Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular

: A new spatio-temporal coordinate framework for studying three-dimensional patterns of gene expression in the Drosophila blastoderm is presented that takes account of previously undetected morphological movements.Background The dynamic Drosophila blastoderm <p>A new spatio-temporal coordinate framework for studying three-dimensional patterns of gene expression in the <it>Drosophila </ it>blastoderm is presented that takes account of previously undetected morphological movements. </p> Abstract Background: To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos. Results: Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms. Conclusion: Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis.
Elucidating Temporal Variability in Organic Matter Sources and Cycling in Tropical Rivers

Elucidating Temporal Variability in Organic Matter Sources and Cycling in Tropical Rivers Erin Elizabeth Ellis Co-Chairs of the Supervisory Committee: Associate Professor Anitra E. Ingalls School of Oceanography Professor Jeffrey E. Richey School of Oceanography Tropical rivers are large sources of carbon to the atmosphere and the ocean. The composition of riverine organic matter (OM) affects the size of these fluxes by governing how much carbon will be returned to the atmosphere while in transit versus exported to the ocean, where carbon can be permanently buried in marine sediments. Carbon isotopes coupled with biomarker measurements are powerful tools to elucidate the sources and cycling of OM in rivers, yet few studies have employed them in the tropics. Here I use carbon isotopes (δ 13 C and ∆ 14 C) and biomarker measurements of higher plants and soils to address the following topics: sources of organic carbon respired in rivers; terrestrial OM sources to rivers; the age of riverine OM. In the Amazon Basin, in situ respiration rates are high enough to support the high carbon dioxide gas evasion rates occurring in many white-water rivers. C4 grasses, C3 plants, and phytoplankton fuel respiration, with phytoplankton being important during the low-water season. On the mainstem, C4 grasses are an important substrate for respiration during the rising-water stage, but other sources dominate during falling water. In the Mekong Basin, vascular plants contribute to 15-76% of the particulate organic carbon (POC) exported by the river, with phytoplankton and higher plants dominating OM composition during the dry and rainy seasons, respectively. The age of lignin exported by the Mekong is consistently young (produced within the last 15 years), and it cycles amidst POC of varying ages, ranging from contemporary during the rainy season, to over 3,000 years old during the rising-water period. The aged signal observed during the dry period is likely due to the increasing influence from carbon derived from the Upper Basin (the Chinese mountains and the Tibetan Plateau), whereas the young rainy-season values reflect carbon derived from the Lower Basin. Seasonal variability in the composition of particulate lignin corroborates these findings. Finally, the highest concentrations of branched tetraether lipids were found in floodplains and lake beds, suggesting that anaerobic environments may be a significant source of these biomarkers to the river, with production likely occurring within the river.
Sensitivity analysis of the vestigial signal defence-based civil GNSS spoofing detection method

The vestigial signal defence (VSD) method is used widely for GNSS spoofing detection through monitoring the vestigial signals within the receiver. Though the VSD has been extensively investigated in the open literature, its sensitivity in terms of detection and false alarm probabilities has not been analysed. This is addressed in this study. The sensitivity models including the vestigial signal-to-interference and noise ratio (SINR) and the detection and false alarm probabilities are mathematically formulated. The models are used to quantify and characterise the SINR and the detection and false alarm probabilities. It shows that the VSD is vulnerable to relatively strong spoofing signals. Strong spoofing signals significantly increase the noise floor in turn greatly decreasing the vestigial SINR, resulting in an unacceptable VSD detection performance. It also shows that the sensitivity could be improved with a higher sampling frequency and a longer integration time. It is therefore recommended to use a scheme that combines a long integration time and noise floor monitoring. The sensitivity models together with the recommendation scheme are validated by simulation.
Performance, Histology, and Meat Quality of Coccidiosis-Challenged Broilers Fed Essential Oils

