2,6-DMP were highly oxidized by the enzyme. The enzymatic reaction was significantly enhanced by Co2+ and Mn2+, while activity was strongly inhibited in the presence of Fe2+, Zn2+, and thiol compounds. LacG decolorized 43% of Congo red and 14% of Malachite green, and the addition of ABTS as a redox mediator dramatically increased the dye decolorization efficiency.

Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments.

Proteogenomic searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated, however, mainly due to the difficulty in confirming the existence of identified novel peptides. We simulated a proteogenomic search using a controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using a human cell line data set, we evaluated the performance of six FDR control methods-global, separate, and multistage FDR estimation, respectively, coupled to a target-decoy search and a mixture model-based method-on novel peptide identification. The multistage approach showed the highest accuracy for FDR estimation. However, global and separate FDR estimation with the mixture model-based method showed higher sensitivities than others at the same true FDR. Furthermore, the mixture model-based method performed equally well when applied without or with a reduced set of decoy sequences. Considering different prior probabilities for novel and known protein identification, we recommend using mixture model-based methods with separate FDR estimation for sensitive and reliable identification of novel peptides from proteogenomic searches.

Organics on oxidic metal surfaces: a first-principles DFT study of PMDA and ODA fragments on the pristine and mildly oxidized surfaces of Cu(111).

Metal-organic hybrid materials are ubiquitous and a fundamental understanding of the hybrid-interface is key for the development of these hybrid material systems. In this work, using first-principles density-functional theory (including van der Waals (vdW) corrections), we study the fundamental physico-chemical properties of the molecular fragments of pyromellitic dianhydride oxydianiline (PMDA-ODA) on pristine Cu(111), as well as oxidic p4:O/Cu(111) in order to investigate the effect of mild oxidation of the metal substrate on PMDA-ODA adsorption. Firstly, we report the most favorable adsorption geometries amongst the various surface models and correlate the adsorption behavior with the electronic structure of the molecular fragments and the substrate layer. PMDA adsorbs weakly on both the clean and mildly oxidized copper surface via vdW forces while ODA adsorbs much stronger with a significant charge transfer between the substrates. Here, the oxidic layer is found to reduce the adsorption strength of both fragments and in particular, the ODA molecule interacts with the substrate via additional hydrogen bonding. Finally, our simulated scanning tunneling microscopy (STM) images suggest possible orientations of PMDA and ODA on clean and oxidic Cu surfaces to guide future experiments.

Next Place Prediction Based on Spatiotemporal Pattern Mining of Mobile Device Logs.

Due to the recent explosive growth of location-aware services based on mobile devices, predicting the next places of a user is of increasing importance to enable proactive information services. In this paper, we introduce a data-driven framework that aims to predict the user's next places using his/her past visiting patterns analyzed from mobile device logs. Specifically, the notion of the spatiotemporal-periodic (STP) pattern is proposed to capture the visits with spatiotemporal periodicity by focusing on a detail level of location for each individual. Subsequently, we present algorithms that extract the STP patterns from a user's past visiting behaviors and predict the next places based on the patterns. The experiment results obtained by using a real-world dataset show that the proposed methods are more effective in predicting the user's next places than the previous approaches considered in most cases.

Influence of citric acid molar ratio on the sintering behavior of nanocrystalline BaCe0.8Sm0.2O(3-delta).

The samarium-doped barium cerate (BaCe0.8Sm0.2O(3-delta), BCS) nano crystalline powders were synthesized via citric-nitrate method. The BCS nanopowders were prepared with various molar ratio of citric acid to metal nitrate. The pure perovskite structure was obtained from the BCS calcinated at 1200 degrees C and its crystalline size was increased with increase of the molar ratio citric acid to metal nitrate, while the aggregated particle size was significantly decreased as increasing the molar ratio. Also, excellent densification behavior was observed when high molar ratio of citric acid to metal nitrate was used. It was clarified that the molar ratio of citric acid determines the aggregated particle size and, in turn, finial microstructure after sintering.

