Genome-wide analysis of key gene families in RNA silencing and their responses to biotic and drought stresses in adzuki bean.

BACKGROUND: In plants, RNA silencing is an important conserved mechanism to regulate gene expression and combat against abiotic and biotic stresses. Dicer-like (DCL) and Argonaute (AGO) proteins and RNA-dependent RNA polymerase (RDR) are the core elements involved in gene silencing and their gene families have been explored in many plants. However, these genes and their responses to stresses have not yet been well characterized in adzuki bean. RESULTS: A total of 11 AGO, 7 DCL and 6 RDR proteins were identified, and phylogenetic analyses of these proteins showed that they clustered into six, four and four clades respectively. The expression patterns of these genes in susceptible or resistant adzuki bean cultivars challenged with drought, bean common mosaic virus and Podosphaera xanthii infections were further validated by quantitative RT-PCR. The different responses of these proteins under abiotic and biotic stresses indicated their specialized regulatory mechanisms. CONCLUSIONS: In this study, 24 genes of the DCL, AGO and RDR gene families in adzuki bean were identified, and the sequence characterization, structure of the encoded proteins, evolutionary relationship with orthologues in other legumes and gene expression patterns under drought and biotic stresses were primarily explored, which enriched our understanding of these genes in adzuki bean. Our findings provide a foundation for the comparative genomic analyses of RNA silencing elements in legume plants and further new insights into the functional complexity of RNA silencing in the response to various stresses in adzuki bean.

Dynamics in Diffusive Emissions of Dissolved Gases from Groundwater Induced by Fluctuated Ground Surface Temperature.

During the lateral transport with subsurface flow, amounts of manufactured volatile organic chemicals and gases dissolved in groundwater are emitted into the atmosphere via upward diffusion through soils. Quantifying gas emissions is important for assessing environmental risk associated with these constituents (e.g., air pollution and global warming). It is widely recognized that the temperature would affect gas spreading in soils, which in turn regulates the gas emission from groundwater. However, the upward diffusive gas emission induced by the fluctuated ground surface temperature (GST) remains unexplored. A coupled heat transfer and gas transport model is developed to investigate emissions of tetrachloroethylene (PCE) and N2O, a typical manufactured volatile organic chemical and a natural gas, from groundwater with seasonally fluctuating GSTs. The results indicate that both PCE and N2O emissions vary significantly from month to month. Moreover, fluctuations of emissions lag obviously behind the fluctuation of GST due to the damping effects of both capillary fringe and soil sorption. The proposed model agrees with the observed data from a monolith lysimeter experiment well. The model is also applied to the estimations of N2O emissions from 12 aquifers in Walloon Region, Belgium. The estimated N2O emission is 12.6 µg N/m2/d that falls in the estimated range (9.0-21.5 µg N/m2/d) using the IPCC emission factor approach that commonly accounts for the N2O emission of groundwater discharge to surface water only. It suggests that the upward diffusion is non-negligible for estimations of N2O emission from groundwater.

Genome sequence assembly algorithms and misassembly identification methods.

The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.

Early impact of the COVID-19 pandemic on outpatient migraine care in Hawaii: Results of a quality improvement survey.

