Miracle-dz/UniFAR-FTUs huggingface dataset:
Tissue-engineered microenvironment systems for modeling human vasculature

The high attrition rate of drug candidates late in the development process has led to an increasing demand for test assays that predict clinical outcome better than conventional 2D cell culture systems and animal models. Government agencies, the military, and the pharmaceutical industry have started initiatives for the development of novel in-vitro systems that recapitulate functional units of human tissues and organs. There is growing evidence that 3D cell arrangement, co-culture of different cell types, and physico-chemical cues lead to improved predictive power. A key element of all tissue microenvironments is the vasculature. Beyond transporting blood the microvasculature assumes important organ-specific functions. It is also involved in pathologic conditions, such as inflammation, tumor growth, metastasis, and degenerative diseases. To provide a tool for modeling this important feature of human tissue microenvironments, we developed a microfluidic chip for creating tissue-engineered microenvironment systems (TEMS) composed of tubular cell structures. Our chip design encompasses a small chamber that is filled with an extracellular matrix (ECM) surrounding one or more tubular channels. Endothelial cells (ECs) seeded into the channels adhere to the ECM walls and grow into perfusable tubular tissue structures that are fluidically connected to upstream and downstream fluid channels in the chip. Using these chips we created models of angiogenesis, the blood–brain barrier (BBB), and tumor-cell extravasation. Our angiogenesis model recapitulates true angiogenesis, in which sprouting occurs from a “parent” vessel in response to a gradient of growth factors. Our BBB model is composed of a microvessel generated from brain-specific ECs within an ECM populated with astrocytes and pericytes. Our tumor-cell extravasation model can be utilized to visualize and measure tumor-cell migration through vessel walls into the surrounding matrix. The described technology can be used to create TEMS that recapitulate structural, functional, and physico-chemical elements of vascularized human tissue microenvironments in vitro.
3D printing of highly fluorinated methacrylates for the rapid prototyping of transparent and chemically-resistant microfluidic devices

The raising importance of stereolithography printers for rapid prototyping of microfluidic chips is due to the combination of affordable machinery and high resolution. However most commercial printing materials have low chemical resistance to solvents and strong acids. Perfluoropolyethers (PFPE) are a class of materials which show a high chemical resistance. Here we present a new resin formulation using PFPE methacrylates which allows 3D printing of microfluidic structures with a channel size of 200 μm and a transparency of 90% in the visible light region. We further show that using an adapted PFPE resin formulation superhydrophobic surfaces can be printed.
On-chip high-Q solenoid inductors embedded in WL-CSP

On-chip Cu solenoid inductors on Si substrate with thick resin layer have been fabricated. These inductors were fabricated by dual Cu electroplating layers and separated more than 10 /spl mu/m from Si substrate by thick resin layer. The self-resonance frequency of 17.7 and higher than 20 GHz with peak-Q of 18.5 and 24.2 were obtained for a 5 turn solenoid inductor in the resistivity of 4, 1k /spl Omega/cm, respectively. This technology realizes that high performance inductors are embedded in wafer-level chip-scale packages.
P-type Cu2ZnSnS4 as Multifunctional Material for Photovoltaic and Thermoelectric Application: Theoretical Investigation

In this work, a detailed information about physical properties of Cu2ZnSnS4 stannite phase by first principles calculation has been presented. Using density functional theory based on the generalized gradient approximation GGA, the structural properties such as lattice parameters and bulk modulus has been determined. In addition, structure electronic and partial density of state to characterize the electronic properties was also calculated. For the optical properties investigation, the absorption coefficient and the efficiency of energy conversion has been calculated. Finally, we have investigated on thermoelectric properties such as electrical conductivity, Seebeck coefficient, thermal conductivity and figure of merit to evaluate the potential of this material in different applications. From our results presented herein, we conclude that this material can be considered potential multifunctional material for thermoelectric and photovoltaic applications.
Novel Approach to High Throughput Screening for Activators of Transcription Factors

