Miracle-dz/UniFAR-FTUs huggingface dataset:
EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.
CD4 T Cell Epitope Specificity and Cytokine Potential Are Preserved as Cells Transition from the Lung Vasculature to Lung Tissue following Influenza Virus Infection

ABSTRACT Pulmonary CD4 T cells are critical in respiratory virus control, both by delivering direct effector function and through coordinating responses of other immune cells. Recent studies have shown that following influenza virus infection, virus-specific CD4 T cells are partitioned between pulmonary vasculature and lung tissue. However, very little is known about the peptide specificity or functional differences of CD4 T cells within these two compartments. Using a mouse model of influenza virus infection in conjunction with intravascular labeling in vivo, the cell surface phenotype, epitope specificity, and functional potential of the endogenous polyclonal CD4 T cell response was examined by tracking nine independent CD4 T cell epitope specificities. These studies revealed that tissue-localized CD4 cells were globally distinct from vascular cells in expression of markers associated with transendothelial migration, residency, and micropositioning. Despite these differences, there was little evidence for remodeling of the viral epitope specificity or cytokine potential as cells transition from vasculature to the highly inflamed lung tissue. Our studies also distinguished cells in the pulmonary vasculature from peripheral circulating CD4 T cells, providing support for the concept that the pulmonary vasculature does not simply reflect circulating cells that are trapped within the narrow confines of capillary vessels but rather is enriched in transitional cells primed in the draining lymph node that have specialized potential to enter the lung tissue. IMPORTANCE CD4 T cells convey a multitude of functions in immunity to influenza, including those delivered in the lymph node and others conveyed by CD4 T cells that leave the lymph node, enter the blood, and extravasate into the lung tissue. Here, we show that the transition of recently primed CD4 cells detected in the lung vasculature undergo profound changes in expression of markers associated with tissue localization as they establish residence in the lung. However, this transition does not edit CD4 T cell epitope specificity or the cytokine potential of the CD4 T cells. Thus, CD4 T cells that enter the infected lung can convey diverse functions and have a sufficiently broad viral antigen specificity to detect the complex array of infected cells within the infected tissue, offering the potential for more effective protective function.
A silicon carbide array for electrocorticography and peripheral nerve recording

Objective. Current neural probes have a limited device lifetime of a few years. Their common failure mode is the degradation of insulating films and/or the delamination of the conductor–insulator interfaces. We sought to develop a technology that does not suffer from such limitations and would be suitable for chronic applications with very long device lifetimes. Approach. We developed a fabrication method that integrates polycrystalline conductive silicon carbide with insulating silicon carbide. The technology employs amorphous silicon carbide as the insulator and conductive silicon carbide at the recording sites, resulting in a seamless transition between doped and amorphous regions of the same material, eliminating heterogeneous interfaces prone to delamination. Silicon carbide has outstanding chemical stability, is biocompatible, is an excellent molecular barrier and is compatible with standard microfabrication processes. Main results. We have fabricated silicon carbide electrode arrays using our novel fabrication method. We conducted in vivo experiments in which electrocorticography recordings from the primary visual cortex of a rat were obtained and were of similar quality to those of polymer based electrocorticography arrays. The silicon carbide electrode arrays were also used as a cuff electrode wrapped around the sciatic nerve of a rat to record the nerve response to electrical stimulation. Finally, we demonstrated the outstanding long term stability of our insulating silicon carbide films through accelerated aging tests. Significance. Clinical translation in neural engineering has been slowed in part due to the poor long term performance of current probes. Silicon carbide devices are a promising technology that may accelerate this transition by enabling truly chronic applications.
On the Convergence of Alternating Direction Lagrangian Methods for Nonconvex Structured Optimization Problems

Nonconvex and structured optimization problems arise in many engineering applications that demand scalable and distributed solution methods. The study of the convergence properties of these methods is, in general, difficult due to the nonconvexity of the problem. In this paper, two distributed solution methods that combine the fast convergence properties of augmented Lagrangian-based methods with the separability properties of alternating optimization are investigated. The first method is adapted from the classic quadratic penalty function method and is called the alternating direction penalty method (ADPM). Unlike the original quadratic penalty function method, where single-step optimizations are adopted, ADPM uses an alternating optimization which, in turn, makes it scalable. The second method is the well-known alternating direction method of multipliers (ADMM). It is shown that ADPM for nonconvex problems asymptotically converges to a primal feasible point under mild conditions and an additional condition ensuring that it asymptotically reaches the standard first-order necessary conditions for local optimality is introduced. In the case of the ADMM, novel sufficient conditions under which the algorithm asymptotically reaches the standard first-order necessary conditions are established. Based on this, complete convergence of the ADMM for a class of low-dimensional problems is characterized. Finally, the results are illustrated by applying ADPM and ADMM to a nonconvex localization problem in wireless-sensor networks.
MESOSCALE MICROSTRUCTURE EVOLUTION, RELIABILITY AND FAILURE ANALYSIS OF HIGH TEMPERATURE TRANSIENT LIQUID PHASE SINTERING JOINTS

