An in vivo method for assessing the antimicrobial properties of topical antiseptics using artifically contaminated skin

A method is described for assessing the antimicrobial activity of topical antiseptics on human skin. The test, carried out on the forearms of volunteers, uses an inoculum of Stuphylococcus aureus . Up to four preparations may be tested at one time plus a placebo and untreated control site. The method has been used to compare four proprietary antiseptics and to evaluate their activity for up to one hour and has demonstrated a chloroxylenol, triclosan, EDTA combination product to be the most effective. The method is highly adaptable and may be used to evaluate activity versus other organisms and to examine other factors affecting antiseptic efficacy     

An application for assessing quality of RNA hybridized to Affymetrix GeneChips

This paper describes a stand-alone application for estimating the 3' to 5' ratio by fitting a mixed effects model to the interior pixel intensities of perfect match probes for selected control probe sets from an Affymetrix *.DAT file. The effectiveness of this method was demonstrated previously by an application of the method to two microarray datasets for which external verification of RNA quality was known. This application provides a more objective assessment of sample quality in that both a point estimate and 95% confidence interval about the 3' to 5' ratio are provided. AVAILABILITY: The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm     

An electrophoretic method to deliver topical drugs to the eye

It is possible that many patients avoid complete ophthalmic exams because pupil dilation is slow, reversal sluggish, and vision blurred. Others experience incomplete dilation during exams or prior to surgery when good dilation is essential to successful outcome. Iontophoresis, the application of low-level electrical current to promote traversal of desired molecules across a boundary, has been used for many years and has recently become common in transdermal drug delivery. We now investigate iontophoresis as a method of accelerating drug absorption into the ocular anterior segment. In vivo rabbit studies assessed iontophoresis effects on the performance of dilators and constrictors. 1-mA and 4-mA direct current levels applied for 2-minute durations yielded dilation time-history measurements. Subsequent in vitro tests at a wide range of current densities showed minimal chemical modifications in ocular pharmaceuticals. Drug samples processed through high-performance liquid chromatography (HPLC) pinpointed minimal structural changes. Detailed in vivo rabbit testing is under way. Using 2 dilators and constrictors in crossed testing with 0.5-mA to 1.25-mA current levels and 20-sec to 60-sec durations, we recorded dilation progress by digital photography. Initial studies showed faster, larger dilations and quicker reversal using iontophoresis. Drug testing showed chemical structures remaining constant for clinically useful current levels, < or = 1 mA (< or = 1.25 mA/cm2 current density). Drug pH and HPLC retention times were constant within this range, and resistivity varied linearly as expected for increasing current. Rabbit testing will quantify improved drug speed and efficacy, validate the charge delivery electrode design, and indicate iontophoretic current and duration for further use. Tested ocular drugs showed no degradation when exposed to clinically useful iontophoretic currents. Preliminary results indicate significant time reductions for dilation and reversal, plus increases in maximum dilation. This procedure may aid clinicians by allowing more rapid complete examinations and surgical preparations for patients. Making dilation more convenient will also improve patient acceptance of exams, aiding earlier detection and treatment of ocular disease.     

A method for preparation of dry thrombin for topical application

Thrombin for topical hemostasis can be prepared from bovine or human blood plasma. The prothrombin is isolated by means of adsorption on DEAE-Sephadex A-50 and consecutively activated by CaCl₂ and thromboplastin. Thrombin is precipitated and purified by acetone. The specific activity of the thrombin preparation is 122 + 23 IU/mg protein while the yield is 36,360 ± 6623 IU/liter plasma.     

An improved method for assessing soil-fungus population density

Summary A rapid method for determining soil fungal populations is described. A 25-g equivalent of oven-dry soil, in 225 ml of water in a 500-ml aspirator bottle, is agitated on a magnetic stirrer and samples withdrawn with a syringe while the suspension is in motion. Individual drops are placed in petri dishes and mixed with a suitable culture medium. The average weight of soil per drop is determined and colony counts related to dry weight of soil as usual. This syringe method is simple, eliminates much of the error common in serial dilution and pipetting, and allows for a high degree of reproducibility and possible standardization.     

Tumor necrosis factor-alpha in temporomandibular joint synovial fluid predicts treatment effects on pain by intra-articular glucocorticoid treatment

The aim of this study was to investigate the influence of tumor necrosis factor-alpha (TNF-alpha) in temporomandibular joint (TMJ) synovial fluid and blood on the treatment effect on TMJ pain by intra-articular injection of glucocorticoid in patients with chronic inflammatory TMJ disorders. High pretreatment level of TNF-alpha in the synovial fluid was associated with a decrease of TNF-alpha and elimination of pain upon maximal mouth opening. Elimination of this TMJ pain was accordingly associated with decrease in synovial fluid level of TNF-alpha. There was also a significant decrease of C-reactive protein and TMJ resting pain after treatment. In conclusion, this study indicates that presence of TNF-alpha in the synovial fluid predicts a treatment effect of intra-articular injection of glucocorticoid on TMJ movement pain in patients with chronic TMJ inflammatory disorders.     

