Ensemble Detection of DNA Engineering Signatures

Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.

A new scoring system to predict mortality in community-acquired pneumonia: CURB (S)-65

OBJECTIVE

The first decision to be made in the case of community-acquired pneumonia (CAP) is whether hospitalization of the patient is mandatory. In this study, we aimed to investigate whether the addition of oxygenation parameters to CURB-65 has diagnostic value in predicting mortality in CAP.

PATIENTS AND METHODS

A total of 903 CAP patients were included in the study. Patients with a CURB-65 score of 0 and 1 were classified as Group 1 and patients with a CURB-65 score of 2 or more were classified as Group 2. The prediction of mortality through Pneumonia Severity Index (PSI), CURB-65 and CURBS-65/CURBP-65 with the addition of SaO2 and PaO2 values; hence the four different models, was compared among all patient groups.

RESULTS

As a result, 3.3% of the cases in Group 1 and 12.7% of the cases in Group 2 died. In both CURB-65 groups, it was noted that the frequency of patients with SaO2 <90% was significantly higher in the dead group than in the alive patient group (p=0.009 and p=0.001, respectively). In the univariate analysis, PaO2<60, and SaO2<90 were significantly associated with mortality. Model 2 (CURBS-65) and Model 3 (CURBP- 65) were examined, SaO2<90 (OR 2.08) was found to have an effect on death. In predicting mortality by the receiver operating characteristics (ROC) analysis, it was understood that the CURBS-65 score had a slightly higher area under the curve (AUC) value than CURB-65.

CONCLUSIONS

As a result, it has been shown that the use of CURBS-65 scoring instead of CURB-65 clinical scoring may be more useful in predicting mortality.

TASBE Flow Analytics: A Package for Calibrated Flow Cytometry Analysis

Flow cytometry is a powerful method for high-throughput precision measurement of cell fluorescence and size. Effective use of this tool for quantification of synthetic biology devices and circuits, however, generally requires careful application of complex multistage workflows for calibration, filtering, and analysis with appropriate statistics. The TASBE Flow Analytics package provides a free, open, and accessible implementation of such workflows in a form designed for high-throughput analysis of large synthetic biology data sets. Given a set of experimental samples and controls, this package can process them to output calibrated data, quantitative analyses and comparisons, automatically generated figures, and detailed debugging and diagnostic reports in both human-readable and machine-readable forms. TASBE Flow Analytics can be used through a simple user-friendly interactive Excel interface, as a library supporting Matlab, Octave, or Python interactive sessions, or as a component integrated into automated workflows.

Reports of the 2018 AAAI Fall Symposium

The AAAI 2018 Fall Symposium Series was held Thursday through Saturday, October 18–20, at the Westin Arlington Gateway in Arlington, Virginia, adjacent to Washington, D.C. The titles of the eight symposia were Adversary-Aware Learning Techniques and Trends in Cybersecurity; Artificial Intelligence for Synthetic Biology; Artificial Intelligence in Government and Public Sector; A Common Model of Cognition; Gathering for Artificial Intelligence and Natural System; Integrating Planning, Diagnosis, and Causal Reasoning; Interactive Learning in Artificial Intelligence for HumanRobot Interaction; and Reasoning and Learning in Real-World Systems for Long-Term Autonomy. The highlights of each symposium (except the Gathering for Artificial Intelligence and Natural System symposium, whose organizers failed to submit a summary) are presented in this report.

Accurate predictions of genetic circuit behavior from part characterization and modular composition

A long-standing goal of synthetic biology is to rapidly engineer new regulatory circuits from simpler devices. As circuit complexity grows, it becomes increasingly important to guide design with quantitative models, but previous efforts have been hindered by lack of predictive accuracy. To address this, we developed Empirical Quantitative Incremental Prediction (EQuIP), a new method for accurate prediction of genetic regulatory network behavior from detailed characterizations of their components. In EQuIP, precisely calibrated time-series and dosage-response assays are used to construct hybrid phenotypic/mechanistic models of regulatory processes. This hybrid method ensures that model parameters match observable phenomena, using phenotypic formulation where current hypotheses about biological mechanisms do not agree closely with experimental observations. We demonstrate EQuIP's precision at predicting distributions of cell behaviors for six transcriptional cascades and three feed-forward circuits in mammalian cells. Our cascade predictions have only 1.6-fold mean error over a 261-fold mean range of fluorescence variation, owing primarily to calibrated measurements and piecewise-linear models. Predictions for three feed-forward circuits had a 2.0-fold mean error on a 333-fold mean range, further demonstrating that EQuIP can scale to more complex systems. Such accurate predictions will foster reliable forward engineering of complex biological circuits from libraries of standardized devices.

