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The volume and complexity of biological and biomedical research continues to grow exponentially with cutting-edge technologies such as high-throughput sequencing. Unfortunately, bioinformatics analysis is often considered only after data have been generated, which significantly limits the ability to make sense of complex big data. This unique book introduces the idea of No-Boundary Thinking (NBT) in biological and biomedical research, which aims to access, integrate, and synthesize data, information, and knowledge from bioinformatics to define important problems and articulate impactful research questions. This interdisciplinary volume brings together a team of bioinformatics specialists who draw on their own experiences with NBT to illustrate the importance of collaborative science. It will help stimulate discussion and application of NBT, and will appeal to all biomedical researchers looking to maximize their use of bioinformatics for making scientific discoveries.
As a result of the wildfire that engulfed Fort McMurray (FMM), Alberta, Canada in May 2016, over 90,000 residents were evacuated from the city. Approximately 2400 homes, or 10% of the housing stock, were destroyed in Fort McMurray. About 200,000 hectors of forest were destroyed by the fire, which reached into Saskatchewan. In the aftermath of a major disaster, a community’s infrastructure is disrupted, and psychological, economic, and environmental effects can last for many years.
Intensive research was conducted in Fort McMurray five years after the wildfire disaster to determine the prevalence of major depressive disorder (MDD) and post-traumatic stress disorder (PTSD) among residents of the community and to determine the demographic, clinical, and other risk factors of probable MDD and PTSD.
An online questionnaire administered via REDCap was used to collect data in a quantitative cross-sectional study between 24 April and 2 June 2021. Patients were asked to complete the Patient Health Questionnaire (PHQ-9) in order to assess the presence of symptoms associated with MDD. An assessment of likely PTSD in respondents was conducted using the PTSD Checklist for DSM-5 (PCL-C). In this study, descriptive, univariate, and multivariate regression analyses were conducted.
Out of 249 people who accessed the survey link, 186 completed it (74.7% response rate). There was a median age of 42 among the subscribers. A majority of the sample consisted of 159 (85.5%) females; 98 (52.7%) over the age of 40; 136 (71%) in a relationship; and 175 (94.1%) employed. Our study sample had an overall prevalence of 45.0% (76) of MDD symptoms. The multivariate logistic regression model revealed four variables that were independently associated with MDD symptoms, including being unemployed, diagnosed with MDD, taking sedative-hypnotics, and willingness to receive mental health counseling. A total of 39.6% of our respondents (65) reported having likely PTSD. Three independent variables: received a mental health depression diagnosis from a health professional, would like to receive mental health counseling, and have only limited or no support from familycontributed significantly to the model for predicting likely PTSD among respondents while controlling the other factors in the regression model.
The findings of this study indicate that unemployment, the use of sleeping pills, the presence of a previous depression diagnosis, and the willingness to seek mental health counseling are significant factors associated with the increase in the prevalence of MDD and PTSD following wildfires. Support from family members may prevent these conditions from developing.
As a result of the floods in Fort McMurray (FMM) and the surrounding area in 2020, more than $228 million in insured damage was sustained, over 1200 structures were damaged, and more than 13,000 people were evacuated from their homes.
The aim of the study was to determine the prevalence of post-traumatic stress disorder (PTSD)-like symptoms among the population of FMM one year after the flood in 2020 and the risk predictors associated with such symptoms.
In order to collect sociodemographic, clinical, and flood-related information from residents of FMM via REDCap, an online quantitative cross-sectional survey was administered between April 24 and June 02, 2021. Respondents were assessed for probable PTSD using the PTSD Checklist for DSM-5 (PCL-C).
An overall response rate of 74.7% was achieved among 186 of 249 respondents. The prevalence of likely post-traumatic stress disorder was 39.6% (65). There was a significantly increased likelihood of developing PTSD symptoms in respondents with a history of depression (OR= 5.71; 95% CI: 1.68 - 19.36). As well, disaster responders experiencing limited and no family support after the disaster were more likely to report PTSD symptoms (OR= 2.87; 95% CI: 1.02 - 8.05) and (OR= 2.87; 95% CI: 1.06 - 7.74), respectively.