There is growing body of evidence that many diseases require a systemic treatment approach rather than targeting just a single enzyme or receptor. Neurodegenerative diseases affect a wide spectrum of the population and, in most cases, lead to physical and/or mental incapacity, involving memory, cognition, language and personality. Aging contributes to the development of neurodegeneration by shifting the equilibrium between oxygendependent and independent mechanisms of energy production towards mitochondriagenerated ATP. Mitochondrial capacity degenerates with aging, making cells susceptible to both ischemic and oxidative insults. Although all mechanisms of hypoxic preconditioning are very far from complete understanding, it is clear that cell is equipped with the necessary molecular machinery to respond to the changes in intracellular oxygen content. However, aging significantly compromises this response. Turning on the existent molecular machinery to compensate for hypoxic and oxidative stress may lead to comprehensive and safe therapeutic strategy for age-related neurodegenerative disorders. To restore homeostatic balance destroyed as a result of acute or chronic injury, one needs to activate intrinsic genetic programs silent or insufficiently active in the damaged cells. Activation of cellular defensive systems requires stabilization of corresponding transcription factors which govern expression of cassettes of genes turning on a particular program such as antioxidant, anti-inflammatory, or anti-hypoxic one. Hence, one of the emerging strategies in drug screening becomes a hunt for activators (or inhibitors) of transcription factors. In some cases there is an enzyme responsible for a rate-limiting conversion of a transcription factor, in some not. The well-known and commonly used approach to screening of activators of transcription factors is the use of luciferase gene cloned under the promoter activated by a specified transcription factor. For example, cell-based screening for activators of hypoxia induced factor 1 (HIF1) is performed using HRE (hypoxia response element)-luciferase (Semenza et al 1996), and for Nrf2 – using ARE (antioxidant response element)-luciferase reporter assay (Moehlenkamp & Johnson 1999). Promega has just begun to offer commercially such type of constructs with any desired promoter for research and drug screening purposes.
Statistical Discrimination in Labor Markets: An Experimental Analysis

Statistical discrimination occurs when distinctions between demographic groups are made on the basis of real or imagined statistical distinctions between the groups. While such discrimination is legal in some cases (e.g., insurance markets), it is illegal and/or controversial in others (e.g., racial profiling and gender-based labor market discrimination). First moment statistical discrimination occurs when, for example, female workers are offered lower wages because females are perceived to be less productive, on average, than male workers. Second moment discrimination occurs when risk averse employers offer female workers lower wages based not on lower average productivity but on a higher variance in their productivity. Empirical work on statistical discrimination is hampered by the difficulty of obtaining suitable data from naturally-occurring labor markets. This article reports results from controlled laboratory experiments designed to study second moment statistical discrimination in a simulated labor marker setting. Since decision-makers may not view risk in the same way as economists or statisticians (i.e., risk=variance of distribution), we also examine two possible alternative measures of risk: the support of the distribution, and the probability of earning less than the expected (maximum) profits for the employer. Our results indicate that individuals do respond to these alternative measures of risk, and employers made statistically discriminatory wage offers consistent with loss-aversion in our full sample (though differences between male and female employers can be noted). If one can transfer these results outside of the laboratory, they indicate that labor market discrimination based only on first moment discrimination is biased downward. The public policy implication is that efforts and legislation aimed at reducing discrimination of various sorts face an additional challenge in trying to identify and limit relatively hidden, but significant, forms of statistical discrimination.
ER/Golgi Intermediates Acquire Golgi Enzymes by Brefeldin a–Sensitive Retrograde Transport in Vitro

