Single-Cell Measurements and Modeling and Computation of Decision-Making Errors in a Molecular Signaling System with Two Output Molecules

A cell constantly receives signals and takes different fates accordingly. Given the uncertainty rendered by signal transduction noise, a cell may incorrectly perceive these signals. It may mistakenly behave as if there is a signal, although there is none, or may miss the presence of a signal that actually exists. In this paper, we consider a signaling system with two outputs, and introduce and develop methods to model and compute key cell decision-making parameters based on the two outputs and in response to the input signal. In the considered system, the tumor necrosis factor (TNF) regulates the two transcription factors, the nuclear factor κB (NFκB) and the activating transcription factor-2 (ATF-2). These two system outputs are involved in important physiological functions such as cell death and survival, viral replication, and pathological conditions, such as autoimmune diseases and different types of cancer. Using the introduced methods, we compute and show what the decision thresholds are, based on the single-cell measured concentration levels of NFκB and ATF-2. We also define and compute the decision error probabilities, i.e., false alarm and miss probabilities, based on the concentration levels of the two outputs. By considering the joint response of the two outputs of the signaling system, one can learn more about complex cellular decision-making processes, the corresponding decision error rates, and their possible involvement in the development of some pathological conditions.

Early Detection of Risk of Neo-Sinus Blood Stasis Post-Transcatheter Aortic Valve Replacement Using Personalized Hemodynamic Analysis

Background

Despite the demonstrated benefits of transcatheter aortic valve replacement (TAVR), subclinical leaflet thrombosis and hypoattenuated leaflet thickening are commonly seen as initial indications of decreased valve durability and augmented risk of transient ischemic attack.

Methods

We developed a multiscale patient-specific computational framework to quantify metrics of global circulatory function, metrics of global cardiac function, and local cardiac fluid dynamics of the aortic root and coronary arteries.

Results

Based on our findings, TAVR might be associated with a high risk of blood stagnation in the neo-sinus region due to the lack of sufficient blood flow washout during the diastole phase (e.g., maximum blood stasis volume increased by 13, 8, and 2.7 fold in the left coronary cusp, right coronary cusp, and noncoronary cusp, respectively [N = 26]). Moreover, in some patients, TAVR might not be associated with left ventricle load relief (e.g., left ventricle load reduced only by 1.2 % [N = 26]) and diastolic coronary flow improvement (e.g., maximum coronary flow reduced by 4.94%, 15.05%, and 23.59% in the left anterior descending, left circumflex coronary artery, and right coronary artery, respectively, [N = 26]).

Conclusions

The transvalvular pressure gradient amelioration after TAVR might not translate into adequate sinus blood washout, optimal coronary flow, and reduced cardiac stress. Noninvasive personalized computational modeling can facilitate the determination of the most effective revascularization strategy pre-TAVR and monitor leaflet thrombosis and coronary plaque progression post-TAVR.

On the Fabrication of High-Performance Additively Manufactured Copper Winding Using Laser Powder Bed Fusion

Due to its exceptional electrical and thermal conductivity, pure copper is frequently employed in industry as the base metal for thermal management and electromagnetic applications. The growing need for complicated and efficient motor designs has recently accelerated the development of copper additive manufacturing (AM). The present work aims to improve the power density of the copper laser powder bed fusion (Cu-LPBF) coil by increasing the slot-filling factor (SFF) and the electrical conductivity. Firstly, the dimensional limitation of Cu-LPBF fabricated parts was identified. Sample contouring and adjusting beam offset associated with optimum scan track morphology upgraded the minimum feature spacing to 80 μm. Accordingly, the printed winding's slot-filling factor increased to 79% for square wire and 63% for round wire. A maximum electrical conductivity of 87% (IACS) was achieved by heat treatment (HT). The electrical impedance of full-size Cu-LPBF coils, newly reported in this study, was measured and compared with solid wire. It can reflect the performance of Cu-LPBF coils (power factor) in high-frequency applications. Furthermore, surface quality benefited from either sample contouring and HT, where the side surface roughness was lowered by 45% and an additional reduction of 25% after HT.

