Miracle-dz/UniFAR-FTUs huggingface dataset:
Early neural ectodermal genes are activated by siamois and twin during blastula stages

BMP signaling distinguishes between neural and non‐neural fates by activating epidermis‐specific transcription and repressing neural‐specific transcription. The neural ectoderm forms after the Organizer secrets antagonists that prevent these BMP‐mediated activities. However, it is not known whether neural genes also are transcriptionally activated. Therefore, we tested the ability of nine Organizer transcription factors to ectopically induce the expression of four neural ectodermal genes in epidermal precursors. We found evidence for two pathways: Foxd4 and Sox11 were only induced by Sia and Twn, whereas Gmnn and Zic2 were induced by Sia, Twn, as well as seven other Organizer transcription factors. The induction of Foxd4, Gmnn and Zic2 by Sia/Twn was both non‐cell autonomous (requiring an intermediate protein) and cell autonomous (direct), whereas the induction of Sox11 required Foxd4 activity. Because direct induction by Sia/Twn could occur endogenously in the dorsal‐equatorial blastula cells that give rise to both the Organizer mesoderm and the neural ectoderm, we knocked down Sia/Twn in those cells. This prevented the blastula expression of Foxd4 and Sox11, demonstrating that Sia/Twn directly activate some neural genes before the separation of the Organizer mesoderm and neural ectoderm lineages. genesis 53:308–320, 2015. © 2015 Wiley Periodicals, Inc.
Growth Mechanism of 3C-SiC Heteroepitaxial Layers on α-SiC by VLS

We report on the heteroepitaxial growth of 3C-SiC layers by Vapor-Liquid-Solid (VLS) mechanism on Si face 6H-SiC substrates, on-axis and 3.5° off. The Si-Ge melts, which Si content was varied from 10 to 50 at%, were fed by 3 sccm of propane. The growth temperature was varied from 1200 to 1600°C. It was found that 3C-SiC layers (either twinned or twinned free) form at low temperature while homoepitaxy is achieved at high temperature. The proposed growth mechanism involves the initial formation of 3C islands during the heating ramp (below 1200°C) and the dissolution of these islands when temperature increases. Geometrical aspects, such as the step density at the surface and the vertical component of the growth, are also considered to explain the difference observed between the on and off axis substrates.
In Vivo Identification of Sumoylation Sites by a Signature Tag and Cysteine-targeted Affinity Purification*

Small ubiquitin-like modifier (SUMO) is conjugated to its substrates via an enzymatic cascade consisting of three enzymes, E1, E2, and E3. The active site of the E2 enzyme, Ubc9, recognizes the substrate through binding to a consensus tetrapeptide ΨKXE. However, recent proteomics studies suggested that a considerable part of sumoylation occurs on non-consensus sites. Current unbiased sumoylation site identification techniques typically require high stoichiometry in vitro sumoylation, mass spectrometry, and complex data analysis. To facilitate in vivo analysis, we have designed a mass spectrometric method based on an engineered human SUMO-1 construct that creates a signature tag on SUMO substrates. This construct enables affinity purification by covalent binding to cysteine residues in LysC/trypsin-cleaved peptides and site identification by diglycyl lysine tagging of sumoylation sites. As a proof of concept, site-specific and substrate-unbiased in vivo sumoylation analysis of HeLa cells was performed. We identified 14 sumoylation sites, including well known sites, such as Lys524 of RanGAP1, and novel non-consensus sites. Only 3 of the 14 sites matched consensus sites, supporting the emerging view that non-consensus sumoylation is a common event in live cells. Six of the non-consensus sites had a nearby SUMO interaction motif (SIM), which emphasizes the role of SIM in non-consensus sumoylation. Nevertheless, the lack of nearby SIM residues among the remaining non-consensus sites indicates that there are also other specificity determinants of non-consensus sumoylation. The method we have developed proved to be a useful tool for sumoylation studies and will facilitate identification of novel SUMO substrates containing both consensus and non-consensus sites.
Multi-resolution 3D Mesh Coding in MPEG

This paper introduces a novel scalable 3D mesh compression technique based on a shape approximation prediction strategy. The proposed approach, so-called Shape Approximation Compression (SAC), directly compresses the levels of detail (LoDs) defined by the content creators, while exploiting their inter-correlations. Here, the geometry of each LoD is used in order to compute a smooth approximation of the next layer. A progressive mesh hierarchy is then built on the top of the approximated version making it possible to efficiently predict and progressively transmit the geometry approximation errors. The SAC codec was evaluated within the framework of the MPEG core experiments on Multi-Resolution 3D Mesh Coding (MR3DMC) and was preliminarily accepted for future standardization.
INSTRUCTIONAL DESIGN AND ASSESSMENT Using a Human Patient Simulation Mannequin to Teach Interdisciplinary Team Skills to Pharmacy Students

