Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic Value of Microvessel Density in Tumor and Peritumoral Area as Evaluated by CD31 Protein Expression and Argyrophilic Nucleolar Organizer Region Count in Endothelial Cells in Uterine Leiomyosarcoma

The objective of this study was to investigate the prognostic value of microvessel density (MVD) in uterine leiomyosarcoma (LMS) and peritumoral area (PA) as evaluated by CD31 expression and argyrophilic nucleolar organizer region (AgNOR) count in endothelial cells. Tissue specimens from 66 patients with uterine LMS were examined. There were no significant differences in the mean MVD between tumor itself and the PA (P = 0.9); moreover, the MVD in the PA often exceeded that in the tumor. No correlation or significant differences were also found in the MVD between different grades of malignancy of LMS (r = 0.1; P = 0.07). The number of AgNORs in tumor endothelial cells was significantly higher in tumor vessels than in the peritumoral area (P < 0.005) and increased with the tumor grade. Analysis of the prognostic value of MVD in uterine LMS and PA showed that the density of tumor vessels was not an independent criterion, while the MVD in the PA affected 10-year survival to a significantly greater extent (χ 2 = 27.5; P = 0.0003). The number of AgNORs also had an important effect on survival of LMS patients: when the threshold of 11.6 granules was exceeded, prognosis was significantly more unfavorable than that prior to exceeding the threshold.
Practice for Life: Making Decisions in College

Based on research from a five-year multi-institutional study of undergraduate students at liberal arts colleges, Practice for Life: Making Decisions in College is an important contribution to the literature on today’s college students. The authors examined what it is like to be a college student at a liberal arts college and the process of becoming liberally educated. To explore this, the book is framed around decision making in college, focusing on what decisions students make, how students make these decisions, and how students reflect upon and learn from their decisions. Some decisions came from big questions such as: “What should I major in? ” or “Should I apply to graduate school? ” Other decisions were less substantial, such as: “Should I talk to my parents about this? ” or “What should I do this weekend? ” Although the book is framed, and titled, as if it focuses solely on decision making, the findings presented extend beyond decision making, providing insight into what drives students to be engaged with their education, how students experience transitions into and during college, and how they make meaning of their experiences.
Resistance of content-dependent video watermarking to watermark-estimation attacks

One of the key challenges for a watermarking scheme to be mandated in a digital right management (DRM) system is the robustness. This paper is focused on exploring the robustness against the watermark-estimation attacks (WEAs) that are clever at disclosing hidden information for unauthorized purposes without sacrificing media's quality. In WEAs, the collusion attack naturally occurs in video watermarking while the copy attack adapts to any media watermarking. In view of this, the aim of this study is to deal with the WEAs by means of a video frame-dependent watermark (VFDW). We begin by gaining insight into the WEAs, leading to formal definitions of "optimal watermark prediction" and "perfect cover data recovery". Subject to these definitions, the video-frame hash is addressed as a constituent component of the VFDW for antiestimation of hidden watermarks. Both mathematical analyses and experiment results consistently verify the antidisclosure capability of the video content-dependent watermarking scheme. Our approach is the first work that takes resistance to both the collusion and copy attacks into consideration.
Differential Transceiver Design for Quasi-Orthogonal Space-Time Block Codes

In this paper, we report a general and simple differential modulation scheme that can be applied to both partial-diversity quasi-orthogonal space-time block codes and full-diversity quasi-orthogonal space-time block codes for four transmit antennas. The differential encoding and decoding can be simplified to differential Alamouti codes by grouping the signals in the transmitted matrix and decoupling the detection of data symbols, respectively. For the codes with partial transmit diversity, the new scheme can achieve constant amplitude of transmitted signals, and avoid signal constellation expansion, and it has a linear signal detector with very low complexity. Simulation results show that these partial-diversity codes can provide very useful results at low SNR for current communication systems. For the codes with full transmit diversity achieved by constellation rotation, our scheme has performance equal to the best full-rate quasi-orthogonal schemes previously described in the literature with a simpler detector.
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

MOTIVATION Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has been widely used. Recently, massively parallel sequencing coupled with ChIP experiments (ChIP-seq) has been increasingly used as an alternative to ChIP-chip, offering cost-effective genome-wide coverage and resolution up to a single base pair. For many well-studied TFs, both ChIP-seq and ChIP-chip experiments have been applied and their data are publicly available. Previous analyses have revealed substantial technology-specific binding signals despite strong correlation between the two sets of results. Therefore, it is of interest to see whether the two data sources can be combined to enhance the detection of TFBS. RESULTS In this work, hierarchical hidden Markov model (HHMM) is proposed for combining data from ChIP-seq and ChIP-chip. In HHMM, inference results from individual HMMs in ChIP-seq and ChIP-chip experiments are summarized by a higher level HMM. Simulation studies show the advantage of HHMM when data from both technologies co-exist. Analysis of two well-studied TFs, NRSF and CCCTC-binding factor (CTCF), also suggests that HHMM yields improved TFBS identification in comparison to analyses using individual data sources or a simple merger of the two. AVAILABILITY Source code for the software ChIPmeta is freely available for download at http://www.umich. edu/~hwchoi/HHMMsoftware.zip, implemented in C and supported on linux.
Merging Tangible Buttons and Spatial Augmented Reality to Support Ubiquitous Prototype Designs

