Viable Sample Research Articles

Integrated studies of soil, termites, vegetation and groundwater to understand metal migration at the Kintyre U deposits, Western Australia

Transported cover is a persistent problem for mineral exploration in Australia and elsewhere in the world. Explorers are not confident in the current understanding of where, when, and how geochemical anomalies form (or don't form) in the cover and how to make the critical interpretive link to buried mineral deposits. Understanding how elements move through transported cover and their link to buried mineralization is increasingly important for exploration success in many regions of the world. At the Kintyre U deposits, groundwater, regolith, soil, Triodia basedowii (spinifex), Acacia ancistrocarpa foliage and litter, and termite ( Nasutitermes triodiae ) mound materials were sampled and analysed to test if near surface methods can detect mineralization through <1 to 80 m of cover. Near surface soil geochemistry, biogeochemistry and hydrogeochemistry weak anomalies did not correlate with primary mineralization through cover except in residual subcropping zones and the thin (<5 m) cover adjacent to these sites. Termite mounds, and to a lesser degree, A. ancistocarpa appear to reflect the mineralized signature in shallow cover (<10 m). A postulated metal migration model for this site links mechanical and chemical weathering and surface colluvial/alluvial down-slope dispersion, with U migration from the Kintyre Hill outcrop to the near surface environment. Plants, soils and groundwater are most likely cycling (near-background levels of) U in the cover at Kintyre. In shallow cover, plants and termite mounds are potential viable sample media. However, for exploration on sites with deep heterogeneous cover, geophysical responses or other new techniques will need to be developed to provide a traceable surface signature.

Abstract 3346: Testing the cancer stem cell hypothesis using the hybrid spheroid assay and Koch's postulates

Abstract We tested the Cancer Stem Cell (CSC) hypothesis using the patented Hybrid Spheroid (HS) Assay (HSA) and by applying Koch's postulates to test its validity. The HSA is an in vitro assay that enables one to take a viable sample of an individual patient's tumor, make a single cell suspension, mix it in known proportions with human fibroblasts (AG1522) and dispense a known number of cells of the mixture into each well of Ultra Low Attachment (ULA) 96-well plates to agglomerate into 1 HS/well, each containing an average of <1 CSC. The HS provides an analog of the CSC niche, enabling the CSC to proliferate (with some daughters differentiating into Amplifying Transit Cells (ATCs)) and undergo 10-15 symmetric divisions before exhausting the nutrients. This satisfies the McCulloch and Till (spleen colony assay) requirements for a stem cell. Applying Koch's postulates: (1) Does the patient's tumor contain cells with CSC properties? Yes: (a) The HSs grow to a size consistent with containing a CSC, (b) those that grew contain cells expressing ≥ 1 OKSM factor(s), and (c) such HSs contain differentiated progeny of the initial CSC. (2) Can we isolate and propagate these cells? In progress: testing HS serial growth, dissociation and reculture. (3) Can these cells induce the tumor in vivo? In progress: testing by xenografting individual CSC-containing HSs in NSG mice. (4) Do these cells contain and express specific gene products that give them CSC properties? Yes: Demonstrated for Oct4 and Nanog. (5) If we disrupt these genes, do the cells lose their CSC properties? In progress: (shRNA). (6) If we eliminate the CSCs do we eliminate the cancer? Yes: tested by (a) mathematical modeling of single CSC growth, differentiation of some progeny into ATCs capable of a limited number of divisions, that then become terminal non-proliferative tumor cells in the HSA; if a single CSC survives/remains, the HS will grow, i.e., the cancer will recur (63% for an average of 1 CSC in a HS, with a Poisson distribution, assuming that niche sites remain available), and (b) by measuring surviving fractions after exposure to radiation and/or chemotherapy agents (where sterilization of the CSC prevents the HS from growing ≥ 10 divisions. The HSA was applied to tumor samples taken from individual endometrial adenocarcinoma patients and correctly predicted, based on CSC radioresistance, which patients would fail their standard-of-care treatments. Conclusion: The CSC hypothesis is validated in the HSA. Citation Format: Christopher S. Lange, Talal Syed, Mike Zhang, Christian Sabalvaro, Hana I. Lim, Ghadir Salame, Bhargava Chitti, Ifeanyi Ilonzo, Arsalaan Ansari, Michelle Chan, Catherine Li, Jing Xu, Xiaotong Chen. Testing the cancer stem cell hypothesis using the hybrid spheroid assay and Koch's postulates. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3346.