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads.

Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially for long or complex repeats. Here, we introduce LongTR, which accurately genotypes tandem repeats from high-fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr and https://zenodo.org/doi/10.5281/zenodo.11403979 .

Genome-wide profiling of genetic variation at tandem repeat from long reads.

Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or complex repeats. Here we introduce LongTR, which accurately genotypes tandem repeats from high fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr.

Analysis and benchmarking of small and large genomic variants across tandem repeats.

Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes. However, they are often excluded from at-scale studies because of challenges with variant calling and representation, as well as a lack of a genome-wide standard. Here, to promote the development of TR methods, we created a catalog of TR regions and explored TR properties across 86 haplotype-resolved long-read human assemblies. We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 'truth-set' TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies.

Scalable Scheduling of Semiconductor Packaging Facilities Using Deep Reinforcement Learning.

Reinforcement learning (RL) has emerged as a promising approach for scheduling semiconductor operations. Yet, it is still challenging to solve large-scale scheduling problems based on an RL method since learning complexity grows fast as the size of shop floor increases. This challenge becomes more apparent when solving the scheduling problems with a diverse number of job types, which leads to the difficulties in exploration and function approximation in RL. This article presents a scheduling method for semiconductor packaging facilities using deep RL in which an agent allocates a job to one of machines in a centralized manner. Specifically, a novel state representation is introduced to effectively accommodate the variations in the number of available machines and the production requirements. Furthermore, we propose a continuous representation of an action to maintain the size of the action space even when the numbers of jobs, machines, and operation types are subject to change. Extensive experiments on large-scale datasets demonstrate that the proposed method mostly outperforms the metaheuristics and rule-based methods, as well as the other RL approaches considered in terms of makespan while requiring much less computation time than the metaheuristics.

TRviz: a Python library for decomposing and visualizing tandem repeat sequences.

Summary: TRviz is an open-source Python library for decomposing, encoding, aligning and visualizing tandem repeat (TR) sequences. TRviz takes a collection of alleles (TR containing sequences) and one or more motifs as input and generates a plot showing the motif composition of the TR sequences. Availability and implementation: TRviz is an open-source Python library and freely available at https://github.com/Jong-hun-Park/trviz. Detailed documentation is available at https://trviz.readthedocs.io. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Variable number tandem repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG.

Despite substantial efforts in identifying both rare and common variants affecting disease risk, in the majority of diseases, a large proportion of unexplained genetic risk remains. We propose that variable number tandem repeats (VNTRs) may explain a proportion of the missing genetic risk. Herein, in a pilot study with a retrospective cohort design, we tested whether VNTRs are causal modifiers of breast cancer risk in 347 female carriers of the BRCA1 185delAG pathogenic variant, an important group given their high risk of developing breast cancer. We performed targeted-capture to sequence VNTRs, called genotypes with adVNTR, tested the association of VNTRs and breast cancer risk using Cox regression models, and estimated the effect size using a retrospective likelihood approach. Of 303 VNTRs that passed quality control checks, 4 VNTRs were significantly associated with risk to develop breast cancer at false discovery rate [FDR] < 0.05 and an additional 4 VNTRs had FDR < 0.25. After determining the specific risk alleles, there was a significantly earlier age at diagnosis of breast cancer in carriers of the risk alleles compared to those without the risk alleles for seven of eight VNTRs. One example is a VNTR in exon 2 of LINC01973 with a per-allele hazard ratio of 1.58 (1.07-2.33) and 5.28 (2.79-9.99) for the homozygous risk-allele genotype. Results from this first systematic study of VNTRs demonstrate that VNTRs may explain a proportion of the unexplained genetic risk for breast cancer.

Continuous cuffless blood pressure monitoring using photoplethysmography-based PPG2BP-net for high intrasubject blood pressure variations.