The industrial design prototyping process has previously shown promising enhancements using Spatial Augmented Reality to increase the fidelity of concept visualizations. This paper explores further improvements to the process by incorporating tangible buttons to allow dynamically positioned controls to be employed by the designer. The tangible buttons are equipped with RFID tags that are read by a wearable glove sensor system to emulate button activation for simulating prototype design functionality. We present a new environmental setup to support the low cost development of an active user interface that is not restricted to the two-dimensional surface of a traditional computer display. The design of our system has been guided by the requirements of industrial designers and an expert review of the system was conducted to identify its usefulness and usability aspects. Additionally, the quantitative performance evaluation of the RFID tags indicated that the concept development using our system to support a simulated user interface functionality is an improvement to the design process.
A Rule-Based System for Unrestricted Bridging Resolution: Recognizing Bridging Anaphora and Finding Links to Antecedents

Bridging resolution plays an important role in establishing (local) entity coherence. This paper proposes a rule-based approach for the challenging task of unrestricted bridging resolution, where bridging anaphors are not limited to definite NPs and semantic relations between anaphors and their antecedents are not restricted to meronymic relations. The system consists of eight rules which target different relations based on linguistic insights. Our rule-based system significantly outperforms a reimplementation of a previous rule-based system (Vieira and Poesio, 2000). Furthermore, it performs better than a learning-based approach which has access to the same knowledge resources as the rule-based system. Additionally, incorporating the rules and more features into the learning-based system yields a minor improvement over the rule-based system.
Gear fault diagnosis of wind turbine based on discrete wavelet transform

The feature-frequency technique based on discrete wavelet transform (DWT) is proposed to diagnose the gear faults of wind turbine. Discrete wavelet decomposition to the vibration acceleration signal, combined with the analysis of energy distribution in different frequency band, is applied to determine the characteristic frequency band of the fault, and then the type of fault is determined by the frequency spectrum of the reconstructed signal on the characteristic frequency band. Large simulation experiments show that the featurefrequency technique based on DWT can effectively extract the characteristics of the gear faults of wind turbine and then accurately determine the type of fault.
Escherichia coli RNA and DNA polymerase bypass of dihydrouracil: mutagenic potential via transcription and replication.

Dihydrouracil (DHU) is a DNA base damage product produced in significant amounts by ionizing radiation damage to cytosine under anoxic conditions. DHU represents a model for pyrimidine base damage (ring saturation products) of the type recognized and repaired by Escherichia coli endonuclease III and its homologs in other species. We have built this lesion into synthetic oligonucleotides, with DHU placed at a single location downstream from an E.coli RNA polymerase promoter. This construct was used to determine the effect of DHU when encountered on a DNA template strand by either E.coli RNA or DNA polymerase (Klenow fragment). Single round transcription experiments or primer extension-type replication experiments were conducted in order to make a direct comparison between RNA and DNA polymerases with DHU placed within the same sequence context. Both DNA and RNA polymerase efficiently bypass DHU and insert adenine opposite this lesion. These results suggest that DHU is mutagenic with respect to both replication and transcription and have implications for DNA repair as well the routes leading to generation of mutant proteins in dividing and non-dividing cells.
Article (refereed) -postprint Title Phenology Predicts the Native and Invasive Range Limits of Common Ragweed Running Head Phenology Determines Ragweed Range Limits

The NERC and CEH trademarks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. Abstract Accurate models for species' distributions are needed to forecast the progress and impacts of alien invasive species and assess potential range-shifting driven by global change. Although this has traditionally been achieved through data-driven correlative modelling, robustly extrapolating these models into novel climatic conditions is challenging. Recently, a small number of process-based or mechanistic distribution models have been developed to complement the correlative approaches. However, tests of these models are lacking, and there are very few process-based models for invasive species. We develop a method for estimating the range of a globally-invasive species, common ragweed (Ambrosia artemisiifolia L.), from a temperature-and photoperiod-driven phenology model. The model predicts the region in which ragweed can reach reproductive maturity before frost kills the adult plants in autumn. This aligns well with the poleward and high-elevation range limits in its native North America and in invaded Europe, clearly showing that phenological constraints determine the cold range margins of the species. Importantly, this is a 'forward' prediction made entirely independently of the distribution data. Therefore, it allows a confident and biologically-informed forecasting of further invasion and range shifting driven by climate change. For ragweed, such forecasts are extremely important as the species is a serious crop weed and its airborne pollen is a major cause of allergy and asthma in humans. Our results show that phenology can be a key determinant of species' range margins, so integrating phenology into species distribution models offers great potential for the mechanistic modelling of range dynamics.
Visualising Layout of a Container Terminal