Computational model of a synovial joint morphogenesis

Biomechanics and Modeling in Mechanobiology - Joints enable the relative movement between the connected bones. The shape of the joint is important for the joint movements since they facilitate and...     

Emerging intra-articular drug delivery systems for the temporomandibular joint

Temporomandibular joint (TMJ) disorders are a heterogeneous group of diseases that cause progressive joint degeneration leading to chronic pain and reduced quality of life. Both effective pain reduction and restoration of TMJ function remain unmet challenges. Intra-articular injections of corticosteroids and hyaluronic acid are currently used to treat chronic pain, but these methods require multiple injections that increase the risk of iatrogenic joint damage and other complications. The small and emerging field of TMJ tissue engineering aims to reduce pain and disability through novel strategies that induce joint tissue regeneration. Development of methods for sustained, intra-articular release of growth factors and other pro-regenerative signals will be critical for the success of TMJ tissue engineering strategies. This review discusses methods of intra-articular drug delivery to the TMJ, as well as emerging injectable controlled release systems with potential to improve TMJ drug delivery, to encourage further research in the development of sustained release systems for both long-term pain management and to enhance tissue engineering strategies for TMJ regeneration.     

Two-dimensional cryostat section electrophoresis: a novel method and its application to the diseased synovial membrane

Summary A two-dimensional electrophoresis technique for analysing sections of human tissue is described. Cryostat sections, 10 μm thick, are placed on an isoelectric focusing gel and then transfered to an SDS gel in the second dimension. The protein pattern is visualized by silver staining and is thought to represent soluble proteins. The silver-stained proteins were found to be both reproducible and, to the extent tested, organ-specific. This method was used to analyse 43 synovial membranes from patients suffering from rheumatoid arthritis or degenerative joint diseases. The analysis did not reveal any specific protein pattern for rheumatoid arthritis. The protein spot number was not related to the cause of arthritis. However, the total protein spot number was related to the histomorphological synovitis type, with those exhibiting either an exudative or proliferative synovitis pattern possessing significantly higher protein spot numbers than those specimens exhibiting a sero-fibrous or lympho-plasmacytic pattern of synovitis.     

An alternative method for assessing early mortality in contemporary populations

Biological anthropologists are interested in a population's early mortality rates for a variety of reasons. Early mortality (infant or juvenile) is of obvious importance to those interested in demography, but early mortality statistics are useful for life history analysis, paleodemography, and human adaptability studies, among others. In general, the form of mortality statistics is derived from demography, where chronological age is the gold standard for statistical calculation and comparison. However, there are numerous problems associated with the collection, analysis, and interpretation of early mortality statistics based on age, particularly for anthropological research, which is often conducted in small or non-calendrical-age numerate populations. The infant mortality rate (IMR), for example, is notoriously difficult to determine in populations where accurate accounting of age is not routine, and yet it is widely used in demography, public health, medicine, and social science research. Here we offer an alternative to age-based early mortality statistics that makes use of human biologists' interest in, and skill at, assessing human growth and development. Our proposal is to use developmental stages of juveniles instead of relying exclusively on age as the basis for mortality statistics. Death or survival according to a developmental stage (such as crawling or weaning) may provide more accurate data that are also more closely related to the cause of death. Developmental stages have the added advantage of putting infants and children back at the center of the discussion of early mortality by focusing on their activities in relation to their environment. A case study from the Turkana population of Kenya illustrates the use of developmental stages in describing early mortality. Am J Phys Anthropol 107:315–330, 1998. © 1998 Wiley-Liss, Inc.     

An experimental method for measuring force on the spinal facet joint: description and application of the method.

