Common Research Tool Research Articles

Qualitative Thematic Analysis of Transcripts in Social Change Research: Reflections on Common Misconceptions and Recommendations for Reporting Results

This paper, on qualitative thematic analysis (QTA) in social change research, falls somewhere between a reflective piece and a how-to guide. Using two examples from my own previous research, I discuss why QTA in the field of social change or social justice, which often analyzes the words of vulnerable, marginalized, or underserved populations, is so fraught, so contested, and so often dismissed. Qualitative thematic analysis of interviews or focus groups is a common research tool used in the field, but the guidelines, scope, and practices of this tool are varied and ill-defined. I have witnessed in my students’ papers and in peer reviewing for journals that there are a handful of assumptions and misconceptions that appear repeatedly, for example around intercoder reliability and frequency counting, that reduce the quality of analysis. This paper focuses on how to conduct QTAs that address social change: complex social problems faced by underserved populations, such as those dealing with poverty and inequality. By discussing the methods used in two of my own social change research projects, this paper offers a balanced method for both promoting rigor and understanding the limits and strengths of this method.

Validation of an RNAscope assay for the detection of avian influenza A virus.

Highly pathogenic avian influenza (HPAI) is an acute viral disease associated with high mortality and great economic losses. Immunohistochemistry (IHC) is a common diagnostic and research tool for the demonstration of avian influenza A virus (AIAV) antigens within affected tissues, supporting etiologic diagnosis and assessing viral distribution in both naturally and experimentally infected birds. RNAscope in situ hybridization (ISH) has been used successfully for the identification of a variety of viral nucleic acids within histologic samples. We validated RNAscope ISH for the detection of AIAV in formalin-fixed, paraffin-embedded (FFPE) tissues. RNAscope ISH targeting the AIAV matrix gene and anti-IAV nucleoprotein IHC were performed on 61 FFPE tissue sections obtained from 3 AIAV-negative, 16 H5 HPAIAV, and 1 low pathogenicity AIAV naturally infected birds, including 7 species sampled between 2009 and 2022. All AIAV-negative birds were confirmed negative by both techniques. All AIAVs were detected successfully by both techniques in all selected tissues and species. Subsequently, H-score comparison was assessed through computer-assisted quantitative analysis on a tissue microarray comprised of 132 tissue cores from 9 HPAIAV-infected domestic ducks. Pearson correlation of r = 0.95 (0.94-0.97), Lin concordance coefficient of ρc = 0.91 (0.88-0.93), and Bland-Altman analysis indicated high correlation and moderate concordance between the 2 techniques. H-score values were significantly higher with RNAscope ISH compared to IHC for brain, lung, and pancreatic tissues (p ≤ 0.05). Overall, our results indicate that RNAscope ISH is a suitable and sensitive tool for in situ detection of AIAV in FFPE tissues.

Nicotine dependence and visceral adiposity as risk factors for the development and severity of carotid artery stenosis.

Nicotine dependence (ND) and visceral adiposity are emerging as independent risk factors for cardiovascular diseases, including carotid artery stenosis (CAS). This study aimed to determine the relationship between ND and the contribution of abdominal fat to the onset of CAS, which is indicated by a luminal narrowing of at least 60% as determined by duplex and/or Doppler ultrasound. We prospectively collected data from 60 patients with CAS and 60 age- and gender-matched healthy subjects. The Fagerström Test for Nicotine Dependence (FTND), a common research tool, was used in the study. The original questionnaire was designed to gather social and demographic data. Anthropometric measurements, visceral adiposity index (VAI), and lipid accumulation products (LAP) were used to assess obesity. Most patients showed a high or mild-moderate degree of ND: 46.67% and 35%, respectively. The median visceral adiposity index (VAI) and lipid accumulation product (LAP) in patients was 3.92 and 32.83, respectively. Prolonged smoking duration, increased intensity, and high ND are hallmarks of CAS patients.

Cot-side imaging of functional connectivity in the developing brain during sleep using wearable high-density diffuse optical tomography

Studies of cortical function in newborn infants in clinical settings are extremely challenging to undertake with traditional neuroimaging approaches. Partly in response to this challenge, functional near-infrared spectroscopy (fNIRS) has become an increasingly common clinical research tool but has significant limitations including a low spatial resolution and poor depth specificity. Moreover, the bulky optical fibres required in traditional fNIRS approaches present significant mechanical challenges, particularly for the study of vulnerable newborn infants. A new generation of wearable, modular, high-density diffuse optical tomography (HD-DOT) technologies has recently emerged that overcomes many of the limitations of traditional, fibre-based and low-density fNIRS measurements. Driven by the development of this new technology, we have undertaken the first cot-side study of newborn infants using wearable HD-DOT in a clinical setting. We use this technology to study functional brain connectivity (FC) in newborn infants during sleep and assess the effect of neonatal sleep states, active sleep (AS) and quiet sleep (QS), on resting state FC. Our results demonstrate that it is now possible to obtain high-quality functional images of the neonatal brain in the clinical setting with few constraints. Our results also suggest that sleep states differentially affect FC in the neonatal brain, consistent with prior reports.

Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms.

Panting score (PS) is a common research tool used to assess the physiological state of cows exposed to heat stress, but it is subjective. Infrared temperature (IRT), measured by either infrared thermometers or cameras, may be a more objective and reliable alternative. Very few studies thus far have evaluated the associations between PS, IRT, and milk production. We investigated the applicability of IRT compared with PS as a means of assessing heat stress and milk yield reduction in dairy cows in tropical smallholder dairy farms (SDF). In autumn 2017, SDF located across 4 typical dairy regions of Vietnam were each visited once to collect farm (n = 32) and individual cow data (n = 344). For each SDF, heat load index (HLI) inside the cowsheds, an indicator of environmental heat load calculated from ambient temperature, humidity, and wind speed, was measured. For each cow, PS (0 indicates a cow breathing normally, not panting; 4.5 indicates an extremely heat-stressed cow with excessive panting, tongue fully extended, and excessive drooling), IRT of the cow's body, single-day energy-corrected milk yield (ECM), body weight, and body condition score were measured. Cow genotype, age, lactation number, and days in milk were recorded. The IRT of the cows' inner vulval lip (IVuT) were measured with an infrared thermometer; and the IRT of the cows' vulval surface (OVuT), inner tail base surface (ITBT), ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, fore hoof, and hind hoof were also measured with an infrared camera. Multivariate mixed-effects models were used to assess the associations between HLI with PS and IRT, and associations between PS and IRT with ECM while accounting for the effects of other cow variables. All IRT correlated positively with PS (Pearson correlation, r = 0.23-0.50). Each unit increase in HLI was associated with increases of 0.07 units in PS and 0.09 to 0.23°C in IRT. Each degree (°C) increase in IVuT, OVuT, and ITBT was associated with decreases of 0.75, 0.87, and 0.70 kg/cow per day in ECM, respectively, whereas PS and other IRT were not significantly associated with ECM. Thus, all IRT showed potential to assess the heat stress level of cows; and IVuT, OVuT, and ITBT, but not PS and other IRT, showed potential to predict ECM reduction in cows during heat stress. First cross (F1) Holstein Brown Swiss and F1 Holstein Jersey showed lower PS and yielded higher ECM than the third backcross (B3) Holstein Zebu (7/8 Holstein + 1/8 Zebu) and pure Holstein. Thus, F1 Holstein Brown Swiss and F1 Holstein Jersey could be more suitable for tropical SDF than B3 Holstein Zebu and pure Holstein.

COVID -19 pandemic, surveys on elderly about vaccination. National and European perspectives

COVID -19 pandemic, surveys on elderly about vaccination. National and European perspectives

Substrate-activated expression of a biosynthetic pathway in Escherichia coli.

Microbes can facilitate production of valuable chemicals more sustainably than traditional chemical processes in many cases: they utilize renewable feedstocks, require less energy intensive process conditions, and perform a variety of chemical reactions using endogenous or heterologous enzymes. In response to the metabolic burden imposed by production pathways, chemical inducers are frequently used to initiate gene expression after the cells have reached sufficient density. While chemically inducible promoters are a common research tool used for pathway expression, they introduce a compound extrinsic to the process along with the associated costs. We developed an expression control system for a biosynthetic pathway for the production of d-glyceric acid that utilizes galacturonate as both the inducer and the substrate, thereby eliminating the need for an extrinsic chemical inducer. Activation of expression in response to the feed is actuated by a galacturonate-responsive transcription factor biosensor. We constructed variants of the galacturonate biosensor with a heterologous transcription factor and cognate hybrid promoter, and selected for the best performer through fluorescence characterization. We showed that native E. coli regulatory systems do not interact with our biosensor and favorable biosensor response exists in the presence and absence of galacturonate consumption. We then employed the control circuit to regulate the expression of the heterologous genes of a biosynthetic pathway for the production d-glyceric acid that was previously developed in our lab. Productivity via substrate-induction with our control circuit was comparable to IPTG-controlled induction and significantly outperformed a constitutive expression control, producing 2.13±0.03g L-1 d-glyceric acid within 6h of galacturonate substrate addition. This work demonstrated feed-activated pathway expression to be an attractive control strategy for more readily scalable microbial biosynthesis.

