Recovery of Small DNA Fragments from Serum Using Compaction Precipitation

Background: While most nucleic acids are intracellular, trace amounts of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), including micro RNAs, can also be found in peripheral blood. Many studies have suggested the potential utility of these circulating nucleic acids in prenatal diagnosis, early cancer detection, and the diagnosis of infectious diseases. However, DNA circulating in blood is usually present at very low concentrations (ng/ml), and is in the form of relatively small fragments (,1,000 bp), making its isolation challenging. Methods: Here we report an improved method for the isolation of small DNA fragments from serum using selective precipitation by quaternary ammonium compaction agents. A 151 bp fragment of double-stranded DNA from the Escherichia coli bacteriophage lambda served as the model DNA in our experiments. DNA was serially diluted in serum until undetectable by conventional polymerase chain reaction (PCR), before being enriched by compaction precipitation. Results: Starting with concentrations two to three orders of magnitude lower than the PCR-detectable level (0.01 ng/ml), we were able to enrich the DNA to a detectable level using a novel compaction precipitation protocol. The isolated DNA product after compaction precipitation was largely free of serum contaminants and was suitable for downstream applications. Conclusions: Using compaction precipitation, we were able to isolate and concentrate small DNA from serum, and increase the sensitivity of detection by more than four orders of magnitude. We were able to recover and detect very low levels (0.01 ng/ml) of a small DNA fragment in serum. In addition to being very sensitive, the method is fast, simple, inexpensive, and avoids the use of toxic chemicals

Bayesian Active Learning With Abstention Feedbacks

We study pool-based active learning with abstention feedbacks where a labeler can abstain from labeling a queried example with some unknown abstention rate. This is an important problem with many useful applications. We take a Bayesian approach to the problem and develop two new greedy algorithms that learn both the classification problem and the unknown abstention rate at the same time. These are achieved by simply incorporating the estimated average abstention rate into the greedy criteria. We prove that both algorithms have near-optimality guarantees: they respectively achieve a ${(1-\frac{1}{e})}$ constant factor approximation of the optimal expected or worst-case value of a useful utility function. Our experiments show the algorithms perform well in various practical scenarios.Comment: Poster presented at 2019 ICML Workshop on Human in the Loop Learning 2019 (non-archival). arXiv admin note: substantial text overlap with arXiv:1705.0848

Increasing Binding Efficiency via Reporter Shape and Flux in a Viral Nanoparticle Lateral-Flow Assay

To identify factors controlling the performance of reporter particles in a sensitive lateral-flow assay (LFA), we investigated the effect of the flux and shape of filamentous bacteriophage (phage) on the performance of phage LFAs. Phage of three different lengths and diameters were modified with biotin and AlexaFluor 555 as binding and read-out elements, respectively. The binding efficiencies of the functionalized phage were tested in a fibrous glass LFA membrane modified with avidin. The total binding rate, quantified using real-time particle counting and particle image velocimetry, decreased monotonically with the average bulk flux of phage through the membrane. At the pore scale, more phage bound in regions with faster local flow, confirming that both average and local flux increased binding. The number of bound phage increased with the aspect ratio of the phage and scaled with the phage surface area, consistent with a binding interaction controlled by the number of recognition elements on the surface. Together, these results indicate that increasing the likelihood that recognition elements on the surface of phage encounter the fibers enhances the assay binding efficiency and suggests one origin for the improved performance of nonspherical phage reporters

A low-cost smartphone-based platform for highly sensitive point-of-care testing with persistent luminescent phosphors

Through their computational power and connectivity, smartphones are poised to rapidly expand telemedicine and transform healthcare by enabling better personal health monitoring and rapid diagnostics. Recently, a variety of platforms have been developed to enable smartphone-based point-of-care testing using imaging-based readout with the smartphone camera as the detector. Fluorescent reporters have been shown to improve the sensitivity of assays over colorimetric labels, but fluorescence readout necessitates incorporating optical hardware into the detection system, adding to the cost and complexity of the device. Here we present a simple, low-cost smartphone-based detection platform for highly sensitive luminescence imaging readout of point-of-care tests run with persistent luminescent phosphors as reporters. The extremely bright and long-lived emission of persistent phosphors allows sensitive analyte detection with a smartphone by a facile time-gated imaging strategy. Phosphors are first briefly excited with the phone's camera flash, followed by switching off the flash, and subsequent imaging of phosphor luminescence with the camera. Using this approach, we demonstrate detection of human chorionic gonadotropin using a lateral flow assay and the smartphone platform with strontium aluminate nanoparticles as reporters, giving a detection limit of ?45 pg mL?1 (1.2 pM) in buffer. Time-gated imaging on a smartphone can be readily adapted for sensitive and potentially quantitative testing using other point-of-care formats, and is workable with a variety of persistent luminescent materials