OBJECTIVE: A survey was implemented for early assessment of pandemic-related practice processes and quality improvement (QI). BACKGROUND: In response to the public health measures in Hawaii to curtail the coronavirus 2019 pandemic, Hawaii Pacific Neuroscience (HPN) adapted their patient care to ensure continuity of neurological treatment. METHODS: The telephone survey was conducted on patients seen at HPN during the period of April 22, 2020-May 18, 2020 to address four areas related to patients' outpatient experience: delivery of care, general well-being, experience with telemedicine, and disease-specific questions. RESULTS: A total of 928 patients were contacted of which 429 (46.2%) patients responded and 367 (85.5%) agreed to participate. A total of 133 patients with migraine and 234 patients with other neurological conditions provided responses. Our migraine patients' survey responses suggest that their well-being was disproportionately negatively affected by the pandemic. Survey respondents with migraine were significantly more likely than their non-migraine peers to report worsening anxiety and sleep problems [62/132 (47.0%) vs. 78/234 (33.3%), χ2  = 6.64, p = 0.010, and 64/132 (48.5%) vs. 73/234 (31.2%), χ2  = 10.77, p = 0.001]; migraine patients also reported worsening of depression as a result of the pandemic more than patients with other diagnoses, though this was not statistically significant [44/132 (33.3%) vs. 57/234 (24.4%), χ2  = 3.40, p = 0.065]. In regard to access to healthcare, significantly more migraine patients reported running out of medications than those with other diagnoses [20/133 (15.0%) vs. 18/234 (7.7%), χ2  = 4.93, p = 0.026]. More avoided seeking medical help for new health problems because of the pandemic [30/133 (22.6%) vs. 30/234 (12.8%), χ2  = 5.88, p = 0.015]. Migraine patients were also significantly impacted economically by the pandemic; 43/132 (32.4%) of migraine patients reported losing their jobs as the result of the pandemic versus 34/234 (14.5%) of their peers (χ2  = 11.20, p < 0.001). An increase in headache severity or frequency was reported in 39/118 (33.1%) of respondents and 19/118 (16.1%) reported to using more abortive therapy than usual. Telemedicine was well received by almost all patients who took advantage of the option. Most of those patients found telemedicine to be easy to use and as valuable as an in-person visit. Migraine patients indicated with more frequency that without the telemedicine option, they would have missed their medical appointments [37/68 (54.4%) vs. 56/144 (38.6%), χ2  = 4.31, p = 0.038]; a majority would prefer or consider telemedicine for future appointments over in-person visits. CONCLUSIONS: Insights gained from this QI survey to the practice's new pandemic-related processes include stressing lifestyle modification, optimizing treatment plans, and continuing the option of telemedicine.

Intraparticle sorption and desorption of antibiotics.

Intraparticle domains are the critical locations for storing contaminants and retarding contaminant transport in subsurface environments. While the kinetics and extent of antibiotics sorption and desorption in subsurface materials have been extensively studied, their behaviors in intraparticle domains have not been well understood. This study investigated the sorption and desorption of antibiotics (ATs) in the intraparticle domains using quartz grains and clay, and antibiotic tetracycline (TC) and levofloxacin (LEV) as examples that are commonly present in groundwater systems. Batch experiments coupled with the analyses using various microscopic and spectroscopic techniques were performed to investigate the sorption and desorption kinetics, and to provide insights into the intraparticle sorption and desorption of TC and LEV. Results indicated that both TC and LEV with different physiochemical properties can migrate into intraparticle domains that were consistent with sorptive diffusion. The rate and extent of the sorption are a function of intraparticle surface area and properties, pore volume and connectivity, and ionic properties of the ATs. The sorptive diffusion led to the slow desorption of both TC and LEV after their sorption, apparently showing an irreversible desorption behavior (with desorption percentage about 1.86-20.51%). These results implied that intraparticle domains can be important locations for storing ATs, retarding ATs transport, and may serve as a long-term secondary source for groundwater contamination.

A comparative analysis of TCR immune repertoire in COVID-19 patients.

The coronavirus disease 2019 (COVID-19) has merged as a global health threat since its outbreak in December 2019. Despite widespread recognition, there has been a paucity of studies focusing on the T cell receptor (TCR) bias in adaptive immunity induced by SARS-CoV-2. This research conducted a comparative analysis of the TCR immune repertoire to identify notable αß TCR bias sequences associated with the SARS-CoV-2 virus antigen. The present study encompassed 73 symptomatic COVID-19 patients, categorized as moderate/mild or severe/critical, along with 9 healthy controls. Our findings revealed specific TCR chains prominently utilized by moderate and severe patients, identified as TRAV30-J34-TRBV3-1-J2-7 and TRAV12-3-J6-TRBV28-J1-1, respectively. Additionally, our research explored critical TCR preferences in the bronchoalveolar lavage fluid (BALF) of COVID-19 patients at various disease stages. Indeed, monitoring the dynamics of immune repertoire changes in COVID-19 patients could serve as a crucial biomarker for predicting disease progression and recovery. Furthermore, the study explored TCR bias in both peripheral blood mononuclear cells (PBMCs) and BALF. The most common αß VJ pair observed in BALF was TRAV12-3-J18-TRBV7-6-J2-7. In addition, a comparative analysis with the VDJdb database indicated that the HLA-A*02:01 allele exhibited the widest distribution and highest frequency in COVID-19 patients across different periods. This comprehensive examination provided a global characterization of the TCR immune repertoire in COVID-19 patients, contributing significantly to our understanding of TCR bias induced by SARS-CoV-2.