Sample sizes and precision of estimates of sensitivity and specificity from primary studies on the diagnostic accuracy of depression screening tools: a survey of recently published studies.

Depression screening tools are useful to the extent that they accurately discriminate between depressed and non-depressed patients. Studies without enough patients to generate precise estimates make it difficult to evaluate accuracy. We conducted a survey of recently published studies on depression screening tool accuracy to evaluate the percentage with sample size calculations; the percentage that provided confidence intervals; and precision, based on the width and lower bounds of 95% confidence intervals for sensitivity and specificity. We calculated 95% confidence intervals, if possible, when not provided. Only three of 89 studies (3%) described a viable sample size calculation. Only 30 studies (34%) provided reasonably accurate confidence intervals. Of 86 studies where 95% confidence intervals were provided or could be calculated, only seven (8%) had interval widths for sensitivity of ≤ 10%, whereas 53 (62%) had widths of ≥ 21%. Lower bounds of confidence intervals were < 80% for 84% of studies for sensitivity and 66% of studies for specificity. Overall, few studies on the diagnostic accuracy of depression screening tools reported sample size calculations, and the number of patients in most studies was too small to generate reasonably precise accuracy estimates. The failure to provide confidence intervals in published reports may obscure these shortcomings. Copyright © 2016 John Wiley & Sons, Ltd.

Acute pyelonephritis in children.

Acute pyelonephritis is one of the most serious bacterial illnesses during childhood. Escherichia coli is responsible in most cases, however other organisms including Klebsiella, Enterococcus, Enterobacter, Proteus, and Pseudomonas species are being more frequently isolated. In infants, who are at major risk of complications such as sepsis and meningitis, symptoms are ambiguous and fever is not always useful in identifying those at high risk. A diagnosis of acute pyelonephritis is initially made on the basis of urinalysis; dipstick tests for nitrites and/or leukocyte esterase are the most accurate indicators of infection. Collecting a viable urine sample for urine culture using clean voided methods is feasible, even in young children. No gold standard antibiotic treatment exists. In children appearing well, oral therapy and outpatient care is possible. New guidelines suggest less aggressive imaging strategies after a first infection, reducing radiation exposure and costs. The efficacy of antibiotic prophylaxis in preventing recurrence is still a matter of debate and the risk of antibiotic resistance is a warning against its widespread use. Well-performed randomized controlled trials are required in order to better define both the imaging strategies and medical options aimed at preserving long-term renal function.

Assessment of tumour viability in human lung cancer xenografts with texture-based image analysis

AimsTo build and evaluate an automated method for assessing tumour viability in histological tissue samples using texture features and supervised learning.MethodsH&E-stained sections (n=56) of human non-small cell lung adenocarcinoma xenografts...

Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments

Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the application of such forces decreases the sample lifetime, hindering data acquisition. To provide experimentally viable sample lifetimes in the face of high pulling forces, we have designed a novel anchoring strategy for DNA in magnetic tweezers. Our approach, which exploits covalent functionalization based on heterobifunctional poly(ethylene glycol) crosslinkers, allows us to strongly tether DNA while simultaneously suppressing undesirable non-specific adhesion. A complete force and lifetime characterization of these covalently anchored DNA-tethers demonstrates that, compared to more commonly employed anchoring strategies, they withstand 3-fold higher pulling forces (up to 150 pN) and exhibit up to 200-fold higher lifetimes (exceeding 24 h at a constant force of 150 pN). This advance makes it possible to apply the full range of biologically relevant force scales to biomolecular processes, and its straightforward implementation should extend its reach to a multitude of applications in the field of single-molecule force spectroscopy.

