Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Seq Data Mining: Downregulation of NeuroD6 Serves as a Possible Biomarker for Alzheimer's Disease Brains

Alzheimer's disease (AD) is the most common cause of dementia worldwide with no curative therapies currently available. Previously, global transcriptome analysis of AD brains by microarray failed to identify the set of consistently deregulated genes for biomarker development of AD. Therefore, the molecular pathogenesis of AD remains largely unknown. Whole RNA sequencing (RNA-Seq) is an innovative technology for the comprehensive transcriptome profiling on a genome-wide scale that overcomes several drawbacks of the microarray-based approach. To identify biomarker genes for AD, we analyzed a RNA-Seq dataset composed of the comprehensive transcriptome of autopsized AD brains derived from two independent cohorts. We identified the core set of 522 genes deregulated in AD brains shared between both, compared with normal control subjects. They included downregulation of neuronal differentiation 6 (NeuroD6), a basic helix-loop-helix (bHLH) transcription factor involved in neuronal development, differentiation, and survival in AD brains of both cohorts. We verified the results of RNA-Seq by analyzing three microarray datasets of AD brains different in brain regions, ethnicities, and microarray platforms. Thus, both RNA-Seq and microarray data analysis indicated consistent downregulation of NeuroD6 in AD brains. These results suggested that downregulation of NeuroD6 serves as a possible biomarker for AD brains.
Brno University of Technology at TRECVid 2012 Interactive Surveillance Event Detection Pilot

In the paper, we describe our experiments in the interactive surveillance event detection pilot (SED) of the 2009 TRECVid evaluation. Our approach inherits functionality of the Surveillance Network Augmented by Retrieval (SUNAR) system, which is an information retrieval based wide area (video) surveillance system being developed at FIT, Brno University of Technology. It contains both standard and experimental techniques evaluated at the AVSS 2009/10 Multi-Camera Tracking Challenge. We have deployed active learning functionality based on moving objects' trajectory statistics and shape classification using VTApi (Video Terror Application programming interface), which was created to unify and accelerate the intelligent vision applications development. The paper is organized as follows. The first section provides a motivation and a brief introduction. Section 2 is dedicated to the active learning approach used and some other theoretical aspects of the work. Details on the technology is presented in Section 3. Section 4 shows some experimental results achieved during the training. Finally, Section 5 discusses achieved results and concludes the paper. Evaluation results are attached at the end of the paper.
A polarization-agile aperture-coupled patch antenna using quad-mode reconfigurable feeding network

This paper presents a new polarization-agile antenna that can switch between four various polarizations. The proposed antenna is based on a quad-mode reconfigurable feeding network with four dynamic transmission modes. At each mode, the measured insertion loss of the feeding network is less than 0.8 dB at the target frequency. Meanwhile, a dual-polarized aperture-coupled patch antenna with good isolation and the same gain between two ports is designed for the realization of the polarization diversity. The feeding network can be integrated into the dual-polarized antenna to form the polarization-agile antenna. By switching the PIN diodes on the feeding network, the proposed antenna can exhibit two orthogonal linear polarizations and two orthogonal circular polarizations. Measured results of the polarization-agile antenna are shown in detail, which verify its performance.
Multiple Facets of Inequity in Racial and Ethnic Achievement Gaps

This article provides a critical look into national trends of the achievement gaps between Whites and Blacks and between Whites and Hispanics over the last 3 decades based on the National Assessment of Educational Progress mathematics assessments. It examines multiple facets of inequity underlying the racial and ethnic achievement gaps from 3 perspectives: equality, adequacy, and reciprocity. Although the Black-White and Hispanic-White mathematics achievement gaps narrowed significantly over the last 3 decades, there was some setback in the national progress during the last decade and the achievement gaps remain substantially large. The study finds that the racial and ethnic achievement gaps are highly inequitable, as it turns out that schools do not measure up to essential conditions of equity: Minority students do not (a) get fairly equal educational opportunities, (b) achieve minimally adequate level of competency, and (c) learn in a racially integrated school. The recent trend of widening racial achievement gaps is also seen as a real setback in equity as there was little systemic improvement in those 3 conditions of equity during the last decade. Implications of the findings for educational policies to enhance broader equity and justice are discussed.
A Parametric Study of Scalable Interconnects on FPGAs

