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Early descriptions of clinical reasoning have described a dual process model that relies on analytical or nonanalytical approaches to develop a working diagnosis. In this classic research, clinical reasoning is portrayed as an individual‐driven cognitive process based on gathering information from the patient encounter, forming mental representations that rely on previous experience and engaging developed patterns to drive working diagnoses and management plans. Indeed, approaches to patient safety, as well as teaching and assessing clinical reasoning focus on the individual clinician, often ignoring the complexity of the system surrounding the diagnostic process. More recent theories and evidence portray clinical reasoning as a dynamic collection of processes that takes place among and between persons across clinical settings. Yet, clinical reasoning, taken as both an individual and a system process, is insufficiently supported by theories of cognition based on individual clinicals and lacks the specificity needed to describe the phenomenology of clinical reasoning. In this review, we reinforce that the modern healthcare ecosystem – with its people, processes and technology – is the context in which health care encounters and clinical reasoning take place. [ABSTRACT FROM AUTHOR]

Background: Poor functional status is a key marker of morbidity, yet is not routinely captured in clinical encounters. We developed and evaluated the accuracy of a machine learning algorithm that leveraged electronic health record (EHR) data to provide a scalable process for identification of functional impairment. Methods: We identified a cohort of patients with an electronically captured screening measure of functional status (Older Americans Resources and Services ADL/IADL) between 2018 and 2020 (N = 6484). Patients were classified using unsupervised learning K means and t‐distributed Stochastic Neighbor Embedding into normal function (NF), mild to moderate functional impairment (MFI), and severe functional impairment (SFI) states. Using 11 EHR clinical variable domains (832 variable input features), we trained an Extreme Gradient Boosting supervised machine learning algorithm to distinguish functional status states, and measured prediction accuracies. Data were randomly split into training (80%) and test (20%) sets. The SHapley Additive Explanations (SHAP) feature importance analysis was used to list the EHR features in rank order of their contribution to the outcome. Results: Median age was 75.3 years, 62% female, 60% White. Patients were classified as 53% NF (n = 3453), 30% MFI (n = 1947), and 17% SFI (n = 1084). Summary of model performance for identifying functional status state (NF, MFI, SFI) was AUROC (area under the receiving operating characteristic curve) 0.92, 0.89, and 0.87, respectively. Age, falls, hospitalization, home health use, labs (e.g., albumin), comorbidities (e.g., dementia, heart failure, chronic kidney disease, chronic pain), and social determinants of health (e.g., alcohol use) were highly ranked features in predicting functional status states. Conclusion: A machine learning algorithm run on EHR clinical data has potential utility for differentiating functional status in the clinical setting. Through further validation and refinement, such algorithms can complement traditional screening methods and result in a population‐based strategy for identifying patients with poor functional status who need additional health resources. [ABSTRACT FROM AUTHOR]

The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources. [ABSTRACT FROM AUTHOR]

Landspraying while drilling (LWD) is an approved disposal method for water‐based drilling mud (WBM) systems in western Canada, where the mud is applied either on arable or vegetated land. This study examined the effects of a single LWD application (0, 15, 20, 40, or 80 m3 ha−1) on native prairie soil properties. Results from the study showed a significant increase in Na concentration and sodium adsorption ratio (SAR) in the 0‐ to 7.5‐cm depth. However, the highest SAR attained (3.46) after application at the 80 m3 ha−1 rate remained below levels considered detrimental to soil structure. Electrical conductivity (EC) also increased with the LWD rate but peaked at levels (447 μS cm−1 in the 0‐ to 2.5‐cm depth) much lower than the threshold for most plant species, and the effects on EC had disappeared by the end of the first year of mud application. Available P concentration (modified Kelowna method), averaged across sampling times and the two depths (0‐ to 2.5‐ and 2.5‐ to 7.5‐cm), increased from 7.4 to 11 mg kg−1 as LWD rate increased from 0 to 80 m3 ha−1. Although the available P remained at concentrations suboptimum for most crops, such concentrations may impact native prairie vegetation adapted to very low P. Drilling mud applications generally had no significant effect on available N. The application of WBM systems on the native prairie at recommended rates in western Canada may not be detrimental to soil quality and plant growth in this ecosystem. [ABSTRACT FROM AUTHOR]