Title of Dissertation: MESOSCALE MICROSTRUCTURE EVOLUTION, RELIABILITY AND FAILURE ANALYSIS OF HIGH TEMPERATURE TRANSIENT LIQUID PHASE SINTERING JOINTS Seyed Ali Moeini, Doctor of Philosophy, 2017 Dissertation directed by: Professor F. P. McCluskey, Department of Mechanical Engineering The continuous increase in application temperature of power electronic devices, due to the growing power density, miniaturization, and functionality in military and commercial applications, requires new packaging technologies with high temperature and reliability capabilities. Currently, the traditional maximum allowable temperature of power electronics (125°C) is a limiting factor for high temperature applications, such as space exploration, drilling, avionics, and electronic vehicles. Substitution of Silicon devices with wide bandgap (e.g., SiC) devices has extended the maximum allowable temperatures to 475 ̊C. However, this created the need for robust high temperature packaging materials, especially interconnects and attachments. High temperature solders are often too expensive, too brittle, or environmentally toxic to be used, leading to increased study of low temperature joining techniques, such as solid phase sintering and Transient Liquid Phase Sintering (TLPS), for producing high temperature stable attachments. TLPS is an emerging electronic interconnect technology enabling the formation of high temperature robust joints between metallic surfaces at low temperatures by the consumption of a transient, low temperature, liquid phase to form high temperature stable intermetallic compounds (IMCs). The performance and durability of these materials strongly depend on their microstructure, which is determined by their processing. The complicated process of IMC formation through eutectic solidification and the extensive number of parameters affecting the final microstructure make it impractical to experimentally study the effect of each factor. In this work, phase field modeling of the microstructure of TLPS materials fabricated by different processing methods will be conducted. Phase-field modeling (PFM) is a powerful thermodynamic consistent method in mesoscale modeling that simulates the evolution of intermetallic compounds during the solidification process, providing insight into the final microstructure. Application of this method facilitates the optimization of influential processing factors. Efforts will also be conducted to identify failure modes and mechanisms experimentally under dynamic, power and thermal cycling loads as a function of critical microstructural features, facilitating the optimization of joining parameters to obtain higher durability TLPS interconnections. The objective of this dissertation is to provide an insight into the processing of a reliable high temperature TLPS and facilitate their application in power electronic industries. MESOSCALE MICROSTRUCTURE EVOLUTION, RELIABILITY AND FAILURE ANALYSIS OF HIGH TEMPERATURE TRANSIENT LIQUID PHASE SINTERING JOINTS
Optimal plant water‐use strategies under stochastic rainfall

Plant hydraulic traits have been conjectured to be coordinated, thereby providing plants with a balanced hydraulic system that protects them from cavitation while allowing an efficient transport of water necessary for photosynthesis. In particular, observations suggest correlations between the water potentials at which xylem cavitation impairs water movement and the one at stomatal closure, and between maximum xylem and stomatal conductances, begging the question as to whether such coordination emerges as an optimal water‐use strategy under unpredictable rainfall. Here mean transpiration is used as a proxy for long‐term plant fitness and its variations as a function of the water potentials at 50% loss of stem conductivity due to cavitation and at 90% stomatal closure are explored. It is shown that coordination between these hydraulic traits is necessary to maximize , with rainfall patterns altering the optimal range of trait values. In contrast, coordination between ecosystem‐level conductances appears not necessary to maximize . The optimal trait ranges are wider under drier than under mesic conditions, suggesting that in semiarid systems different water use strategies may be equally successful. Comparison with observations across species from a range of ecosystems confirms model predictions, indicating that the coordinated functioning of plant organs might indeed emerge from an optimal response to rainfall variability.
A Genetic Algorithm with Evolutionary Path-relinking for the SONET Ring Assignment Problem