Reducing Long-Term Mortality Post Transcatheter Aortic Valve Replacement Requires Systemic Differentiation of Patient-Specific Coronary Hemodynamics

Background Despite the proven benefits of transcatheter aortic valve replacement (TAVR) and its recent expansion toward the whole risk spectrum, coronary artery disease is present in more than half of the candidates for TAVR. Many previous studies do not focus on the longer-term impact of TAVR on coronary arteries, and hemodynamic changes to the circulatory system in response to the anatomical changes caused by TAVR are not fully understood. Methods and Results We developed a multiscale patient-specific computational framework to examine the effect of TAVR on coronary and cardiac hemodynamics noninvasively. Based on our findings, TAVR might have an adverse impact on coronary hemodynamics due to the lack of sufficient coronary blood flow during diastole phase (eg, maximum coronary flow rate reduced by 8.98%, 16.83%, and 22.73% in the left anterior descending, left circumflex coronary artery, and right coronary artery, respectively [N=31]). Moreover, TAVR may increase the left ventricle workload (eg, left ventricle workload increased by 2.52% [N=31]) and decrease the coronary wall shear stress (eg, maximum time averaged wall shear stress reduced by 9.47%, 7.75%, 6.94%, 8.07%, and 6.28% for bifurcation, left main coronary artery, left anterior descending, left circumflex coronary artery, and right coronary artery branches, respectively). Conclusions The transvalvular pressure gradient relief after TAVR might not result in coronary flow improvement and reduced cardiac load. Optimal revascularization strategy pre-TAVR and progression of coronary artery disease after TAVR could be determined by noninvasive personalized computational modeling.

Combined Molecular and Biochemical Identification of Alpha Toxin in Local Isolated Clostridium novyi from the Sheep Liver

Clostridium novyi (C. novyi) causes deadly Black disease in sheep and rarely in other animals. Alpha toxin (α-toxin), the most apparent pathogen of this disease, is produced by C. novyi type B. Economic damages of C. novyi include sheep mortality costs, depreciation of affected farms, and health problems with infected carcasses. The identification of C. novyi and isolation of its pathogens by conventional methods is a time-consuming process, necessitating a simple and rapid method for isolating and detecting pathogenic C. novyi. Therefore, this study aimed to molecularly identify α-toxin in local C. novyi isolates from the sheep livers. In this study, 75 livers suspected of Black disease were sampled. The samples of the liver were cultured under anaerobic conditions. Some of the cultured colonies were used in biochemical tests. For molecular confirmation, the DNA of isolates was extracted, and the isolates were confirmed by the polymerase chain reaction (PCR) on the liver tissue and cultured samples using specific α-toxin primers. The PCR on α-toxin produced a band in the range of 609 bp, indicating that the samples belonged to C. novyi. According to the results, of 75 isolates, 18 isolates were confirmed as C. novyi. C. novyi type B was isolated from the liver and confirmed by biochemical and molecular characterization. The PCR assay ensured a sensitive and specific tool for the detection of C. novyi in the samples.

A hybrid model to study how late long-term potentiation is affected by faulty molecules in an intraneuronal signaling network regulating transcription factor CREB

Systems biology analysis of intracellular signaling networks has tremendously expanded our understanding of normal and diseased cell behaviors and has revealed paths to finding proper therapeutic molecular targets. When it comes to neurons in the human brain, analysis of intraneuronal signaling networks provides invaluable information on learning, memory and cognition-related disorders, as well as potential therapeutic targets. However, neurons in the human brain form a highly complex neural network that, among its many roles, is also responsible for learning, memory formation and cognition. Given the impairment of these processes in mental and psychiatric disorders, one can envision that analyzing interneuronal processes, together with analyzing intraneuronal signaling networks, can result in a better understanding of the pathology and, subsequently, more effective target discovery. In this paper, a hybrid model is introduced, composed of the long-term potentiation (LTP) interneuronal process and an intraneuronal signaling network regulating CREB. LTP refers to an increased synaptic strength over a long period of time among neurons, typically induced upon occurring an activity that generates high-frequency stimulations (HFS) in the brain, and CREB is a transcription factor known to be highly involved in important functions of the cognitive and executive human brain such as learning and memory. The hybrid LTP-signaling model is analyzed using a proposed molecular fault diagnosis method. It allows to study the importance of various signaling molecules according to how much they affect an intercellular phenomenon when they are faulty, i.e. dysfunctional. This paper is intended to suggest another angle for understanding the pathology and therapeutic target discovery by classifying and ranking various intraneuronal signaling molecules based on how much their faulty behaviors affect an interneuronal process. Possible relations between the introduced hybrid analysis and the previous purely intracellular analysis are investigated in the paper as well.