An experiment was conducted to determine the effects of Ralco’s Microfused Essential Oils (MEO) on growth, jejunal histology, and meat quality of coccidiosis-challenged broilers. Day old broilers (n = 768; 64 pens; 12 broilers/pen) were randomly allotted to 1 of 5 dietary treatments fed in 4 phases: starter (d0–16), grower (d17–27), finisher (d28–34), and withdrawal (d35–41). Diets were a corn-soybean meal basal diet (CON), CON+BMD50/Coban90 at 55/121, 250/550, 250/495 and 0 mg/kg (ANTI), CON+MEO at 375, 250, 125, and 100 mg/kg (MEOD), CON+MEO at constant 500 mg/kg (MEO500), and CON+MEO at constant 250 mg/kg (MEO250). Broilers were offered a 10X dose of a coccidiosis vaccine on d 3, 15, 22, and 29. On d 14, jejunal histology was measured. Two broilers per pen were harvested on d 41 and breast pH was measured. Rancidity compounds (TBARS) were measured on whole breasts at d 7 postmortem and ground thighs on d 0, 3, 5, and 7 postmortem. Overall, MEO250-fed broilers had a tendency for greater gain over CON-fed (63.6 vs. 61.3 ± 0.87 g; P < 0.08). MEOD-fed broilers tended to have greater villus height compared to MEO500-fed (806.6 vs. 716.3 ± 27.7 μm; P = 0.09. No differences were observed for pH or TBARS of breasts (P > 0.05). There were differences in L*, a*, and b* color values of breasts and there was an interaction for color values of thighs. ANTI, MEO500, and MEO250 had decreased TBARS values for thighs compared to CON at d 7 postmortem (P ≤ 0.05). Overall, growth performance of MEO250 was not different than ANTI during peak challenge (P > 0.05). MEO250 could improve growth performance and meat quality when broilers are subjected to a coccidiosis disease challenge.
Meat and Muscle BiologyTM Introduction

Extended aging increases browning and decreases redness in fresh beef. The goal of this study was to test an already proven combination of antioxidants (0.05% ascorbic acid + 0.1% rosemary extract) using a method that could be applied at the retail level to simply and effectively extend the shelf-life of extended aged beef. The specific objective was to analyze the effect of topical application of ascorbic acid and rosemary extract on color, lipid oxidation, microbial growth, and sensory perception of beef longissimus lumborum (LL; n = 12) and semimembranosus (SM; n = 12) muscles wet aged at 0°C for 14, 28, and 42 (extended aging period) days. After aging, steaks were cut, sprayed with 2 mL of a 0.05% ascorbic acid + 0.1% rosemary extract solution (treated) or untreated (control), and subjected to retail display. Antioxidant treated LL steaks had greater (P < 0.05) L* (lightness) values, but lower (P < 0.05) a* (redness) and b* (yellowness) values than control steaks. Furthermore, antioxidant treatment decreased (P < 0.05) browning on d 4 of retail display compared to control steaks. Consumers scored antioxidant treated SM steaks as less tender on d 28, more juicy on d 14 but less juicy on d 18 and 42. Antioxidant treatment did not affect lipid oxidation, microbial growth, or sensory flavor scores. As expected, longer aging periods resulted in less color stability of LL and SM steaks. Although the antioxidant treatment resulted in measurable subjective color improvements, these improvements are likely not detectable by the consumer.
2020-02412-PhD Position F/M Tactile User Interfaces for Virtual Reality using High- Density Electrotactile Feedback

Inria, the French national research institute for the digital sciences, promotes scientific excellence and technology transfer to maximise its impact. It employs 2,400 people. Its 200 agile project teams, generally with academic partners, involve more than 3,000 scientists in meeting the challenges of computer science and mathematics, often at the interface of other disciplines. Inria works with many companies and has assisted in the creation of over 160 startups. It strives to meet the challenges of the digital transformation of science, society and the economy.
An Experiment on Personal Archiving and Retrieving Image System ( PARIS )

System) is an experiment personal photograph library, which includes more than 80,000 of consumer photographs accumulated within a duration of approximately five years, metadata based on our proposed MPEG-7 annotation architecture, Dozen Dimensional Digital Content (DDDC), and a relational database structure. The DDDC architecture is specially designed for facilitating the managing, browsing and retrieving of personal digital photograph collections. In annotating process, we also utilize a proposed Spatial and Temporal Ontology (STO) designed based on the general characteristic of personal photograph collections. This paper explains PRAIS system.
The use of streak observations to detect space debris

ABSTRACT Man-made space debris orbit around the Earth at many altitudes in different orbits and many launches add further debris to already congested orbits. The European Space Agency (ESA) GSTP-funded Optical IN-SITU Monitor project started in 2016 and aims to analyse the end-to-end processing pipeline from image acquisition to the extracted positions of space debris. A camera will take images and an on-board data processor will filter and compress the images obtained, which – in case of a future flight model of the instrument – shall be downlinked to the ground station. For the image filtering and compression, several data reduction algorithms are considered and also two different kinds of processors are considered. The difficulty of the images is to differentiate between stars in the background (which have to be filtered out) and the debris. A short overview of the project is presented in this paper: its current status, the hardware choices and the data reduction algorithm trade-off.
Overview of the NTCIR-16 Session Search (SS) Task

