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 αβ 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 αβ 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.

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.

Lifestyle behaviour patterns in the prevention of type 2 diabetes mellitus: the Fukushima Health Database 2015-2020

OBJECTIVES

Lifestyle behaviours associated with the incidence of type 2 diabetes mellitus (T2DM) need further clarification using health insurance data.

STUDY DESIGN

This is a cohort study.

METHODS

In 2015, 193,246 participants aged 40-74 years attended the specific health checkups and were observed up to 2020 in Fukushima, Japan. Using the principal component analysis, we identified two patterns from ten lifestyle behaviour questions, namely, the "diet-smoking" pattern (including smoking, alcohol drinking, skipping breakfast, eating fast, late dinner, and snacking) and the "physical activity-sleep" pattern (including physical exercise, walking equivalent activity, walking fast, and sufficient sleep). Then, individual pattern scores were calculated; the higher the scores, the healthier the behaviours.

RESULTS

The accumulative incidence rate of T2DM was 630.5 in men and 391.9 in women per 100,000 person-years in an average of 4 years of follow-up. Adjusted for the demographic and cardiometabolic factors at the baseline, the hazard ratio (95% confidence interval) of the highest versus lowest quartile scores of the "diet-smoking" pattern for T2DM risk was 0.82 (0.72, 0.92; P for trend = 0.002) in men and 0.87 (0.76, 1·00; P for trend = 0.034) in women; that of the "physical activity-sleep" pattern was 0.92 (0.82, 1·04; P for trend = 0.0996) in men and 0.92 (0.80, 1·06; P for trend = 0.372) in women. The "physical activity-sleep" pattern showed a significant inverse association in non-overweight men.

CONCLUSIONS

Lifestyle behaviour associated with a healthy diet and lack of smoking may significantly lower the risk of T2DM in middle-aged Japanese adults.

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.

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.

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.

Prevalence trends of metabolic syndrome in residents of postdisaster Fukushima: a longitudinal analysis of Fukushima Health Database 2012-2019

OBJECTIVES

The study aimed to evaluate the long-term metabolic risk profiles of Fukushima residents after the Great East Japan Earthquake of March 2011.

STUDY DESIGN

This was a cross-sectional and a longitudinal design.

METHODS

The Fukushima Health Database (FDB) contains 2,331,319 annual health checkup records of participants aged 40-74 years between 2012 and 2019. We checked the validity of the FDB by comparing the prevalence of metabolic factors with the National Database of Health Insurance Claims and Specific Health Checkups (NDB). We applied a regression analysis to determine the changes and project the trends of metabolic factors over the years.

RESULTS

Compared to the NDB, the prevalence of metabolic factors in Fukushima was higher than the country average from 2013 to 2018, and they showed the same trends as those from the FDB. The prevalence of metabolic syndrome (MetS) increased from 18.9% in 2012 to 21.4% in 2019 (an annual increase of 2.74%) in men and from 6.8 to 7.4% (an annual increase of 1.80%) in women in Fukushima. The standardized prevalence of MetS, being overweight, and diabetes is projected to continue increasing, with disparities among subareas being higher in evacuees than in non-evacuees. An annual decrease of 0.38-1.97% in hypertension was mainly observed in women.

CONCLUSIONS

The prevalence of metabolic risk is higher in Fukushima as compared to the country average. The increasing metabolic risk in subareas, including the evacuation zone, highlights the need to control MetS in Fukushima residents.

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.

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.

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.

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.

