MBAT: A scalable informatics system for unifying digital atlasing workflows

Background  

Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.     

Comparison of Isoflurane and α-Chloralose in an Anesthetized Swine Model of Acute Pulmonary Embolism Producing Right Ventricular Dysfunction

Pulmonary embolism (PE) is a leading cause of sudden cardiac death, and a model is needed for testing potential treatments. In developing a model, we compared the hemodynamic effects of isoflurane and α-chloralose in an acute swine model of PE because the choice of anesthesia will likely affect the cardiovascular responses of an animal to PE. At baseline, swine that received α-chloralose (n = 6) had a lower heart rate and cardiac output and higher SpO_2, end-tidal CO_2, and mean arterial pressure than did those given isoflurane (n = 9). After PE induction, swine given α-chloralose compared with isoflurane exhibited a lower heart rate (63 ± 10 compared with 116 ± 15 bpm) and peripheral arterial pressure (52 ± 12 compared with 61 ± 12 mm Hg); higher SpO₂ (98% ± 3% compared with 95% ± 1%), end-tidal CO₂ (35 ± 4 compared with 32 ± 5), and systolic blood pressure (121 ± 8 compared with 104 ± 20 mm Hg); and equivalent right ventricular:left ventricular ratios (1.32 ± 0.50 compared with 1.23 ± 0.19) and troponin I mean values (0.09 ± 0.07 ng/mL compared with 0.09 ± 0.06 ng/mL). Isoflurane was associated with widely variable fibrinogen and activated partial thromboplastin time. Intraexperiment mortality was 0 of 6 animals for α-chloralose and 2 of 9 swine for isoflurane. All swine anesthetized with α-chloralose survived with sustained pulmonary hypertension, RV-dilation-associated cardiac injury without the confounding vasodilatory or coagulatory effects of isoflurane. These data demonstrate the physiologic advantages of α-chloralose over isoflurane for anesthesia in a swine model of severe submassive PE.Abbreviations: LV, left ventricle; PAP, pulmonary arterial pressure; PE, pulmonary embolism; RV, right ventriclePulmonary embolism (PE) is one of the leading causes of noncardiac sudden death in Western nations and is the third most common cause of cardiovascular morbidity.^4,6,7,18 In survivors, severe PE damages the right heart, leading to a clinical course complicated by hypotension and circulatory shock, suggesting acute right heart failure in about 10% of patients and followed by persistent pulmonary hypertension or right ventricular dysfunction and dyspnea in at least 15% of patients.^{9,15,16,23,29} To test treatments to reduce right heart failure, a standardized model that is repeatable, accurate, and precise and that mimics the gross pathologic, cardiovascular, pulmonary, autonomic, hematologic, biochemical, and cellular characteristics of PE in humans with disease is needed.⁸Three lines of rationale favor domestic pigs as a model for PE. Several publications, using different methods of anesthesia, have found that swine manifest hemodynamic responses similar to those of humans in the presence of autologous PE, including elevated heart rate, decreased cardiac output, and reduced oxygen saturation.^2,12,30 Swine have similar platelet concentrations, and their coagulation profile on thromboelastography has been shown to be similar to humans, with the exception of higher fibrin crosslinking but less fibrin, leading to resistance to plasmin.^5,11,19,34 Market swine, which would otherwise be destined for slaughter, are relatively cost effective compared with other large animals and are of sufficient size for placement of an adult pulmonary arterial catheter for measurement of pulmonary vascular resistance in a closed-chest preparation.In view of the differences in the hemodynamic effects of different anesthetic agents, the choice of anesthesia will likely affect the cardiovascular responses of an animal to PE. However, current literature lacks a methodologic publication that compares the cardiovascular, right ventricular, pulmonary, and hematologic responses to PE in closed-chest swine models incorporating different anesthetic regimens.Figure 1 presents features of an ideal animal model for the purpose of testing treatments for PE. To develop a swine model of PE that closely resembles this physiologic ideal model, we induced PE in swine maintained in a surgical plane of anesthesia with either isoflurane or α-chloralose. Each of these agents has potential advantages and disadvantages. Isoflurane can be titrated minute by minute but causes undesirable vasodilation, whereas α-chloralose is believed to preserve cardiovascular reflexes but requires heating to dissolve and continuous infusion or repeated boluses.^26,35 We hypothesized that, compared with isoflurane, α-chloralose would meet more of the features described in Figure 1.Open in a separate windowFigure 1.Desirable features of large animal model of severe submassive PE designed for translational research.     

Engaging the Public to Identify Opportunities to Improve Critical Care: A Qualitative Analysis of an Open Community Forum

Objective

To engage the public to understand how to improve the care of critically ill patients.

Design

A qualitative content analysis of an open community forum (Café Scientifique).

Setting

Public venue in Calgary, Alberta, Canada.

Participants

Members of the general public including patients, families of patients, health care providers, and members of the community at large.