Background Medical students traditionally learn physical examination skills as a rote list of manoeuvres. Alternatives like hypothesis-driven physical examination ( HDPE) may promote students' understanding of the contribution of physical examination to diagnostic reasoning. We sought to determine whether first-year medical students can effectively learn to perform a physical examination using an HDPE approach, and then tailor the examination to specific clinical scenarios. Context First-year medical students at the University of Minnesota were taught both traditional and HDPE approaches during a required 17-week clinical skills course in their first semester. The end-of-course evaluation assessed HDPE skills: students were assigned one of two cardiopulmonary cases. Each case included two diagnostic hypotheses. During an interaction with a standardised patient, students were asked to select physical examination manoeuvres in order to make a final diagnosis. Items were weighted and selection order was recorded. Innovation First-year students with minimal pathophysiology performed well. All students selected the correct diagnosis. Importantly, students varied the order when selecting examination manoeuvres depending on the diagnoses under consideration, demonstrating early clinical decision-making skills. Implications An early introduction to HDPE may reinforce physical examination skills for hypothesis generation and testing, and can foster early clinical decision-making skills. This has important implications for further research in physical examination instruction. [ABSTRACT FROM AUTHOR]

Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition., Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues., Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length., Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process. [ABSTRACT FROM AUTHOR]

Rain runoff from windrowed or stockpiled manure may contain antimicrobials with the potential to contaminate surface and ground water. To quantify the concentration of antimicrobials transported in runoff from windrowed manure, antimicrobials were administered continuously in feed to beef cattle (Bos taurus) as follows: 44 mg of chlortetracycline kg-1 feed (dry weight), a 1:1 mixture of 44 mg of chlortetracycline and 44 mg sulfamethazine kg-1 feed, and 11 mg of tylosin kg-1 feed. Cattle in a fourth treatment group received no antimicrobials (control). Manure from the cattle was used to construct two windrows per treatment. On Days 2 and 21 of composting, a portable Guelph Rainfall Simulator II was used to apply deionized water at an intensity of 127 mm h-1 to each windrow, and the runoff was collected. Manure samples were collected before rain simulations on Days 2 and 21 of composting for antimicrobial analysis. On Day 2, average concentrations of chlortetracycline, sulfamethazine, and tylosin in manure were 2580, 450, and 120 mg kg-1, respectively, with maximum concentrations in runoff of 2740, 3600, and 4930 mg L-1, respectively. Concentrations of all three antimicrobials in runoff were higher (P < 0.05) on Day 2 than on Day 21, reflecting the higher concentrations in manure on Day 2. Maximum estimated masses of chlortetracycline, sulfamethazine, and tylosin that could be transported in runoff from a windrow (3 m long, 2.5 m wide, 1.5 m high) were approximately 0.87 to 0.94, 1.57, and 1.23 g, respectively. This study demonstrates the importance of windrow composting in reducing antimicrobial concentrations in manure. The runoff from windrows can be a source of antimicrobials and demonstrates the need for containment of runoff from composting facilities to mitigate antimicrobial contamination of surface and groundwater resources. [ABSTRACT FROM AUTHOR]

Windrow composting or stockpiling reduces the viability of pathogens and antimicrobial residues in manure. However, the impact of these manure management practices on the persistence of genes coding for antimicrobial resistance is less well known. In this study, manure from cattle administered 44 mg of chlortetracycline kg-1 feed (dry wt. basis) (CTC), 44 mg of CTC and 44 mg of sulfamethazine kg-1 feed (CTCSMZ), 11 mg of tylosin kg-1 feed (TYL), and no antimicrobials (control) were composted or stockpiled over 102 d. Temperature remained ≥55°C for 35 d in compost and 2 d in stockpiles. Quantitative PCR was used to measure levels of 16S rRNA genes and tetracycline [tet(B), (C), (L), (M), (W)], erythromycin [erm(A), (B), (F), (X)], and sulfamethazine [sul(1), (2)] resistance determinants. After 102 d, 16S rRNA genes and all resistance determinants declined by 0.5 to 3 log10 copies per gram dry matter. Copies of 16S rRNA genes were affected (P < 0.05) by antimicrobials with the ranking of control > CTC = TYL > CTCSMZ. Compared with the control, antimicrobials did not increase the abundance of resistance genes in either composted or stockpiled manure, except tet(M) and sul(2) in CTCSMZ (P < 0.05). The decline in 16S rRNA genes and resistance determinants was higher (P < 0.05) in composted than in stockpiled manure. We conclude that composting may be more effective than stockpiling in reducing the introduction of antimicrobial resistance genes into the environment before land application of manure. [ABSTRACT FROM AUTHOR]