As a result of our study, we found that those who had a history of depression and had sought health counseling were significantly more likely to develop PTSD symptoms following flooding, while those with family support were less likely to suffer from PTSD symptoms. There is a need for further studies to investigate the relationship between the need for counseling and the presentation of potential symptoms of post-traumatic stress disorder.
The critical effect of the windward interior angles of elastically mounted trapezoidal bodies on a galloping instability is numerically investigated in this paper using two methodologies of high-fidelity computational fluid dynamics simulations and data-driven stability analysis using the eigensystem realization algorithm. A micro exploration of the dynamical response is processed to understand the mechanism underpinning the structural amplification at the initial stage of the galloping instability and the competition between wake and structural modes. It is observed that very small changes in the windward interior angle of an isosceles-trapezoidal body can provoke or suppress galloping – indeed, a small decrease or increase (low to $1^\circ$) of the windward interior angle from a right angle ($90^\circ$) can result in a significant enhancement and complete suppression, respectively, of the galloping oscillations. This supports our hypothesis that the contraction and/or expansion (viz., fore-aft tapering and/or widening) of the cross-section in the streamline direction has potential influences on galloping triggering from the geometrical perspective. The data-driven stability analysis is also applied to verify and analyse this phenomenon from the perspective of modal analysis. The experimental measurements are also conducted in the wind tunnel to support this hypothesis.
The target backsheath field acceleration mechanism is one of the main mechanisms of laser-driven proton acceleration (LDPA) and strongly depends on the comprehensive performance of the ultrashort ultra-intense lasers used as the driving sources. The successful use of the SG-II Peta-watt (SG-II PW) laser facility for LDPA and its applications in radiographic diagnoses have been manifested by the good performance of the SG-II PW facility. Recently, the SG-II PW laser facility has undergone extensive maintenance and a comprehensive technical upgrade in terms of the seed source, laser contrast and terminal focus. LDPA experiments were performed using the maintained SG-II PW laser beam, and the highest cutoff energy of the proton beam was obviously increased. Accordingly, a double-film target structure was used, and the maximum cutoff energy of the proton beam was up to 70 MeV. These results demonstrate that the comprehensive performance of the SG-II PW laser facility was improved significantly.
The control of a wing-in-ground craft (WIG) usually allows for many needs, like cruising, speed, survival and stealth. Various degrees of emphasis on these requirements result in different trajectories, but there has not been a way of integrating and quantifying them yet. Moreover, most previous studies on other vehicles’ multi-objective trajectory is planned globally, lacking for local planning. For the multi-objective trajectory planning of WIGs, this paper proposes a multi-objective function in a polynomial form, in which each item represents an independent requirement and is adjusted by a linear or exponential weight. It uses the magnitude of weights to demonstrate how much attention is paid relatively to the corresponding demand. Trajectories of a virtual WIG model above the wave trough terrain are planned using reward shaping based on the introduced multi-objective function and deep reinforcement learning (DRL). Two conditions are considered globally and locally: a single scheme of weights is assigned to the whole environment, and two different schemes of weights are assigned to the two parts of the environment. Effectiveness of the multi-object reward function is analysed from the local and global perspectives. The reward function provides WIGs with a universal framework for adjusting the magnitude of weights, to meet different degrees of requirements on cruising, speed, stealth and survival, and helps WIGs guide an expected trajectory in engineering.
The paper addresses the six-degree-of-freedom coupled control problem for spacecraft formation flying subject to actuator saturation and input quantisation whilst considering limited communication resources. Firstly, a novel event-triggered distributed observer without continuous communications is presented to recover the information of the virtual leader. Remarkably, by embedding a hyperbolic tangent function-based nonlinear term into the triggering condition, the event-based observer realises a more reasonable trigger threshold. Subsequently, an adding-a-power-integrator-based fixed-time control algorithm is proposed for the follower spacecraft. Further, the control scheme ingeniously compensates for the actuator saturation and the input quantisation problems without embedding auxiliary systems. Finally, numerical simulations are carried out to highlight the advantages of the theoretical results.
To evaluate risk factors for poor prognosis in vocal fold leukoplakia.
Clinical data were collected for 344 patients with vocal fold leukoplakia who received surgical treatment in our otolaryngology department from October 2010 to June 2019. Univariate and multivariate logistic regression analyses of the relevant factors were conducted.