Hepatitis C testing and status among opioid substitution treatment clients in New South Wales

In Australia about half of the people who inject drugs (PWID) are hepatitis C (HCV) antibody positive (anti-HCV+). The prevalence among opioid substitution treatment (OST) clients specifically is unclear, despite OST clinics being a potential setting for HCV care. This study aimed to report the prevalence of HCV among a large sample of NSW OST clients, understand whether HCV testing is translating into knowledge of status, and identify the correlates of inaccurate self-reporting of HCV status. Participants completed an interview that included self-reported HCV status. Participants also provided a blood sample that was tested for HCV IgG antibodies, and for viral load using a quantitative real-time reverse-transcriptase polymerase chain reaction. Valid interviews and viable blood sample were provided by 1,484 participants. Logistic regression modelling was used to identify independent predictors of knowledge of HCV antibody status. Overall, 84% of participants were anti-HCV+. Of these, 65% were RNA+. Four per cent of anti-HCV negative participants were RNA+. One-quarter of anti-HCV+ participants did not know their status or reported it incorrectly, compared with 14.5% of anti-HCV negative participants. The prevalence of HCV in this sample was higher than that found among other samples of people who inject drugs, suggesting the need for greater prevention efforts with OST clients. Anti-HCV+ individuals are less accurate at reporting their HCV status than those who are anti-HCV-. Inaccurate knowledge is associated with different variables for anti-HCV+ vs. anti-HCV- individuals. There are opportunities to improve knowledge of HCV status and to therefore improve health outcomes and reduce transmission among this at-risk population.

Adapting dried blood spot sampling for an anti-therapeutic antibody immunogenicity assay

Dried blood spot sampling is a microvolume sampling technique with many potential advantages. It allows for easier handling and less expensive shipment and storage of biological samples. Additionally, it can provide ethical benefits in the pre-clinical setting through a reduction in animal usage by allowing intensive serial sample collection from the same animals. In the clinical setting, ease of sample collection, greater flexibility of sample storage, and shipping are distinct advantages. These advantages can enhance preclinical and clinical data quality, where immunogenicity monitoring plays an important role in the interpretation of pharmacokinetic data. To date, a method for usage of dried blood spot sampling with an immunogenicity assay has not been published. Herein we demonstrate that the measurement of anti-drug antibodies (ADA) using DBS was comparable to traditional methods in terms of reproducibility, assay sensitivity and drug tolerance. The data demonstrate that DBS is a viable sample collection method, and in some cases may be preferred, over classic serum or plasma sampling for antidrug antibody assays.

Multiple liquid chromatography separations and nanoESI‐ion trap detection of plasma proteins in search of stroke biomarkers: A pilot study

Stroke is the most common cause of morbidity and death in the Western world, following ischemic heart disease and cancer. Stroke can be of two types, ischemic or hemorrhagic, with ischemic stroke accounting for approximately 85% of the total number of strokes. Well-recognized environmental risk factors for stroke include hypertension, smoking, diabetes mellitus, atrial fibrillation, and atherosclerosis. Computed tomography (CT) scanning is used to diagnose hemorrhagic stroke but is relatively ineffective and may remain normal in patients with mild ischemic strokes. Magnetic Resonance Imaging (MRI) is more sensitive in detecting ischemia than CT, especially in the diagnosis of mild stroke but it is still not 100% sensitive or precise. A simple and low-cost, rapid blood test to confirm a clinical and imaging diagnosis of ischemic stroke would be extremely useful. Based on this, the central idea of this paper is to develop a method that would be applicable to a statistically viable sample set to provide candidate biomarkers for distinguishing stroke types. In search of these candidate biomarkers, different analytical separation techniques have been used to screen for major differences in the proteomes of patients plasma samples with proteomics for identification.