Development of a cost-effective automated platform to produce human liver spheroids for basic and applied research

Liver disease represents an increasing cause of global morbidity and mortality. Currently, liver transplant is the only treatment curative for end-stage liver disease. Donor organs cannot meet the demand and therefore scalable treatments and new disease models are required to improve clinical intervention. Pluripotent stem cells represent a renewable source of human tissue. Recent advances in three-dimensional cell culture have provided the field with more complex systems that better mimic liver physiology and function. Despite these improvements, current cell-based models are variable in performance and expensive to manufacture at scale. This is due, in part, to the use of poorly defined or cross-species materials within the process, severely affecting technology translation. To address this issue, we have developed an automated and economical platform to produce liver tissue at scale for modelling disease and small molecule screening. Stem cell derived liver spheres were formed by combining hepatic progenitors with endothelial cells and stellate cells, in the ratios found within the liver. The resulting tissue permitted the study of human liver biology 'in the dish' and could be scaled for screening. In summary, we have developed an automated differentiation system that permits reliable self-assembly of human liver tissue for biomedical application. Going forward we believe that this technology will not only serve as anin vitroresource, and may have an important role to play in supporting failing liver function in humans.

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 (t_c) 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 t_c 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.

Abstract P5-09-12: Germline mutation in TP53 gene in a cohort of 2,561 Chinese high-risk breast cancer patients using multigene panel testing

Background: Li-Fraumeni syndrome (LFS) is a rare autosomal genetic disorder with germline TP53 mutations. Patients with TP53 mutations have a higher risk of developing breast cancer than those harboring BRCA mutations. Although limited studies have shown that TP53 mutation carriers are less responsive to low dose radiation and more susceptible to induce new malignancies from radiotherapy. Moreover screening strategies allows early detection of a spectrum of cancers related to TP53 mutations. From work of BRCA mutations where over 40% novel mutations were detected in Chinese cohort, it is important to evaluate the frequency of TP53 mutation in Chinese to better understand the spectrum to guide appropriate clinical management of these high risk individuals.

Methods: TP53 gene mutation screening was performed on 2,561 high-risk breast cancer patients using multigene panel testing. The patients were accrued by Hong Kong Hereditary and High Risk Breast Cancer Program from March 2007 to May 2018. All detected pathogenic mutations were further validated by bi-directional DNA sequencing and analyzed by our in-house developed bioinformatics pipeline.

Results: Sixteen distinct pathogenic or likely pathogenic variants were identified, and 3 of them were de novo TP53 mutations (18.75%). The mean age of patients who harbored TP53 mutation was 30.44 years (range 18-44), and 50% of the tumors were bilateral breast cancer. Of sixteen different pathogenic mutations, majority of them were missense mutation (87.5%), and 2 were nonsense mutation (12.5%). Four of the sixteen TP53 mutation carriers had family history of breast cancer, while others had a family history of lung cancer (43.75%).

Conclusion: This study revealed that seven patients were found to habor TP53 mutation even when they did not meet the criteria of LFS of LFS-like phenotype, implicated the importance of using multigene panel test for probands and their relatives to offer a comprehensive surveillance programe for TP53 carriers.

Citation Format: Kwong A, Shin V, Au CH, Ho C, Slavin T, Weitzel J, Chan TL, Ma E. Germline mutation in TP53 gene in a cohort of 2,561 Chinese high-risk breast cancer patients using multigene panel testing [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-12.

Structural Parameter of Orientational Order to Predict the Boson Vibrational Anomaly in Glasses

It has so far remained a major challenge to quantitatively predict the boson peak, a THz vibrational anomaly universal for glasses, from features in the amorphous structure. Using molecular dynamics simulations of a model Cu_{50}Zr_{50} glass, we decompose the boson peak to contributions from atoms residing in different types of Voronoi polyhedra. We then introduce a microscopic structural parameter to depict the "orientational order," using the vector pointing from the center atom to the farthest vertex of its Voronoi coordination polyhedron. This order parameter represents the most probable direction of transverse vibration at low frequencies. Its magnitude scales linearly with the boson peak intensity, and its spatial distribution accounts for the quasilocalized modes. This correlation is shown to be universal for different types of glasses.

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.