A technique is described for measuring load magnitude and resultant load contact location in the facet joint in response to applied loads and moments, and the technique applied to the canine lumbar spine motion segment. Due to the cantilever beam geometry of the cranial articular process, facet joint loads result in surface strains on the lateral aspect of the cranial articular process. Strains were quantified by four strain gages cemented to the bony surface of the process. Strain measured at any one gage depended on the loading site on the articular surface of the caudal facet and on the magnitude of the facet load. Determination of facet loads during in vitro motion segment testing required calibration of the strains to known loads of various magnitudes applied to multiple sites on the caudal facet. The technique is described in detail, including placement of the strain gages. There is good repeatability of strains to applied facet loads and the strains appear independent of load distribution area. Error in the technique depends on the location of the applied facet loads, but is only significant in nonphysiologic locations. The technique was validated by two independent methods in axial torsion. Application of the technique to five in vitro canine L2-3 motion segments testing resulted in facet loads (in newtons, N) of 74+ / -23 N (mean + / -STD) in 2 newton-meter, Nm, extension, to unloaded in flexion. Lateral bending resulted in loads in the right facet of 40+ / -32 N for 1 Nm right lateral bending and 54+ / -29 N for 1 Nm left lateral bending. 4 Nm Torsion with and without 100 N axial compression resulted in facet loads of 92+ / -27 N and 69+ / -19 N, respectively. The technique is applicable to dynamic and in vivo studies.     

An immunocytochemical method for histamine: application to the planarians

Histamine-immunoreactivity was investigated in the planarians Dugesia tigrina and Polycelis nigra. Specific antisera against a histamine-protein conjugate were used, and 1-ethyl—3 (3-dimethyl-aminopropyl) carbodiimide was used both as coupling agent to prepare the antigen and as a tissue fixative. In D. tigrina, histamine-immunoreactivity was restricted to photoreceptor cells in the cerebral eye. In P. nigra, nerve fibers were found in the ventral nerve cord and nerves running laterally from these. The epidermal eyes did not display histamine-immunoreactivity. The results suggest that histamine may be a transmitter in some of the most primitive animals. They also suggest that the distribution of histamine may differ in planarians.     

An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

The environmental risks associated with genetically-engineered （GE） organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment （ERA） model that follows the 1998 USEPA guidelines, focusing on potential adverse effects to biological diversity. The approach starts by （ 1 ） identifying the local environmental values so the ERA addresses specific concerns associated with local biological diversity. The model simplifies the indicator endpoint selection problem by （2） classifying biological diversity into ecological functional groups and selecting those that deliver the identified environmental values. （3） All of the species or ecosystem processes related to the selected functional groups are identified and （4） multi-criteria decision analysis （MCDA） is used to rank the indicator endpoint entities, which may be spe- cies or ecological processes. MCDA focuses on those species and processes that are critical for the identified ecological functions and are likely to be highly exposed to the GE organism. The highest ranked indicator entities are selected for the next step. （5） Rele- vant risk hypotheses are identified. Knowledge about the specific transgene and its possible environmental effects in other countries can be used to assist development of risk hypotheses. （6） The risk hypotheses are ranked using MCDA with criteria related to the severity of the potential risk. The model emphasizes transparent, expert-driven, ecologically-based decision-making and provides formal methods for completing a screening level-ERA that can focus ERA on the most significant concerns. The process requires sub- stantial human input but the human capital is available in most countries and regions of the world.     

An automatic method for assessing structural importance of amino acid positions

Background  

A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose.     

Techniques for assessing knee joint pain in arthritis

Background

In general, opioids that induce the recycling of μ-opioid receptors (MORs) promote little desensitization, although morphine is one exception to this rule. While morphine fails to provoke significant internalization of MORs in cultured cells, it does stimulate profound desensitization. In contrast, morphine does promote some internalization of MORs in neurons although this does not prevent this opioid from inducing strong antinociceptive tolerance.

Results

In neurons, morphine stimulates the long-lasting transfer of MOR-activated Gα subunits to proteins of the RGS-R7 and RGS-Rz subfamilies. We investigated the influence of this regulatory process on the capacity of morphine to promote desensitization and its association with MOR recycling in the mature nervous system. In parallel, we also studied the effects of [D-Ala², N-MePhe⁴, Gly-ol⁵] encephalin (DAMGO), a potent inducer of MOR internalization that promotes little tolerance. We observed that the initial exposure to icv morphine caused no significant internalization of MORs but rather, a fraction of the Gα subunits was stably transferred to RGS proteins in a time-dependent manner. As a result, the antinociception produced by a second dose of morphine administered 6 h after the first was weaker. However, this opioid now stimulated the phosphorylation, internalization and recycling of MORs, and further exposure to morphine promoted little tolerance to this moderate antinociception. In contrast, the initial dose of DAMGO stimulated intense phosphorylation and internalization of the MORs associated with a transient transfer of Gα subunits to the RGS proteins, recovering MOR control shortly after the effects of the opioid had ceased. Accordingly, the recycled MORs re-established their association with G proteins and the neurons were rapidly resensitized to DAMGO.

