Traditional Buffers Research Articles

Accuracy of buffers and self-drawn neighbourhoods in representing adolescent GPS measured activity spaces: An exploratory study.

There continues to be a lack of understanding as to the geographical area at which the environment exerts influence on behaviour and health. This exploratory study compares different potential methods of both researcher- and participant-defined definitions of neighbourhood reflect an adolescent's activity space. Seven consecutive days of global positioning system (GPS) tracking data were collected at 15s intervals using a small exploratory adolescent sample of 14-18 year olds (n=69) in West Yorkshire, England. A total of 304,581 GPS tracking points were collected and compared 30 different definitions of researcher-defined neighbourhoods including radial, network and ellipse buffers at 400m, 800m, 1000m, 1600m and 3000m, as well as participant-defined self-drawn neighbourhoods. This exploratory study supports emerging evidence cautioning against the use of static neighbourhood definitions for defining exposure. Traditional buffers (network and radial) capture at most 67% of activity space (home radial), and at worst they captured only 3.5% (school network) and range from capturing between 3 and 88% of total time. Similarly, self-drawn neighbourhoods captured only 10% of actual daily movement. Interestingly, 40% of an adolescent's self-drawn neighbourhood was not used. We also demonstrate that buffers capture a range of space (22-95%) where adolescents do not go, thus misclassifying the exposure. Our exploratory findings demonstrate that neither researcher- nor participant-defined definition of neighbourhood adequately captures adolescent activity space. Further research with larger samples are needed to confirm the findings of this exploratory study.

Nitrous Oxide Emissions from Saturated Riparian Buffers: Are We Trading a Water Quality Problem for an Air Quality Problem?

Reestablishing perennial vegetation along riparian areas in agroecosystems reduces nutrient and sediment losses from agricultural lands. However, subsurface (tile) drains bypass traditional buffers routing the majority of shallow groundwater straight to surface waters, limiting their nutrient removal capabilities. Saturated riparian buffers (SRBs) reconnect subsurface drainage water with the soil profile to remove NO in tile water through microbial denitrification. One concern of enhancing denitrification on agricultural landscapes is the potential increase in NO emissions from incomplete denitrification. Our objective was to compare NO emissions from SRBs to traditional buffers and bordering crop fields at two sites, Bear Creek Site 1 and Iowa Site 1, in Central Iowa. We measured NO emissions directly from the soil surface and dissolved in shallow groundwater and estimated indirect emissions from downstream denitrification from 2015 through 2017. Nitrous oxide emissions from soil surfaces were greatest from fertilized corn ( L.). Saturated riparian buffers were only significantly greater ( < 0.05) than traditional buffers in one out of six site-years. Dissolved NO in shallow groundwater seeping from SRBs was not significantly greater ( < 0.05) than dissolved NO from the tile outlet among site years. Indirect NO emissions from rivers and estuaries were significantly reduced from NO removal in both SRBs. Overall, total NO emissions from SRBs were similar to those from traditional buffers and less than those from fertilized corn-soybean [ (L.) Merr.] agriculture. Replacing cultivated land in riparian areas with a SRB has shown potential to subsequently remove NO from surface waters and reduce NO emissions from agricultural landscapes.

Ionic Liquids as Bifunctional Cosolvents Enhanced CO2 Conversion Catalysed by NADH-Dependent Formate Dehydrogenase

Efficient CO2 conversion by formate dehydrogenase is limited by the low CO2 concentrations that can be reached in traditional buffers. The use of ionic liquids was proposed as a manner to increase CO2 concentration in the reaction system. It has been found, however, that the required cofactor (NADH) heavily degraded during the enzymatic reaction and that acidity was the main reason. Acidity, indeed, resulted in reduction of the conversion of CO2 into formic acid and contributed to overestimate the amount of formic acid produced when the progression of the reaction was followed by a decrease in NADH absorbance (method N). Stability of NADH and the mechanism of NADH degradation was investigated by UV, NMR and by DFT calculations. It was found that by selecting neutral–basic ionic liquids and by adjusting the concentration of the ionic liquid in the buffer, the concentration of NADH can be maintained in the reaction system with little loss. Conversion of CO2 to methanol in BmimBF4 (67.1%) was more than twice as compared with the conversion attained by the enzymatic reaction in phosphate buffer (24.3%).