Assessing screening criteria for the radiocarbon dating of bone mineral

Radiocarbon dating of bone mineral (carbonate in the apatite lattice) has been the target of sporadic research for the last 40years. Results obtained by different decontamination protocols have, however, failed to provide a consistent agreement with reference ages. In particular, quality criteria to assess bone mineral radiocarbon dating reliability are still lacking.Systematic research was undertaken to identify optimal preservation criteria for bone mineral in archeological bones. Six human long bones, originating from a single site, were radiocarbon-dated both for collagen and apatite, with the level of agreement between the dates providing an indication of exogenous carbon contamination. Several techniques (Histology, FTIR, TEM, LA-ICP-MS) were employed to determine the preservation status of each sample.Research results highlight the importance of a micro-scale approach in establishing bone preservation, in particular the use of trace element concentration profiles demonstrated its potential use as a viable sample selection criterion for bone carbonate radiocarbon dating.

Tigecycline Penetration into Skin and Soft Tissue

Tigecycline, a derivative of minocycline, has antibacterial activity against common pathogens associated with complicated skin and soft tissue infections (cSSTIs), including methicillin-resistant Staphylococcus aureus. At present, there is a paucity of data concerning its penetration into skin and soft tissue (SST). This study evaluated the penetration of tigecycline into SST in 25 patients (mean age, 52 years) with cSSTIs requiring surgical intervention. After a 100-mg loading dose, each patient received 50 mg of tigecycline infused intravenously over 1 h every 12 h. Blood samples were obtained on the day of surgery at 1 h (peak), during surgery, and 12 h (trough) after the beginning of a 50-mg infusion. A viable SST sample was harvested at the infection site. Tissue and concomitant serum concentrations were grouped into three time intervals: 2-4 h (median, 3 h), 5-7 h (median, 7 h), and 8-10 h (median, 9h), and analyzed for tissue penetration. Tissue and blood samples were obtained one to six days (mean 2.5 days) after initiation of tigecycline treatment. The mean serum peak and trough concentrations of tigecycline were 0.56±0.25 mg/L and 0.26±0.12 mg/L, respectively. The mean tissue:serum ratios at the three study time periods were 3.8 (range 0.7-5.5), 5.2 (range 0.8-7.1), and 2.8 (range 0.8-8.8). In general, we found higher concentrations of tigecycline in SST than in the serum at the same time point.

Developing a Biomonitoring Educational Pamphlet for Potential Participants in a Breast Milk Biomonitoring Study

Over the past decade, biomonitoring research initiatives in the United States have increased because of growing concern over the accumulation of environmental chemicals in the human body. One matrix that has become a viable biological sample for estimating human exposure to environmental chemicals is breast milk. However, breast milk biomonitoring research can induce anxiety and confusion about breastfeeding if communication is lacking between researchers, community partners, and participants. To bridge this communication gap, an informative, reassuring 8-page pamphlet was developed to educate community partners and potential participants about research on 1 class of environmental chemicals-polybrominated diphenyl ethers. Not only did the pamphlet assist in participant recruitment, but it forged positive relationships with valuable community partners.

Low-Cost QCM Sensor System for Screening Semen Samples

Artificial insemination is a well-established part of modern agricultural practice. A viable semen sample is judged by the total number of spermatozoa (sperm) in the sample and the motility of the sperm. In this paper, we report the development of a reusable measurement cell and electronics for screening semen samples based on the Quartz Crystal Microbalance (QCM) and Universal Frequency to Digital Converter (UFDC-1) to produce a low-cost sensor system. After introducing the semen sample at one end of the measurement cell, sperm swim down a channel before causing a frequency change on the QCM. Data is presented that shows the different frequency changes using a commercial frequency counter caused by porcine semen samples, one two days old and one twenty one days old. Similar data is presented for a motile semen sample measurement using the low-cost UFDC-1.