Methods

A panel of researchers, decision-makers, and a family member led a Café Scientifique, an informal dialogue between the populace and experts, over three-hours to engage the public to understand how to improve the care of critically ill patients. Conventional qualitative content analysis was used to analyze the data. The inductive analysis occurred in three phases: coding, categorizing, and developing themes.

Results

Thirty-eight members of the public (former ICU patients, family members of patients, providers, community members) attended. Participants focused the discussion and provided concrete suggestions for improvement around communication (family as surrogate voice, timing of conversations, decision tools) and provider well-being and engagement, as opposed to medical interventions in critical care.

Conclusions

Café participants believe patient and family centered care is important to ensure high-quality care in the ICU. A Café Scientifique is a valuable forum to engage the public to contribute to priority setting areas for research in critical care, as well as a platform to share lived experience. Research stakeholders including health care organizations, governments, and funding organizations should provide more opportunities for the public to engage in meaningful conversations about how to best improve healthcare.     

抗花叶病烟草种质资源的鉴定与筛选

本研究以不同来源、不同类型的46个烟草品种为试验材料,进行抗烟草普通花叶病（TMV）特性的田间鉴定和分子鉴定,为筛选抗病烟草种质奠定基础。结果表明,22个品种的烟草抗TMV特性田间鉴定结果与前人鉴定结果基本相同,从24个前人未鉴定的烟草品种中初步筛选出14个中抗品种,8个中感品种和2个感病品种;通过抗TMV基因（CN）的特异引物进行扩增,36个烟草品种的基因组DNA具有特异性片段;通过分子鉴定和田间鉴定的结果比较,62.9%的具有CN或其同源基因的烟草品种田间鉴定表现为中抗或高抗,83.3%的具有CN或其同源基因的选育烟草品种田间鉴定表现为中抗或高抗;结合两种方法,初步确定了3个中感品种和11个中抗品种。     

What really matters in end-of-life discussions? Perspectives of patients in hospital with serious illness and their families

Background:

The guideline-recommended elements to include in discussions about goals of care with patients with serious illness are mostly based on expert opinion. We sought to identify which elements are most important to patients and their families.

Methods:

We used a cross-sectional study design involving patients from 9 Canadian hospitals. We asked older adult patients with serious illness and their family members about the occurrence and importance of 11 guideline-recommended elements of goals-of-care discussions. In addition, we assessed concordance between prescribed goals of care and patient preferences, and we measured patient satisfaction with goals-of-care discussions using the Canadian Health Care Evaluation Project (CANHELP) questionnaire.

Results:

Our study participants included 233 patients (mean age 81.2 yr) and 205 family members (mean age 60.2 yr). Participants reported that clinical teams had addressed individual elements of goals-of-care discussions infrequently (range 1.4%–31.7%). Patients and family members identified the same 5 elements as being the most important to address: preferences for care in the event of life-threatening illness, values, prognosis, fears or concerns, and questions about goals of care. Addressing more elements was associated with both greater concordance between patients’ preferences and prescribed goals of care, and greater patient satisfaction.

Interpretation:

We identified elements of goals-of-care discussions that are most important to older adult patients in hospital with serious illness and their family members. We found that guideline-recommended elements of goals-of-care discussions are not often addressed by health care providers. Our results can inform interventions to improve the determination of goals of care in the hospital setting.In Canada, dying is often an in-hospital, technology-laden experience.^1–4 Rates of cardiopulmonary resuscitation (CPR) before death continue to increase among older adult patients in hospital,⁵ and one-fifth of deaths in hospital occur in an intensive care unit.^1,2,6,7 These observations contrast sharply with patient-reported preferences. A recent Canadian study found that 80% of older adult patients in hospital with a serious illness prefer a less aggressive and more comfort-oriented end-of-life care plan that does not include CPR.⁸Such patients and their families have identified communication with health care providers and decision-making about goals of care as high priorites for improving end-of-life care in Canada.^9,10 We define “decision-making about goals of care” as an end-of-life communication and decision-making process that occurs between a clinician and a patient (or a substitute decision-maker if the patient is incapable) in an institutional setting to establish a plan of care. Often, this process includes deciding whether to use life-sustaining treatments.¹¹ Current guidelines recommend that health care providers address 11 key elements when discussing goals of care with patients and families (Box 1).^12–14 However, these elements are mostly based on expert opinion and lack input from patients and their families.

Box 1:

Key elements of goals-of-care discussions with patients in hospital with serious illness^12–14

• Ask about previous discussions or written documentation about the use of life-sustaining treatments
• Offer a time to meet to discuss goals of care
• Provide information about advance care planning to review before conversations with the physician
• Disclose prognosis
• Ask about patients’ values (i.e., what is important to them when considering health care decisions)
• Provide information about outcomes, benefits and risks of life-sustaining treatments
• Provide information about outcomes, benefits and risks of comfort measures
• Prompt for additional questions about goals of care
• Provide an opportunity to express fears or concerns
• Ask about preferences for care in the event of a life-threatening illness
• Facilitate access to legal documents to record patients’ wishes

Our primary objective was to determine which of these elements are most important to patients and their families. In addition, we examined whether these discussions were associated with concordance between patients’ (or family members’) preferences and prescribed goals of care, and with satisfaction with end-of-life communication and decision-making.     