The SONET ring assignment problem (SRAP) arises in telecommunications network design, specically on the infrastructure planning phase of a network project. In a SONET network, each client site is associated or assigned to exactly one SONET ring, called local ring. The communication among clients in dierent rings is done through a special ring, called federal ring, that interconnects the local rings. A capacity constraint on each ring, including the federal ring, is imposed. The objective is to nd an assignment of the clients that attends to all constraints and minimizes the total cost of the network. As the majority of this cost comes from the equipment used to connect local rings to the federal ring, the problem is simplied to nd a feasible assignment that reduces the number of local rings in the network. We propose a genetic algorithm with evolutionary path-relinking for nding good-quality solutions. The heuristics included in the algorithm, as well as the evolutionary path-relinking, are detailed. Experimental results illustrate the eectiveness of the proposed method to obtain very good solutions in a short period of time.
Inhibitory activity of Cinnamomum cassia bark-derived component against rat lens aldose reductase.

PURPOSE To evaluate the inhibitory activity of active compounds isolated from Cinnamomum cassia bark against lens aldose reductase and compare to that of three commercially available compounds (cinnamyl alcohol, trans -cinnamic acid, and eugenol) and quercitrin as aldose reductase inhibitors. The IC (50) value of cinnamaldehyde was determined. METHODS Active compound was purified on repeated silica gel column and HPLC (Waters Delta Prep 4000). Aldose reductase was prepared from lenses of Sprague-Dawley male rat eyes. The incubation mixture contained 135 mM Na, K-phosphate buffer (pH 7.0), 100 mM lithium sulfate, 0.03 mM NADPH, 0.04 mM DL-glyceraldehyde and 50 micro L of an enzyme preparation, with or without a plant extract. The reaction was initiated by adding NADPH at 37 degrees C and stopped by adding 0.5 N hydrochloric acid. Subsequently, 6 N NaOH containing 10 mM imidazole was added, and the mixture was incubated at 60 degrees C for 10 min to convert NADP into a fluorescent product. The fluorescence was measured with a spectrofluorophotometer. RESULTS The biologically active constituents of C. cassia extract against lens aldose reductase were characterized as trans -cinnamaldehyde by spectral analysis. The IC (50) value of cinnamaldehyde is 0.003 mg/mL. However, cinnamyl alcohol, trans -cinnamic acid and eugenol exhibited only weak inhibition against aldose reductase. In comparison, quercitrin was 6 times more potent than cinnamaldehyde. CONCLUSIONS These results suggest that cinnamaldehyde isolated from C. cassia barks may be useful as a lead compound and a medicinal foodstuff for aldose reductase inhibition.
The Price of Oil Risk

We solve a Pareto risk-sharing problem with heterogeneous agents with recursive utility over multiple goods. We use this optimal consumption allocation to derive a pricing kernel and the price of oil and related futures contracts. This gives us insight into the dynamics of risk premia in commodity markets for oil. As an example, in a calibrated version of our model we show how rising oil prices and falling oil risk premium are an outcome of the dynamic properties of the optimal risk sharing solution. We also compute portfolios that implement the optimal consumption policies and demonstrate that large and variable open interest is a property of optimal risk sharing.
The Pharmacology of Acute Respiratory Distress Syndrome

Acute Respiratory Distress Syndrome (ARDS) is a common respiratory complication of critical severe illness or injury. Despite steady improvement in outcomes over the last three decades, ARDS remains a common cause of morbidity and mortality in pediatric and adult intensive care units. Due to its extensive burden, ARDS has been the focus of numerous multi-center clinical trials which have attempted to translate animal, ex vivo, and small single center studies into wider practice. Since the results of several of these large studies have been recently published, we sought to review the pharmacology of ARDS, summarize the major non-pharmacologic interventions shown to improve outcome, and update the reader on evolving therapies which may enter clinical practice in the coming decade.
Assessing Suicide Risk and Emotional Distress in Chinese Social Media: A Text Mining and Machine Learning Study

