Miracle-dz/UniFAR-FTUs huggingface dataset:
Higher order oligomerization is required for H-NS family member MvaT to form gene-silencing nucleoprotein filament

MvaT from Pseudomonas aeruginosa is a member of the histone-like nucleoid structuring protein (H-NS) family of nucleoid-associated proteins widely spread among Gram-negative bacteria that functions to repress the expression of many genes. Recently, it was reported that H-NS from Escherichia coli can form rigid nucleoproteins filaments on DNA, which are important for their gene-silencing function. This raises a question whether the gene-silencing function of MvaT, which has only ∼18% sequence similarity to H-NS, is also based on the formation of nucleoprotein filaments. Here, using magnetic tweezers and atomic force microscopy imaging, we demonstrate that MvaT binds to DNA through cooperative polymerization to form a nucleoprotein filament that can further organize DNA into hairpins or higher-order compact structures. Furthermore, we studied DNA binding by MvaT mutants that fail to repress gene expression in P. aeruginosa because they are specifically defective for higher-order oligomer formation. We found that, although the mutants can organize DNA into compact structures, they fail to form rigid nucleoprotein filaments. Our findings suggest that higher-order oligomerization of MvaT is required for the formation of rigid nucleoprotein filaments that silence at least some target genes in P. aeruginosa. Further, our findings suggest that formation of nucleoprotein filaments provide a general structural basis for the gene-silencing H-NS family members.
Capacity-Approaching Superposition Coding for Optical Fiber Links

We report on the first experimental demonstration of superposition coded modulation (SCM) for polarization-multiplexed coherent-detection optical fiber links. The proposed coded modulation scheme is combined with phase-shifted bit-to-symbol mapping (PSM) in order to achieve geometric and passive shaping of the signal's waveform. The output constellations in SCM-PSM exhibit nonbijective quasi-Gaussian statistical distributions that asymptotically reach the Shannon capacity limit, showing up to 0.7 dB sensitivity improvement for 256-ary SCM-PSM with respect to 256-ary quadrature amplitude modulation (QAM). The characteristic wave formation based on superposition of antipodal symbols and the lack of need for additional encoders for signal shaping, greatly reduces the transmitter and receiver processing complexity in comparison to conventional alternatives. Single-level coding strategy (SL-SCM) is employed in the framework of bit-interleaved coded modulation with iterative decoding (BICM-ID) for forward error correction. The fiber transmission system is characterized in terms of signal-to-noise ratio for back-to-back case and correlated with simulated results for ideal transmission over additive white Gaussian noise channel. Thereafter, successful demodulation and decoding after dispersion-unmanaged transmission over 240-km standard single mode fiber of dual-polarization 6-Gbaud 16-, 32- and 64-ary SCM-PSM is experimentally demonstrated.
Advances in Panel Scalable Planarization and High Throughput Differential Seed Layer Etching Processes for Multilayer RDL at 20 Micron I/O Pitch for 2.5D Glass Interposers

This paper describes the improvement of advanced semi-additive processes (SAP) to demonstrate 1.5-5 μm lines and spaces with 4-5 μm diameter photo-vias for multiple re-distribution layers (RDL) at 20 μm bump pitch on glass interposers. High performance computing systems for networking and graphics are driving ultra-high bandwidth interconnections between logic and memory devices. This signal bandwidth need with lowest power consumption has enabled the application of 2.5D interposers for high density chip-to-chip interconnections. Silicon interposers with through-silicon-vias (TSVs) are capable of ultra-high density wiring between logic and memory chips, but use back end of line (BEOL) dual damascene processes, requiring chemical mechanical polishing (CMP), leading to high process cost, which limits their expansion into lower cost and higher volume applications. On the other hand, organic substrates processed on large panels have large capture pads for via landing due to their poor dimensional stability, limiting the bump pitch scaling at chip level. Glass interposers have been proposed to address the limitations of both silicon interposers and organic substrates in recent years. This paper reports on research to extend low cost and large panel semi-additive processes (SAP) to below 5um lines and vias. To achieve this, high resolution lithography processes combined with photosensitive dry film polymer dielectrics were optimized to form fine patterns and ultra-small micro-vias. A major challenge for multilayer RDL is the non co-planarity of copper electroplating, and a new cost-effective copper surface planarization process was proposed and evaluated for surface co-planarity improvement, leading to better yields for multi-layer RDL fabrication.
The Formalization of Theory and Method