The Utilization of Consensus Techniques in Education and Research in Medical Professions

ABSTRACT Study Design This is a narrative review. Introduction Consensus techniques are an increasingly common research tool used to define levels of expert agreement on a topic where evidence is inconsistent or lacking. An assessment of commonly used consensus techniques can inform future education and research. Objective The aim of this study was to describe the use of various consensus techniques used in education and research in orthotics and prosthetics and closely related medical professions, to aid in choosing the most appropriate consensus technique for future research. Methods A systematic search of the literature was conducted using specific terms and keywords related to various consensus techniques, applications of consensus techniques in research and education, and medical disciplines related to orthotics and prosthetics. Studies were included if they described the use of a consensus technique for medical education or research and explained why the specific technique was used. Results Common consensus techniques were identified in the literature. To allow comparison of the techniques, the advantages, disadvantages, limitations, and previous applications of each were extracted from the literature. Conclusion Using the information from the literature, the most prevalent consensus techniques can be compared, aiding educators and researchers in choosing the technique most suitable for their topic of inquiry.

Using cognitive mapping to understand conservation planning.

We considered a common research tool for understanding the mental models behind conservation decisions: cognitive mapping. Developed by cognitive psychologists, the elicitation of mental models with cognitive mapping has been used to understand soil management in Spain, invasive grass management in Australia, community forest management in the Bolivian Amazon, and small‐scale fisheries access in Belize, among others. A generalized cognitive mapping process considers specific factors associated with the design, data‐collection, data‐analyses, and interpretation phases of research. We applied this tool in a study about the integration of social data in shoreline master plans of Washington State. Fourteen policy makers and managers (approximately 85% of the region's potential sample) were asked to identify the factors they considered when making their plans. Researchers coded these factors into mental‐model objects and summarized mental‐object frequency and co‐occurrence trends. Although managers prioritized the perceived needs of social groups in their mental model of shoreline master plans, they focused specifically on tribal and private property rights, even though existing social data identified a diversity of interests around timber harvesting, tourism, and agriculture. Understanding their mental models allowed us to more effectively present this social data so that it could fit within their existing thoughts around planning. Although our case study provides a description of the cognition of a particular policy process, cognitive mapping can be used to understand cognitive processes that influence any conservation planning context.

Light scattering methods for tissue diagnosis.

Light scattering has become a common biomedical research tool, enabling diagnostic sensitivity to myriad tissue alterations associated with disease. Light-tissue interactions are particularly attractive for diagnostics due to the variety of contrast mechanisms that can be used, including spectral, angle-resolved, and Fourier-domain detection. Photonic diagnostic tools offer further benefit in that they are non-ionizing, non-invasive, and give real-time feedback. In this review, we summarize recent innovations in light scattering technologies, with a focus on clinical achievements over the previous ten years.

Cannabinoid Ligands Targeting TRP Channels.

Transient receptor potential (TRP) channels are a group of membrane proteins involved in the transduction of a plethora of chemical and physical stimuli. These channels modulate ion entry, mediating a variety of neural signaling processes implicated in the sensation of temperature, pressure, and pH, as well as smell, taste, vision, and pain perception. Many diseases involve TRP channel dysfunction, including neuropathic pain, inflammation, and respiratory disorders. In the pursuit of new treatments for these disorders, it was discovered that cannabinoids can modulate a certain subset of TRP channels. The TRP vanilloid (TRPV), TRP ankyrin (TRPA), and TRP melastatin (TRPM) subfamilies were all found to contain channels that can be modulated by several endogenous, phytogenic, and synthetic cannabinoids. To date, six TRP channels from the three subfamilies mentioned above have been reported to mediate cannabinoid activity: TRPV1, TRPV2, TRPV3, TRPV4, TRPA1, and TRPM8. The increasing data regarding cannabinoid interactions with these receptors has prompted some researchers to consider these TRP channels to be “ionotropic cannabinoid receptors.” Although CB1 and CB2 are considered to be the canonical cannabinoid receptors, there is significant overlap between cannabinoids and ligands of TRP receptors. The first endogenous agonist of TRPV1 to be discovered was the endocannabinoid, anandamide (AEA). Similarly, N-arachidonyl dopamine (NADA) and AEA were the first endogenous TRPM8 antagonists discovered. Additionally, Δ9-tetrahydrocannabinol (Δ9-THC), the most abundant psychotropic compound in cannabis, acts most potently at TRPV2, moderately modulates TRPV3, TRPV4, TRPA1, and TRPM8, though Δ9-THC is not reported to modulate TRPV1. Moreover, TRP receptors may modulate effects of synthetic cannabinoids used in research. One common research tool is WIN55,212-2, a CB1 agonist that also exerts analgesic effects by desensitizing TRPA1 and TRPV1. In this review article, we aim to provide an overview and classification of the cannabinoid ligands that have been reported to modulate TRP channels and their therapeutic potential.