Background Early identification and intervention are imperative for suicide prevention. However, at-risk people often neither seek help nor take professional assessment. A tool to automatically assess their risk levels in natural settings can increase the opportunity for early intervention. Objective The aim of this study was to explore whether computerized language analysis methods can be utilized to assess one’s suicide risk and emotional distress in Chinese social media. Methods A Web-based survey of Chinese social media (ie, Weibo) users was conducted to measure their suicide risk factors including suicide probability, Weibo suicide communication (WSC), depression, anxiety, and stress levels. Participants’ Weibo posts published in the public domain were also downloaded with their consent. The Weibo posts were parsed and fitted into Simplified Chinese-Linguistic Inquiry and Word Count (SC-LIWC) categories. The associations between SC-LIWC features and the 5 suicide risk factors were examined by logistic regression. Furthermore, the support vector machine (SVM) model was applied based on the language features to automatically classify whether a Weibo user exhibited any of the 5 risk factors. Results A total of 974 Weibo users participated in the survey. Those with high suicide probability were marked by a higher usage of pronoun (odds ratio, OR=1.18, P=.001), prepend words (OR=1.49, P=.02), multifunction words (OR=1.12, P=.04), a lower usage of verb (OR=0.78, P<.001), and a greater total word count (OR=1.007, P=.008). Second-person plural was positively associated with severe depression (OR=8.36, P=.01) and stress (OR=11, P=.005), whereas work-related words were negatively associated with WSC (OR=0.71, P=.008), severe depression (OR=0.56, P=.005), and anxiety (OR=0.77, P=.02). Inconsistently, third-person plural was found to be negatively associated with WSC (OR=0.02, P=.047) but positively with severe stress (OR=41.3, P=.04). Achievement-related words were positively associated with depression (OR=1.68, P=.003), whereas health- (OR=2.36, P=.004) and death-related (OR=2.60, P=.01) words positively associated with stress. The machine classifiers did not achieve satisfying performance in the full sample set but could classify high suicide probability (area under the curve, AUC=0.61, P=.04) and severe anxiety (AUC=0.75, P<.001) among those who have exhibited WSC. Conclusions SC-LIWC is useful to examine language markers of suicide risk and emotional distress in Chinese social media and can identify characteristics different from previous findings in the English literature. Some findings are leading to new hypotheses for future verification. Machine classifiers based on SC-LIWC features are promising but still require further optimization for application in real life.
Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis

Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored. In the present study, a comparative proteome analysis based on iTRAQ (isobaric Tags for Relative and Absolute Quantification) was performed to identify the critical candidate factors involved in OA formation. A total of 389 differentially expressed proteins (DEPs) were identified between high-oleate cultivar Kainong176 and low-oleate cultivar Kainong70. Among these DEPs, 201 and 188 proteins were upregulated and downregulated, respectively. In addition, these DEPs were categorized into biosynthesis pathways of unsaturated FAs at the early stage during the high-oleic peanut seed development, and several DEPs involved in lipid oxidation pathway were found at the stage of seed maturation. Meanwhile, 28 DEPs were sporadically distributed in distinct stages of seed formation, and their molecular functions were directly correlated to FA biosynthesis and degradation. Fortunately, the expression of FAB2 (stearoyl-acyl carrier protein desaturase), the rate-limiting enzyme in the upstream biosynthesis process of OA, was significantly increased in the early stage and then decreased in the late stage of seed development in the high-oleate cultivar Kainong176. Furthermore, real-time PCR verified the expression pattern of FAB2 at the mRNA level, which was consistent with its protein abundance. However, opposite results were found for the low-oleate cultivar Kainong70. Overall, the comparative proteome analysis provided valuable insight into the molecular dynamics of OA accumulation during peanut seed development.
Astragalus polysaccharides exerts anti‐infective activity by inducing human cathelicidin antimicrobial peptide LL‐37 in respiratory epithelial cells

Astragalus polysaccharides (APS), one of the major active components in Astragalus membranaceus, is an effective immunomodulator used in the treatment of immunological diseases in China. However, the anti‐infective action and mechanism of APS is not fully known. In the present study, we found that APS induced the expression of human cathelicidin antimicrobial peptide LL‐37, a key host anti‐infective molecule, in both mRNA and protein levels in respiratory epithelial cells HBE16 and A549. Furthermore, the lysate and supernatant from APS‐treated HBE16 cells both exhibited an obvious antibacterial action, which was partially neutralizated by LL‐37 monoclonal antibody. In addition, APS also significantly elevated the phosphorylation of p38 MAPK and JNK and caused the degradation of IκBα. Specific inhibitors of p38 MAPK, JNK, or NF‐κB obviously abolished APS‐induced LL‐37 synthesis and antibacterial activity, respectively. Taken together, our results confirmed the enhancement of APS on LL‐37 induction and antibacterial action in respiratory epithelial cells, which may be attributed to activation of p38 MAPK/JNK and NF‐κB pathways. Furthermore, these results also supported the clinical application of APS in the treatment of infectious diseases.