One of the most significant developments in American sociology since World War II has been the growth of systematic-formal theories and quantitative methods for empirical research-in short, the formalization of theory and method. This development affords an opportunity to advance an evolutionary thesis: If a tradition of sociological inquiry is oriented to discovering laws and if it tends to formalize its theory or method, it is more likely to give birth to concentrated research
APOLN : A Par tial Parser Of Unrestr icted Text

In this paper, we present APOLN (Analizador Parcial de Oraciones en Lenguaje Natural): a partial parser of unrestricted natural language sentences based on finite-state techniques. Partial parsing has been used in several applications: syntactic parsing of unrestricted texts, data extraction systems, machine translation, solving the attachment ambiguity, speech recognition systems, text summarization, etc. The main attractiveness of partial parsing is that is able to handle unrestricted sentences, that contain lexical errors or that present constructions not accepted by the defined grammar. Partial parsing is an alternative to the definition of wide coverage grammars whose definition is an expensive and complex task and that present well -known problems such as overgeneration, undergeneration and ambiguity. We present APOLN as a tool that can be used to construct syntactically annotated corpora from lexically tagged corpora. We also present the results (precision and recall rates) of applying APOLN on unrestricted Spanish corpora, and how tagging errors influence the performance of the parser.
On the Role of Prestimulus Alpha Rhythms over Occipito-Parietal Areas in Visual Input Regulation: Correlation or Causation?

The posterior alpha rhythm (8–14 Hz), originating in occipito-parietal areas through thalamocortical generation, displays characteristics of visual activity in anticipation of visual events. Posterior alpha power is influenced by visual spatial attention via top-down control from higher order attention areas such as the frontal eye field. It covaries with visual cortex excitability, as tested through transcranial magnetic stimulation (TMS), and predicts the perceptual fate of a forthcoming visual stimulus. Yet, it is still unknown whether the nature of the relationship between this prestimulus alpha oscillation and upcoming perception is causal or only correlative. Here, we tested in the human brain whether the oscillation in the alpha band is causally shaping perception through directly stimulating visual areas via short trains of rhythmic TMS. We compared stimulation at alpha frequency (10 Hz) with two control frequencies in the theta (5 Hz) and beta bands (20 Hz), and assessed immediate perceptual outcomes. Target visibility was significantly modulated by alpha stimulation, relative to both control conditions. Alpha stimulation selectively impaired visual detection in the visual field opposite to the stimulated hemisphere, while enhancing detection ipsilaterally. These frequency-specific effects were observed both for stimulation over occipital and parietal areas of the left and right hemispheres and were short lived: they were observed by the end of the TMS train but were absent 3 s later. This shows that the posterior alpha rhythm is actively involved in shaping forthcoming perception and, hence, constitutes a substrate rather than a mere correlate of visual input regulation.
I know where you are and what you are sharing: exploiting P2P communications to invade users' privacy

In this paper, we show how to exploit real-time communication applications to determine the IP address of a targeted user. We focus our study on Skype, although other real-time communication applications may have similar privacy issues. We first design a scheme that calls an identified-targeted user inconspicuously to find his IP address, which can be done even if he is behind a NAT. By calling the user periodically, we can then observe the mobility of the user. We show how to scale the scheme to observe the mobility patterns of tens of thousands of users. We also consider the linkability threat, in which the identified user is linked to his Internet usage. We illustrate this threat by combining Skype and BitTorrent to show that it is possible to determine the filesharing usage of identified users. We devise a scheme based on the identification field of the IP datagrams to verify with high accuracy whether the identified user is participating in specific torrents. We conclude that any Internet user can leverage Skype, and potentially other real-time communication systems, to observe the mobility and filesharing usage of tens of millions of identified users.
Movement Times of Right and Left Handers Using Preferred and Non-Preferred Hands