The proposed paper summarises the work done in a container terminal project where the needs of small to medium sized ports / terminals with 'multi-purpose' capability had to be addressed. To this end the following had to be considered: The absence of extensive IT support and how to deal with it, Information flows to/from and within the terminal, Cargo flows to/from and within the terminal and in association with this, Layout of land and maritime approaches including berths, Position of in-and out gates, Terminal and yard layout in conjunction with selected cargo handling equipment. The above resulted in an electronic terminal planning board (TPB) with generic applicability.
Spatial Patterns of Canopy Disturbance, Structure, and Species Composition in a Multi-Cohort Hardwood Stand

Multi-cohort stands are increasingly recognized and valued because of their biological functioning, biological diversity, and resistance and resiliency to perturbations. These forest ecosystems are epitomized by multiple age classes, and often contain multiple canopy layers, a range of tree size classes, and large amounts of woody debris. Disturbance history reconstructions in multi-cohort stands provide an understanding of the processes that create these systems. In this study, we documented structure and composition, and used dendroecological techniques to reconstruct disturbance history on a 1 ha plot in a multi-cohort hardwood stand in the Fall Line Hills of Alabama. The stand was dominated by Quercus alba L. and Liriodendron tulipifera L. Mingling index and stem maps indicated that most species were well dispersed throughout the stand, with the exception of L. tulipifera and Carya tomentosa (Poiret) Nuttal, which were relatively clustered. The oldest trees in the stand established in the 1770s, however, the largest recruitment event occurred ca. 1945 in conjunction with a stand-wide canopy disturbance. We posit that spatial heterogeneity of canopy removal during this event was largely responsible for the observed compositional and spatial complexity documented in the stand. In addition to the 1945 event, we recorded another stand-wide canopy disturbance in 1906 and 84 gap-scale disturbance events from 1802 to 2003. The conditions documented in the stand can be used as a benchmark to guide the creation and maintenance of complex multi-cohort stand characteristics, an increasingly popular management goal.
Validation of the Spanish Version of the Psychological Sense of School Membership (PSSM) Scale in Chilean Adolescents and Its Association with School-Related Outcomes and Substance Use

School membership appears to be an important factor in explaining the relationship between students and schools, including school staff. School membership is associated with several school-related outcomes, such as academic performance and expectations. Most studies on school membership have been conducted in developed countries. The Psychological Sense of School Membership (PSSM) scale (18 items: 13 positively worded items, 5 negatively worded items) has been widely used to measure this construct, but no studies regarding its validity and reliability have been conducted in Spanish-speaking Latin American countries. This study investigates the psychometric properties, factor structure and reliability of this scale in a sample of 1250 early adolescents in Chile. Both exploratory and confirmatory factor analyses provide evidence of an excellent fit for a one-factor solution after removing the negatively worded items. The internal consistency of this new abbreviated version was 0.92. The association analyses demonstrated that high school membership was associated with better academic performance, stronger school bonding, a reduced likelihood of school misbehavior, and reduced likelihood of substance use. Analyses showed support for the reliability and validity of the PSSM among Chilean adolescents.
A popularity-based neighbor selection model in P2P file-sharing system

In the past few years, P2P file distribution applications (e.g., Bit Torrent) are becoming so popular that they are the dominating source of Internet traffic. This brings significant problems not only because the increasing P2P traffic costs most of network bandwidth, but also the overmuch P2P connections increase the burden on the end-users. In this paper we present a peers' popularity model that rank these peers by performance and then select the strong peers, those who can provide efficient uploading and who have sufficient load capacity. To achieve this goal, we design a general definition to peers' popularity and analyze it with a Zipf-like distribution. Furthermore, we carry out the implementation proposals in most P2P systems with tracker server. Through this model we can reduce the superfluous P2P connections and increase the efficiency of P2P download.
Model transformations to satisfy all-configurations-transitions on statecharts

Existing applicable coverage criteria in model-based testing for statecharts do not require test suites to include all transitions between state configurations. This excludes potentially important test cases, reduces the quality of the generated test suite, and leaves parts of the system-under-test untested. We propose a new coverage criterion called All-Configurations-Transitions, which includes these missing test cases and propose test model transformation to enable existing test generators to satisfy the criterion. The new criterion improves the quality of generated test suites for statecharts using parallelism and reduces the amount of untested functionality of the system-under-test.
A Particle Swarm approach for the Design of Variable Structure Stabilizer for a Nonlinear Model of SMIB System