Objectives.To determine the effectiveness and student acceptance of using a human patient simulation (HPS) training module focused on interdisciplinary teamwork skills. Design. During their second-professional year, all pharmacy students were in enrolled in Principles of Pharmacotherapy 4: Cardiovascular Diseases and Patient Care Lab IV, a problem-based learning course. As part of the patient care laboratory, students participated in a simulated case of an acutely ill patient with a hypertensive emergency. During the simulation, students performed a history and physical examination. They then worked as a team to make treatment recommendations to the nursing and physician staff members. Following the exercise, a facilitated debriefing session was conducted. Students completed satisfaction surveys to assess the quality and effectiveness of the session. Assessment.Over 98% of students agreed or strongly agreed that they learned material relevant to their current studies. When compared to student lectures, 90% of students felt that they learned clinical patient care better when using a HPS mannequin in simulated patient scenarios. Conclusion. HPS-based learning offers a realistic training experience through which clinical knowledge and interpersonal teamwork skills can be taught. Students enjoy the experience and find it relevant to their future practice. Simulation-based training may teach certain topics better than traditional lecture formats and as such could help to fill gaps in the current pharmacy curriculum.
Random Walks on Regular and Irregular Graphs

For an undirected graph and an optimal cyclic list of all its vertices, the cyclic cover time is the expected time it takes a simple random walk to travel from vertex to vertex along the list until it completes a full cycle. The main result of this paper is a characterization of the cyclic cover time in terms of simple and easy-to-compute graph properties. Namely, for any connected graph, the cyclic cover time is $\Theta(n^2 d_{ave} (d^{-1})_{ave})$, where $n$ is the number of vertices in the graph, $d_{ave}$ is the average degree of its vertices, and $(d^{-1})_{ave}$ is the average of the inverse of the degree of its vertices. Other results obtained in the processes of proving the main theorem are a similar characterization of minimum resistance spanning trees of graphs, improved bounds on the cover time of graphs, and a simplified proof that the maximum commute time in any connected graph is at most $4n^3/27 + o(n^3)$.
Capacity region and optimum power control strategies for fading Gaussian multiple access channels with common data

A Gaussian multiple access channel (MAC) with common data is considered. Capacity region when there is no fading is known in an implicit form. We provide an explicit characterization of the capacity region and provide a simpler encoding/decoding scheme than that mentioned in work by Slepian and Wolf. Next, we give a characterization of the ergodic capacity region when there is fading, and both the transmitters and the receiver know the channel perfectly. Then, we characterize the optimum power allocation schemes that achieve arbitrary rate tuples on the boundary of the capacity region. Finally, we provide an iterative method for the numerical computation of the ergodic capacity region and the optimum power control strategies
Persistent pointer information

Pointer information, indispensable for static analysis tools, is expensive to compute and query. We provide a query-efficient persistence technique, Pestrie, to mitigate the costly computation and slow querying of precise pointer information. Leveraging equivalence and hub properties, Pestrie can compress pointer information and answers pointer related queries very efficiently. The experiment shows that Pestrie produces 10.5X and 17.5X smaller persistent files than the traditional bitmap and BDD encodings. Meanwhile, Pestrie is 2.9X to 123.6X faster than traditional demand-driven approaches for serving points-to related queries.
A simplified treatment of Kanatani's renormalisation method

The renormalisation method of Kanatani is intended to find the minimisers of cost functions of a certain form. As such, it has applicability to a wide spectrum of computer vision problems that may be couched in these terms. However, despite its sophistication, the method of Kanatani has been slow to gain broad acceptance, perhaps because of the complexity of its original derivation. In this paper we present an alternative and simpler treatment of this important method.
Thermosensitive PEG–PCL–PEG (PECE) hydrogel as an in situ gelling system for ocular drug delivery of diclofenac sodium