Description of Otolaryngology (OTO) Disease in Houseless Patients on O'ahu, Hawai'i.

This retrospective study assesses the prevalence of otolaryngology (OTO) disease in houseless patients on O'ahu based on data from the Houseless Outreach and Medical Education (HOME) clinics, a medical student-run, primary health care service. It is important to note that this data represents only a snapshot in time of the OTO diseases present in this population. Records were examined from September 3, 2020 to September 30, 2021. Patients with at least 1 OTO disease were included in this study. A total of 597 patient records were reviewed; a total of 58 patients were included in this study. The most common OTO diagnoses in this sample were facial trauma (n = 12, 21%), dental caries (n = 7, 12%), cerumen impaction (n = 6, 10%), viral upper respiratory infection (n = 5, 9%), otitis media (n = 4, 7%), and allergic conjunctivitis (n = 3, 5%). Roughly 10% of patients seen in HOME clinics between September 2020 and September 2021 were seen for OTO disease.

Abnormal Temporal Slowing on EEG Findings in Preclinical Alzheimer's Disease Patients With the ApoE4 Allele: A Pilot Study.

INTRODUCTION: Currently, there are limited accessible and cost-effective biomarkers for preclinical Alzheimer's disease (AD) patients. However, the apolipoprotein E (ApoE) polymorphic alleles can predict if someone is at high (e4), neutral (e3), or low (e2) genetic risk for developing AD. This study analyzed electroencephalogram (EEG) reports from individuals with various ApoE genotypes, aiming to identify EEG changes and patterns that could potentially serve as predictive markers for preclinical AD progression. METHODS: Participants aged 64-78 were selected from the patient database at an outpatient neurology clinic. Genotype studies were performed to determine ApoE status, followed by EEG analysis to identify any apparent trends. A case-control design was used, categorizing participants into cases (e2e3, e2e4, e3e4, e4e4) and controls (e3e3). EEG recordings were compared between the groups to identify potential differences in EEG characteristics, including abnormal temporal slowing, frequency, and ApoE genotype association. RESULTS: Among 43 participants, 49% demonstrated evidence of abnormal temporal slowing on EEG. Of these, 48% displayed focal left temporal slowing, and 52% displayed bilateral temporal slowing. The right-sided temporal slowing was not observed. Among participants with abnormal slowing, 95% exhibited theta frequency (4-8 Hz) slowing, while only 4.8% displayed delta frequency (0-4 Hz) slowing. Among participants with the ApoE4 allele, 61.5% demonstrated evidence of abnormal slowing, compared to 43.3% without it. Furthermore, the presence of an ApoE4 allele was associated with a significantly higher proportion of males (54%) compared to those without it (13%) (p=0.009). CONCLUSIONS: Although we did not find a statistically significant difference in temporal EEG slowing among different ApoE genotypes, our findings suggest a potential association between temporal slowing on EEG and the presence of an ApoE4 allele in individuals with preclinical AD. These observations highlight the need for further exploration into the potential influence of the ApoE4 allele on EEG findings and the utility of EEG as a complementary diagnostic tool for AD. Longitudinal studies with large sample sizes are needed to establish the precise relationship between EEG patterns, ApoE genotypes, and AD progression.

Intraoperative In Vivo Imaging Modalities in Head and Neck Cancer Surgical Margin Delineation: A Systematic Review.

Surgical margin status is one of the strongest prognosticators in predicting patient outcomes in head and neck cancer, yet head and neck surgeons continue to face challenges in the accurate detection of these margins with the current standard of care. Novel intraoperative imaging modalities have demonstrated great promise for potentially increasing the accuracy and efficiency in surgical margin delineation. In this current study, we collated and analyzed various intraoperative imaging modalities utilized in head and neck cancer to evaluate their use in discriminating malignant from healthy tissues. The authors conducted a systematic database search through PubMed/Medline, Web of Science, and EBSCOhost (CINAHL). Study screening and data extraction were performed and verified by the authors, and more studies were added through handsearching. Here, intraoperative imaging modalities are described, including optical coherence tomography, narrow band imaging, autofluorescence, and fluorescent-tagged probe techniques. Available sensitivities and specificities in delineating cancerous from healthy tissues ranged from 83.0% to 100.0% and 79.2% to 100.0%, respectively, across the different imaging modalities. Many of these initial studies are in small sample sizes, with methodological differences that preclude more extensive quantitative comparison. Thus, there is impetus for future larger studies examining and comparing the efficacy of these intraoperative imaging technologies.