Field Emission from Self-Assembled Arrays of Lanthanum Monosulfide Nanoprotrusions

The field emission properties of LaS nanoprotrusions called nanodomes, formed by pulsed laser deposition on porous anodic alumina films, have been analyzed with scanning anode field emission microscopy. The voltage necessary to produce a given field emission current is 3.5 times less for nanodomes than for thin films. Assuming the same work function for LaS thin films and nanoprotrusions, that is, 1 eV, a field enhancement factor of 5.8 is extracted for the nanodome emitters from Fowler-Nordheim plots of the field emission data. This correlates well with the aspect ratio of the tallest nanodomes observed in atomic force micrograph measurements

The clinical features of osteogenesis imperfecta in Vietnam

Purpose Osteogenesis imperfecta (OI) has not been studied in a Vietnamese population before. The aim of this study was to systematically collect epidemiological information, investigate clinical features and create a clinical database of OI patients in Vietnam for future research and treatment strategy development. Method Participants underwent clinical and physical examinations; also medical records were reviewed. Genealogical information was collected and family members’ phenotypical manifestations recorded. Cases were classified according to the Sillence classification. Results In total, 146 OI patients from 120 families were studied: 46 with OI Type I, 46 with Type III and 54 with Type IV. Almost patients had skeletal deformations. One hundred and forty-two had a history of fractures, 117 blue sclera, 89 dentinogenesis imperfecta and 26 hearing loss. The total number of fractures was 1,932. Thirty-four patients had intra-uterine fractures and nine had perinatal fractures. Surgery was performed 163 times in 58 patients; 100 osteosyntheses and 63 osteotomies. Bisphosphonate treatment was used in 37 patients. The number of affected individuals and predominance of severe forms of OI indicate that the disease is under diagnosed in Vietnam, especially in cases without a family history or with mild form of OI. Deformities appeared in all patients with different severity and localisation, affecting mostly the lower limbs. OI medical and surgical treatment rates are low and in most cases surgery was performed due to fractures. Conclusions Compared to previous studies, our results indicate a lower OI prevalence and greater severity of symptoms in the Vietnamese population when compared with other areas. Further investigation, improved diagnosis and treatment are needed to increase the patients’ quality of life

Field Emission from Self-Assembled Arrays of Lanthanum Monosulfide Nanoprotrusions