Influence of caffeic acid phenethyl ester on bone healing in a rat model

OBJECTIVE

To examine the effects of caffeic acid phenethyl ester (CAPE; a component of honey bee-hive propolis with antioxidant, anti-inflammatory, antiviral and anticancer properties) on bone regeneration and fibrotic healing in a rat model.

METHODS

Male Sprague-Dawley rats (n = 63; mean age 7 weeks; weight 280-490 g) were randomly divided into three groups: A, cranial defect with no bone healing treatment (n = 21); B, cranial defect treated with CAPE (n = 21); C, cranial defect treated with CAPE and β-tricalcium phosphate/hydroxyl apatite (n = 21). Rats were anaesthetized with ketamine (8 mg/100 g) by intraperitoneal injection and a cranial critical size bone defect was created. Following surgery, CAPE (10 µmol/kg) was administered by daily intraperitoneal injection. Seven rats in each group were killed at days 7, 15 and 30 following surgery. Bone regeneration, fibrotic healing and osteoblast activity were evaluated by histopathology.

RESULTS

Statistically significant differences in healing were found between all groups. There were no statistically significant within-group differences between day 7 and 15. At day 30, bone healing scores were significantly higher in groups B and C compared with group A.

CONCLUSION

CAPE significantly improved bone-defect healing in a rat model, suggesting that CAPE has beneficial effects on bone healing.

Frequency of respiratory function disorders among dental laboratory technicians working under conditions of high dust concentration

BACKGROUND AND OBJECTIVES

Dental laboratory technicians (DLTs) have much exposure to mineralogical dust that may have adverse effects on their lung health. The aim of our study was to investigate occupational dust exposure, and to determine the frequency of respiratory function disorders and radiologic abnormalities among DLTs.

MATERIALS AND METHODS

The study enrolled 94 DLTs who were exposed to dust in dental laboratories and 94 control subjects. Dust concentrations in the workplaces were measured.

RESULTS

The mean age of DLTs was 30.70 ± 9.84 years. No significant difference was found between the DLTs and the control groups for age or smoking status (p > 0.05). Spirometric values for the DLTs were found to be lower than the control group (p < 0.05). The mean working period for DLTs was 9.19±5.9 years. The pulmonary function test results for the DLTs showed that 65.9% had a normal pattern, 22.4% were restrictive, and 11.7% showed obstructive type pulmonary function disorder. Negative correlations were found between the working period time and Forced Expiratory Volume in 1 second in the DLTs (R = -0.675 p = 0.000). Negative correlations were also found between working period time and Forced Vital Capacity in the DLTs (R = -0.720 p = 0.000). All DLTs had chest X-rays and 16 (17%) of them showed radiological pneumoconiosis.

CONCLUSIONS

This study showed a negative association between level of respiratory function and working period in DLTs.

An end-to-end workflow for engineering of biological networks from high-level specifications

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

Automated selection of synthetic biology parts for genetic regulatory networks

Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps.

MR T1 and T2 relaxations in cysts and abscesses measured by 1.5 T MRI

OBJECTIVES

The main objective of this study was to make a comparison between the relaxation rates in jaw cysts and abscesses. Such a comparison should provide quantitative information for MR image analysis.

METHODS

A phantom containing 20 odontogenic jaw cysts and 11 jaw abscesses was imaged with 1.5 T MR. T(1) measurements were performed by using a mixed sequence of inversion recovery and spin echo, while T(2) measurements were carried out by the Carr-Purcell Meiboom-Gill (CPMG) sequence. Cystic fluids and abscesses were compared statistically.

RESULTS

In cysts and abscesses, respectively, the mean 1/T(1) was 0.9355 s(-1) and 0.8245 s(-1) and the mean 1/T(2) was 2.4575 s(-1) and 4.7073 s(-1). The 1/T(2) in cysts was very highly significantly different from that in abscesses (p = 0.0001). Both T(1) and T(2) were linearly proportional to material contents. T(2) relaxivities [26.458 ml (g s)(-1) for abscesses and 21.455 ml (g s)(-1) for cysts] were higher than T(1) relaxivities [5.4766 ml (g s)(-1) for abscesses and 10.075 ml (g s)(-1) for cysts].

DISCUSSION

Present T(2) measurements differentiate cysts from abscesses with a confidence interval of 95%. Because in vivo and in vitro image contrasts are changed by the same parameters, the T(2) findings should present valuable information for in vivo MRI. Hence the significant difference and the relaxivities may provide quantitative information for clinicians and researchers making image analyses.