Dance Dance Education and Rites of Passage

The experience of a successful adolescent learner will be described from the student’s perspective about learning the video game Dance Dance Revolution (DDR) through selected passages from a phenomenological interview. The question driving this investigation is, “Why did she sustain engagement in learning?” The importance of this question came out of the need for background on how to create an afterschool program that was to use DDR as an after school activity that might engage adolescents and tweens to become more physically active and reduce the risk of adult obesity, and to increase bone density for these developing young people through playing the game over time. The difficulty of creating this program was the risk that the students would not sustain engagement in the activity, and thus we would not have a viable sample for the bone density adolescent obesity study. Implications of this study include understanding the potential construction of learning environments that motivate and sustain engagement in learning and the importance of identity construction for teachers to motivate and engage their students. In addition to the analysis of sustained engagement through the four socio- and cultural-cognitive theories, four major principals were extracted from the operationalized themes into a framework for instructional design techniques and theory for engaging learners for game design, training, and in classroom learning.

Microscale membrane extraction of diverse antibiotics from water

Antibiotics include a wide range of compounds that in addition to having high solubility in water may be basic, acidic or neutral. Therefore, it is anticipated that no single method would be effective in simultaneously extracting all of these compounds. In recent times, microscale membrane extraction has evolved as a viable sample preparation alternative. The two major approaches are microscale supported liquid membrane extraction (μ-SLME) and microscale liquid–liquid membrane extraction (μ-LLME). An approach that includes μ-LLME as well as μ-SLME for acidic and basic compounds is presented for the extraction and concentration of diverse antibiotics in water. Enrichment factors as high as 2700 were achieved. Relative standard deviations ranged from 1.5% to 2.0%, and detection limits were as low as 92 ng/L.

R58fs Mutation in the HGD Gene in a Family with Alkaptonuria in the UAE

This study was conducted to determine the prevalence of alkaptonuria in the UAE population and to identify the genotype of affected individuals. In a 3 stage sampling technique 2981 pupils from Government schools in Al Ain and private schools in Dubai were selected to take part in the study, of whom 2857 provided urine samples. Urine collected was analysed for homogentisic acid by gas chromatography-mass spectrometry. Genomic DNA was isolated from the white blood cells of all family members of the affected case following standard established protocols. Specific PRC primers were designed to amplify all 14 exons of the HGD gene with the flanking intronic sequences including the splice site sequences. 2857 children returned a viable urine sample, of which one was highly positive for homogentisic acid. All 12 members of this girl's family were studied and one, a 22 year old brother, was found to excrete HGA. Another, a sister who had not provided a urine sample, was discovered by genetic testing. There were no complaints of joint pain or other symptoms in any member of this family. Parents were first cousins. We found a single nucleotide deletion c.342delA, located in exon 3, which resulted in a frameshift at amino acid position 58 (p.Arg58fs or p.R58fs). Alkaptonuria may be more common than it is thought to be with an allele prevalence estimated at 0.0107 (95% CI 0.000392-0.03473). The R58fs mutation is old, perhaps having occurred several thousand years ago, and has spread over a large geographical area.

Assessment of the atmospheric fungal prevalence through field ergosterol measurement II: Establishing the conversion factor

A general empirical conversion factor for estimating ambient fungal prevalence from filter ergosterol concentration data is proposed. The derivation was based on 28 high-volume filter samples, each with six viable samples collected simultaneously, over a period of 6 months, and specific ergosterol content data previously determined for 12 common airborne fungal species. A number of simplifying assumptions were made to arrive at the weighted-average ergosterol content based on the specific ergosterol content and the corresponding fraction in the viable sample. The filter ergosterol concentrations and the viable counts varied by one order of magnitude, but the general empirical conversion factor derived from the weighted-average ergosterol content data was relatively constant at 0.191±0.040 pg spore −1 (mean±s.d., n=28). Using this factor to calculate the total spore number concentrations for the 28 filter samples gave a mean value of 1211 spores m −3, which was not significantly different from the mean calculated from the individual weighted-average ergosterol values (1236 spores m −3). Comparison with literature reports confirmed that such conversion factors are experiment and environment specific.