Memantine mediates astrocytic activity in response to excitotoxicity induced by PP2A inhibition

Reduced activity of protein phosphatase 2 A (PP2A) is a common feature in Alzheimer’s disease (AD) and non-AD tauopathies. The administration of okadaic acid (OKA), a potent PP2A and PP1 inhibitor, is a common research tool for inducing AD-like alterations such as tau hyperphosphorylation and cognitive decline. Recently, we showed that OKA increases cerebrospinal fluid (CSF) glutamate levels, which was strongly correlated with cognitive decline. Also, we demonstrated that memantine (MN), a glutamatergic NMDAR channel blocker, was capable of preventing the increase in CSF glutamate levels and cognitive decline. Here, we aimed to analyze whether the protective effects of MN involve intrinsic astrocytic properties, particularly related to glutamate uptake and astrocytic reactivity – indexed by the expression of S100B and glial fibrillary acidic protein (GFAP). Rats received intraperitoneal injections of MN or saline over 3 consecutive days before receiving intrahippocampal infusion of OKA or saline. Afterward, they were submitted to behavioral tasks and then, euthanatized for neurochemical analysis. Here, we showed that the neuroprotective effects of MN in response to OKA neurotoxicity involve astrocytic activation. MN decreased glutamate uptake in the hippocampus and increased the release of S100B protein in the CSF in response to OKA neurotoxicity, which indicates a possible neurons-astrocyte coupling protective mechanism. These findings shed light on astrocytes as potential targets for treating neurological disorders associated with decreased PP2A activity.

Isolation and Purification of Satellite Cells from Young Rats by Percoll Density Gradient Centrifugation.

Satellite cells (SCs) are myogenic stem cells that play an important role in skeletal muscle regeneration and hypertrophy. Primary cultures of SCs are useful to analyze cell functions; however, it is difficult to obtain highly pure SCs from young rats with the conventional procedures. The purpose of this study is to establish a purification method for SC isolation from young rats and quantitatively evaluate the purification procedure employing Percoll, a common research tool to purify cells. We elucidated the purity of SCs collected by Percoll density gradient centrifugation using real-time RT-qPCR and immunocytochemistry for desmin. Percoll treatment increased the purity of SCs isolated from young rats to nearly 90%, which was comparable to that achieved with the conventional method using middle-aged rats.

Field trip to an MRI

This is the second of two articles on MRI physics. In this article I discuss what a class of physics students might expect to see and learn from a field trip to a full-scale MRI. Magnetic resonance imaging is not only becoming a more common medical diagnostic tool—it is now a more common research tool. Being such an important application of physics, many universities have their own MRI for their medical physics programs.

Efficacy of eperisone and tizanidine on visual and auditory reaction time: A prospective, double-blind randomized controlled trial

Background: Musculoskeletal diseases with painful reflex muscle spasm have a high prevalence. Because of reflex muscle spasm, muscle relaxants are frequently used either alone or in combination with analgesics. Eperisone inhibits voltage-gated sodium channels in brain stem and tizanidine acts on imidazoline and α2-adrenergic receptor to relax muscle spasm and relieves pain. The development of sedation seems to be the major limiting factor in the use of muscle relaxants for treatment as they can affect daily activity and decrease working capability. Aims and Objectives: The present trial conducted to evaluate the effect of eperisone and tizanidine on visual and auditory reaction time. Materials and Methods: This was a prospective, double-blind, parallel group, randomized clinical trial. A total of 115 patients were randomized into two groups. Patients in Group A received tablet eperisone 100 mg and patients in Group B received tablet tizanidine 2 mg for 7 days. Primary outcome measures were changed in visual and auditory reaction time from baseline to day 7. Secondary outcome measure of the trial was change in the visual analog scale (VAS) is the most common research tool used to measure pain. VAS score of the sedation from baseline to day 7. Results: On day 7, the difference in visual reaction time in Group A and B was 0.014 and 0.077, respectively, and this difference is statistically significant (P = 0.029). Difference in Auditory reaction time on day 7 in Group A and B were 0.007 and 0.091, respectively, and it is statistically significant (P = 0.004). There was increase in sedation score in Group B by 0.34 and it is statistically significant (P = 0.015). Conclusion: Tizanidine increases visual and auditory reaction time and sedation which is not seen with eperisone. Eperisone is a preferred alternative for muscle relaxation to avoid these effects.