Abstract Development of efficient ocular drug delivery systems was still a challenging task. The objective of this article was to develop a thermosensitive PEG–PCL–PEG (PECE) hydrogel and investigate its potential application for ocular drug delivery of diclofenac sodium (DIC). PECE block polymers were synthesized by coupling MPEG-PCL co-polymer using IPDI reagent, and then its sol–gel transition as a function with temperature was investigated by a rheometer. The results showed that 30% (w/v) PECE aqueous solution exhibited sol–gel transition at approximately 35 °C. In vitro release profiles showed the entrapped DIC was sustained release from PECE hydrogels up to 7 days and the initial drug loading greatly effect on release behavior of DIC from PECE hydrogels. MTT assay results indicated that no matter PECE or 0.1% (w/v) DIC-loaded PECE hydrogels were nontoxic to HCEC and L929 cells after 24 h culturing. In vivo eye irritation test showed that the instillation of either 30% (w/v) PECE hydrogels or 0.1% (w/v) DIC-loaded PECE hydrogels to rabbit eye did not result in eye irritation within 72 h. In vivo results showed that the AUC0–48 h of 0.1% (w/v) DIC-loaded PECE hydrogels exhibited 1.6-fold increment as compared with that of commercial 0.1% (w/v) DIC eye drops, suggesting the better ophthalmic bioavailability could be obtained by the instillation of 0.1% (w/v) DIC-loaded PECE hydrogels.
Analytical model for Software Defined Network delay estimation

Traditional IP networks are becoming more complex to satisfy the demands of modern applications and it draws communication providers to exploit a wide range of specialized hardware. Commissioning of a new network service implies additional room for new equipment, power sources, cooling systems, etc. Besides, there is need for increase of qualified stuff. This results in the escalation of capital and operational expenses that eventually exceeds the revenue growth rates for which these expenses are initially intended. To overcome such a deadlock, it is no more sufficient to introduce new protocols for network enhancement, it is necessary to reconsider the network architecture. Software-Defined Networking (SDN) is a new network paradigm that allows managing network services by separating data and control planes. Herein network planning and traffic management are performed by software what makes installation of new network services, such as routing, resource management and security more simple and agile. Interaction between the two planes can be provided by means of OpenFlow protocol that allows manipulating data plane and collecting various statistics used to form global state of a network. In this paper we present an overview of SDN and OpenFlow, their key features and main concepts. Next, we present a model of SDN-network in the form of a queuing network and propose the approach to mean delay time estimation.
Risk of selecting K65R in antiretroviral-naive HIV-infected individuals with chronic hepatitis B treated with adefovir

Seven antiretroviral-naive HIV-infected individuals with chronic hepatitis B treated with adefovir for longer than 6 months were assessed. Using bulk population sequencing and a sensitive limiting dilution analysis, the selection of K65R or other resistance mutations did not occur in HIV, suggesting that adefovir can be confidently used as hepatitis B virus (HBV) therapy in HIV/HBV-co-infected patients who do not require antiretroviral therapy.
Performance Analysis of Space-Shift Keying in Decode-and-Forward Multihop MIMO Networks

In this paper, space-shift keying (SSK) is considered for multihop multiple-input-multiple-output (MIMO) networks. In SSK, only one among ns = 2m available transmit antennas, chosen on the basis of m information bits, is activated during transmission. We consider two different systems of multihop cooperation, where each node has multiple antennas and employs SSK. In system I, a multihop diversity relaying scheme is considered. In system II, a multihop multibranch relaying scheme is considered. In both systems, we adopt decode-and-forward (DF) relaying, where each relay forwards the signal only when it correctly decodes. We analyze the end-to-end bit error rate (BER) and diversity order of both the systems with SSK. For binary SSK (ns = 2), our analytical BER expression is exact, and our numerical results show that the BERs evaluated through the analytical expression overlap with those obtained through Monte Carlo simulations. For nonbinary SSK (ns > 2), we derive an approximate BER expression, where the analytically evaluated BER results closely follow the simulated BER results. We show the comparison of the BERs of SSK and conventional phase-shift keying (PSK) and also show the instances where SSK outperforms PSK. We also present the diversity analyses for SSK in systems I and II, which predict the achievable diversity orders as a function of system parameters.
The microbiome in urogenital schistosomiasis and induced bladder pathologies

Background Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies. Methodology Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline. Principal findings The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism. Conclusion The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.
Efficient computation of temporal aggregates with range predicates

