Miracle-dz/UniFAR-FTUs huggingface dataset:
An eﬀicient spectra processing method for metabolite identification from (1)H-NMR metabolomics data.

The spectra processing step is crucial in metabolomics approaches, especially for proton NMR metabolomic profiling. During this step, noise reduction, baseline correction, peak alignment and reduction of the 1D 1 H-NMR spectral data are required in order to allow biological information to be highlighted through further statistical analyses. Above all, data reduction (binning or bucketing) strongly impacts subsequent statistical data analysis and potential biomarker discovery. Here, we propose an efficient spectra processing method which also brings a helpful support for compound identification using a new data reduction algorithm that produces relevant variables, called buckets. These buckets are the result of the extraction of all relevant peaks contained in the complex mixture spectra, rid of any non-significant signal. Taking advantage of the concentration variability of each compound in a series of samples and based on significant correlations that link these buckets together into clusters, the method further proposes automatic assignment of metabolites by matching these clusters with the spectra of reference compounds from HMDB or a home-made database. This new method is applied to a set of simulated 1 H-NMR spectra to determine the effect of some processing parameters and, as a proof of concept, to a tomato 1 H-NMR dataset to test its ability to recover the fruit extract compositions. The implementation code for both clustering and matching steps is available upon request to the corresponding author.
Edinburgh Research Explorer Patient-reported outcomes in the ProtecT randomized trial of clinically localized prostate cancer treatments

(12-item short-form health survey [SF-12]; EuroQol quality-of-life survey, the EQ-5D-3L) were assessed at prostate biopsy clinics before randomization. Descriptive statistics are presented by treatment allocation and by men ’ s age at biopsy and PSA testing time points for selected measures.
University of Birmingham An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7

Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneﬁcial or pathogenic, and the adaptive processes involved. Isolation of bacterial m RNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial m RNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample.To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial m RNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.
Performance Analysis of Lot Release and Dispatching Decisions in Wafer Fabrication

Controlling semiconductor wafer fabrications (wafer fabs) is a difficult task because the water fabs have several distinct characteristics such as a large number of processes involved, long lead time, and re-entrant product flow. Typical operational control issues in the wafer fabs include job releasing, dispatching and batch loading decisions. Most of the research works on operational control problems in the fab studied so far address these control problems separately. This paper is motivated by the belief that an operational control decision affects the performance of the other control decisions, and the existence of bottleneck machines is a core factor for this mutual influence of the control schemes. To examine the impact of the control rules on the system-wide performance, we present bottleneck machine-focused control rules and construct simulation models where these control rules are incorporated. Through simulation studies, the performance of the presented control policies is evaluated, and some insights on the performance of the control policies and their interactions are discussed.
Interannual sea surface salinity variations observed in the tropical North Pacific Ocean

Analysis of observational data sets reveals pronounced interannual variations of sea surface salinity (SSS) in the tropical North Pacific (7°N–15°N) during 2000–2012. SSS anomalies with maximum magnitudes >0.2 occur in the central Pacific and translate westward at a speed of 15–20 cm s–1. The signals are weakened during their westward movement but reinforced in the Philippine Sea. Budget analysis for the mixed layer salinity suggests that in the central Pacific, El Niño–Southern Oscillation‐related atmospheric freshwater forcing and ocean advection changes are both important in generating and maintaining these large SSS anomalies. In the advection term, the most contributing component is the meridional Ekman advection induced by trade winds. These SSS anomalies are subsequently carried westward by the North Equatorial Current, which is the primary cause of SSS variations in the Philippine Sea. Freshwater forcing is also at work in the Philippine Sea, but its role is generally secondary.
Dynamic Difficulty Adjustment in Computer Games Through Real-Time Anxiety-Based Affective Feedback

A number of studies in recent years have investigated the dynamic difficulty adjustment (DDA) mechanism in computer games to automatically tailor gaming experience to individual player's characteristics. Although most of these existing works focus on game adaptation based on player's performance, affective state experienced by the players could play a key role in gaming experience and may provide a useful indicator for a DDA mechanism. In this article, an affect-based DDA was designed and implemented for computer games. In this DDA mechanism, a player's physiological signals were analyzed to infer his or her probable anxiety level, which was chosen as the target affective state, and the game difficulty level was automatically adjusted in real time as a function of the player's affective state. Peripheral physiological signals were measured through wearable biofeedback sensors and several physiological indices were explored to determine their correlations with anxiety. An experimental study was conducted to evaluate the effects of the affect-based DDA on game play by comparing it with a performance-based DDA. This is the first time, that is known, that the impact of a real-time affect-based DDA has been demonstrated experimentally.
Dialogues concerning a ( possibly ) new science

The three characters, Dreamer, Experimentalist and Realistic, meet in an ideal place of Toscana. They come from different places of the old, decadent and altogether fundamentally renewing Europe of the early 21 century. They were invited in this place to discuss matters of high importance: Do agent based computer simulations offer a venue for a new social science? On what basis such a new science would stand? What role would play experimental approaches developed in social psychology? How to use case studies from the real world? Is there a need to develop a specific methodology of simulation?
The Operating Microscope : Why is It Essential for Microsurgery ?

f bstract ndodontic surgery has now evolved into endodontic icrosurgery. By using state-of-the-art equipment, nstruments and materials that match biological conepts with clinical practice, we believe that microurgical approaches produce predictable outcomes in he healing of lesions of endodontic origin. In this eview we attempted to provide the most current oncepts, techniques, instruments and materials with he aim of demonstrating how far we have come. Our ltimate goal is to assertively teach the future genration of graduate students and also train our coleagues to incorporate these techniques and conepts into everyday practice. (J Endod 2006;32: 01– 623)
Reviews and perspectives Why we may not ﬁ nd intentions in the brain