CONCLUSION

T(2) may differentiate cysts from abscesses. The difference in T(2) is related to the material content of samples.

Assesment of correlation between bispectral index and four common sedation scales used in mechanically ventilated patients in ICU

PURPOSE

The aim of this study was to compare the correlation between bispectral index (BIS) monitor and four commonly used subjective clinical scales (Ramsay Sedation Scale (RSS), Richmond Agitation Sedation Scale (RASS), Sedation Agitation Scale, Adaptation to Intensive Care Environment scale) in mechanically ventilated patients in intensive care unit (ICU). In addition, comparison of responsiveness of the clinical scales in respect to BIS changes is another goal of this study.

MATERIALS AND METHODS

Mechanically ventilated thirty patients who required sedation for any reason were enrolled to study. Patients who needed neuromuscular blockade, patients with known hearing and visual problems, neurological diseases, anoxic encephalopathy, mental retardation and who developed hemodynamic instability (mean arterial pressure below 60 mmHg) and hypoxemia (sPO2 below 90%) during follow-up were excluded. Starting before the initiation of sedation, first BIS scores then clinical sedation scales were evaluated. This procedure is repeated every 2 hours for 24 hours.

RESULTS

All of the four clinical scales were significantly correlated with BIS. BIS and clinical scale values, except Adaptation to Intensive Care Environment scale, showed significant changes compared to baseline after the initiation of sedation. Ramsay and Richmond scales showed the highest correlation with BIS (respectively, r = 0.758, r = 0.750). Adaptation to Intensive Care Environment revealed the lowest correlation (r = 0.565).

CONCLUSIONS

All of the scales were significantly correlated with BIS. RSS and RASS showed higher correlation than other scales. As a conclusion: RSS and RASS can be used for monitoring the depth of sedation in mechanically ventilated patients in ICU.

Bruxism: is it a new sign of the cardiovascular diseases?

AIM

To determine the relationship between bruxism and cardiovascular diseases.

MATERIALS AND METHODS

120 patients who referred to the Dentistry Faculty with the complaint of bruxism were selected. All patients gave informed consent for participation in the study. All of the patients were examined and bruxism was classified. And also these were examined by B-mode ultrasound to measure the Intima Media Thickness (IMT) at the far wall of the common carotid artery. A wide range of vascular risk factors including age, gender, body mass index, and previous history were surveyed. Spearman correlation analysis was performed to ascertain quantitative comparison, Mann-Whitney U and Kruskal-Wallis test were used for comparison of means

RESULTS

There were 66 (55%) male and 54 (45%) female patients, with a female to male ratio of 1/1.2. The mean age was 35.6 +/- 1,25 years (range 18-65 years). In the analysis of bruxism classification and IMT there was a statistical significance between bruxism classification subgroup 1, 2, 3 and IMT. There was no statistical significance between bruxism classification Subgroup 4 and IMT due to the small number of the patients (n = 12).

CONCLUSIONS

Stressful situations can cause both bruxism and cardiovascular disease such as coronary artery diseases, hypertension, arrhythmias, cardiomyopathy. The statistical analysis supported this hypothesis. However, we need to new studies with large number of samples to confirm this hypothesis. Clearly, future studies in this field will need to take into consideration the influence of the following variables: age, use of medication or drugs, smoking habits, and other sleep disorders.

Phosphodiesterase-5 inhibitors may facilitate bone defect recovery

BACKGROUND AND OBJECTIVES

Bone healing is still one of the most important problems of the oral and maxillofacial surgery procedures. This study was designed to evaluate the effect of sildenafil citrate (which is used for erectile dysfunction) on bone defect healing in an experimental animal model.

MATERIALS AND METHODS

A total of 42 male Wistar-albino rats were randomly assigned to the control group (n=21) or the study group (n=21). The control group was fed on a standard laboratory diet until 12 h before surgery, whereas the study group received Sildenafil citrate via orogastric tube 10 mg/kg once a day for 30 days. Under anaesthesia, a 3 x 3 x 2 mm depth defect was made on tibia of each rat. 7 animals from each group were euthanised on postoperative days 7,15 and 30. Bone samples were taken for examination, histologically on day 7, by 3D dental tomography on day 15, and for bone strength resistance on day 30.

RESULTS

Statistically significant differences were determined between the groups from the inflammatory and repair phase, with the healing process being more advanced in the Sildenafil group.