The field emission properties of LaS nanoprotrusions called nanodomes, formed by pulsed laser deposition on porous anodic alumina films, have been analyzed with scanning anode field emission microscopy. The voltage necessary to produce a given field emission current is ∼3.5 times less for nanodomes than for thin films. Assuming the same work function for LaS thin films and nanoprotrusions, that is, ∼1 eV, a field enhancement factor of ∼5.8 is extracted for the nanodome emitters from FowlerNordheim plots of the field emission data. This correlates well with the aspect ratio of the tallest nanodomes observed in atomic force micrograph measurements. The promise of producing extremely high current densities in near-vacuum with no external source (such as heater, primary electron-beam, or intense light source) has generated significant interest in robust, reproducible, and fieldemission-based cold cathodes Recently, we reported the first successful deposition of lanthanum monosulfide (LaS) thin films on Si substrates using pulsed laser deposition (PLD) The nanodomes are cone-shaped LaS structures with base diameter 2r ranging from 50 to 100 nm and height h ranging from 100 to 150 nm. They were found to grow on the boundaries separating regions of the anodic alumina film that have near perfect pore ordering. Their density is ∼10 9 /cm 2 , as extracted from the field emission-scanning electron micrographs (FE-SEM) and atomic force micrographs (AFM) such as those shown in The SAFEM technique was used to measure the FE current-voltage (I-V) characteristics at different surface locations. As the nanowires are buried inside the pores, they contribute very little, if any at all, to the net FE current. Moreover, FE measurements from the arrays of nanodomes and nanodots were possible because the regions joining adjacent nanodomes and nanodots are covered with a thin percolating network of LaS over the entire array. Its presence was confirmed by measuring a low resistance value of about 2 Ohms between two electrical contacts about 1 cm apart. For each location, a full set of I-V characteristics (total measured current versus applied voltage) for different values of d, the distance between the cathode surface and the probe ball, was measured. This set of measurements was then analyzed in order to extract the apparent current density αJ versus actual applied local field γF, where γ is the local geometrical field enhancement at the surface of the cathode In order to assess the FE properties from LaS nanoprotrusions, we have compared the FE from nanodome cathodes with that from planar thin film LaS cathodes. This comparative methodology was chosen because a precise quantitative estimation of γ from topographic measurements is still subject to controversy, except for a flat surface. These experimental measurements were performed for both LaS thin films of 100 nm thickness on Si wafers and LaS nanodomes on anodic alumina films. The analysis consisted of the following steps. (1) In order to restrict the analysis of the differences in the I-V data to the surface morphology of the cathodes, both SAFEM measurements were performed with the same probe ball-to-cathode distance d = 3.65 μm. Typical I-V characteristics are shown in (2) The total FE current versus applied voltage (I-V) characteristics were measured for different values of the probe-ball-to-cathode-surface distance d. From these data, the apparent current densities (α t f J and α nd J) as a a function of the applied local field were extracted ACKNOWLEDGMEN

Field Emission from Self-Assembled Arrays of Lanthanum Monosulfide Nanoprotrusions

The field emission properties of LaS nanoprotrusions called nanodomes, formed by pulsed laser deposition on porous anodic alumina films, have been analyzed with scanning anode field emission microscopy. The voltage necessary to produce a given field emission current is ∼3.5 times less for nanodomes than for thin films. Assuming the same work function for LaS thin films and nanoprotrusions, that is, ∼1 eV, a field enhancement factor of ∼5.8 is extracted for the nanodome emitters from Fowler-Nordheim plots of the field emission data. This correlates well with the aspect ratio of the tallest nanodomes observed in atomic force micrograph measurements

Impact of Education and Network for Avian Influenza H5N1 in Human: Knowledge, Clinical Practice, and Motivation on Medical Providers in Vietnam

BACKGROUND: Knowledge, clinical practice, and professional motivation of medical providers relating to H5N1 infection have an important influence on care for H5N1 patients who require early diagnosis and early medical intervention. METHODS/PRINCIPAL FINDINGS: Novel educational programs including training and workshops for medical providers relating to H5N1 infection in Vietnam were originally created and implemented in 18 provincial hospitals in northern Vietnam between 2008 and 2010. A self-administered, structured questionnaire survey was conducted in 8 provincial hospitals where both educational training and workshops were previously provided. A total of 326 medical providers, including physicians, nurses, and laboratory technicians who attended or did not attend original programs were enrolled in the survey. Knowledge, clinical attitudes and practice (KAP), including motivation surrounding caring for H5N1 patients, were evaluated. The study indicated a high level of knowledge and motivation in all professional groups, with especially high levels in laboratory technicians. Conferences and educational programs were evaluated to be the main scientific information resources for physicians, along with information from colleagues. The chest radiographs and the initiation of antiviral treatment in the absence of RT-PCR result were identified as gaps in education. Factors possibly influencing professional motivation for caring for H5N1 patients included healthcare profession, the hospital where the respondents worked, age group, attendance at original educational programs and at educational programs which were conducted by international health-related organizations. CONCLUSIONS: Educational programs provide high knowledge and motivation for medical providers in Vietnam caring for H5N1 patients. Additional educational programs related to chest radiographs and an initiation of treatment in the absence of RT-PCR are needed. Networking is also necessary for sharing updated scientific information and practical experiences. These enhanced KAPs by educational programs and integrated systems among hospitals should result in appropriate care for H5N1 patients and may reduce morbidity and mortality