Accumulation of metals in GOLD4 COPD lungs is associated with decreased CFTR levels

Background

The Cystic Fibrosis Transmembrane conductance Regulator (CFTR) is a chloride channel that primarily resides in airway epithelial cells. Decreased CFTR expression and/or function lead to impaired airway surface liquid (ASL) volume homeostasis, resulting in accumulation of mucus, reduced clearance of bacteria, and chronic infection and inflammation.

Methods

Expression of CFTR and the cigarette smoke metal content were assessed in lung samples of controls and COPD patients with established GOLD stage 4. CFTR protein and mRNA were quantified by immunohistochemistry and quantitative RT-PCR, respectively. Metals present in lung samples were quantified by ICP-AES. The effect of cigarette smoke on down-regulation of CFTR expression and function was assessed using primary human airway epithelial cells. The role of leading metal(s) found in lung samples of GOLD 4 COPD patients involved in the alteration of CFTR was confirmed by exposing human bronchial epithelial cells 16HBE14o- to metal-depleted cigarette smoke extracts.

Results

We found that CFTR expression is reduced in the lungs of GOLD 4 COPD patients, especially in bronchial epithelial cells. Assessment of metals present in lung samples revealed that cadmium and manganese were significantly higher in GOLD 4 COPD patients when compared to control smokers (GOLD 0). Primary human airway epithelial cells exposed to cigarette smoke resulted in decreased expression of CFTR protein and reduced airway surface liquid height. 16HBE14o-cells exposed to cigarette smoke also exhibited reduced levels of CFTR protein and mRNA. Removal and/or addition of metals to cigarette smoke extracts before exposure established their role in decrease of CFTR in airway epithelial cells.

Conclusions

CFTR expression is reduced in the lungs of patients with severe COPD. This effect is associated with the accumulation of cadmium and manganese suggesting a role for these metals in the pathogenesis of COPD.     

The Importance of Intraoperative Selenium Blood Levels on Organ Dysfunction in Patients Undergoing Off-Pump Cardiac Surgery: A Randomised Controlled Trial

Introduction

Cardiac surgery is accompanied by an increase of oxidative stress, a significantly reduced antioxidant (AOX) capacity, postoperative inflammation, all of which may promote the development of organ dysfunction and an increase in mortality. Selenium is an essential co-factor of various antioxidant enzymes. We hypothesized a less pronounced decrease of circulating selenium levels in patients undergoing off-pump coronary artery bypass (OPCAB) surgery due to less intraoperative oxidative stress.

Methods

In this prospective randomised, interventional trial, 40 patients scheduled for elective coronary artery bypass grafting were randomly assigned to undergo either on-pump or OPCAB-surgery, if both techniques were feasible for the single patient. Clinical data, myocardial damage assessed by myocard specific creatine kinase isoenzyme (CK-MB), circulating whole blood levels of selenium, oxidative stress assessed by asymmetric dimethylarginine (ADMA) levels, antioxidant capacity determined by glutathionperoxidase (GPx) levels and perioperative inflammation represented by interleukin-6 (IL-6) levels were measured at predefined perioperative time points.

Results

At end of surgery, both groups showed a comparable decrease of circulating selenium concentrations. Likewise, levels of oxidative stress and IL-6 were comparable in both groups. Selenium levels correlated with antioxidant capacity (GPx: r = 0.720; p<0.001) and showed a negative correlation to myocardial damage (CK-MB: r = −0.571, p<0.001). Low postoperative selenium levels had a high predictive value for the occurrence of any postoperative complication.

Conclusions

OPCAB surgery is not associated with less oxidative stress and a better preservation of the circulating selenium pool than on-pump surgery. Low postoperative selenium levels are predictive for the development of complications.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01409057","term_id":"NCT01409057"}}NCT01409057     

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark''s Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.     

Fewer peak trials per session facilitate acquisition of peak responding despite elimination of response rate differences

It has been shown in previous research [Kaiser, D.H., 2008. The proportion of fixed interval trials to probe trials affects acquisition of the peak procedure fixed interval timing task. Behav. Process., 77 (1), 100-108] that rats acquired peak responding sooner when fewer peak trials were presented during sessions of training with the peak procedure timing task. One potential problem with that research was that there were large differences in response rates among the groups. The present experiment attempted to examine the effect of proportion of peak trials when differences in response rate were controlled. Two groups of rats were each simultaneously tested with two versions of the peak procedure. One group was tested with 10% peak trials per session, and the other group was tested with 50% peak trials per session. For both of the groups, one of the panel lights and levers was associated with the traditional peak procedure. The other panel light and lever was associated with a similar peak procedure; however, reinforcement was provided at the end of each peak trial. This manipulation eliminated differences in response rate among the groups, however, Group 10% acquired peak responding more quickly than Group 50%, effectively replicating previous work in the absence of a response bias.