With the constantly increasing gate capacity of FPGAs, a single FPGA chip is able to employ large-scale applications. To connect a large number of computational nodes, NetworkOn-Chip (NoC), in which different flows share a point-to-point link, becomes advantageous in terms of scalability. Although fixed regular network infrastructures are only used in recent FPGAbased NoCs, the network topology can be optimized to fit the target application on FPGAs. In this paper, we investigate the suitable interconnects based on the typical implementation of NoC router with various number of wires per channel on FPGAs. In order to clearly illustrate the trade-off between network throughput and hardware amount for network components, we evaluate the amount of hardware for various networks, which are composed by routers with different port numbers, and their throughput using a flitlevel simulation. Evaluation results show that for small systems with 16 cores or less, a large router is advantageous from the viewpoint of both performance and cost. On the other hand, when systems become large, the partitioned networks are efficient from the viewpoint of cost.
Clustering by Ordering Density-Based Subspaces

Finding clusters on the basis of density distribution is a traditional approach to discover clusters with arbitrary shape. Some density-based clustering algorithms such as DBSCAN, OPTICS, DENCLUE, and CLIQUE etc have been explored in recent researches. This paper presents a new approach which is based on the ordered subspace to find clusters. The key idea is to sort the subspaces according to their density, and set a new cluster for the maximal subspace of the subspace list. Since the number of the subspaces is much less than that of the data, very large databases with high-dimensional data sets can be processed with high efficiency. We also present a new method to project high-dimensional data, and then some results of clustering with visualization are demonstrated in this paper.
A Dense Microcluster of Class 0 Protostars in NGC 2264 D-MM1

We present sensitive and high angular resolution (~1'') 1.3 mm continuum observations of the dusty core D-MM1 in the Spokes cluster in NGC 2264 using the Submillimeter Array. A dense microcluster of seven Class 0 sources was detected in a 20′′ × 20′′ region with masses between 0.4 and 1.2 M☉ and deconvolved sizes of ~600 AU. We interpret the 1.3 mm emission as arising from the envelopes of the Class 0 protostellar sources. The mean separation of the 11 known sources (SMA Class 0 and previously known infrared sources) within D-MM1 is considerably smaller than the characteristic spacing between sources in the larger Spokes cluster and is consistent with hierarchical thermal fragmentation of the dense molecular gas in this region.
Chemical Abundances of Planetary Nebulae in the Bulge and Disk of M31

We derive abundances and central star parameters for 15 planetary nebulae (PNe) in M31: 12 in the bulge and three in a disk field 14 kpc from the nucleus. No single abundance value characterizes the bulge stars: although the median abundances of the sample are similar to those seen for PNe in the LMC, the distribution of abundances is several times broader, spanning over one decade. None of the PNe in our sample approach the super-metal-rich ([Fe/H]~0.25) expectations for the bulge of M31, although a few PNe in the sample of Stasińska, Richer, & Mc Call come close. This [O/H] versus [Fe/H] discrepancy is likely due to a combination of factors, including an inability of metal-rich stars to produce bright PNe, a luminosity selection effect, and an abundance gradient in the bulge of M31. We show that PNe that are near the bright limit of the [O III] λ5007 planetary nebula luminosity function (PNLF) span nearly a decade in oxygen abundance and, thus, support the use of the PNLF for deriving distances to galaxies (in the work by Jacobi and collaborators) with differing metallicities. We also identify a correlation between central star mass and PN dust formation that partially alleviates any dependence of the PNLF maximum magnitude on population age. In addition, we identify a spatially compact group of five PNe having unusually high O/H; this subgroup may arise from a recent merger, but velocity information is needed to assess the true nature of the objects.
Predicates are predicate transformers: a unified compositional theory for concurrency