The aim of the present work was to quantify the difference in performance of hands when doing tasks of defined difficulty. Results of five experiments are reported in which strongly lateralised subjects performed movement tasks with their preferred and non-preferred hands. These tasks were (i) ballistic movements (ii) Fitts' task (iii) pin-to-hole transfer (iv) Drury tracking task (v) a modified form of the Drury tracking task in which subjects cut paper with scissors. The results showed that in ballistic tasks there was no significant effect of handedness or of hand used. With visually-controlled tasks, where there was considerable control of accuracy required, the preferred hand generally performed better than the non-preferred hand. There was however no significant difference, in any of the tests, between right and left handers when using their preferred hands. Left handers, in some tasks, performed better with their non-preferred hands than did right handed persons using the non-preferred hand.
Standards-based accountability in South Africa

The implementation of standards-based accountability (SBA) interventions aimed at improving school performance often focuses on the testing component, at the expense of capacity building. This was the case in South Africa when a SBA programme was instituted by government in 2000, which was accompanied by substantial rises in senior certificate pass rates between 2000 and 2003. Our analysis indicates that the bulk of these effects was achieved by manipulating the results by means of 4 measures: eliminating high-risk candidates, encouraging candidates to register at the easier standard grade, lowering the standard of examination questions, and raising raw scores during the moderation process. However, research results from other school improvement programmes in the country indicate that significant improvement in school performance is possible when capacity-building elements are combined with accountability measures.
Targeting Interleukin-11 Receptor-α Impairs Human Endometrial Cancer Cell Proliferation and Invasion In Vitro and Reduces Tumor Growth and Metastasis In Vivo

Endometrial cancer contributes to significant morbidity and mortality in women with advanced stage or recurrent disease. IL11 is a cytokine that regulates cell cycle, invasion, and migration, all hallmarks of cancer. IL11 is elevated in endometrial tumors and uterine lavage fluid in women with endometrial cancer, and alters endometrial epithelial cancer cell adhesion and migration in vitro, but its role in endometrial tumorigenesis in vivo is unknown. We injected mice subcutaneously with human-derived Ishikawa or HEC1A endometrial epithelial cancer cells (ectopic), or HEC1A cells into the uterus (orthotopic) to develop endometrial cancer mouse models. Administration of anti-human IL11 receptor (R) α blocking antibody dramatically reduced HEC1A-derived tumor growth in both models and reduced peritoneal metastatic lesion spread in the orthotopic model, compared with IgG. Anti-human IL11Rα retained a well-differentiated, endometrial epithelial phenotype in the HEC1A ectopic mice, suggesting it prevented epithelial-to-mesenchymal transition. Blockade of mouse IL11Rα with anti-mouse IL11Rα antibody did not alter tumor growth, suggesting that cancer epithelial cell IL11 signaling is required for tumor progression. In vitro, anti-human IL11Rα antibody significantly reduced Ishikawa and HEC1A cell proliferation and invasion and promoted apoptosis. Anti-human, but not anti-mouse, IL11Rα antibody reduced STAT3, but not ERK, activation in HEC1A cells in vitro and in endometrial tumors in xenograft mice. We demonstrated that targeted blockade of endometrial cancer epithelial cell IL11 signaling reduced primary tumor growth and impaired metastasis in ectopic and orthotopic endometrial cancer models in vivo. Our data suggest that therapeutically targeting IL11Rα could inhibit endometrial cancer growth and dissemination. Mol Cancer Ther; 15(4); 720–30. ©2016 AACR.
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In the companion paper, Watson et al. (1997), we demonstrated the effectiveness of using perceptual criteria to select the amount of detail that is displayed in an immersive virtual reality (VR) system. Based upon this determination, we will now attempt to develop a principled, perceptually oriented framework to automatically select the appropriate level of detail (LOD) for each object in a scene, taking into consideration the limitations of the human visual system. We apply knowledge and theories from the domain of visual perception to the field of VR, thus optimizing the visual information presented to the user based upon solid metrics of human vision. Through a series of contrast grating experiments a user's visual acuity may be assessed in terms of spatial frequency (c/deg) and contrast. The results of these tests can be modeled mathematically using a contrast sensitivity function (CSF). Therefore, we can use the CSF results to estimate how much visual detail the user can perceive in an object at any instant. Then, if we could describe this object in terms of its spatial frequencies, this would enable us to select the lowest LOD available without the user being able to perceive any visual change.
Analysis of Magnetic Gearing Effect in Partitioned Stator Switched Flux PM Machines