Among the 344 patients, 98 exhibited recurrence and 30 underwent a malignant change. Multivariate logistic regression analysis showed that size of the lesion (p = 0.03, odds ratio = 2.14), form of the lesion under white light (p < 0.001), surgical method (p < 0.001, odds ratio = 0.28) and pathological type (p < 0.001) were independent factors that affected the recurrence of vocal fold leukoplakia. In both univariate and multivariate analyses, the sole independent risk factor for malignant transformation of vocal fold leukoplakia was pathological type (p < 0.001).
The outlook for vocal fold leukoplakia depends on several clinical factors, especially pathological type. The more severe the pathological type, the more likely it is to recur or become cancerous.
OBJECTIVES/GOALS: Our long-term goal is to understand how both genetic and environmental (GxE) factors contribute to neurodevelopmental disorders (NDDs) so that we may potentially intervene in disease pathogenesis and design therapies to address functional deficiencies. METHODS/STUDY POPULATION: Our studies use a novel GxE model to determine how cephalosporin antibiotic exposure alters the gut microbiome, hippocampal neurogenesis, and behavior in the genetically vulnerable 16p11.2 microdeletion (16pDel) mouse. This mouse models one of the most frequently observed genetic risk variants implicated in NDDs, including ~1% of autism diagnoses. Wildtype and 16pDel littermates were exposed to saline or the cephalosporin, cefdinir, from postnatal days 5-9. We quantified changes in gut microbiota composition using 16S rRNA gene sequencing and utilized immunoblotting, immunohistochemistry, and bulk RNA gene sequencing to assess changes in hippocampal neurogenesis. An additional cohort of saline or cefdinir-exposed mice were subjected to a behavioral battery to assess changes in sociability and anxiety. RESULTS/ANTICIPATED RESULTS: We leveraged the next-generation microbiome bioinformatics platform, Quantitative Insights Into Microbial Ecology 2 (QIIME2) to analyze 16S rRNA gene sequencing datasets of P13 cecal samples from saline- and cefdinir-exposed mice. We found successful perturbations to the gut microbiome following early life cefdinir exposure. Further, we found a robust 50% reduction in hippocampal cyclin E protein in cefdinir-exposed 16pDel male mice, which was replicated in a second independent experiment. This reduction extended to the S-phase cell entry and general stem cell population, quantified by EdU+ and Ki67+ cell numbers, respectively. Lastly, in our first cohort of mice for behavioral studies, we found reduced sociability and increased anxiety-like behaviors in cefdinir-exposed mice. DISCUSSION/SIGNIFICANCE: The findings from this GxE model will provide mechanistic insights into the causes of NDDs; they may inform practice guidelines so as to reduce this environmental exposure; and may suggest interventions like probiotics for those at risk in order to overcome altered gut microbiome composition and restore hippocampal neurogenesis defects.
To examine the perspectives of caregivers that are not part of the antibiotic stewardship program (ASP) leadership team (eg, physicians, nurses, and clinical pharmacists), but who interact with ASPs in their role as frontline healthcare workers.
Qualitative semistructured interviews.
The study was conducted in 2 large national healthcare systems including 7 hospitals in the Veterans’ Health Administration and 4 hospitals in Intermountain Healthcare.
We interviewed 157 participants. The current analysis includes 123 nonsteward clinicians: 47 physicians, 26 pharmacists, 29 nurses, and 21 hospital leaders.
Interviewers utilized a semistructured interview guide based on the Consolidated Framework for Implementation Research (CFIR), which was tailored to the participant’s role in the hospital as it related to ASPs. Qualitative analysis was conducted using a codebook based on the CFIR.
We identified 4 primary perspectives regarding ASPs. (1) Non-ASP pharmacists considered antibiotic stewardship activities to be a high priority despite the added burden to work duties: (2) Nurses acknowledged limited understanding of ASP activities or involvement with these programs; (3) Physicians criticized ASPs for their restrictions on clinical autonomy and questioned the ability of antibiotic stewards to make recommendations without the full clinical picture; And (4) hospital leaders expressed support for ASPs and recognized the unique challenges faced by non-ASP clinical staff.
Further understanding these differing perspectives of ASP implementation will inform possible ways to improve ASP implementation across clinical roles.