CONCLUSIONS

Sildenafil citrate can be used as a supporting factor to accelerate the healing process of bone. In future comprehensive studies will need to demonstrate the Sildenafil citrate affect on bone defect healing.

RECYCLE

A workflow is a model of a process that systematically describes patterns of activity. Workflows capture a sequence of operations, their enablement conditions, and data flow dependencies among them. It is hard to design a complete and correct workflow from scratch, while it is much easier for humans to demonstrate the solution than to state the solution declaratively.

This article presents RECYCLE, our approach to learning workflow models from example demonstration traces. RECYCLE captures control flow, data flow, and enablement conditions of an underlying workflow process. Unlike prior work from workflow mining and AI planning literature, (1) RECYCLE can learn from a single demonstration trace with loops, (2) RECYCLE learns both loop and conditional branch structure, and (3) RECYCLE handles data flow among actions.

In this article, we describe the phases of RECYCLE's learning algorithm: substructure analysis and node abstraction. To ground the discussion, we present a simplified flight reservation system with some of the important characteristics of the real domains we worked with. We present some results from a patient transport domain.

Photon-pair generation by four-wave mixing in optical fibers

We present a theory to quantify a fundamental limit on correlated photon pairs generated through four-wave mixing inside optical fibers in the presence of spontaneous Raman scattering (SpRS). Our theory is able to explain current experimental data. We show that if correlated photon pairs are generated with polarization orthogonal to the pump the effect of SpRS is significantly reduced over a broad spectral region extending from 5 to 15 THz.

Pump-noise transfer in dual-pump fiber-optic parametric amplifiers: walk-off effects

Transfer of intensity noise from pumps to signal in dual-pump fiber-optic parametric amplifiers is simulated numerically for a realistic configuration in which both pumps are amplified and filtered before they enter the fiber. The walk-off effects induced by different group velocities of pumps, signal, and idler are fully taken into account. It is found that the optical signal-to-noise ratio can be as low as 15 dB when the amplifier length is close to 0.5 km, but it can be improved by 3 dB or so by use of longer fibers.

SHOP2: An HTN Planning System

The SHOP2 planning system received one of the awards for distinguished performance in the 2002 International Planning Competition. This paper describes the features of SHOP2 which enabled it to excel in the competition, especially those aspects of SHOP2 that deal with temporal and metric planning domains.

Nonlinear theory of polarization-mode dispersion for fiber solitons

We consider the evolution of optical solitons inside a nonlinear dispersive fiber with random birefringence, causing polarization-mode dispersion. We convert the pair of coupled nonlinear Schrödinger equations satisfied by the orthogonally polarized components into a Fokker-Planck equation using the collective-variable approach. We solve this equation and derive expressions for the probability density functions associated with the differential group delay and the pulse width in the limit of large propagation distances.

Treatment of aggressive non-Hodgkin's lymphoma with dose-intensified epirubicin in combination of cyclophosphamide, vincristine, and prednisone (CEOP-100): a phase II study

Epirubicin is an agent with a lower incidence of cardiotoxicity and myelotoxicity compared with doxorubicin; and it is active in patients with non-Hodgkin's lymphoma (NHL). Our aim was to define the therapeutic efficacy and toxicity of dose-intensified epirubicin in combination with cyclophosphamide, vincristine, and prednisone (CEOP) in patients with diffuse large-cell NHL. Previously untreated patients aged between 15 and 75 years, with at least one measurable lesion, adequate liver, renal, cardiac functions, and no central nervous system involvement were included in the study. The planned chemotherapy regimen CEOP consisted of cyclophosphamide 750 mg/m2, epirubicin 100 mg/m2, and vincristine 1.4 mg/m2 intravenously on day 1 and 100 mg prednisone taken orally on days 1 to 5. Courses were repeated every 21 days. Patients with stage I and II received four cycles of chemotherapy followed by involved-field radiotherapy, and patients with stage III and IV received six cycles of chemotherapy followed by radiotherapy to bulky lymph node sites. Seventy-five patients were enrolled in the study. The complete response rate was 83.8%, and 72 patients were assessable for toxicity. The most common toxicity was myelosuppression; 13.9% of the patients had grade III-IV neutropenia. Severe mucositis, diarrhea, and emesis were uncommon (<10%). At a median follow-up period of 41 months, the 5-year progression-free survival and overall survival rates were 63.5% and 65.3%, respectively. Increasing the dose intensity of epirubicin can yield a similar complete response rate compared with the regimens used in NHL without significantly increasing the toxicity rate associated with chemotherapy. The role of dose-intensive epirubicin should be investigated further in future randomized trials.