Extracting the barbs from complement assays: Identification and optimisation of a safe substitute for traditional buffers

Complement assays have for many years utilised buffers based on barbitone (veronal) despite the well-recognised toxicity of this agent and the tight regulations on its use in most countries. The use of barbitone in complement assay buffers is steeped in history, from a time when no other suitable buffers were available. This is no longer the case, encouraging us to explore alternatives to barbitone for complement assays. We compared a simple, non-toxic HEPES buffer with commercially sourced complement fixation test diluent (CFD), the “gold standard” barbitone buffer, in several clinically relevant complement activity assays and across species.In classical pathway haemolysis assays in human and non-human serum, there was no difference in haemolytic curves or calculated haemolytic activity (CH50) between CFD and an optimised HEPES buffer (HBS) supplemented with cations. Alternative pathway haemolysis assays in human serum were also identical in the two buffers. In a complement fixation test for anti-erythrocyte antibodies, complement consumption was identical for the two buffer systems.The data demonstrate that barbitone-based buffers are unnecessary for assays of complement activity and can readily be replaced with safe and simple alternatives.

Rural-urban correlates of reproductive health with mental health in women in Odisha, India

Background: Mental health and reproductive health are closely related. Women of reproductive age are most vulnerable. Odisha has poor maternal health indicators. Very few Indian studies comparing urban-rural differences in women’s mental health. Methods: Random sampling from respective field practice areas. GHQ-12 Mental Health screening tool used to assess health status. Pre-tested questionnaire applied to enquire about domestic and familial status, reproductive health morbidities. Results: Proportion of reported extramarital relationships of the respondents’ husband was observed to be more than twice as much in urban as compared to rural areas. Prevalence of domestic violence was found to be 43.2% in urban area as compared to 27.2% in rural areas. Significant differences were seen between urban and rural arms of the study regarding adverse pregnancy outcomes (p&lt;0.001), induced abortion (p&lt;0.0001), menstrual problems (p&lt;0.0004) and gynaecological problems (p=0.0031). In these cases, rural women were observed to have significantly more combined (reproductive and mental health) morbidity than their urban counterparts. Conclusions: Findings of the study indicate that though familial and spousal and social support parameters were more adverse in urban women, reproductive health problems and their association with poor mental health was strikingly more common in the rural populace. This may indicate an erosion of the traditional buffers against adverse mental health outcomes in the rural setting and needs further investigation.

Statistical Methods to Study Variation in Associations Between Food Store Availability and Body Mass in the Multi-Ethnic Study of Atherosclerosis.

Research linking characteristics of the neighborhood environment to health has relied on traditional regression methods where prespecified distances from participant's locations or areas are used to operationalize neighborhood-level measures. Because the relevant spatial scale of neighborhood environment measures may differ across places or individuals, using prespecified distances could result in biased association estimates or efficiency losses. We use novel hierarchical distributed lag models and data from the Multi-Ethnic Study of Atherosclerosis (MESA) to (1) examine whether and how the association between the availability of favorable food stores and body mass index (BMI) depends on continuous distance from participant locations (instead of traditional buffers), thus allowing us to indirectly infer the spatial scale at which this association operates; (2) examine if the spatial scale and magnitude of the association differs across six MESA sites, and (3) across individuals. As expected, we found that the association between higher availability of favorable food stores within closer distances from participant's residential location was stronger than at farther distances, and that the magnitude of the adjusted association declined quickly from zero to two miles. Furthermore, between-individual heterogeneity in the scale and magnitude of the association was present; the extent of this heterogeneity was different across the MESA sites. Individual heterogeneity was partially explained by sex. This study illustrated novel methods to examine how neighborhood environmental factors may be differentially associated with health at different scales, providing nuance to previous research that ignored the heterogeneity found across individuals and contexts.