A temporal aggregation query is an important but costly operation for applications that maintain time-evolving data (data warehouses, temporal databases, etc.). Due to the large volume of such data, performance improvements for temporal aggregation queries are critical. In this paper we examine techniques to compute temporal aggregates that include key-range predicates (range temporal aggregates). In particular we concentrate on SUM, COUNT and AVG aggregates. This problem is novel; to handle arbitrary key ranges, previous methods would need to keep a separate index for every possible key range. We propose an approach based on a new index structure called the Multiversion SB-Tree, which incorporates features from both the SB-Tree and the Multiversion B-Tree, to handle arbitrary key-range temporal SUM, COUNT and AVG queries. We analyze the performance of our approach and present experimental results that show its efficiency.
A note on a phase-field model for anisotropic systems

We investigate, using the framework of Γ -convergence, a phase-field model proposed in (Proc. R. Soc. A 465 (2009), 1337-1359) for strongly anisotropic systems; in particular, we prove a full Γ -convergence result for an anisotropic Modica- Mortola-type energy.
Transcytosis of Staphylococcal Superantigen Toxins

Staphylococcus aureus produces a set of proteins (e.g., staphylococcal enterotoxin A [SEA], SEB, toxic shock syndrome toxin 1 [TSST-1]) which act both as superantigens (SAgs) and toxins. Although their mode of action as SAgs is well understood, little is known about how they enter the body via the intestine and cause food poisoning. To examine this problem we used an in vitro culture system to study the capacity of class II MHC-negative human intestinal epithelial cells (Caco-2) to transcytose several staphylococcal toxins. We found that Caco-2 cells are capable of dosedependent, facilitated transcytosis of SEB and TSST-1, but not SEA. We extended these studies in vivo in mice by showing that ingested SEB appears in the blood more efficiently than SEA. Our data suggest that these toxins can cross the epithelium in an immunologically intact form. These results may have important implications for the pathogenesis of food poisoning.
English as a Second Language Students and English Language Anxiety : Issues in the Mainstream

RESEARCH IN THE TEACHING OF ENGLISH • VOLUME 36 • FEBRUARY 2002 This study addresses issues of English language anxiety in two settings: English as a second language and mainstream classrooms. Participants were 178 middle-school Mexican immigrant students attending school in the U.S. Participants were given the English Language Anxiety Scale, which was analyzed with three statistical tests: paired t-tests to analyze broad levels of anxiety between ESL and mainstream classes; ANCOVAs to identify how levels of anxiety correlated with the specific factors of years in the U.S., levels of academic achievement, listening and speaking skills, reading and writing skills, and gender; and an exploratory factor analysis to identify additional factors contributing to anxiety. A second data set, focus group transcripts, was analyzed to identify additional factors and coping strategies. Results showed several related but different types of English language anxiety and a significant gender difference. The focus groups revealed that interaction with Chicano students raised anxiety levels and that such strategies as avoidance were used to reduce anxiety. The paper concludes with recommendations for teaching and research that recognize the complexity of anxiety for English language learners.
Transforming Open-Source Documents to Terror Networks: The Arizona TerrorNet

Homeland security researchers and analysts more than ever must process large volumes of textual information. Information extraction techniques have been proposed to help alleviate the burden of information overload. Information extraction techniques, however, require retraining and/or knowledge re-engineering when document types vary as in the homeland security domain. Also, while effectively reducing the volume of the information, information extraction techniques do not point researchers to unanticipated interesting relationships identified within the text. We present the Arizona TerrorNet, a system that utilizes less specified information extraction rules to extract less choreographed relationships between known terrorists. Extracted relations are combined in a network and visualized using a network visualizer. We processed 200 unseen documents using the TerrorNet which extracted over 200 relationships between known terrorists. An Al Qaeda network expert made a preliminary inspection of the network and confirmed many of the network links.
Semi-Automatic Extraction of Training Examples From Sensor Readings for Fall Detection and Posture Monitoring

While inexpensive wearable motion-sensing devices have shown great promise for fall detection and posture monitoring, two major problems still exist and have to be solved: a framework for the development of firmware and software to make intelligent decisions. We address both the problems. We propose a generic framework for developing the firmware. We also demonstrate that the k-means clustering algorithm can semi-automatically extract training examples from motion data. Moreover, we trained and evaluated several one- and two-level classification networks to monitor non-fall activities and to detect fall events. The proposed classification networks are the combinations of neural networks and softmax regression. These networks are trained offline with examples extracted by our proposed method. The cross-validation of trained two-level networks shows 100% accuracy for non-fall activities and fall events. The data sets for training and testing have been collected using the devices we assembled with four off-the-shelf components. We have programmed them using a prototype of our proposed framework. The data sets include seven types of non-fall activities and four types of fall events. This paper advances the state of the art for the development and training of wearable devices for monitoring non-fall activities and detecting fall events.