A distributed system of services assembled according to a service-oriented architecture requires an efficient mechanism to discover appropriate services deployed over a network. The recent emergence of many service marketplaces makes the case for the existence of such a discovery service. These marketplaces typically provide rudimentary techniques to publish service information and associated matching activities. Such simple matching techniques are typically not suitable to address complex user requirements. Therefore, it is a challenge to discover relevant services, with a high degree of accuracy, out of existing choices. This paper discusses experiments performed on a discovery service whose search techniques incorporate learning profiles to accomplish these complex tasks. The UniFrame Resource Discovery System, which searches for required services, provided an experimental test bed for these experiments. The article describes these techniques and explains their algorithms. Experimental results illustrate the gains in the quality of selected services and reduction in the discovery time using the proposed techniques. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

With increased availability of dried distillers' grains with solubles (DDGS) as cattle feed and the need to recycle organic wastes, this research investigated the feasibility of co-composting DDGS cattle feedlot manure with construction and demolition (C&D) waste. Manure was collected from cattle fed a typical western Canadian finishing diet (CK) of 860 g rolled barley (Hordeum vulgare L) grain, 100 g barley silage, and 40 g vitamin and mineral supplement kg-1 dry matter (DM) and from cattle fed the same diet but (DG manure) with 300 g kg-1 DM barley grain being replaced by DDGS. The CK and DG manures were co-composted with and without C&D waste in 13 m³ bins. Compost materials were turned on Days 14, 37, and 64, and terminated on Day 99. Adding C&D waste led to higher compost temperatures (0.4 to 16.3°C, average 7.2°C) than manure alone. Final composts had similar total C, total N, C/N ratios, and water-extractable K, Mg, and NO3- content across all treatments. However, adding C&D waste increased δ13C, δ15N, water-extractable SO42-, and Ca+ contents and decreased pH, total P (TP), water-extractable C, N, and P and most volatile fatty acids (VFA). The higher C&D compost temperatures should reduce pathogens while reduced VFA content should reduce odors. When using the final compost product, the increased SO42- and reduced TP and available N and P content in C&D waste compost should be taken into consideration. Increased S content in C&D compost may be beneficial for some crops grown on S-deficient soils. [ABSTRACT FROM AUTHOR]

Dissipation of veterinary antimicrobials is known to occur during aerated windrow composting of beef cattle manure. However, it is unclear if a similar dissipation occurs during stockpiling. Chlortetracycline, tylosin, and sulfamethazine are three of the most commonly used veterinary antimicrobials in beef cattle production in western Canada. Their dissipation in stockpiled manure was investigated over 140 d during winter in Alberta, Canada. Beef cattle housed in pens were administered 44 mg of chlortetracycline kg-1 feed (dry weight), 44 mg of chlortetracycline + 44 mg sulfamethazine kg-1 feed, 11 mg of tylosin kg-1 feed, or feed without antimicrobials (control). Manure samples were extracted using pressurized liquid extraction, and the extracts were analyzed for chlortetracycline, sulfamethazine, and tylosin by LC-MS-MS. Dissipation of all three antimicrobials in the manure was explained by exponential decay kinetics. Times for 50% dissipation (DT50) were 1.8 ± 0.1 d for chlortetracycline alone or 6.0 ± 0.8 d when mixed with sulfamethazine, 20.8 ± 3.8 d for sulfamethazine, and 4.7 ± 1.2 d for tylosin. After 77 d, <1% of initial chlortetracycline and <2% of sulfamethazine remained. Tylosin residues were more variable, decreasing to approximately 12% of initial levels after 28 d, with 20% present after 77 d and 13% after 140 d. Temperatures within stockpiles reached maximum values within 6 d of establishment and varied with location (bottom, 62.5°C; middle, 63.8°C; and top, 42.9°C). Antimicrobials in the manure did not inhibit microbial activity, as indicated by temperature and mass losses of carbon (C) and nitrogen (N). The C/N ratio in the manure decreased over the stockpiling period, indicating decomposition of manure to a more stable state. Dissipation of excreted residues with DT50 values 1.8 to 20.8 d showed that stockpiling can be as effective as windrow composting in mitigating the transfer of these three veterinary antimicrobials into the environment during land application of processed manure. [ABSTRACT FROM AUTHOR]