Universal intracellular biomolecule delivery with precise dosage control

Intracellular delivery of mRNA, DNA, and other large macromolecules into cells plays an essential role in an array of biological research and clinical therapies. However, current methods yield a wide variation in the amount of material delivered, as well as limitations on the cell types and cargoes possible. Here, we demonstrate quantitatively controlled delivery into a range of primary cells and cell lines with a tight dosage distribution using a nanostraw-electroporation system (NES). In NES, cells are cultured onto track-etched membranes with protruding nanostraws that connect to the fluidic environment beneath the membrane. The tight cell-nanostraw interface focuses applied electric fields to the cell membrane, enabling low-voltage and nondamaging local poration of the cell membrane. Concurrently, the field electrophoretically injects biomolecular cargoes through the nanostraws and into the cell at the same location. We show that the amount of material delivered is precisely controlled by the applied voltage, delivery duration, and reagent concentration. NES is highly effective even for primary cell types or different cell densities, is largely cargo agnostic, and can simultaneously deliver specific ratios of different molecules. Using a simple cell culture well format, the NES delivers into >100,000 cells within 20 s with >95% cell viability, enabling facile, dosage-controlled intracellular delivery for a wide variety of biological applications.

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.

Melt fluxing to elevate the forming ability of Al-based bulk metallic glasses

Salt-fluxing treatment is an effective technique to improve the glass-forming ability (GFA) of bulk metallic glass (BMG)-forming melts, as demonstrated before in Pd- and Fe-based systems. However, it has been challenging to develop similar fluxing protocol for more reactive melts, such as Al-rich BMG-forming systems. Here we design new fluxing agents, from a thermodynamics perspective that takes into account combined effects of physical absorption and chemical absorption (reaction) between the fluxing agents and oxide inclusions. MgCl₂-CaCl₂ composite salts were selected, and their fluxing effects were systematically studied on an Al₈₆Ni_6.75Co_2.25Y_3.25La_1.75 alloy, the best BMG-forming composition reported thus far for Al-rich alloy systems. The oxygen content was found to continuously decrease in the master alloy with increasing cycles of salt-fluxing treatment, with chlorate products on the surface suggesting concurrent physical absorption and chemical reaction. The fluxing treatment developed has enabled a record critical size (diameter) of 2.5 mm for Al-based BMGs. Our finding is thus an advance in developing highly desirable Al-based BMGs, and also provides guidance for designing processing protocol to produce larger-sized BMGs in other reactive systems.

Nanostructured high-strength molybdenum alloys with unprecedented tensile ductility

The high-temperature stability and mechanical properties of refractory molybdenum alloys are highly desirable for a wide range of critical applications. However, a long-standing problem for these alloys is that they suffer from low ductility and limited formability. Here we report a nanostructuring strategy that achieves Mo alloys with yield strength over 800 MPa and tensile elongation as large as ~ 40% at room temperature. The processing route involves a molecular-level liquid-liquid mixing/doping technique that leads to an optimal microstructure of submicrometre grains with nanometric oxide particles uniformly distributed in the grain interior. Our approach can be readily adapted to large-scale industrial production of ductile Mo alloys that can be extensively processed and shaped at low temperatures. The architecture engineered into such multicomponent alloys offers a general pathway for manufacturing dispersion-strengthened materials with both high strength and ductility.

Microstructural fingerprints of phase transitions in shock-loaded iron

The complex structural transformation in crystals under static pressure or shock loading has been a subject of long-standing interest to materials scientists and physicists. The polymorphic transformation is of particular importance for iron (Fe), due to its technological and sociological significance in the development of human civilization, as well as its prominent presence in the earth's core. The martensitic transformation α→ε (bcc→hcp) in iron under shock-loading, due to its reversible and transient nature, requires non-trivial detective work to uncover its occurrence. Here we reveal refined microstructural fingerprints, needle-like colonies and three sets of {112}<111> twins with a threefold symmetry, with tell-tale features that are indicative of two sequential martensitic transformations in the reversible α→ε phase transition, even though no ε is retained in the post-shock samples. The signature orientation relationships are consistent with previously-proposed transformation mechanisms, and the unique microstructural fingerprints enable a quantitative assessment of the volume fraction transformed.