Destinations That Older Adults Experience Within Their GPS Activity Spaces Relation to Objectively Measured Physical Activity.

Identifying the relevant geography is an ongoing obstacle to effectively evaluate the influence of neighborhood built environment on physical activity. We characterized density and diversity of destinations that 77 older adults experienced within individually representative GPS activity spaces and traditional residential buffers and assessed their associations with accelerometry-measured physical activity. Traditional residential buffers had lower destination density and diversity than activity spaces. Activity spaces based only on pedestrian and bicycling trips had higher destination densities than all-mode activity spaces. Regardless of neighborhood definition, adjusted associations between destinations and physical activity generally failed to reach statistical significance. However, within pedestrian and bicycling-based activity spaces each additional destination type was associated with 243.3 more steps/day (95% confidence interval (CI) 36.0, 450.7). Traditional buffers may not accurately portray the geographic space or neighborhood resources experienced by older adults. Pedestrian and bicycling activity spaces elucidate the importance of destinations for facilitating active transportation.

Abstract 4904: Developing a universal target retrieval solution and protocol for RNA in situ hybridization based on RNAscope technology

Abstract Heat induced target retrieval (HITR) is a widely adopted approach for Immunohistochemistry (IHC) and in situ hybridization (ISH) applications on formalin fixed and paraffin embedded (FFPE) tissues to facilitate target access and increase detection sensitivity. A variety of factors, such as fixative type, fixation time, tissue type, epitope abundance, antibody affinity, and probe length greatly affect the efficiency of HITR. Given such variability, over the decades, multiple HITR buffer formulations and protocols were invented to fit the needs in different experimental scenarios. We have developed a novel HITR solution that allows highly efficient target retrieval for RNA ISH application based on the RNAscope technology. When tested on 15 different tumor types, the new HITR solution resulted in significantly better sensitivity and/or tissue morphology comparing to using traditional HITR buffers, including Citrate, EDTA, and Tris based buffers with various pH. Furthermore, this new HITR solution is highly tolerant to sample variability. When used on multiple human tumor tissue microarrays (TMAs), including breast, colon, lung, and gastric cancers, the new HITR solution improved overall signal-to-noise ratio and reduced core disqualification rate, compared to traditional citrate based HITR buffer for ISH. Moreover, when tested on multiple mouse tissues fixed with different types of fixatives for varying periods of time (6 - 72 hours), a single experimental condition with the new HITR solution showed comparable results in both detection sensitivity and morphological integrity in all the samples. It also allowed detection of a target (Tbp) with extremely low abundance (&amp;lt;5 copies/cell). Given that all the RNAscope probes are synthetic oligonucleotide probes with length shorter than 60 bases, the new HITR solution, in combination with the RNAscope technology, will allow universal detection of any RNA targets with single molecule detection sensitivity in FFPE tissues with minimal requirement for analytical condition optimization. Citation Format: Li-chong Wang, Liuliu Pan, Kuang-Jung Chang, Daniel Kim, Xingyong Wu, Hongwei Wang, Casey Kernag, Bingqing Zhang, Mingxiao He, Nan Su, Xiao-Jun Ma, Yuling Luo. Developing a universal target retrieval solution and protocol for RNA in situ hybridization based on RNAscope technology. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4904. doi:10.1158/1538-7445.AM2015-4904

Developing suitable buffers to capture transport cycling behavior.