An economic model comparison of EMSI and IMPLAN

Economic Modeling Specialist International (EMSI) model is a common economic development research tool that has begun to be utilized for tourism research. Therefore, it is important to examine the differences between the EMSI model and the commonly used Impact Analysis for Planning (IMPLAN) model. The multiplier effects of the default version of EMSI and IMPLAN were compared using data obtained from a visitor expenditure survey of the Jackson Mississippi Mistletoe Marketplace. The results revealed that IMPLAN estimated larger multiplier effects (both type I and type II) than EMSI for the total output and employment (job supports).

Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography

ABSTRACTAnalysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.

Effects of different routes of application on ethylenediurea persistence in tobacco leaves

Ethylenediurea (EDU) is a common research tool for investigating ozone impacts on vegetation, although the role of different application routes (foliar spray vs soil drench) on EDU persistence in the leaves is unknown. We quantified EDU concentrations in leaves of the O3-sensitive Bel-W3 cultivar of tobacco treated with EDU as either foliar spray or soil drench. Foliar EDU concentrations were measured by Q-TOF LC/MS. When EDU was applied as foliar spray, 1 h was enough for reaching a measurable concentration within the leaf. EDU concentration increased over the 21-day period when the leaf was not washed after the application (treatment #1), while it decreased when the leaf was washed after the application (treatment #2). These results suggest that: a) dry deposition of EDU onto the leaf surface was gradually absorbed into the unwashed leaf, although the mechanisms of such uptake were unclear; b) concentration of EDU was decreased quickly (−35%) during the first 24 h from application and more slowly during the following three days (−20%) in the washed leaves. Degradation did not involve enzymatic reactions and was not affected by the presence of ROS. When EDU was applied as soil drench, foliar concentrations increased over time, likely due to adsorption onto soil organic matter and gradual re-solubilization by irrigation water. An analysis of EDU concentration in protoplast and intercellular washing fluid showed that EDU did not enter the cells, but was retained in the apoplast only. Possible implications of EDU in the apoplast and recommendations for EDU application are discussed.

Computation of ground reaction force using Zero Moment Point

Motion analysis is a common clinical assessment and research tool that uses a camera system or motion sensors and force plates to collect kinematic and kinetic information of a subject performing an activity of interest. The use of force plates can be challenging and sometimes even impossible. Over the past decade, several computational methods have been developed that aim to preclude the use of force plates. Useful in particular for predictive simulations, where a new motion or change in control strategy inherently means different external contact loads. These methods, however, often depend on prior knowledge of common observed ground reaction force (GRF) patterns, are computationally expensive, or difficult to implement. In this study, we evaluated the use of the Zero Moment Point as a computationally inexpensive tool to obtain the GRFs for normal human gait. The method was applied on ten healthy subjects walking in a motion analysis laboratory and predicted GRFs are evaluated against the simultaneously measured force plate data. Apart from the antero–posterior forces, GRFs are well-predicted and errors fall within the error ranges from other published methods. Joint extension moments were underestimated at the ankle and hip but overestimated at the knee, attributable to the observed discrepancy in the predicted application points of the GRFs. The computationally inexpensive method evaluated in this study can reasonably well predict the GRFs for normal human gait without using prior knowledge of common gait kinetics.

Low incidence of leg and foot injuries in colour-ringed Marsh Tits Poecile palustris

Marking birds with individually identifiable metal leg-rings (bands) is a common research tool, and the additional use of plastic colour rings has facilitated numerous studies of bird ecology, yet there is limited information for the impact of these methods on individuals and populations. Despite generally being considered to have a negligible effect upon birds, recent literature shows that leg rings can cause injuries to some passerines. This creates an ethical problem and may also bias research results by influencing individual behaviour and survival. The incidence of leg injuries was monitored on colour-ringed and unringed Marsh Tits Poecile palustris over 12 years. The overall incidence of permanent injury did not differ between ringed and unringed birds, but six of 404 colour-ringed birds (1.5%) carried a leg or foot injury, which was significantly greater than the background rate (0.2%) among 515 unringed birds. Some injuries on ringed birds were temporary or may have been unrelated to the rings; however, one fatality and two serious injuries were recorded, probably resulting from colour rings becoming caught on thorns or other objects. Although ring-related injuries were very rare, it is recommended that ringers studying Marsh Tits try to minimise the number of rings on each leg.