Pressure tunes electrical resistivity by four orders of magnitude in amorphous Ge2Sb2Te5 phase-change memory alloy

Ge-Sb-Te-based phase-change memory is one of the most promising candidates to succeed the current flash memories. The application of phase-change materials for data storage and memory devices takes advantage of the fast phase transition (on the order of nanoseconds) and the large property contrasts (e.g., several orders of magnitude difference in electrical resistivity) between the amorphous and the crystalline states. Despite the importance of Ge-Sb-Te alloys and the intense research they have received, the possible phases in the temperature-pressure diagram, as well as the corresponding structure-property correlations, remain to be systematically explored. In this study, by subjecting the amorphous Ge(2)Sb(2)Te(5) (a-GST) to hydrostatic-like pressure (P), the thermodynamic variable alternative to temperature, we are able to tune its electrical resistivity by several orders of magnitude, similar to the resistivity contrast corresponding to the usually investigated amorphous-to-crystalline (a-GST to rock-salt GST) transition used in current phase-change memories. In particular, the electrical resistivity drops precipitously in the P = 0 to 8 GPa regime. A prominent structural signature representing the underlying evolution in atomic arrangements and bonding in this pressure regime, as revealed by the ab initio molecular dynamics simulations, is the reduction of low-electron-density regions, which contributes to the narrowing of band gap and delocalization of trapped electrons. At P > 8 GPa, we have observed major changes of the average local structures (bond angle and coordination numbers), gradually transforming the a-GST into a high-density, metallic-like state. This high-pressure glass is characterized by local motifs that bear similarities to the body-centered-cubic GST (bcc-GST) it eventually crystallizes into at 28 GPa, and hence represents a bcc-type polyamorph of a-GST.

The design of long-term effective uranium bioremediation strategy using a community metabolic model

Acetate amendment at uranium contaminated sites in Rifle, CO. leads to an initial bloom of Geobacter accompanied by the removal of U(VI) from the groundwater, followed by an increase of sulfate-reducing bacteria (SRBs) which are poor reducers of U(VI). One of the challenges associated with bioremediation is the decay in Geobacter abundance, which has been attributed to the depletion of bio-accessible Fe(III), motivating the investigation of simultaneous amendments of acetate and Fe(III) as an alternative bioremediation strategy. In order to understand the community metabolism of Geobacter and SRBs during artificial substrate amendment, we have created a genome-scale dynamic community model of Geobacter and SRBs using the previously described Dynamic Multi-species Metabolic Modeling framework. Optimization techniques are used to determine the optimal acetate and Fe(III) addition profile. Field-scale simulation of acetate addition accurately predicted the in situ data. The simulations suggest that batch amendment of Fe(III) along with continuous acetate addition is insufficient to promote long-term bioremediation, while continuous amendment of Fe(III) along with continuous acetate addition is sufficient to promote long-term bioremediation. By computationally minimizing the acetate and Fe(III) addition rates as well as the difference between the predicted and target uranium concentration, we showed that it is possible to maintain the uranium concentration below the environmental safety standard while minimizing the cost of chemical additions. These simulations show that simultaneous addition of acetate and Fe(III) has the potential to be an effective uranium bioremediation strategy. They also show that computational modeling of microbial community is an important tool to design effective strategies for practical applications in environmental biotechnology.