This is an overview of the NTCIR-16 Session Search (SS) task. The task features the Fully Observed Session Search subtask (FOSS) and the Partially Observed Session Search subtask (POSS). This year, we received 28 runs from 6 teams in total. This paper will describe the task background, data, subtasks, evaluation measures, and the evaluation results, respectively.
On the use of structures in language models for dialogue, Specific solutions for specific problems

: Availability of large corpora for training language models to develop dialogue systems is rare. Fortunately, for specific dialogue application, many sentences follow a limited number of typical patterns. In a language like French, frequent errors are due to homophones.Three paradigms are proposed in this paper to rescore a trellis of hypothesized words. They are based on sentence patterns detected in the most likely sentence hypothesized in a first recognition phase.
Imprint of management on microbial communities in arable soil

Arable soils are a major source of the greenhouse gas nitrous oxide (N2O), emissions of which are directly linked to increased use of N fertilizers. Microbial communities that drive N cycle processes in soil ultimately determine the fate of reactive N inputs and control N2O emissions. Under anoxic conditions, two processes compete for nitrate (NO3-): denitrification, the stepwise reduction of NO3- to N2O or atmospheric nitrogen, and dissimilatory nitrate reduction to ammonium (DNRA), in which NO3- is reduced to ammonium (NH4+). The reduction of N2O by denitrifiers and non-denitrifying N2O reducers is the only known biological sink for N2O. The aim of this thesis was to investigate how edaphic factors that are altered by soil management practices influence the diversity, structure and activity of the soil microbiota regulating anaerobic N cycling, and thereby N2O emissions. We hypothesised that N replete conditions and long-term fertilization promote incomplete denitrifiers, whereas high C content increases the abundance of DNRA bacteria and N2O reducing organisms, enhancing soil N2O sink capacity. Inoculation of soil microcosms with a non-denitrifying N2O reducing strain confirmed that increased abundance of these organisms can mitigate soil N2O emissions. A survey of long-term fertilization trials showed a consistent increase in the relative abundance of taxonomic groups previously inferred from genomic evidence to produce or consume N2O in fertilized soil. Nevertheless, the abundance of organisms comprising a truncated denitrification remained dominant, concomitant with increased potential N2O emissions. Another field study including fertilization and different crop rotations suggested that changes in soil C/N ratio due to cropping system influenced the competition between DNRA and denitrification, with higher C/N promoting DNRA and N2O reducing community abundance and activity. This was confirmed in controlled manipulations of C/N in a microcosm study, suggesting that soils covering higher C/N ratios sustain a greater abundance of DNRA and N2O reducing bacteria and therefore have a lower N2O emission potential.
Collective Information Extraction with Relational Markov Networks

Most information extraction (IE) systems treat separate potential extractions as independent. However, in many cases, considering in uences between di erent potential extractions could improve overall accuracy. Statistical methods based on undirected graphical models, such as conditional random elds (CRFs), have been shown to be an e ective approach to learning accurate IE systems. We present a new IE method that employs Relational Markov Networks (a generalization of CRFs), which can represent arbitrary dependencies between extractions. This allows for \collective information extraction" that exploits the mutual inuence between possible extractions. Experiments on learning to extract protein names from biomedical text demonstrate the advantages of this approach.
Detecting Defects in Textile Fabrics with Optimal Gabor Filters

detection for textile fabrics and proposes a new optimal filter design method to solve this problem. Gabor Wavelet Network (GWN) is chosen as the major technique to extract the texture features from textile fabrics. Based on the features extracted, an optimal Gabor filter can be designed. In view of this optimal filter, a new semi-supervised defect detection scheme is proposed, which consists of one real-valued Gabor filter and one smoothing filter. The performance of the scheme is evaluated by using an offline test database with 78 homogeneous textile images. The test results exhibit accurate defect detection with low false alarm, thus showing the effectiveness and robustness of the proposed scheme. To evaluate the detection scheme comprehensively, a prototyped detection system is developed to conduct a real time test. The experiment results obtained confirm the efficiency and effectiveness of the proposed detection scheme.
Viaduct: An Extensible, Optimizing Compiler for Secure Distributed Programs (Technical Report)