Personalized intervention cardiology with transcatheter aortic valve replacement made possible with a non-invasive monitoring and diagnostic framework

One of the most common acute and chronic cardiovascular disease conditions is aortic stenosis, a disease in which the aortic valve is damaged and can no longer function properly. Moreover, aortic stenosis commonly exists in combination with other conditions causing so many patients suffer from the most general and fundamentally challenging condition: complex valvular, ventricular and vascular disease (C3VD). Transcatheter aortic valve replacement (TAVR) is a new less invasive intervention and is a growing alternative for patients with aortic stenosis. Although blood flow quantification is critical for accurate and early diagnosis of C3VD in both pre and post-TAVR, proper diagnostic methods are still lacking because the fluid-dynamics methods that can be used as engines of new diagnostic tools are not well developed yet. Despite remarkable advances in medical imaging, imaging on its own is not enough to quantify the blood flow effectively. Moreover, understanding of C3VD in both pre and post-TAVR and its progression has been hindered by the absence of a proper non-invasive tool for the assessment of the cardiovascular function. To enable the development of new non-invasive diagnostic methods, we developed an innovative image-based patient-specific computational fluid dynamics framework for patients with C3VD who undergo TAVR to quantify metrics of: (1) global circulatory function; (2) global cardiac function as well as (3) local cardiac fluid dynamics. This framework is based on an innovative non-invasive Doppler-based patient-specific lumped-parameter algorithm and a 3-D strongly-coupled fluid-solid interaction. We validated the framework against clinical cardiac catheterization and Doppler echocardiographic measurements and demonstrated its diagnostic utility by providing novel analyses and interpretations of clinical data in eleven C3VD patients in pre and post-TAVR status. Our findings position this framework as a promising new non-invasive diagnostic tool that can provide blood flow metrics while posing no risk to the patient. The diagnostic information, that the framework can provide, is vitally needed to improve clinical outcomes, to assess patient risk and to plan treatment.

Relevance of carbohydrate-deficient transferrin as a predictor of alcoholism in intensive care patients following trauma

Every second traumatized patient is a chronic alcoholic. Chronic alcoholics are at risk due to an increased morbidity and mortality. Reliable and precise diagnostic methods for detecting alcoholism are mandatory to prevent posttraumatic complications by adequate prophylaxis. The patient's history, however, is often not reliable, and conventional laboratory markers are not sensitive or specific enough. The aim of this study was to investigate whether carbohydrate-deficient transferrin (CDT) is a sensitive and specific marker to detect alcoholism in traumatized patients. One hundred and five male traumatized patients or their relatives gave their written informed consent to participate in this institutionally approved study. All patients were transferred to the intensive care unit after admission to the emergency room, followed by surgical treatment. Diagnostics included an alcoholism-related questionnaire, conventional laboratory markers (mean corpuscular volume, gamma-glutamyltransferase, aspartate aminotransferase, and alanine aminotransferase), and CDT sampling (microanion-exchange chromatography, turbidimetry, and radioimmunoassay, respectively). Only patients in whom a reliable history could be obtained were included. Alcoholism was diagnosed if the patients met the Diagnostic and Statistical Manual of Mental Disorders criteria for chronic alcohol abuse or dependence. The administration of fluids before CDT sampling was carefully documented. Patients did not differ significantly regarding age, Trauma and Injury Severity Score, and Acute Physiology and Chronic Health Evaluation score. The sensitivity of the CDT research kit was 70% and of the commercially available kit CDTect was 65%. Early sampling in the emergency room and before administration of large volumes of fluid increased the sensitivity to 83% for the CDT research kit and 74% for CDTect, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)