The partitioned stator switched-flux permanent magnet (PM) (SFPM) (PS-SFPM) machine is a novel stator-PM machine in which PMs and armature windings are separately placed in two different stators. Compared with the conventional SFPM machine with a single stator in which both PMs and armature windings are located, the PS-SFPM machine can generate higher torque density due to the utilization of the machine's inner space. In this paper, the magnetic gearing effect in the PS-SFPM machine is investigated in terms of air-gap field harmonics based on a simple magnetomotive force (MMF)-permeance model. It is found that the PS-SFPM machine is one type of magnetically-geared machine, in which the modulations of rotor iron pieces to the open-circuit PM and armature reaction fields are similar to those found in the magnetic gear and the conventional magnetically geared machine. The pole-pair numbers and rotating speeds of the air-gap field harmonics obtained by the MMF-permeance model are verified by finite element (FE) analysis. More than 93% of the average electromagnetic torque is contributed by the main air-gap field harmonics having pole-pair numbers (2i - 1)pPM and |Nr ± (2i-1)pPM| (i = 1,2,3) in a PS-SFPM machine with pPM-pole-pair PMs and Nr-rotor-pole. A prototype machine is fabricated and tested to verify the FE analysis.
Developing libraries using software transactional memory

Software transactional memory is a promising programming model that adapts many concepts borrowed from the databases world to control concurrent accesses to main memory (RAM). This paper discusses how to support revertible operations, such as memory allocation and release, within software libraries that will be used in software memory transactional contexts. The proposal is based in the extension of the transaction life cycle state diagram with new states associated to the execution of user-defined handlers. The proposed approach is evaluated in terms of functionality and performance by way of a use case study and performance tests. Results demonstrate that the proposal and its current implementation are flexible, generic and efficient.
Statistical Inference for Topological Data Analysis

Topological Data Analysis (TDA) is an emerging area of research at the intersection of algebraic topology and computational geometry, aimed at describing, summarizing and analyzing possibly high-dimensional data using low-dimensional algebraic representations. Recent advances in computational topology have made it possible to actually compute topological invariants from data. These novel types of data summaries have been used successfully in a variety of applied problems, and their potential for highdimensional statistical inference appears to be significant. Nonetheless, the statistical properties of the data summaries produced in TDA and, more generally, of the usually heuristic data-analytic methods they are part of, have remained largely unexplored by statisticians. Our analysis involves the tools of persistent homology, the main method of TDA for measuring the topological features of shapes and functions at different resolutions. A major part of our research also focuses on cluster trees and Reeb graphs, which provide a simple yet meaningful abstraction of the input domain of a function by means of the topological changes in its level sets. The main goal of this thesis is to contribute to the development of a statistical theory for TDA and to further propose new and statistically principled methodologies to improve and extend the applicability of the algorithms of TDA. In particular, we will (1) study tests of significance and confidence intervals to separate topological signal from topological noise; (2) explore new methods for topological dimensional reduction; (3) determine how our methods contribute to reduce computational costs, which currently represent an obstacle in TDA.
Increased Protein Oxidation in Human Substantia Nigra Pars Compacta in Comparison with Basal Ganglia and Prefrontal Cortex Measured with an Improved Dinitrophenylhydrazine Assay