Secretory proteins exit the ER in transport vesicles that fuse to form vesicular tubular clusters (VTCs) which move along microtubule tracks to the Golgi apparatus. Using the well-characterized in vitro approach to study the properties of Golgi membranes, we determined whether the Golgi enzyme NAGT I is transported to ER/Golgi intermediates. Secretory cargo was arrested at distinct steps of the secretory pathway of a glycosylation mutant cell line, and in vitro complementation of the glycosylation defect was determined. Complementation yield increased after ER exit of secretory cargo and was optimal when transport was blocked at an ER/Golgi intermediate step. The rapid drop of the complementation yield as secretory cargo progresses into the stack suggests that Golgi enzymes are preferentially targeted to ER/Golgi intermediates and not to membranes of the Golgi stack. Two mechanisms for in vitro complementation could be distinguished due to their different sensitivities to brefeldin A (BFA). Transport occurred either by direct fusion of preexisting transport intermediates with ER/Golgi intermediates, or it occurred as a BFA-sensitive and most likely COP I–mediated step. Direct fusion of ER/Golgi intermediates with cisternal membranes of the Golgi stack was not observed under these conditions.
Capsule Biosynthesis and Basic Metabolism inStreptococcus pneumoniae Are Linked through the Cellular Phosphoglucomutase

ABSTRACT Synthesis of the type 3 capsular polysaccharide ofStreptococcus pneumoniae requires UDP-glucose (UDP-Glc) and UDP-glucuronic acid (UDP-GlcUA) for production of the [3)-β-d-GlcUA-(1→4)-β-d-Glc-(1→]npolymer. The generation of UDP-Glc proceeds by conversion of Glc-6-P to Glc-1-P to UDP-Glc and is mediated by a phosphoglucomutase (PGM) and a Glc-1-P uridylyltransferase, respectively. Genes encoding both a Glc-1-P uridylyltransferase (cps3U) and a PGM homologue (cps3M) are present in the type 3 capsule locus, but these genes are not essential for capsule production. In this study, we characterized a mutant that produces fourfold less capsule than the type 3 parent. The spontaneous mutation resulting in this phenotype was not contained in the type 3 capsule locus but was instead located in a distant gene (pgm) encoding a second PGM homologue. The function of this gene product as a PGM was demonstrated through enzymatic and complementation studies. Insertional inactivation ofpgm reduced capsule production to less than 10% of the parental level. The loss of PGM activity in the insertion mutants also caused growth defects and a strong selection for isolates containing second-site suppressor mutations. These results demonstrate that most of the PGM activity required for type 3 capsule biosynthesis is derived from the cellular PGM.
Anti-proliferation of triple-negative breast cancer cells with physagulide P: ROS/JNK signaling pathway induces apoptosis and autophagic cell death

Physagulide P (PP), a new natural compound, was isolated from Physalis angulate L. in our laboratory. In this study, we demonstrated that PP potently suppressed cell proliferation by inducing G2/M phase arrest in MDA-MB-231 and MDA-MB-468 cells. Moreover, PP provoked apoptosis by decreasing the mitochondrial membrane potential and elevating the Bax/Bcl-2 protein expression ratio. The caspase inhibitor Z-VAD-FMK partly restore cell viability, suggesting that apoptosis plays as an important role in the anti-proliferative effect of PP. PP-treated cells also underwent autophagy, as evidenced by the formation of autophagosomes and the accumulation of LC3BII. Furthermore, the knockdown of LC3B reduced PP-induced cytotoxicity, indicating that autophagy played an anticancer effect. PP also induced the generation of reactive oxygen species (ROS) and resulted in c-Jun N-terminal kinases (JNK) activation. Accordingly, JNK siRNA significantly attenuated PP-triggered apoptosis and autophagy, and ROS scavengers almost completely reverse this apoptosis and autophagy. The ROS scavenger also blocked PP-induced G2/M phase arrest and the phosphorylation of JNK. Our results revealed that PP induced G2/M phase arrest, apoptosis and autophagy via the ROS/JNK signaling pathway in MDA-MB-231 and MDA-MB-468 cells. Therefore, PP is a promising candidate for the development of antitumor drugs for the treatment of triple-negative breast cancer.
Exploring the Mind with the Aid of Personal Genome - Citizen Science Genetics to Promote Positive Well-Being

