Fine needle aspiration cytology of salivary gland lesions: advantages and pitfalls

Fine needle aspiration cytology (FNAC) was performed on 52 patients with salivary gland lesions. A definitive cytodiagnosis was possible in 45 cases: a sensitivity of 89% and a specificity of 94% was achieved. The pitfalls of FNAC of salivary gland lesions are reflected by the false positive and false negative rates which were 4%. Errors of cytodiagnosis are due to the morphological variability of these tumours which make sampling and interpretation difficult.     

Epidemiological designs for vaccine safety assessment: methods and pitfalls

Three commonly used designs for vaccine safety assessment post licensure are cohort, case-control and self-controlled case series. These methods are often used with routine health databases and immunisation registries. This paper considers the issues that may arise when designing an epidemiological study, such as understanding the vaccine safety question, case definition and finding, limitations of data sources, uncontrolled confounding, and pitfalls that apply to the individual designs. The example of MMR and autism, where all three designs have been used, is presented to help consider these issues.     

Molecular methods used in clinical laboratory: prospects and pitfalls

The role of molecular detection, identification and typing or fingerprinting of microorganisms has shifted gradually from the academic world to the routine diagnostic laboratory. Molecular methods have been used increasingly over the past decade to improve the sensitivity, specificity and turn-around time in the clinical laboratory. Molecular methods have also been used to identify new and nonculturable agents. Many high-throughput molecular tests are now available commercially, which impacts on the infrastructure in many of the diagnostic laboratories. In this paper, we take an overall look at the use of molecular methods (prospects vs. pitfalls) based on our clinical and public health experience, particularly as they related to Borrelia burgdorferi, a vector-borne pathogen, Treponema pallidum, a re-emerging sexually transmitted global pathogen, and West Nile virus, a newly recognized virus in North America.     

Nanoparticles labeled with positron emitting nuclides: advantages, methods, and applications

Over the past decade, positron emitter labeled nanoparticles have been widely used in and substantially improved for a range of diagnostic biomedical research. However, given growing interest in personalized medicine and translational research, a major challenge in the field will be to develop disease-specific nanoprobes with facile and robust radiolabeling strategies and that provide imaging stability, enhanced sensitivity for disease early stage detection, optimized in vivo pharmacokinetics for reduced nonspecific organ uptake, and improved targeting for elevated efficacy. This review briefly summarizes the major applications of nanoparticles labeled with positron emitters for cardiovascular imaging, lung diagnosis, and tumor theranostics.     

On risk and plant-based biopharmaceuticals

Research into plant-based expression of pharmaceutical proteins is proceeding at a blistering pace. Indeed, plants expressing pharmaceutical proteins are currently being grown in field environments throughout the USA. But how are these plants and proteins being assessed for environmental risk and how are they being regulated? Here, we examine the applicability of the risk assessment paradigm for assessing human and ecological risks from field-grown transgenic plants that express pharmaceutical proteins.     

Use of fractal theory in neuroscience: methods, advantages, and potential problems

Fractal analysis has already found widespread application in the field of neuroscience and is being used in many other areas. Applications are many and include ion channel kinetics of biological membranes and classification of neurons according to their branching characteristics. In this article we review some practical methods that are now available to allow the determination of the complexity and scaling relationships of anatomical and physiological patterns. The problems of describing fractal dimensions are discussed and the concept of fractal dimensionality is introduced. Several related methodological considerations, such as preparation of the image and estimation of the fractal dimensions from the data points, as well as the advantages and problems of fractal geometric analysis, are discussed.     

A reverse double-isotope enzymatic histamine assay: advantages over single-isotope methods.

High concentrations of codeine necessary to demonstrate histamine release from leukocytes interfere with histamine methylation, producing a concentration-dependent flattening of the histamine standard curves obtained from single-isotope (³H) assays. For this reason, the use of uniformly labeled ¹⁴C-histamine was investigated as an internal standard. This isotope serves as an internal standard and accurately predicts the recovery of histamine in the presence of up to 70% enzyme inhibition. The use of this reverse double-isotope procedure allows the assay of histamine without direct external recovery measurements in the presence of various drug concentrations.     

Decomposition methods for scheduling semiconductor testing facilities

We present decomposition procedures for scheduling semiconductor testing facilities. These facilities are characterized by the presence of different types of work centers, some of which have sequence-dependent setup times and some parallel identical machines. We exploit the structure of the routings in semiconductor testing to develop tailored decomposition procedures that decompose the shop into a number of work centers that are scheduled using specialized procedures. Extensive computational experiments show that these procedures significantly outperform existing methods in reasonable CPU times. These results indicate that decomposition methods can be successfully applied to complex scheduling problems of the type addressed in this paper, as well as the classical job shop problems addressed in previous research.     

Metabolomics: towards acceleration of antibacterial plant-based leads discovery

Phytochemistry Reviews - The wide and not yet fully uncovered potential of plant secondary metabolites make plants a rich source of drug leads. Metabolomics enables the study of the metabolic...     

Advances in plant-based inhibitors of P-glycoprotein

Multidrug resistance (MDR) has emerged as the main problem in anti-cancer therapy. Although MDR involves complex factors and processes, the main pivot is the expression of multidrug efflux pumps. P-glycoprotein (P-gp) belongs to the family of adenosine triphosphate (ATP)-binding cassette (ABC) transporters. It functions in cellular detoxification, pumping a wide range of xenobiotic compounds out of the cell. An attractive therapeutic strategy for overcoming MDR is to inhibit the transport function of P-gp and thus, increase intracellular concentration of drugs. Recently, various types of P-gp inhibitors have been found and used in experiments. However, none of them has passed clinical trials due to their high side-effects. Hence, the search for alternatives, such as plant-based P-gp inhibitors have gained attention recently. Therefore, we give an overview of the source, function, structure and mechanism of plant-based P-gp inhibitors and give more attention to cancer-related studies. These products could be the future potential drug candidates for further research as P-gp inhibitors.     