Abstract: The dopaminergic phenotype of neurons in human substantia nigra deteriorates during normal aging, and loss of these neurons is prominent in Parkinson's disease. These degenerative processes are hypothesized to involve oxidative stress. To compare oxidative stress in the nigra and related regions, we measured carbonyl modifications of soluble proteins in postmortem samples of substantia nigra, basal ganglia, and prefrontal cortex from neurologically normal subjects, using an improved 2,4‐dinitrophenylhydrazine assay. The protein carbonyl content was found to be about twofold higher in substantia nigra pars compacta than in the other regions. To further analyze this oxidative damage, the distribution of carbonyl groups on soluble proteins was determined by western immunoblot analysis. This method revealed that carbonyl content of the major proteins in each region was linearly dependent on molecular weight. This distribution raises the possibility that protein carbonyl content is controlled by a size‐dependent mechanism in vivo. Our results suggest that oxidative stress is elevated in human substantia nigra pars compacta in comparison with other regions and that oxidative damage is higher within the dopaminergic neurons. Elevated oxidative damage may contribute to the degeneration of nigral dopaminergic neurons in aging and in Parkinson's disease.
Mapping X-Disease Phytoplasma Resistance in Prunus virginiana

Phytoplasmas such as “Candidatus Phytoplasma pruni,” the causal agent of X-disease of stone fruits, lack detailed biological analysis. This has limited the understanding of plant resistance mechanisms. Chokecherry (Prunus virginiana L.) is a promising model to be used for the plant-phytoplasma interaction due to its documented ability to resist X-disease infection. A consensus chokecherry genetic map “Cho” was developed with JoinMap 4.0 by joining two parental maps. The new map contains a complete set of 16 linkage groups, spanning a genetic distance of 2,172 cM with an average marker density of 3.97 cM. Three significant quantitative trait loci (QTL) associated with X-disease resistance were identified contributing to a total of 45.9% of the phenotypic variation. This updated genetic linkage map and the identified QTL will provide the framework needed to facilitate molecular genetics, genomics, breeding, and biotechnology research concerning X-disease in chokecherry and other Prunus species.
Evidence‐Based Consensus Development and Reduction of Rate of Endoscopic Thoracic Sympathectomy: A National Study

BACKGROUND Endoscopic thoracic sympathectomy (ETS) was overused for treating patients with hyperhidrosis in Taiwan. OBJECTIVES To determine whether use of evidence and a consensus‐building exercise can reduce rates of surgery. METHODS We invited all surgeons in Taiwan who performed five or more ETSs per year for treating patients with hyperhidrosis to join this study. A structured questionnaire was mailed to surgeons asking about their management decisions based on clinical scenarios. Then we provided surgeons with evidence synopses and used the Delphi method to reach consensus. We analyzed healthcare utilization data during 2000 to 2005 and calculated total numbers of ETSs performed per 12 months to examine the effect on surgeons' behavior. RESULTS Of 155 surgeons invited, 61 (40%) completed this study. They agreed that observation or topical therapy was appropriate for patients with mild palmar hyperhidrosis, whereas ETS was appropriate for children, adolescents, and young and middle‐aged adults who had severe symptoms. Surgeons became more willing to recommend botulinum toxin injection after we provided evidence synopses. We found a 52% reduction in mean total ETSs per 12 months in surgeons receiving evidence synopses. A higher percentage of reduction occurred in patients younger than 12 and aged 60 and older. CONCLUSION Evidence‐based consensus development is helpful in decreasing overuse of ETS in treating patients with hyperhidrosis in Taiwan.