Understanding the human mind and increasing individual happiness are important goals in artificial intelligence (AI) and well-being science. The recent revolution in portable self-tracking devices in the data-driven wellness movement and participatory-driven wellness communities, such as the Quantified Self community, provides us with new opportunities to collect psychological or physiological data for understanding the human mind. While new technologies make it possible to track our daily behavior and various biological signals such as physiological or genetic data more easily, one of the important remaining challenges is to discover our own truly meaningful personal values. Citizen science, scientific research by crowdsourcing or human-based computation, is a new and challenging framework that promotes interdisciplinary research in the fields of computer science, life/brain science, and social psychological/behavioral science, which may introduce new paradigms to the AI community. We have been working on citizen science projects related to the area of personal genomics and have developed a personal genomics information environment named MyFinder. The developed platform supports the search for our inherited talents and maximizes our potential for a meaningful life. In particular, we are interested in the human mind and the personal genome. In this paper, we introduce our MyFinder Project and present the results of a recent study on “social intelligence genomics and empathy building”, and discuss issues involved in exploring our mind within the context of personal genomics.
Viral Transcription During Autographa californica Nuclear Polyhedrosis Virus Infection: a Novel RNA Polymerase Induced in Infected Spodoptera frugiperda Cells

Autographa californica nuclear polyhedrosis virus-specific RNA synthesis in isolated nuclei of Spodoptera frugiperda cells in culture was monitored at different times postinfection. Up to 8 h postinfection viral RNA synthesis remained sensitive to 5 μg of α-amanitin per ml. During the course of infection this sensitivity decreased, and at 24 h postinfection RNA synthesis was completely resistant to α-amanitin. DEAE-Sephadex profiles of RNA polymerase isolated at 24 h postinfection showed a new, chromatographically distinct, α-amanitin-resistant form whose kinetics and response to divalent cations differed from those of the host RNA polymerases. The possibility that this enzyme may be responsible for viral late transcription is discussed.
Design and Control of a Variable Stiffness Actuator for Safe and Fast Physical Human/Robot Interaction

This paper is concerned with the design and control of actuators for machines and robots physically interacting with humans, implementing criteria established in our previous work [1] on optimal mechanical-control co-design for intrinsically safe, yet performant machines. In our Variable Impedance Actuation (VIA) approach, actuators control in real-time both the reference position and the mechanical impedance of the moving parts in the machine in such a way to optimize performance while intrinsically guaranteeing safety. In this paper we describe an implementation of such concepts, consisting of a novel electromechanical Variable Stiffness Actuation (VSA) motor. The design and the functioning principle of the VSA are reported, along with the analysis of its dynamic behavior. A novel scheme for feedback control of this device is presented, along with experimental results showing performance and safety of a one-link arm actuated by the VSA motor.
OFDM Based WLAN Systems

This report is intended to provide an overview of the present state of WLANs with respect to physical layer issues and identify some key research issues for future generations of WLANs. The current standards (IEEE 802.11a in USA, HiperLAN/2 in Europe and MMAC in Japan) are all based on OFDM in their PHY layer. Thus, detailed attention on basics of OFDM related WLAN systems are given in the report. This is to introduce the existing techniques that are proposed or implemented in different OFDM based WLANs. A special attention is given on synchronization and channel estimation issues in WLAN due to the fact that virtually it is impossible to obtain a reasonable quality of service without perfect (or near perfect or efficient) synchronization and channel estimation. At the end of the report, some interesting topics that need to be studied in the development of future generation wireless systems based on OFDM are presented. It is worth mentioning here that the explanation on various topics presented here are in no way a complete description. For details, it is suggested to study the references that are mentioned in this report.
Overexpression of fIbA, an early regulator of Aspergillus asexual sporulation, leads to activation of brIA and premature initiation of development