Continuous, comfortable, convenient (C3), and accurate blood pressure (BP) measurement and monitoring are needed for early diagnosis of various cardiovascular diseases. To supplement the limited C3 BP measurement of existing cuff-based BP technologies, though they may achieve reliable accuracy, cuffless BP measurement technologies, such as pulse transit/arrival time, pulse wave analysis, and image processing, have been studied to obtain C3 BP measurement. One of the recent cuffless BP measurement technologies, innovative machine-learning and artificial intelligence-based technologies that can estimate BP by extracting BP-related features from photoplethysmography (PPG)-based waveforms have attracted interdisciplinary attention of the medical and computer scientists owing to their handiness and effectiveness for both C3 and accurate, i.e., C3A, BP measurement. However, C3A BP measurement remains still unattainable because the accuracy of the existing PPG-based BP methods was not sufficiently justified for subject-independent and highly varying BP, which is a typical case in practice. To circumvent this issue, a novel convolutional neural network(CNN)- and calibration-based model (PPG2BP-Net) was designed by using a comparative paired one-dimensional CNN structure to estimate highly varying intrasubject BP. To this end, approximately [Formula: see text], [Formula: see text], and [Formula: see text] of 4185 cleaned, independent subjects from 25,779 surgical cases were used for training, validating, and testing the proposed PPG2BP-Net, respectively and exclusively (i.e., subject-independent modelling). For quantifying the intrasubject BP variation from an initial calibration BP, a novel 'standard deviation of subject-calibration centring (SDS)' metric is proposed wherein high SDS represents high intrasubject BP variation from the calibration BP and vice versa. PPG2BP-Net achieved accurately estimated systolic and diastolic BP values despite high intrasubject variability. In 629-subject data acquired after 20 minutes following the A-line (arterial line) insertion, low error mean and standard deviation of [Formula: see text] and [Formula: see text] for highly varying A-line systolic and diastolic BP values, respectively, where their SDSs are 15.375 and 8.745. This study moves one step forward in developing the C3A cuffless BP estimation devices that enable the push and agile pull services.

Benchmarking of small and large variants across tandem repeats.

Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits, and are linked to over 60 disease phenotypes. However, their complexity often excludes them from at-scale studies due to challenges with variant calling, representation, and lack of a genome-wide standard. To promote TR methods development, we create a comprehensive catalog of TR regions and explore its properties across 86 samples. We then curate variants from the GIAB HG002 individual to create a tandem repeat benchmark. We also present a variant comparison method that handles small and large alleles and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ∼24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 TR benchmark. We work with the GIAB community to demonstrate the utility of this benchmark across short and long read technologies.

A deep population reference panel of tandem repeat variation.

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

A deep population reference panel of tandem repeat variation.

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

Detecting tandem repeat variants in coding regions using code-adVNTR.

The human genome contains more than one million tandem repeats (TRs), DNA sequences containing multiple approximate copies of a motif repeated contiguously. TRs account for significant genetic variation, with 50 + diseases attributed to changes in motif number. A few diseases have been to be caused by small indels in variable number tandem repeats (VNTRs) including poly-cystic kidney disease type 1 (MCKD1) and monogenic type 1 diabetes. However, small indels in VNTRs are largely unexplored mainly due to the long and complex structure of VNTRs with multiple motifs. We developed a method, code-adVNTR, that utilizes multi-motif hidden Markov models to detect both, motif count variation and small indels, within VNTRs. In simulated data, code-adVNTR outperformed GATK-HaplotypeCaller in calling small indels within large VNTRs. We used code-adVNTR to characterize coding VNTRs in the 1000 genomes data identifying many population-specific variants, and to reliably call MUC1 mutations for MCKD1.

High-rate biohydrogen production from xylose using a dynamic membrane bioreactor.