Conclusion

In the nervous system, morphine induces a strong desensitization before promoting the phosphorylation and recycling of MORs. The long-term sequestering of morphine-activated Gα subunits by certain RGS proteins reduces the responses to this opioid in neurons. This phenomenon probably increases free Gβγ dimers in the receptor environment and leads to GRK phosphorylation and internalization of the MORs. Although, the internalization of the MORs permits the transfer of opioid-activated Gα subunits to the RGSZ2 proteins, it interferes with the stabilization of this regulatory process and recycled MORs recover the control on these Gα subunits and opioid tolerance develops slowly.     

An unsupervised machine learning method for assessing quality of tandem mass spectra

Background

In a single proteomic project, tandem mass spectrometers can produce hundreds of millions of tandem mass spectra. However, majority of tandem mass spectra are of poor quality, it wastes time to search them for peptides. Therefore, the quality assessment (before database search) is very useful in the pipeline of protein identification via tandem mass spectra, especially on the reduction of searching time and the decrease of false identifications. Most existing methods for quality assessment are supervised machine learning methods based on a number of features which describe the quality of tandem mass spectra. These methods need the training datasets with knowing the quality of all spectra, which are usually unavailable for the new datasets.

Results

This study proposes an unsupervised machine learning method for quality assessment of tandem mass spectra without any training dataset. This proposed method estimates the conditional probabilities of spectra being high quality from the quality assessments based on individual features. The probabilities are estimated through a constraint optimization problem. An efficient algorithm is developed to solve the constraint optimization problem and is proved to be convergent. Experimental results on two datasets illustrate that if we search only tandem spectra with the high quality determined by the proposed method, we can save about 56 % and 62% of database searching time while losing only a small amount of high-quality spectra.

Conclusions

Results indicate that the proposed method has a good performance for the quality assessment of tandem mass spectra and the way we estimate the conditional probabilities is effective.

     

An implantable telemetry device to measure intra-articular tibial forces

Tibial forces are important because they determine polyethylene wear, stress distribution in the implant, and stress transfer to underlying bone. Theoretic estimates of tibiofemoral forces have varied between three and six times the body weight depending on the mathematical models used and the type of activity analyzed. An implantable telemetry system was therefore developed to directly measure tibiofemoral compressive forces. This system was tested in a cadaver knee in a dynamic knee rig. A total knee tibial arthroplasty prosthesis was instrumented with four force transducers located at the four corners of the tibial tray. These transducers measured the total compressive forces on the tibial tray and the location of the center of pressure. A microprocessor performed analog-to-digital signal conversion and performed pulse code modulation of a surface acoustic wave radio frequency oscillator. This signal was then transmitted through a single pin hermetic feed-through tantalum wire antenna located at the tip of the stem. The radio frequency signal was received by an external antenna connected to a receiver and to a computer for data acquisition. The prosthesis was powered by external coil induction. The tibial transducer accurately measured both the magnitude and the location of precisely applied external loads. Successful transmission of the radio frequency signal up to a range of 3m was achieved through cadaveric bone, bone cement, and soft tissue. Reasonable accuracy was obtained in measuring loads applied through a polyethylene insert. The implant was also able to detect unicondylar loading with liftoff.     

BIPES,a cost-effective high-throughput method for assessing microbial diversity

Pyrosequencing of 16S rRNA (16S) variable tags has become the most popular method for assessing microbial diversity, but the method remains costly for the evaluation of large numbers of environmental samples with high sequencing depths. We developed a barcoded Illumina paired-end (PE) sequencing (BIPES) method that sequences each 16S V6 tag from both ends on the Illumina HiSeq 2000, and the PE reads are then overlapped to obtain the V6 tag. The average accuracy of Illumina single-end (SE) reads was only 97.9%, which decreased from ∼99.9% at the start of the read to less than 85% at the end of the read; nevertheless, overlapping of the PE reads significantly increased the sequencing accuracy to 99.65% by verifying the 3′ end of each SE in which the sequencing quality was degraded. After the removal of tags with two or more mismatches within the medial 40–70 bases of the reads and of tags with any primer errors, the overall base sequencing accuracy of the BIPES reads was further increased to 99.93%. The BIPES reads reflected the amounts of the various tags in the initial template, but long tags and high GC tags were underestimated. The BIPES method yields 20–50 times more 16S V6 tags than does pyrosequencing in a single-flow cell run, and each of the BIPES reads costs less than 1/40 of a pyrosequencing read. As a laborsaving and cost-effective method, BIPES can be routinely used to analyze the microbial ecology of both environmental and human microbiomes.