Aspergillus nidulans reproduces asexually by forming thousands of mitotically derived spores atop highly specialized multicellular organs termed conidiophores. We have identified a gene called flbA (for fluffy low brlA expression) that is required for initiation of A. nidulans conidiophore development. flbA mutants form abnormal colonies that have a distinct fluffy phenotype characterized by tightly interwoven aerial hyphae that autolyse as the colony matures. The requirement for fIbA in conidiophore development precedes activation of brlA, a primary regulator of conidiophore development. The wild‐type flbA gene was isolated and found to encode a 3.0 kb mRNA that is expressed throughout the A. nidulans asexual life cycle. Overexpression of fIbA using an Inducible promoter resulted in misscheduled expression of brlA in vegetative ceils and caused hyphal tips to differentiate into spore‐producing structures. Sequence analysis of a nearly full‐length fIbA cDNA clone showed that fibA is predicted to encode a 717‐amino‐acid polypeptide with 30% identity to the Saccharomyces cerevisiae SST2 protein. SST2 is required by yeast cells for resuming growth following prolonged exposure to yeast mating pheromone and for mating partner discrimination. We propose that fIbA plays a related role in a signalling pathway for Aspergillus conidiophore development.
Exchangeable pairs and Poisson approximation

This is a survery paper on Poisson approximation using Stein's method of exchangeable pairs. We illustrate using Poisson-binomial trials and many variations on three classical problems of combinatorial probability: the matching problem, the coupon collector's problem, and the birthday problem. While many details are new, the results are closely related to a body of work developed by Andrew Barbour, Louis Chen, Richard Arratia, Lou Gordon, Larry Goldstein, and their collaborators. Some comparison with these other approaches is offered.
Notice of RetractionStudent-Centric Evaluation Methodology for Teaching Effect of Teaching Methods in Computer Organization and Design Course

Computer organization and design course is one of the fundamental courses for computer science education. With the rapid progress in semi-conductor, new technologies in computer science are also emerging. It becomes more challenging for universities to design computer organization and design course. More new teaching methods and innovations are used to obtain better teaching effects as the corresponding responses to the continuous development of the research and technology. Though the experiences show that the teaching effects can be improved through the innovative teaching methods, how to evaluate the important factors of these methods accurately is still not clear. In this paper, we describe the methodology used by Zhejiang University to evaluate the teaching effects of teaching methods in computer organization and design course. Our methodology is based on the evaluation from the students. Such methodology can help the teachers find out the advantages and flaws of different teaching methods and then improve their work.
On investigating efficient methodology for Environmental Sound Recognition

This paper presents a comparative study of various methods to identify the environmental sounds. We evaluate two methods for feature extraction: Mel Frequency Cepstral Coefficients (MFCC) which is well known for speaker identification, and Matching Pursuit (MP) with Gabor Dictionary which gives a time frequency representation employed for scene recognition. In the classification stage, we show a comparison among Support Vector Machines (SVM), Logistic Regression, and Backpropagation Artificial Neural Network (BP-ANN). Simulation results show that MFCC gives a higher recognition performance as compared with MP. Furthermore, by concatenating MFCC features with some feature of MP, e.g., scale, might also improve performance in some situations. We observe that SVM show the best performance among the classifiers, for clean as well noisy signals.
Combining machine learning and human judgment in author disambiguation

Author disambiguation in digital libraries becomes increasingly difficult as the number of publications and consequently the number of ambiguous author names keep growing. The fully automatic author disambiguation approach could not give satisfactory results due to the lack of signals in many cases. Furthermore, human judgment on the basis of automatic algorithms is also not suitable because the automatically disambiguated results are often mixed and not understandable for humans. In this paper, we propose a Labeling Oriented Author Disambiguation approach, called LOAD, to combine machine learning and human judgment together in author disambiguation. LOAD exploits a framework which consists of high precision clustering, high recall clustering, and top dissimilar clusters selection and ranking. In the framework, supervised learning algorithms are used to train the similarity functions between publications and a clustering algorithm is further applied to generate clusters. To validate the effectiveness and efficiency of the proposed LOAD approach, comprehensive experiments are conducted. Comparing to conventional author disambiguation algorithms, the LOAD yields much more accurate results to assist human labeling. Further experiments show that the LOAD approach can save labeling time dramatically.