Early Impact of the COVID-19 Pandemic on Outpatient Neurologic Care in Hawai'i.

In March 2020, Hawai'i instituted public health measures to prevent the spread of Coronavirus disease 2019 (COVID-19), including stay-at-home orders, closure of non-essential businesses and parks, use of facial coverings, social distancing, and a mandatory 14-day quarantine for travelers. In response to these measures, Hawai'i Pacific Neuroscience (HPN) modified practice processes to ensure continuity of neurological treatment. A survey of patients was performed to assess the impact of the COVID-19 pandemic and pandemic-related practice processes for quality improvement. Overall, 367 patients seen at HPN between April 22, 2020, and May 18, 2020, were surveyed via telephone. Almost half (49.6%) participated in a telemedicine appointment, with the majority finding it easy to use (87.4%) and as valuable as face-to-face appointments (68.7%). Many (44.5%) patients said they would have missed a health care appointment without the availability of telemedicine, and 47.3% indicated they might prefer to use telemedicine over in-person appointments in the future. Many reported new or worsening mental health problems, including depression (27.6%), anxiety (38.3%), or sleep disturbances (37.4%). A significant number reported worsening of their condition, with 33.1% of patients who experience migraines reporting increased symptom severity or frequency, 45.8% patients with Alzheimer's disease reporting worsened symptoms, 38.5% of patients with Parkinson's disease who had a recent fall, and 50.0% of patients with multiple sclerosis experiencing new or worsened symptoms. Insights from this survey applied to the practice's pandemic-related processes include emphasizing lifestyle modification, screening for changes in mental health, optimizing treatment plans, and continuing the option of telemedicine.

Mapping global lake dynamics reveals the emerging roles of small lakes.

Lakes are important natural resources and carbon gas emitters and are undergoing rapid changes worldwide in response to climate change and human activities. A detailed global characterization of lakes and their long-term dynamics does not exist, which is however crucial for evaluating the associated impacts on water availability and carbon emissions. Here, we map 3.4 million lakes on a global scale, including their explicit maximum extents and probability-weighted area changes over the past four decades. From the beginning period (1984-1999) to the end (2010-2019), the lake area increased across all six continents analyzed, with a net change of +46,278 km2, and 56% of the expansion was attributed to reservoirs. Interestingly, although small lakes (<1 km2) accounted for just 15% of the global lake area, they dominated the variability in total lake size in half of the global inland lake regions. The identified lake area increase over time led to higher lacustrine carbon emissions, mostly attributed to small lakes. Our findings illustrate the emerging roles of small lakes in regulating not only local inland water variability, but also the global trends of surface water extent and carbon emissions.

An analytical model of bubble-facilitated vapor intrusion.

Mass transfer from nonaqueous phase liquid (NAPL) to entrapped air induced by a fluctuating water table commonly occurs in residual NAPL zones in aquifers. Gas bubble expansion and vertical migration due to interphase mass transfer could facilitate the upward transport of volatile organic compounds (VOCs) in the aquifer and result in higher mass fluxes into a building relative to those of diffusion-limited (D-L) VOC transport. However, the current vapor intrusion models have not considered bubble migration. In this study, an analytical solution of bubble-facilitated (B-F) VOC transport in the unsaturated-saturated zone was developed. The analytical solution was tested by a numerical solution using the finite-difference method. Sensitivity analyses of model parameters were implemented to understand the VOC transport behaviors. The effects of bubble migration on vapor intrusion pathway completion time (tc) and the attenuation factor (AF) were investigated by comparison with the D-L VOC transport model. The results indicate that the D-L model significantly overestimates the tc and underestimates the AF because the model neglects the impacts of bubble migration. Therefore, one may make an inappropriate decision and set up an inappropriate response action schedule if using the D-L model to assess the risk of bubble-facilitated vapor intrusion. The analytical solution was applied to a laboratory experiment. The analytical model managed to interpret the laboratory experiment data, showing that the mass flux of B-F VOC transport is two orders of magnitude higher than that of D-L VOC transport.