The association between neighborhood built environment and cycling has received considerable attention in health literature over the last two decades, but different neighborhood definitions have been used and it is unclear which one is most appropriate. Administrative or fixed residential spatial units (e.g., home-buffer-based neighborhoods) are not necessarily representative for environmental exposure. An increased understanding of appropriate neighborhoods is needed. GPS cycling tracks from 78 participants for 7 days form the basis for the development and testing of different neighborhood buffers for transport cycling. The percentage of GPS points per square meter was used as indicator of the effectiveness of a series of different buffer types, including home-based network buffers, shortest route to city center buffers, and city center-directed ellipse-shaped buffers. The results show that GPS tracks can help us understand where people go and stay during the day, which can help us link built environment with cycling. Analysis showed that the further people live from the city center, the more elongated are their GPS tracks, and the better an ellipse-shaped directional buffer captured transport cycling behavior. In conclusion, we argue that in order to be able to link built environment factors with different forms of physical activity, we must study the most likely area people use. In this particular study, to capture transport cycling, with its relatively large radius of action, city center-directed ellipse-shaped buffers yielded better results than traditional home-based network buffer types. The ellipse-shaped buffer types could therefore be considered an alternative to more traditional buffers or administrative units in future studies of transport cycling behavior.

HELIX: a new modular nucleic acid crystallization screen

Crystallization of nucleic acids remains a bottleneck to their structural characterization by X-ray crystallography. A new 96-well-format initial screen for nucleic acids, called HELIX, has been developed at UCL School of Pharmacy, London, on the basis of a detailed analysis of the crystallization conditions from 1450 nucleic acid structures deposited in the Protein Data Bank (PDB), combined with observations and experience acquired in the authors' nucleic acids crystallography laboratory during the crystallization of DNA/RNA quadruplexes and ligand complexes. Despite using traditional buffers, precipitants and salts, the resulting modular screen is designed to offer a variety of approaches to enhance successful crystallization of oligonucleotides with a diverse range of topologies, sequences and molecular weights. HELIX includes a set of 24 conditions divided into four sets that can be mixed (inter- and intra-set) to provide a customizable orthogonal screening tool for experienced users, termed VariX. Additionally, mindful of synchrotron anomalous data collection, cacodylate buffers are avoided in the formulations and an optimized cryocrystallization module is included. This article reviews the crystallization trends and data derived from the PDB and discusses the HELIX screen layout, formulation and results from in-house crystallization trials.

The Coping Paradox: Work, Stress, and Coping in the U.S. Army

The military environment has unique stressors. This study investigates the types of stressors, appraisals, and coping responses of U.S. soldiers and their leaders. A qualitative analysis of interviews indicates that the traditional coping buffers of social drinking and seeking social support from fellow soldiers, family, and leaders can potentially serve as sources of stress. While this paradox may be a result of the unique types of stressors in the military work environment, these results should direct researchers to better understand individuals' perceptions and appraisals of stress, with a focus on the meaning of stress, given contextual factors inherent in the workplace. The findings are discussed in relation to the literature on the impact of stress on physical and psychological health.

Buffer composition changes in background electrolyte during electrophoretic run in capillary zone electrophoresis.

The electrophoretic behaviors of different analytes in capillary zone electrophoresis were studied by the Whole Column Imaging Detection (WCID). For capillary zone electrophoresis (CZE) in conventional buffer systems, non-constant sample plug movement characterized by progressive decrease of peak migration velocity was observed. The appropriate velocity decrease was correlated with a degree of ionization of the analyzed ion, thus the effect observed could be explained by fast buffer composition change resulting in the development of a non-linear pH gradient. To visualize the appropriate pH gradient, the concentration profile of initially uniformly distributed amphoteric substances was also monitored. The evolution of the concentration profile exhibited very complex dynamics. In addition, it was found that the nature of the electrode solutions strongly affect changes in the background electrolyte. In the case of traditional background electrolytes with an acid-base pair for electrode solutions a non-uniform ampholyte concentration developed quickly, leading finally to a quasi-stationary profile similar to those typical of IEF. Possible approaches to suppress a negative impact of the background electrolyte composition changes during electrophoretic run on CE-separation are presented herein. In particular it was observed that zwitterionic buffers are able to withstand prolonged electrolysis much better compared to traditional buffers.