Social learning of nut-cracking behavior in East African sanctuary-living chimpanzees (Pan troglodytes schweinfurthii).

Nut cracking is restricted to communities of wild chimpanzees living in West Africa, suggesting it is an example of a socially transmitted tradition. Detailed study of the acquisition of nut cracking in wild chimpanzees is consistent with this conclusion. However, only 2, small-scale experiments have been carried out in captivity to explore the role of social transmission in the acquisition of this behavior. The study presented here does this with a comparatively larger, statistically viable sample of 11 sanctuary-living chimpanzees (Pan troglodytes schweinfurthii), permitting both between- and within-subjects experimental manipulations. Results confirmed that nut cracking can be acquired in a matter of days by social learning, but only in chimpanzees 3 to 4 years old and older. Direct comparisons are made with a study carried out in the wild, revealing striking similarities in developmental profiles.

Linezolid tissue penetration and serum activity against strains of methicillin-resistant Staphylococcus aureus with reduced vancomycin susceptibility in diabetic patients with foot infections

Linezolid soft tissue penetration and serum antimicrobial activity were analysed in six patients with peripheral vascular disease and severe diabetic foot infections requiring surgical intervention. Blood draws (1, 3, 6, 9 and 12 h after initiation of a 1 h infusion) and a viable soft tissue sample at the site of infection were obtained in patients receiving linezolid (600 mg every 12 h) on the day of surgery. Concentrations of linezolid were determined by HPLC in both tissue (pre-treated with tissue lysis buffer) and serum. In addition, serum inhibitory and bactericidal activity (dilution titres 1:2-1:32) of linezolid was determined in these patients against strains of methicillin-resistant Staphylococcus aureus (MRSA) with reduced susceptibility to vancomycin (vancomycin MICs = 2, 4, 8, 256 and >256 mg/L). Linezolid concentrations in tissue were found to be 51% (range, 18% to 78%) of simultaneous serum concentrations. Rapid (1 h) and prolonged (12 h) inhibitory activity (titres > or = 1:2) was observed for linezolid against each of the study isolates. Furthermore, bactericidal activity (titres > or = 1:2) was observed for at least 6 h (50% of the dosing interval) against four of these five strains. These findings suggest that linezolid could be effective in the treatment of multidrug-resistant MRSA even when concentrations at the infection site are diminished due to impaired blood flow.

Application of Diversity Indices to Appraise Plant Availability in the Traditional Medicinal Markets of Johannesburg, South Africa

The lack of scientific rigour in analysing ethnobotanical surveys has prompted researchers to investigate ways of quantitatively describing their data, including the use of ecological diversity indices. There are numerous indices and measures available to describe sample diversity. Twenty-two measures of species richness, diversity and evenness were reviewed using six sets of ethnomedicinal data derived from 50 formal muti shop traders (of different ethnicities) and 100 informal street traders of traditional medicine in Johannesburg, South Africa, and a seventh data set from traders on the western boundary of the Kruger National Park, South Africa. The diversity measures were coupled with species accumulation curves to construct cumulative diversity curves used to determine the minimum viable sample size on which a diversity index should be based, and to better understand the differences in the relative diversities of the samples. Distinct differences in the relative abundance and diversity of plants sold by street traders and shop traders were evident. Species diversity and evenness was found to be higher in shops, thus resulting in a lower dominance in the sale of certain plant species compared to the street traders. A survey of an informal market should include no less than 35 research participants compared to no less than 20 for the muti shops. The use of selected indices of species richness (Margalef's), diversity (Shannon, Simpson's, Fisher's alpha, Hill's numbers) and evenness are recommended as a means of describing patterns exhibited within ethnobotanical data.