Manure composting has become commonplace in the beef cattle (Bos taurus L.) feedlot industry in Alberta. However, the nitrogen (N) and phosphorus (P) characteristics of runoff from windrows subjected to heavy rainfall at different compost maturities are unknown. On Days 18, 26,40, 54, 81, 109, and 224 of composting, a rainfall simulator generated runoff, which was collected in timed 5-L increments, creating the variable "time during runoff event" (TDRE). The volumetric runoff coefficient of windrows increased from 24% of incident rainfall on Day 0 to 69% by Day 90. Ammonium-nitrogen showed a significant maturity X TDRE interaction on Day 18, increasing from 46 mg L-1 for the 0- to 5-L increment to 172 mg L-1 for the 25- to 30-L increment, as did total dissolved phosphorus (TDP), increasing from 36 to 61 mg L-1. Nitrate-nitrogen had a runoff export coefficient of 19.5 mg m² min-1 on Day 224, which was significantly higher than 1.8 to 6.3 mg m² min-1 on Days 18 to 54. Across the 224-d composting period, compost NO3-N concentration explained 87% of runoff NO3-N, whereas compost water-soluble P explained 68% of runoff TDP. The occurrence and duration of rainfall events relative to the compost maturity spectrum has implications for the magnitude of N and P mobility and overall nutrient losses. [ABSTRACT FROM AUTHOR]

Here, we report the NMR solution structures of Mycobacterium tuberculosis ( M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. © Proteins 2013. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Enzymes of the glyoxylate shunt are important for the virulence of pathogenic organisms such as Mycobacterium tuberculosis and Candida albicans. Two isoforms have been identified for malate synthase, the second enzyme in the pathway. Isoform A, found in fungi and plants, comprises ∼530 residues, whereas isoform G, found only in bacteria, is larger by ∼200 residues. Crystal structures of malate synthase isoform G from Escherichia coli and Mycobacterium tuberculosis were previously determined at moderate resolution. Here we describe crystal structures of E. coli malate synthase A (MSA) in the apo form (1.04 Å resolution) and in complex with acetyl-coenzyme A and a competitive inhibitor, possibly pyruvate or oxalate (1.40 Å resolution). In addition, a crystal structure for Bacillus anthracis MSA at 1.70 Å resolution is reported. The increase in size between isoforms A and G can be attributed primarily to an inserted α/β domain that may have regulatory function. Upon binding of inhibitor or substrate, several active site loops in MSA undergo large conformational changes. However, in the substrate bound form, the active sites of isoforms A and G from E. coli are nearly identical. Considering that inhibitors bind with very similar affinities to both isoforms, MSA is as an excellent platform for high-resolution structural studies and drug discovery efforts. [ABSTRACT FROM AUTHOR]