Modern distributed systems involve interactions between principals with limited trust, so cryptographic mechanisms are needed to protect confidentiality and integrity. At the same time, most developers lack the training to securely employ cryptography. We present Viaduct, a compiler that transforms high-level programs into secure, efficient distributed realizations. Viaduct’s source language allows developers to declaratively specify security policies by annotating their programs with information flow labels. The compiler uses these labels to synthesize distributed programs that use cryptography efficiently while still defending the source-level security policy. The Viaduct approach is general, and can be easily extended with new security mechanisms. Our implementation of the Viaduct compiler comes with an extensible runtime system that includes plug-in support for multiparty computation, commitments, and zero-know-ledge proofs. We have evaluated the system on a set of benchmarks, and the results indicate that our approach is feasible and can use cryptography in efficient, nontrivial ways.
ScholarWorks at WMU

The signiﬁcance of computer architecture simulators in advancing computer architecture research is widely acknowledged. Computer architects have developed numerous simulators in the past few decades and their number continues to rise. This paper explores different simulation techniques and surveys many simulators. Comparing simulators with each other and validating their correctness has been a challenging task. In this paper, we compare and contrast x86 simulators in terms of ﬂexibility, level of details, user friendliness and simulation models. In addition, we measure the experimental error and compare the speed of four contemporary x86 simulators: gem5, Sniper, Multi2sim and PTLsim. We also discuss the strengths and limitations of the different simulators. We believe that this paper provide insights into different simulation strategies and aims to help computer architects understand the differences among the existing simulation tools.
DIDACache: A Deep Integration of Device and Application for Flash Based Key-Value Caching

In recent years, flash-based key-value cache systems have raised high interest in industry, such as Facebook's McDipper and Twitter's Fatcache. These cache systems typically use commercial SSDs to store and manage key-value cache data in flash. Such a practice, though simple, is inefficient due to the huge semantic gap between the key-value cache manager and the underlying flash devices. In this paper, we advocate to reconsider the cache system design and directly open device-level details of the underlying flash storage for key-value caching. This co-design approach bridges the semantic gap and well connects the two layers together, which allows us to leverage both the domain knowledge of key-value caches and the unique device properties. In this way, we can maximize the efficiency of key-value caching on flash devices while minimizing its weakness. We implemented a prototype, called DIDACache, based on the Open-Channel SSD platform. Our experiments on real hardware show that we can significantly increase the throughput by 35.5%, reduce the latency by 23.6%, and remove unnecessary erase operations by 28%.
ACCEPTED MANUSCRIPT

Bio: Andrea Mariuzzo is Research fellow in History at Scuola Normale Superiore, Pisa. In the course of his career, he has worked extensively on the making of political cultures in post-war Italy, and on schools and higher education institutions in Italy between fascism and the Republic. His current project is concerning the influence of American educational and academic models in Italy and Europe in the Twentieth century.
Ai: The Tumultuous History Of The Search For Artificial Intelligence

In the summer of 1956, a group of young scientists sat down to consider the astounding proposition that "every aspect of learning or any other feature of intelligence can, in principle, be so precisely described that a machine can be made to simulate it. " Armed with their own enthusiasm, the excitement of the idea itself, and lots of government money, they predicted that the whole range of human intelligence would be programmable within their own lifetimes. Nearly half a century later, the field has grown tenfold - with mixed results. Based on extensive interviews with the major players in the history of artificial intelligence, including Marvin Minsky, Herbert Simon, Alan Newell, Raj Reddy and Patrick Winston, this book chronicles their successes, from robotics to world-class chess playing and, equally, their failures. With anecdotes about the founders and leaders and their celebrated feuds and intellectual gamesmanship, the book also discusses the next necessary breakthrough - teaching computers "common sense".
Base Restriction 1 : No Inline Scripts Will Execute

The last three years have seen a dramatic increase in both awareness and exploitation of Web Application Vulnerabilities. 2008 and 2009 saw dozens of high-profile attacks against websites using Cross Site Scripting (XSS) and Cross Site Request Forgery (CSRF) for the purposes of information stealing, website defacement, malware planting, clickjacking, etc. While an ideal solution may be to develop web applications free from any exploitable vulnerabilities, real world security is usually provided in layers. We present content restrictions, and a content restrictions enforcement scheme called Content Security Policy (CSP), which intends to be one such layer. Content restrictions allow site designers or server administrators to specify how content interacts on their web sites—a security mechanism desperately needed by the untamed Web. These content restrictions rules are activated and enforced by supporting web browsers when a policy is provided for a site via HTTP, and we show how a system such as CSP can be effective to lock down sites and provide an early alert system for vulnerabilities on a web site. Our scheme is also easily deployed, which is made evident by our prototype implementation in Firefox and on the Mozilla Add-Ons web site.