There are many factors causing the shimmy of the aircraft landing gear and structural clearance of landing gear is a typical factor. Some aircraft in service or operation did not shimmy before, but suddenly appeared after a period of use. To solve the problem of clearance shimmy during the service of a certain aircraft, we established a dynamic model of rotating gear with clearance based on the flexible multi-body dynamics model of landing gear and L-N contact theory. We defined different types of clearance and established a mechanical model of aircraft pendulum vibration considering the clearance of landing gear structure for dynamic simulation, and studied the effects of different clearance types, clearance size of motion pair and different clearance positions on the stability of pendulum. The results show that the axial clearance has little effect on the shimmy performance of landing gear; the radial clearance has a certain effect on the shimmy performance of medium speed running, which slightly improves the shimmy damping required by medium speed running; the rotational clearance affects the shimmy performance of the nose landing gear by affecting the force transmission of structural components. The required shimmy damping coefficient increases at low speed and decreases at high speed. The main reason for the return clearance is that during the return, the shimmy damper does not work, which leads to the decrease of the shimmy damping performance and the increase of the required shimmy damping coefficient in the whole speed range. Meanwhile, the structural clearance will increase the shimmy frequency of the nose landing gear. By analysing the yaw angle of the nose landing gear and the time domain curve of the yaw angle of the yaw damper, we can determine which structure of the landing gear and which type of clearance is the cause of the yaw. Finally, the coupling effect caused by the main structural parameters of the landing gear in “gap shimmy” was analysed according to different mechanical stability distances and strut stiffness of the nose landing gear, providing reference for aircraft anti-shimmy design, nose landing gear fault diagnosis and nose landing gear maintenance support.
As a typical plasma-based optical element that can sustain ultra-high light intensity, plasma density gratings driven by intense laser pulses have been extensively studied for wide applications. Here, we show that the plasma density grating driven by two intersecting driver laser pulses is not only nonuniform in space but also varies over time. Consequently, the probe laser pulse that passes through such a dynamic plasma density grating will be depolarized, that is, its polarization becomes spatially and temporally variable. More importantly, the laser depolarization may spontaneously take place for crossed laser beams if their polarization angles are arranged properly. The laser depolarization by a dynamic plasma density grating may find application in mitigating parametric instabilities in laser-driven inertial confinement fusion.
In this chapter, we study the economic issues of fresh data trading markets, where the data freshness is captured by Age-of-Information (AoI). In our model, a destination user requests, and pays for, fresh data updates from a source provider. In this work, the destination incurs an age-related cost, modeled as a general increasing function of the AoI. To understand economic viability and profitability of fresh data markets, we consider a pricing mechanism to maximize the source’s profit, while the destination chooses a data update schedule to trade off its payments to the source and its age-related cost. The problem is exacerbated when the source has incomplete information regarding the destination’s age-related cost, which requires one to exploit (economic) mechanism design to induce the truthful information. This chapter attempts to build such a fresh data trading framework that centers around the following two key questions: (a) How should a source choose the pricing scheme to maximize its profit in a fresh data market under complete market information? (b) Under incomplete information, how should a source design an optimal mechanism to maximize its profit while ensuring the destination’s truthful report of its age-related cost information?
In the present study, we investigated the influence of different mid-stage N compensation timings on agronomic and physiological traits associated with grain yield and quality in field experiments. Two japonica rice cultivars with a good tasting quality (Nangeng 9108 and Nangeng 5055) were examined under eight N compensation timings (N1–N6: one-time N compensation at 7-2 weeks before heading; N7: split N compensation at 5 and 3 weeks before heading; N8: split N compensation at 4 and 2 weeks before heading) and a control with no N compensation. The highest yield was obtained with N7, followed by N3. The yield advantage is mainly attributable to the improved population structure (higher productive tiller rate with a stable number of effective panicles), higher total number of spikelets per unit area (large panicles with more grains per panicle), larger leaf area index in the late period and higher photosynthetic production capacity (more dry matter accumulation and transportation in the middle and late periods). Delaying N compensation timing improved the processing and nutritional quality of rice, but decreased the quality of appearance and cooking/eating traits. Our results suggest that, from the perspective of achieving relative coordination between high yield and high quality of japonica rice, the optimal N compensation should be divided equally at 5 and 3 weeks before heading. However, if simplifying the number of operations and the pursuit of eating quality were considered, one-time N compensation should be conducted at 5 weeks before heading.