This study aimed a high-rate dark fermentative H2 production from xylose using a dynamic membrane module bioreactor (DMBR) with a 444-µm pore polyester mesh. 20 g xylose/L was fed continuously to the DMBR at different hydraulic retention times (HRTs) from 12 to 3 h at 37 °C. The maximum average H2 yield (HY) and H2 production rate (HPR) at 3 h HRT were found to be 1.40 ± 0.07 mol H2/mol xyloseconsumed and 30.26 ± 1.19 L H2/L-d, respectively. The short HRT resulted in the maximum suspended biomass concentration (8.92 ± 0.40 g VSS/L) along with significant attached biomass retention (7.88 ± 0.22 g VSS/L). H2 was produced by both butyric and acetic acid pathways. Low HY was concurrent with lactic acid production. The bacterial population shifted from non-H2 producers, such as Lactobacillus and Sporolactobacillus spp., to Clostridium sp., when HY increased. Thus, xylose from lignocellulose is a feasible substrate for dark fermentative H2 production using DMBR.

Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study.

Hereditary chronic kidney disease (CKD) appears to be more frequent than the clinical perception. Exome sequencing (ES) studies in CKD cohorts could identify pathogenic variants in ~10% of individuals. Tubulointerstitial kidney diseases, showing no typical clinical/histologic finding but tubulointerstitial fibrosis, are particularly difficult to diagnose. We used a targeted panel (29 genes) and MUC1-SNaPshot to sequence 271 DNAs, selected in defined disease entities and age cutoffs from 5217 individuals in the German Chronic Kidney Disease cohort. We identified 33 pathogenic variants. Of these 27 (81.8%) were in COL4A3/4/5, the largest group being 15 COL4A5 variants with nine unrelated individuals carrying c.1871G>A, p.(Gly624Asp). We found three cysteine variants in UMOD, a novel missense and a novel splice variant in HNF1B and the homoplastic MTTF variant m.616T>C. Copy-number analysis identified a heterozygous COL4A5 deletion, and a HNF1B duplication/deletion, respectively. Overall, pathogenic variants were present in 12.5% (34/271) and variants of unknown significance in 9.6% (26/271) of selected individuals. Bioinformatic predictions paired with gold standard diagnostics for MUC1 (SNaPshot) could not identify the typical cytosine duplication ("c.428dupC") in any individual, implying that ADTKD-MUC1 is rare. Our study shows that >10% of selected individuals carry disease-causing variants in genes partly associated with tubulointerstitial kidney diseases. COL4A3/4/5 genes constitute the largest fraction, implying they are regularly overlooked using clinical Alport syndrome criteria and displaying the existence of phenocopies. We identified variants easily missed by some ES pipelines. The clinical filtering criteria applied enriched for an underlying genetic disorder.

Production and characterization of crude laccase from Irpex sp. JS7 that decolorizes synthetic and natural melanin.

The JS7 strain, isolated from an old forest tree, produces extracellular enzymes that decolorize synthetic and natural melanin from human hair. Phylogenetic analysis based on the internal transcribed spacer (ITS) sequence indicated that JS7 belongs to the genus Irpex. The JS7 strain has laccase activity while it lacks manganese and lignin peroxidase activity, which suggests that the JS7 strain melanin decolorization activity originated from laccase. Laccase production from the Irpex sp. JS7 improved three-fold in the presence of veratryl alcohol, compared to without an inducer. The optimum pH and temperature for melanin decolorization were 7.5 and 40 °C, respectively. The crude enzyme half-life at 25 °C was about 100 days, and it had high storage stability. The melanin decolorization reaction rate by the crude enzyme conformed to typical enzyme kinetic principles. In the presence of syringaldehyde as a redox mediator, the melanin decolorization rate was 75% within 5 days, similar to the decolorization percentage obtained using the enzyme alone. Based on these results, the Irpex sp. JS7 enzyme is suitable for use in melanin decolorization by whitening agents in the cosmetics industry.