Interfacial Reactions of Mo with Al: Ion mixing Versus Thermal Annealing

Interfacial reactions induced by ion beam mixing and furnace annealing in Al/Mo bilayers are investigated. The amount of interfacial ion m'xing, 4Dt, follows a linear dose dependence for irradiation temperatures ≤80 C. Below room temperature, the mixing efficiency, defined as d(4Dt)/dø, is temperature independent, and agrees fairly well with the prediction of the phenomenological model based on chemically biased diffusion in thermal spike. We conclude that thermal spike mixing dominates for Xe irradiation of Al/Mo at low temperatures. The mixing efficiency becomes temperature-dependent above room temperature with an apparent activation enthalpy of about 0.17±0.02eV. A layer of 15–20 at.% Mo forms by ion mixing, while oAl12 Mo forms upon thermal annealing in a nonuniform fashion starting at 500°C. Reaction of Mo with large-grained Al substrates shows the same nonuniform characteristics as in evaporated Al/Mo bilayers, implying a minor role of grain boundary effects. Oxygen gettered in the Mo film could be an important factor that influences the interfacial reaction.

New structural picture of the Ge2Sb2Te5 phase-change alloy

Using electron microscopy and diffraction techniques, as well as first-principles calculations, we demonstrate that as much as 35% of the total Ge atoms in the cubic phase of Ge2Sb2Te5 locate in tetrahedral environments. The Ge-vacancy interactions play a crucial stabilizing role, leading to Ge-vacancy pairs and the sharing of vacancies that clusters tetrahedral Ge into domains. The Ge2Sb2Te5 structure with coexisting octahedral and tetrahedral Ge produces optical and structural properties in good agreement with experimental data and explains the property contrast as well as the rapid transformation in this phase-change alloy.

Role of miR-143 Regulating DNA Methyltransferases 3A in Breast Cancer

Background and Aims: MicroRNAs (miRNAs) are 19-25-nucleotides regulatory non-protein-coding RNA molecules that regulate the expressions of a wide variety of genes including some involved in cancer development. In particular, decreased expression of miR-143 has been reported in various human cancers including colorectal cancer and B-cell lymphomas. The aim of this study was to elucidate the role of miR-143 dysregulation in breast cancer.Methods: Expression levels of human mature microRNAs (miRNAs) were compared with paired breast carcinomas and adjacent normal tissues by TaqMan real-time PCR based expression arrays. Decreased expression of miR-143 was further confirmed in breast cancer cell lines and paired breast tumors and normal adjacent tissues by qRT-PCR. Potential targets of miR-143 were defined. The functional effect of miR-143 and its targets was performed in human breast cancer cell lines to confirm target association.Results: Down-regulation of miR-143 was verified in both human breast cancer cell lines and 80% (12/15) of breast tumors (P &lt; 0.001). DNA methyltranferase 3A (DNMT3A), one of a key enzyme involved in DNA methylation, was defined as a potential target of miR-143 by in-silico analysis. Overexpression of miR-143 in breast cancer cell lines down-regulated expression of DNMT3A, decreased tumor cell growth by MTT assay and soft agar colony formation assay. DNMT3A was demonstrated to be a direct target of miR-143 by luciferase reporter assay. Inverse correlation between DNMT3A protein and miR-143 was found in tumor and normal breast tissues.Conclusions: In this study, we show for the first time in breast cancer that miR-143 specifically targeted DNMT3A and the expression of miR-143 was inversely correlated with DNMT3A expression. Our findings demonstrated that down-regulation of miR-143 and up-regulation of DNMT3A are significant changes in breast tumors. These findings indicate a tumor suppressive role of miR-143 in epigenetic aberration of breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3148.

Nature of atomic bonding and atomic structure in the phase-change Ge2Sb2Te5 glass

Using electronic structure calculations, we demonstrate a global valence alternation in the amorphous Ge2Sb2Te5, a prototype phase-change alloy for data storage. The resulting p bonding profoundly influences the local atomic structure, leading to right-angle components similar to those in the crystalline counterpart of this chalcogenide glass. The dominance of p bonding is revealed by (i) distributions of the coordination number (CN) and the bond angle, for truly bonded atoms determined based on the electron localization function, and (ii) a direct evaluation of the p (and s) orbital occupation probability for the CN=3 Ge atoms that form 90 degree bonds with neighbors.