Drilling mud systems are used by the petroleum industry to facilitate and expedite the drilling of oil and natural gas wells. In western Canada, spent water-based muds (WBM) are often applied to cropland and native prairie at low application rates as a disposal option. We speculate that application of drilling waste on native prairie in semiarid climates will alter the soil surface energy balance and adversely affect soil biophysical processes and subsequently ecosystem productivity. This study was initiated to examine the effect of application rate (0, 40, and 80 m3 ha-1) of summer-applied WBM on surface albedo (α), soil temperature, and soil heat flux at the 0.05-m depth (G005) and at the surface (G) over 42 d following application. Our results provide evidence of a significant alteration of these micrometeorological parameters with WBM application. Surface albedo decreased by 15% (relative to the control) with the application of 40 m3 ha-1 mud and by an additional 3% when this mud rate was doubled. The lower α meant that a greater proportion of incoming shortwave solar radiation (Rsi) was available for partitioning into components of the surface energy balance, including C. This coincides with observed increases in G005, G, and soil temperature at the 0.025-m depth, with higher WBM. By modifiying heat flow and temperature in the root zone, WBM application may alter critical ecosystem biophysical and physiological processes, with important implications for overall biological productivity. The direction and magnitude of such changes, in conjunction with all the other ecological effects of WBM, will ultimately define the sustainability of the practice in this fragile ecosystem. [ABSTRACT FROM AUTHOR]

This article discusses the composting of different bedding materials used in feedlots in Alberta, Canada. The authors compared the chemical and physical properties of wood chip bedded manure with barley straw bedded manures. The found the temperatures were about the same but wood chip composts showed significantly lower nitrogen losses and lower total phosphorus as well as significantly higher total carbon and inorganic nitrogen. They encourage the adoption of wood chips over straw as preferred bedding for Alberta beef cattle feedlots.

Organic amendments have been used to restore productivity to disturbed soils such as those on abandoned oil and natural gas wellsites. A study was conducted on three abandoned well-sites in southern Alberta, Canada to examine the effects of one-time applications of alfalfa (Medicago sativa L.) hay or beef cattle (Bos taurus) feedlot manure compost on soil properties under continuous wheat (Triticum aestivum L.). The base amendment rate (1×) [dry wt.] was 5.3 Mg ha-1 for compost and 3.1 Mg ha-1 for alfalfa. The five amendment rates of 0, 1×, 2×, 4×, and 8× were soil-incorporated at the wellsites. Although approximately twice as much C was applied with alfalfa than with compost, final SOC content was similar for the two amendment treatments, indicating the greater stability of compost-derived C. Nitrate N content in the 0- to 60-cm depth was not affected by compost rate (mean 213 kg ha-1) but increased by 7.78 kg ha-1 for each Mg ha-1 increase in alfalfa rate. This result reflects the greater stability of compost-N compared with alfalfa-N and suggests a lower risk of NO3-N leaching with compost application. Compost rates >20 Mg ha-1 resulted in excessive extractable P build-up in the topsoil (up to 95.7 mg kg-1), which may pose environmental risk to surface water. We recommend amending wellsites with up to 12 Mg ha-1 of alfalfa or <20 Mg ha-1 of compost during reclamation to improve C storage and nutrient cycling while minimizing nutrient loss to water systems. [ABSTRACT FROM AUTHOR]

This article presents a study which analyses chemical and physical changes following co-composting of beef cattle feedlot manure with phosphogypsum (PG). The product of phosphorus (P) fertilizer manufacture and large stockpile currently exist in Alberta. Co-composting PG with manure will obviously result in a final product with significantly lower specific radioactivity due to a dilution effect. In addition to potential nutrient benefits from PG addition, widespread diversion of PG to manure composting could alleviate the accumulation of PG in large stacks. Main and interaction effects of bedding and PG rate were not significant for initial total phosphorus content of the manure-PG mixtures. Aluminum, Arsenic, and lead concentrations were significantly higher in straw-bedded than wood chip-bedded compost. This could be related to additions of these elements in fertilizers and herbicides-pesticides, which would raise concentrations in the barley straw compared to the wood chips. Main and interaction effects were significant for water loss during composting.

Component-based software development offers a promising solution for taming the complexity found in today's distributed applications. Today's and future distributed software systems will certainly require combining heterogeneous software components that are geographically dispersed. For the successful deployment of such a software system, it is necessary that its realization, based on assembling heterogeneous components, not only meets the functional requirements, but also satisfies the non-functional criteria such as the desired quality of service (QoS). In this paper, a framework based on the notions of a meta-component model, a generative domain model and QoS parameters is described. A formal specification based on two-level grammar is used to represent these notions in a tightly integrated way so that QoS becomes a part of the generative domain model. A simple case study is described in the context of this framework. Copyright © 2002 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]