There is a vivid trend in engineering optimization problems towards the adoption of heuristic optimization algorithms to arrive at optimal solutions. This is mainly due to the simplicity of these algorithms and the great cut down of complicated mathematical manipulations that are required in other optimization theory methods. This paper demonstrates the application of an iterative heuristic optimization algorithm, namely, Particle Swarm Optimization (PSO), in the design of variable structure stabilizers for a nonlinear single machine infinite bus system (SMIB). Two versions of PSO, namely the inertia weight method of updating the velocities (PSO-iw) and constriction factor method (PSO-cf) are applied in the optimal design of the stabilizer. The success of the PSO approach is supported by simulation results that confirm the attainment of the stabilizer control objectives.
Giant Chordoma of the Upper Thoracic Spine with Mediastinal Involvement: A Surgical Challenge

Thoracic chordomas are very rare malignant tumours originating from notochordal remnants. These tumours develop within a vertebral body and enlarge involving the mediastinal compartment. Because of their slow-growing attitude, they become symptomatic only when they invade or compress the spinal cord and/or mediastinal organs. We present a rare case of a thoracic spine chordoma presenting with increasing paraparesis with a huge mediastinal component which was surgically debulked to decompress the spinal cord and medistinal organs.
Specific aspartyl and calpain proteases are required for neurodegeneration in C . elegans

Treatment with pharmacological reagents occurred 30–60 min before growth factor or cytokine administration. The reagents were either present throughout the experiment or alternatively the medium was replaced after 6–12 h incubation. Reagents in this study were: LY294002 (10–50 mM; Calbiochem) and okadaic acid (1 nM to 1 mM; Calbiochem and Alomone Laboratories). In vivo and in vitro kinase assays The in vivo kinase assay was performed largely as recommended by the supplier (Akt Kinase Assay Kit, Cell Signaling Technology). In vitro kinase assays were performed using 1 £ buffer (Akt Kinase Assay Kit, Cell Signaling Technology), 100 mM ATP, 0.5 mM peptide (ENNEKQMRQLSVIPPMMFDA), 300 U ml 21 Akt1 protein kinase. For radioactivity incorporation assay, 250 mCi ml 21 [g-32 P]ATP were included in the reaction. The reactions were quenched by addition of SDS gel buffer, and were either spotted on nitrocellulose membranes for immunoblotting, or were analysed by PAGE using 18% acrylamide gels. Transfections were performed with lipofection reagents (Effectene, Qiagen) largely following the supplier's recommendations. Typically, 1–2 mg DNA was lipofected on a 60-mm dish for 6–12 h in the presence of FGF2, after which the cells received fresh medium with growth factors as indicated. Previously unpublished constructs used in this study are: Chromatin immunoprecipitation was performed on neural stem cells largely as described 28. Neural stem cells grown on 150-mm dishes were collected and crosslinked using 1% formalin for 10 min at room temperature, and the extracts were sonicated until the DNA fragments were 500–800 bp in size. Cell extracts were subsequently incubated with 5 mg IgG or antibodies against N-CoR or CBF1 overnight at 4 8C. The extracts were incubated with protein A-sepharose beads (Sigma) for 1 h. After extensive washing of the beads, proteins were eluated and reversed by crosslinking for 6 h at 65 8C.
A 0.7V 194µW 31dB FOM 2.3–2.5 GHz RF frontend for WBAN with mutual noise cancellation using passive coupling

A low power low noise 0.7V mixer first RF frontend for an IEEE 802.15. 6 narrowband receiver is presented which uses passive coupling based frequency translated mutual noise cancellation. Unlike traditional noise cancelling techniques we perform symmetrical noise cancellation of a fully differential structure where each path cancels the noise of the other at IF. This paper tackles the noise figure and power consumption problems of sub 1V mixers. The FOM is 10dB higher and power consumption is 194μW which is 0.5X lower than the state of the art. The LO power used is -14dBm.
Robust Numerical Calibration for Implied Volatility Expansion Models

Implied volatility expansions allow calibration of sophisticated volatility models. They provide an accurate fit and parametrization of implied volatility surfaces that is consistent with empirical observations. Fine-grained higher order expansions offer a better fit but pose the challenge of finding a robust, stable, and computationally tractable calibration procedure due to a large number of market parameters and nonlinearities. We propose calibration schemes for second order expansions that take advantage of the model's structure via exact parameter reductions and recoveries, reuse and scaling between expansion orders where permitted by the model asymptotic regime, and numerical iteration over bounded significant parameters. We perform a numerical analysis over 12 years of real S&P 500 index options data for both multiscale stochastic and general local-stochastic volatility models. Our methods are validated empirically by obtaining stable market parameters that meet the qualitative and numerical constr.