Atomic shuffling dominated mechanism for deformation twinning in magnesium

Deformation twinning is often mediated by partial dislocation activities at the twin boundary. Using molecular dynamics simulations, we have uncovered a new mechanism for the most commonly observed {1012}<101 1> deformation twinning in Mg and other hexagonal close-packed metals. Here the twin growth involves no definable dislocations at the twin boundary, and the twin orientational relationship can be established by local atomic shuffling, directly constructing the twin lattice from the parent lattice.

Atomic level structure in multicomponent bulk metallic glass

The atomic-level structure of a representative ternary Cu-Zr-Al bulk metallic glass (BMG) has been resolved. Cu- (and Al-) centered icosahedral clusters are identified as the basic local structural motifs. Compared with the Cu-Zr base binary, a small percentage of Al in the ternary BMG leads to dramatically increased population of full icosahedra and their spatial connectivity. The stabilizing effect of Al is not merely topological, but also has its origin in the electronic interactions and bond shortening.

Reversible twinning in pure aluminum

Twinning in metals is normally a permanent plastic deformation mechanism. Here we report reversible twinning in high stacking fault energy (SFE) aluminum. Twinning and spontaneous detwinning at the crack tip have been captured in situ during tensile straining under a transmission electron microscope. Both the in situ observation and the molecular dynamics simulations reveal a two-stage detwinning process. The high propensity for detwinning is due to the high SFE and the low frictional forces against the detwinning partial dislocations in Al. This discovery of reversible twinning has implications for the deformation of other high SFE materials.

Novel de novo BRCA1 mutation in a woman with early onset breast cancer

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Background: Germline mutations in BRCA1/2 account for a significant portion of hereditary breast/ovarian cancer. Mutation carriers usually have a family history of breast/ovarian cancer or early onset disease. Rarely, germline mutations are found only in the probands but not in any family members. Such de novo mutations have been reported in diseases such as hemophilia A, thalassaemia and familial adenomatous polyposis. De novo mutations in the BRCA1 or BRCA2 genes are rare and the few reported have been in BRCA2. Here, we describe de novo as well as novel mutation of the BRCA1 gene in a breast cancer patient. Methods: Blood DNA samples from a 30 year old Chinese woman with breast cancer and no family history of cancer was tested for a BRCA1/2 mutation by full gene sequencing and Multiple Ligation-dependent Probe Amplification (MLPA). Family members were analyzed for the same mutation. Paternity was determined by a set of highly polymorphic short tandem repeat (STR) markers. Results: Full gene sequencing found no deleterious mutation. MLPA revealed a large deletion of exons 1 to 12 of BRCA1 in the proband. MLPA performed on 5 family members: proband's mother and father (who were 1st degree relative- cousins), stepmother (mother's biological sister), 2 sisters (1, same parents; 1, same father and stepmother) found no similar deletion. By using a set of highly polymorphic STR markers, the proband's father and mother were confirmed to be her biological parents. Conclusions: We report a novel de novo BRCA1 deletion mutation encompassing exons 1 - 12 in a Chinese breast cancer patient of early onset with no family history. Identification of this large deletion confirms the importance of pursuing rearrangement testing if full gene sequencing fails to detect a point mutation or short insertion deletion. The mutation found in this study is de novo. This may simply be a random mutation event which occurred in the parents' germ cells during their lifetime which passed onto one of their offspring or maybe a result of gene inversion or splicing deficiency. The relations of such mutations with consanguineous marriage cannot be ruled out. Mutation screening is important in early onset breast cancer patients even if there is no family history.

No significant financial relationships to disclose.