He Jifeng and Hoare’s [He Jifeng] approach to integrate theories for “program8 as predicates” and “programs as predicate transformers” in sequential setting i generalieed to a compositional verification theory for concurrency, using idea8 of Zwiers’ [Zwiers]. Due to the generality of the approach, a variety of parallel composition operators, based on shared variables, communication events, interleaving, maximal progress and the like, can be expressed as derived operations.
Scanning Electron Microscopy Studies of Nafion Deformation into Silicon Micro-Trenches for Fuel Cell Applications

ii I hereby declare that I am the sole author of this thesis. I authorize Princeton University to lend this thesis to other institutions or individuals for the purpose of scholarly research. I further authorize Princeton University to reproduce this thesis by photocopying or by other means, in total or in part, at the request of other institutions or individuals for the purpose of scholarly research. Princeton University requires the signatures of all persons using or photocopying this thesis. Please sign below and give address and date. iv To my friends and family and everyone who has helped make my life so exceedingly enjoyable. v Acknowledgements I would like to begin by thanking all of the great teachers I have had over the years who helped spark my passion for math and science. I would also like to thank my parents for sacrificing to send me to the best schools possible. I would like to thank Professor Benziger for allowing me to work under him and always having faith in my ability to work without direct supervision and clear my own path. I would also like to thank Professor Nan Yao for teaching such an elegant class on electron microscopy. Thanks also go to Mikhail Gaevski, Professor Loo, and Professor Register for allowing me to use their respective facilities and labs. A special thank you goes to Joe Palmer for his words of wisdom and warm smile in the clean room, a place normally devoid of smiles. I would like to thank Mr. James Inman and Mr. Roger Lee of the custodial staff of the Friend Center of Engineering. Their kind greetings and friendly faces were a constant reminder that even in the worst of times, life is good. I would like to thank all of my dear friends at the Cap and Gown club, especially my roommates, and my twin sister Lizz for listening to me talk about my thesis even though I'm sure they all secretly found it exceedingly boring. Last, but certainly not least, I would like to thank all of my classmates in the Chemical Engineering Department. Their camaraderie was undoubtedly the key to my simultaneous successful completion of the chemical engineering curriculum and retention of my sanity. Abstract Fuel cells are a potentially viable, clean, renewable source of energy. Polymer Electrolyte Membrane Fuel Cells (PEMFCs), which rely on the electrolyte copolymer Nafion, are particularly promising. …
Inactivation of a tonoplast P-type ATPase reduces vacuolar acidification and results in a blue flower color

The pH control in different cell compartments is essential for the trafficking of vesicles, proteins and small molecules. Vacuolar type H + -ATPases (v-ATPases) and pyrophosphatases (PPases) in plants control the pH of endomembranes compartments whereas P-type H + -ATPases control the pH of the cytosol by pumping protons across the plasma membrane. In this way an electrochemical gradient is created, which is important for transport of ions across membranes. The regulatory proteins ANTHOCYANIN 1 (AN1), AN2 and AN11 control transcription of genes of the anthocyanin biosynthesis pathway. These same regulators, in combination with PH4 and PH3, induce genes of another pathway, which leads to the acidification of the vacuole. Here we report the isolation of one AN1, PH4 and PH3 target gene, MACF55, which encodes a P-type ATPase. Silencing of MACF55 results in blue flowers with a high pH of the crude petal homogenate indicating that MACF55 is directly involved in vacuolar acidification. Isolation of the PH5 locus from a transposon tagged mutant showed that it encodes MACF55. Complementation experiments showed that 35S:PH5 could fully complement ph5 mutants but not an1, ph3 and ph4, indicating that PH5 activity depends on other genes controlled by AN1, PH4 and PH3. PH5-GFP fusion protein localizes the tonoplast of cowpea protoplast, suggesting that PH5 is responsible for proton pumping from the cytosol into the vacuolar lumen. Thus, PH5 plays a key role in a trait (flower color), which is important for plant reproduction.
PI control of laboratory model elevator via ladder logic in PLC