Resource scheduling methods in cloud and fog computing environments: a systematic literature review

In recent years, cloud computing can be considered an emerging technology that can share resources with users. Because cloud computing is on-demand, efficient use of resources such as memory, processors, bandwidth, etc., is a big challenge. Despite the advantages of cloud computing, sometimes it is not a proper choice due to its delay in responding appropriately to existing requests, which led to the need for another technology called fog computing. Fog computing reduces traffic and time lags by expanding cloud services to the network and closer to users. It can schedule resources with higher efficiency and utilize them to impact the user's experience dramatically. This paper aims to survey some studies that have been done in the field of scheduling in fog/cloud computing environments. The focus of this survey is on published studies between 2015 and 2021 in journals or conferences. We selected 71 studies in a systematic literature review (SLR) from four major scientific databases based on their relation to our paper. We classified these studies into five categories based on their traced parameters and their focus area. This classification comprises 1—performance 2—energy efficiency, 3—resource utilization, 4—performance and energy efficiency, and 5—performance and resource utilization simultaneously. 42.3% of the studies focused on performance, 9.9% on energy efficiency, 7.0% on resource utilization, 21.1% on both performance and energy efficiency, and 19.7% on both performance and resource utilization. Finally, we present challenges and open issues in the resource scheduling methods in fog/cloud computing environments.

     

Root-zone constraints and plant-based solutions for dryland salinity

Limitations to agricultural productivity imposed by the root-zone constraints in Australian dryland soils are severe and need redemption to improve the yields of grain crops and thereby meet world demand. Physical, chemical and biological constraints in soil horizons impose a stress on the plant and restrict plant growth and development. Hardsetting, crusting, compaction, salinity, sodicity, acidity, alkalinity, nutrient deficiencies and toxicities due to boron, carbonates and aluminium are the major factors that cause these constraints. Further, subsoils in agricultural regions in Australia have very low organic matter and biological activity. Dryland salinity is currently given wide attention in the public debate and government policies in Australia, but they only focus on salinity induced by shallow groundwater. However, the occurrence of transient salinity in root-zone layers in the regions where water tables are deep is an important issue with potential for larger economic loss than water table-induced seepage salinity. Root-zone constraints pose a challenge for salinity mitigation in recharge as well as discharge zones. In recharge zones, reduced water movement in sodic horizons results in salt accumulation in the root zone resulting in chemical and physical constraints that reduce transpiration that, in turn, upsets salt balance and plant growth. High salinity in soil and groundwater restricts the ability of plants to reduce water table in discharge zones. Thus plant-based strategies must address different kinds of limitations in soil profiles, both in recharge and discharge zones. In this paper we give an overview of plant response to root-zone constraints but with an emphasis on the processes of salt accumulation in the root-zone of soils. We also examine physical and chemical methods to overcome subsoil limitations, the ability of plants to adapt to and ameliorate these constraints, soil modification by management of agricultural and forestry ecosystems, the use of biological activity, and plant breeding for resistance to the soil constraints. We emphasise that soil scientists in cooperation with agronomists and plant breeders should design site-specific strategies to overcome multiple soil constraints, with vertical and lateral variations, and to develop plant-based solutions for dryland salinity.     

DNA barcoding Bromeliaceae: achievements and pitfalls

Background

DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost.

Methodology/Principal Findings

It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH–psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank''s matK data set. Bromeliaceae''s sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling.

Conclusions/Significance

Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.     

Molecular phylogeny: pitfalls and progress.

Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.     

vProtein: identifying optimal amino acid complements from plant-based foods

Background

Indispensible amino acids (IAAs) are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions, but many plant-based foods provide different proportions of IAAs. To explore how these plant-based foods can be better used in human nutrition, we have created the computational tool vProtein to identify optimal food complements to satisfy human protein needs.

Methods

vProtein uses 1251 plant-based foods listed in the United States Department of Agriculture standard release 22 database to determine the quantity of each food or pair of foods required to satisfy human IAA needs as determined by the 2005 daily recommended intake. The quantity of food in a pair is found using a linear programming approach that minimizes total calories, total excess IAAs, or the total weight of the combination.

Results

For single foods, vProtein identifies foods with particularly balanced IAA patterns such as wheat germ, quinoa, and cauliflower. vProtein also identifies foods with particularly unbalanced IAA patterns such as macadamia nuts, degermed corn products, and wakame seaweed. Although less useful alone, some unbalanced foods provide unusually good complements, such as Brazil nuts to legumes.Interestingly, vProtein finds no statistically significant bias toward grain/legume pairings for protein complementation. These analyses suggest that pairings of plant-based foods should be based on the individual foods themselves instead of based on broader food group-food group pairings. Overall, the most efficient pairings include sweet corn/tomatoes, apple/coconut, and sweet corn/cherry. The top pairings also highlight the utility of less common protein sources such as the seaweeds laver and spirulina, pumpkin leaves, and lambsquarters. From a public health perspective, many of the food pairings represent novel, low cost food sources to combat malnutrition. Full analysis results are available online at http://www.foodwiki.com/vprotein.