Tensile ductility and necking of metallic glass

Metallic glasses have a very high strength, hardness and elastic limit. However, they rarely show tensile ductility at room temperature and are considered quasi-brittle materials. Although these amorphous metals are capable of shear flow, severe plastic instability sets in at the onset of plastic deformation, which seems to be exclusively localized in extremely narrow shear bands approximately 10 nm in thickness. Using in situ tensile tests in a transmission electron microscope, we demonstrate radically different deformation behaviour for monolithic metallic-glass samples with dimensions of the order of 100 nm. Large tensile ductility in the range of 23-45% was observed, including significant uniform elongation and extensive necking or stable growth of the shear offset. This large plasticity in small-volume metallic-glass samples did not result from the branching/deflection of shear bands or nanocrystallization. These observations suggest that metallic glasses can plastically deform in a manner similar to their crystalline counterparts, via homogeneous and inhomogeneous flow without catastrophic failure. The sample-size effect discovered has implications for the application of metallic glasses in thin films and micro-devices, as well as for understanding the fundamental mechanical response of amorphous metals.

Characterization of the pathogenic mechanism of a novel BRCA2 variant in a Chinese family

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Background: Despite the identification of a large number of sequences in BRCA1/2 mutation analyses, many genetic alterations are classified as variants of unknown significance (VUS). Increasing data demonstrates ethnic variation of BRCA mutation. We report a novel BRCA2 VUS in a Chinese family with multiple breast cancers and characterized it as pathogenic by RNA analysis. Method: Peripheral blood was collected from the breast cancer proband and her family who were suspected to have a pathogenic mutation due the segregation of the disease phenotype and the young age of presentation of breast cancer. DNA and RNA was extracted from the blood. The entire coding regions and flanking introns of BRCA1/2 were screened for germline mutations using full gene sequencing and Multiplex Ligation -dependent Probe Amplification. Variant DNA alteration leading to an aberrant BRCA transcript was demonstrated by RT-PCR of the RNA and Polyacrylamide Gel Electrophoresis. Abnormal bands were cloned and direct sequencing conducted. Results: A germline mutation c.7806–9T>G was identified in the proband at the BRCA2 intron 16. This mutation was also found in 3 of her 4 sibling sisters with early breast cancer. The proband's mother harbored the same BRCA2 mutation in DNA extracted from archival gastric tumor tissues. Computational analyses showed that this mutation might give rise to a cryptic splice site for alternative RNA splicing. To confirm the pathogenicity, RT- PCR using specific primers flanking the cryptic splice site and sequencing was performed on RNA extracted from the proband's blood. Four different sizes of transcripts were found: wild type, r.7806_7874del , r.7806_7976del and r.7806–8_7806-lins. The latter 3 aberrant transcripts were not found in the 30 controls therefore polymorphism is unlikely. The r.7806–8_7806-lins transcript caused a frameshift which created a truncated protein; whereas the other two short transcripts produced shorter BRCA2 protein isoforms. Conclusion: We identified a novel BRCA2 VUS and classified it as pathogenic. Classification of VUS as neutral or pathogenic, particularly in ethnic groups where limited knowledge is known is a challenge. Research on the spectrum of mutations in diversed ethnic groups has important implications on management. [Genbank: DQ889340 ]

No significant financial relationships to disclose.

Polyamorphism in a metallic glass

A metal, or an alloy, can often exist in more than one crystal structure. The face-centred-cubic and body-centred-cubic forms of iron (or steel) are a familiar example of such polymorphism. When metallic materials are made in the amorphous form, is a parallel 'polyamorphism' possible? So far, polyamorphic phase transitions in the glassy state have been observed only in glasses involving directional and open (such as tetrahedral) coordination environments. Here, we report an in situ X-ray diffraction observation of a pressure-induced transition between two distinct amorphous polymorphs in a Ce(55)Al(45) metallic glass. The large density difference observed between the two polyamorphs is attributed to their different electronic and atomic structures, in particular the bond shortening revealed by ab initio modelling of the effects of f-electron delocalization. This discovery offers a new perspective of the amorphous state of metals, and has implications for understanding the structure, evolution and properties of metallic glasses and related liquids. Our work also opens a new avenue towards technologically useful amorphous alloys that are compositionally identical but with different thermodynamic, functional and rheological properties due to different bonding and structural characteristics.