We summarize the design and implementation of a laboratory model "the Elevator" and its control. We focus on the hardware and software components and on the process of design, actual implementation and application control. The mentioned model is located at the Technical University in Kosice, Department of Cybernetics and Artificial Intelligence at the Center of Modern Control Techniques and Industrial Informatics. The model is used for education offering the possibility to implement various algorithms and programs in ladder diagrams.
The Interplay between Chondrocyte Redifferentiation Pellet Size and Oxygen Concentration

Chondrocytes dedifferentiate during ex vivo expansion on 2-dimensional surfaces. Aggregation of the expanded cells into 3-dimensional pellets, in the presence of induction factors, facilitates their redifferentiation and restoration of the chondrogenic phenotype. Typically 1×105–5×105 chondrocytes are aggregated, resulting in “macro” pellets having diameters ranging from 1–2 mm. These macropellets are commonly used to study redifferentiation, and recently macropellets of autologous chondrocytes have been implanted directly into articular cartilage defects to facilitate their repair. However, diffusion of metabolites over the 1–2 mm pellet length-scales is inefficient, resulting in radial tissue heterogeneity. Herein we demonstrate that the aggregation of 2×105 human chondrocytes into micropellets of 166 cells each, rather than into larger single macropellets, enhances chondrogenic redifferentiation. In this study, we describe the development of a cost effective fabrication strategy to manufacture a microwell surface for the large-scale production of micropellets. The thousands of micropellets were manufactured using the microwell platform, which is an array of 360×360 µm microwells cast into polydimethylsiloxane (PDMS), that has been surface modified with an electrostatic multilayer of hyaluronic acid and chitosan to enhance micropellet formation. Such surface modification was essential to prevent chondrocyte spreading on the PDMS. Sulfated glycosaminoglycan (sGAG) production and collagen II gene expression in chondrocyte micropellets increased significantly relative to macropellet controls, and redifferentiation was enhanced in both macro and micropellets with the provision of a hypoxic atmosphere (2% O2). Once micropellet formation had been optimized, we demonstrated that micropellets could be assembled into larger cartilage tissues. Our results indicate that micropellet amalgamation efficiency is inversely related to the time cultured as discreet microtissues. In summary, we describe a micropellet production platform that represents an efficient tool for studying chondrocyte redifferentiation and demonstrate that the micropellets could be assembled into larger tissues, potentially useful in cartilage defect repair.
CUTI-1: A Novel Tetraspan Protein Involved in C. elegans CUTicle Formation and Epithelial Integrity

The nematode cuticle is a tough extracellular matrix composed primarily of cross-linked collagens and non-collagenous cuticulins. It is required for nematode motility and protection from the external environment. Little is known about how the complex process of cuticle formation has been adapted to the specialized requirements of the nematode cuticle, which is structurally and compositionally unique from other organisms. The C. elegans gene cuti-1 (CUTicle and epithelial Integrity) encodes a nematode-specific protein. We have shown that CUTI-1 is expressed in the epithelia and in seam cells. Within these tissues the expression of cuti-1 mRNA cycles throughout development in line with the molting cycle, a process that involves synthesis of a new cuticle. In addition, knockdown of cuti-1 by RNA interference (RNAi) results in worms that display post-embryonic phenotypes related to cuticle dysfunction and defects in epithelial integrity. This is one of the first reports of a nematode-specific protein involved in extracellular matrix formation. It provides further insight into how novel ways have evolved to regulate the formation of the cuticle, which is the primary protective barrier and skeletal component of nematodes.
Preliminary Evaluation of Thermo-Sensitive Electrical Parameters Based on the Forward Voltage for Online Chip Temperature Measurements of IGBT Devices