A CHARGE RECYCLING TECHNIQUE FOR THE DESIGN OF LOW POWER CMOS CLOCK DRIVERS

The design of low power CMOS clock drivers using a charge recycling technique is introduced in this paper. Considering a clock signal and its complement, the half of the charge stored in the load capacitances is reused in every clock edge. The proposed circuit exploits the inherent input-output delay of the driver for the generation of all necessary control signals, using fully digital logic and conventional technology. Extensive simulations of the circuit have been performed and the influence of various design parameters on its response has been studied. Compared to traditional taper buffers, power savings over 45% are obtained for the output load transitions whereas the total power reduction decreases by 10% to 35% due to control overhead. Moreover, no speed degradation is observed but almost a duplication of the silicon area is required.

High-Efficiency DNA Separation by Capillary Electrophoresis in a Polymer Solution with Ultralow Viscosity

The viscosities of some polymer solutions for DNA separation in capillary electrophoresis are generally very high, which makes them hard to pump into the capillaries. We have developed a novel sieving buffer, based on low-molecular-weight hydroxypropylmethylcellulose, to separate DNA fragments. The viscosity of this sieving matrix was at least 1 order of magnitude lower than that of traditional buffers with similar sieving effect. The influence of additives such as urea and mannitol was investigated. It was found that the double-stranded DNA (ds DNA) fragments began to denature in 3.5 M urea, and 7 M urea can denature the ds DNA completely. The presence of mannitol will decrease the overlap threshold of the polymer solution (the concentration at which the polymer molecules begin to entangle with each other), which makes it possible to separate DNA fragments in a polymer solution of relatively low concentration. The influence of the electrical field was also investigated, and it was found that the mobility of DNA fragments up to 2000 bp in length did not change greatly with different electric fields. This phenomenon implies that the DNA fragments at this range do not change their conformation with the increase of electric field as was previously believed. The possible mechanism for the separation of DNA fragments is also discussed.

The mATPase histochemical profile of rat type IIX fibres: correlation with myosin heavy chain immunolabelling

In the present study we report a novel histochemical method which, by sequential pre-incubations in alkaline and acidic media, selectively differentiates muscle fibres expressing myosin heavy chain IIX, on the basis of a specific profile for myofibrillar actomyosin ATPase (mATPase) activity. The enzyme reactions were tested for specificity by means of anti-myosin heavy chain monoclonal antibodies, which were characterized on Western blots of muscle homogenates. Enzyme histochemical reactions with the traditional pH buffers were compared to those of the new method and, in conjunction with the immunoreactions, used to confirm the relationship between MyHC expression and the distinct profiles for mATPase. Immunohistochemical reactions demonstrated that the new method only differentiates those fibres expressing myosin heavy chain IIX. The method revealed a continuum in which the intermediate staining intensities corresponded to hybrid fibres expressing myosin heavy chain IIX in combination with either the IIA or IIB forms. Quantitative histochemistry and immunohistochemistry (by image analysis), used to examine the relationship between staining intensities for mATPase and amounts of myosin heavy chain IIX expression, revealed that the new method discriminates well between hybrid fibres expressing variable amounts of the IIX isoform (r2 = 0.93).

Fluorescein as a label for non-radioactive in situ hybridization

Non-radioactive techniques can be applied to many in situ hybridization (ISH) applications, and a number of non-radioactive labels for this process have been reported. However, these labels have some inherent problems in terms of both background and signal-to-noise values. We have sought to address these issues by searching for an alternative label that has the following features: efficient incorporation into probes, non-endogenous to biological systems, the availability of a high-affinity, high-specificity antibody. Fluorescein has been shown to meet these requirements. In addition, due to the fluorescent nature of the label, it has been possible to design a rapid, non-radioactive labelling assay and also to view in situ hybridization results by direct fluorescence in certain ISH applications. The hybridization kinetics have been investigated. Significant improvements have been made to the hybridization buffer leading to reduced background and increased rates of hybridization when compared to traditional hybridization buffers.