ATM deficiency promotes progression of CRPC by enhancing Warburg effect.

ATM is a well-known master regulator of double strand break (DSB) DNA repair and the defective DNA repair has been therapeutically exploited to develop PARP inhibitors based on the synthetic lethality strategy. ATM mutation is found with increased prevalence in advanced metastatic castration-resistant prostate cancer (mCRPC). However, the molecular mechanisms underlying ATM mutation-driving disease progression are still largely unknown. Here, we report that ATM mutation contributes to the CRPC progression through a metabolic rather than DNA repair mechanism. We showed that ATM deficiency generated by CRISPR/Cas9 editing promoted CRPC cell proliferation and xenograft tumor growth. ATM deficiency altered cellular metabolism and enhanced Warburg effect in CRPC cells. We demonstrated that ATM deficiency shunted the glucose flux to aerobic glycolysis by upregulating LDHA expression, which generated more lactate and produced less mitochondrial ROS to promote CRPC cell growth. Inhibition of LDHA by siRNA or inhibitor FX11 generated less lactate and accumulated more ROS in ATM-deficient CRPC cells and therefore potentiated the cell death of ATM-deficient CRPC cells. These findings suggest a new therapeutic strategy for ATM-mutant CRPC patients by targeting LDHA-mediated glycolysis metabolism, which might be effective for the PARP inhibitor resistant mCRPC tumors.

Modeling of the transport and deposition of polydispersed particles: Effects of hydrodynamics and spatiotemporal evolution of the deposition rate.

A time-distance-dependent deposition model is built to investigate the effects of hydrodynamic forces on the transport and deposition of polydispersed particles and the evolution of deposition rates with time and distance. Straining and the heterogeneity of the particle population are considered to play important roles in the decreasing distribution of deposition rates. Numerical simulations were applied in a series of sand column experiments at different fluid velocities for three different porous media. The effects of hydrodynamics forces are elaborated with the systematic variations of deposition dynamic parameters of the proposed model. With retention distributions with particle size as well as temporal and spatial evolutions of deposition rates, the transport and deposition mechanisms of polydispersed particles will be elucidated through the interplay of the variation of the particle size distribution of mobile particle populations and the geometrical change of the porous medium due to retention (straining and blocking).

Harvesting energy from low-frequency excitations through alternate contacts between water and two dielectric materials.

Recent studies have demonstrated the benefits of water-dielectric interfaces in electrostatic energy harvesting. Most efforts have been focused on extracting the kinetic energy from the motions of water drops on hydrophobic surfaces, and thus, the resulting schemes inherently prefer cases where the water drops move at a high speed, or vibrate at a high frequency. Here we report a method for directly harvesting ambient mechanical energy as electric potential energy through water droplets by making alternate contacts with CYTOP and PTFE thin films. Because CYTOP and PTFE acquire significantly different surface charge densities during contact with water, such a difference can be utilized to effectively generate electricity. We demonstrate this concept using prototype devices fabricated on silicon substrates with a simple procedure. In the experiments conducted, a water drop of 400 µL alone could generate a peak open-circuit voltage of 42 V under a 0.25 Hz vibration. Under a 2.5 Hz vibration, the peak open-circuit voltage reached 115 V under an external bias of 8 V. The demonstrated efficiency is orders of magnitude higher than those of existing devices of similar dimensions.

Modeling of retention and re-entrainment of mono- and poly-disperse particles: Effects of hydrodynamics, particle size and interplay of different-sized particles retention.

In this paper, numerical simulations of experimental data were performed with kinetic rate coefficients to characterize the retention and re-entrainment dynamics under different hydrodynamic conditions for monodisperse and polydisperse latex particles (3, 10, 16µm and the mixture). The results show that drastic increase in fluid velocity provokes hardly any remarkable decrease in retention in the presence of large energy barriers (>2000kT). Systematical increases in deposition and re-entrainment dynamic rates were observed with fluid velocity and/or particle size. Increased irreversible deposition rate indicates straining and wedging dominate deposition in this study. Excess retention of 3µm particle in the polydisperse particle suspension was observed. The origins are reckoned that deposited larger particles may hinder the re-entrainment of smaller particles near the grain-to-grain contact and can provide additional sites of attachment.