The temperature of power semiconductor devices is one of the main issues affecting the performance, availability, and reliability of power converters. The chip temperature is generally measured using thermosensitive electrical parameters (TSEPs). These parameters are well controlled for laboratory temperature measurements, where the power devices are not used under functional conditions. However, the use of TSEPs for chip temperature measurements in online conditions has yet to be demonstrated. This paper presents an experimental evaluation of two new TSEPs based on measuring the forward voltage, which could be used during operation of the converter. It examines the accuracy of the chip temperature measurement and also discusses the results in terms of robustness to the aging of power devices.
Understanding and Developing Models for Detecting and Differentiating Breakpoints during Task Execution

The ability to detect and differentiate breakpoints during task execution is critical for enabling defer-to-breakpoint policies within interruption management. In this work, we examine the feasibility of building models that are capable of detecting and differentiating three granularities (types) of perceptually meaningful breakpoints, without specifications of users’ tasks. We collected an ecological sample of task execution data, and then asked human observers to review the collected videos and identify perceived breakpoints and their type. Statistical methods were applied to learn models that map features of the ongoing interaction to each type of breakpoint. Results showed that the models were able to detect and differentiate breakpoints with reasonably high accuracy across tasks. Among many uses, such models can enable interruption management systems to better realize defer-to-breakpoint policies for interactive, free-form tasks. CATEGORIES AND SUBJECT DESCRIPTORS H.1. 2 [Models and Principles]: User/Machine Systems – human information processing and human factors
Importance of inharmonicity in the acoustic Guitar

Audibility of inharmonicity in realistic acoustic guitar tones was studied through formal listening experiments. Test tones were synthesized using an FZ-ARMA model of acoustic guitar sounds, which allows accurate control of the inharmonic partials. Inharmonicity was detected fairly easily for the lowest strings if the plucking transient was left out of the sound, but much harder for the full sound with transient. Detection thresholds were measured for two pitches at the low range of the guitar. Mean thresholds were close to, though above, typical amounts of inharmonicity in the guitar. Implications to digital sound synthesis are discussed.
Masses, deformations and charge radii: Nuclear ground-state properties in the relativistic mean field model

We perform a systematic study of the ground-state properties of all the nuclei from the proton drip line to the neutron drip line throughout the periodic table employing the relativistic mean field model. The TMA parameter set is used for the mean-field Lagrangian density, and a state-dependent BCS method is adopted to describe the pairing correlation. The ground-state properties of a total of 6969 nuclei with Z, N ≥ 8a ndZ ≤ 100 from the proton drip line to the neutron drip line, including the binding energies, the separation energies, the deformations, and the rms charge radii, are calculated and compared with existing experimental data and those of the FRDM and HFB-2 mass formulae. This study provides the first complete picture of the current status of the descriptions of nuclear ground-state properties in the relativistic mean field model. The deviations from existing experimental data indicate either that new degrees of freedom are needed, such as triaxial deformations, or that serious effort is needed to improve the current formulation of the relativistic mean field model.
Voices of Pre-Service Teachers: Perspectives on the Performance Assessment for California Teachers (PACT).

Many educators and policy makers find the declining enrollment in California teacher preparation programs alarming (Commission on Teacher Credentialing [CTC], 2008a), especially given a nationwide statistic showing that one-third of all new teachers leave their initial placements after only three years of teaching, and 46% do so within the first five years (Kopkowski, 2008). Eight percent of the total teaching force in public schools and 9% of teachers under age 30 left the teaching profession altogether in 2004-05 (U.S. Department of Education, 2007). Considering the high turnover rates during the first years in the profession and considerable attrition rates among teachers, a constant supply of new teachers is not only essential, but also critical. California’s teacher preparation program enrollments have declined steadily in both Multiple and Single Subject programs since 2001. A CTC report shows a decline of 48% among Multiple Subject and 18% among