Intentions are commonly conceived of as discrete mental states that are the direct cause of actions. In the last several decades, neuroscientists have taken up the project of ﬁ nding the neural implementation of intentions, and a number of areas have been posited as implementing these states. We argue, however, that the processes underlying action initiation and control are considerably more dynamic and context sensitive than the concept of intention can allow for. Therefore, adopting the notion of ‘ intention ’ in neuroscienti ﬁ c explanations can easily lead to misinterpretation of the data, and can negatively in ﬂ uence investigation into the neural correlates of intentional action. We suggest reinterpreting the mechanisms underlying intentional action, and we will discuss the elements that such a reinterpretation needs to account for.
Bile Salts and Nuclear Receptors in Biliary Epithelial Cell Pathophysiology

The liver is a multi-cellular organ in which non-parenchymal cells represent forty percent of the total cell number. Even though less abundant than hepatocytes, alterations of non-parenchymal liver cell function are central to the development of liver diseases. The latter observation highlights the involvement of these cells in hepatic physiology. Among non-parenchymal liver cells, the biliary epithelial cells (BECs) display two major biological functions: protection and secretion.
Consumptive Use Program + (CUP+) Model

Introduction A user-friendly Microsoft Excel application program “Consumptive Use Program +” or “CUP+” was developed to help growers and water agencies determine reference evapotranspiration (ETo), crop coefficient (Kc) values, crop evapotranspiration (ETc), and evapotranspiration of applied water (ETaw), which provides an estimate of the net irrigation water diversion needed to produce a crop. The application also can be used to study the impact of climate change on evapotranspiration and irrigation water needs. CUP+ computes reference evapotranspiration (ETo) from daily solar radiation, maximum and minimum temperature, dew point temperature, and wind speed using the daily Penman-Monteith equation. In addition, the program uses a curve fitting technique to derive one year of daily weather data from the monthly data and to estimate daily ETo. It also uses daily rainfall data to estimate bare soil evaporation as a function of mean of ETo and wetting frequency in days. A bare soil Kc value is calculated to estimate the offseason evapotranspiration and as a baseline for in-season Kc calculations. CUP+ accounts for the influence of orchard cover crops on Kc values and it accounts for immaturity effects on Kc values for tree and vine crops. Further, the program computes and applies all ETo and Kc values on a daily basis to determine crop water requirements by month, by season, by year. The water balance model is similar to that used in the Simulation of ET of Applied Water (SIMETAW) application program, which was also developed as a cooperative effort between the University of California (UC) and the Department of Water Resources (DWR). The application outputs a wide range of tables and charts that are useful for irrigation planning.
The effectiveness of small-scale headwater storage dams and reservoirs on stream water quality and quantity in the Canadian Prairies

In response to flooding and soil erosion impacting the South Tobacco Creek watershed in southcentral Manitoba, local landowners constructed a network of small dams and reservoirs in the headwaters. Between 1999 and 2007, two of the small dams/reservoirs (Steppler multipurpose dam and Madill dry dam) were intensively monitored for their effectiveness in reducing peak flows and downstream sediment and nutrient loading during spring snowmelt (typically mid-March to mid-April) and summer rainfall (typically May to November) periods. These small-scale headwater storage dams were effective in reducing peak flows from agricultural land. The two dams/reservoirs monitored also reduced annual concentrations of sediment and total nitrogen (TN) to downstream receiving waters. However, annual concentrations of total phosphorus (TP) were only significantly reduced at the Madill dry dam, and the average concentrations of nitrogen (N) and phosphorus (P) within outflow water samples still exceeded guidelines for freshwater in the Canadian Prairies. Both dams/reservoirs significantly reduced annual loads of sediment, TN, and TP (Steppler dam, average of 77%, 15%, and 12%, respectively; Madill dam, average of 66%, 20%, and 9%, respectively). This corresponded to an average annual retention of 25 Mg y−1 (28 tn yr−1) of sediment, 166 kg N y−1 (366 lb N yr−1) and 17 kg P y−1 (37 lb P yr−1) by the Steppler dam, while 6 Mg y−1 (7 tn yr−1) of sediment, 181 kg N y−1 (399 lb N yr−1) and 10 kg P y−1 (22 lb P yr−1) were retained by the Madill dam. Both reservoirs reduced annual loads of dissolved N and P to downstream water bodies (Steppler, average of 14% and 10%, respectively; Madill, average of 23% and 15%, respectively), and were generally effective in removing dissolved N and P during both snowmelt and rainfall-generated runoff. The percent retention of dissolved nutrients was consistently higher during the summer than the spring. While the reservoirs removed particulates during snowmelt-generated runoff, they were often sources of suspended nutrients during rainfall-generated events. However, since dissolved nutrients were the dominant form of both N and P (>70% for both snowmelt and rainfall events), the two dams/reservoirs successfully reduced overall nutrient loads to downstream water bodies, annually and seasonally. In combination with improving flood and erosion control for the region, small headwater storage dams and reservoirs deserve consideration when developing watershed nutrient management plans, especially for undulating and hummocky regions on the Great Plains.
Syllables without vowels: Phonetic and phonological evidence from Tashlhiyt Berber

It has been proposed that Tashlhiyt is a language which allows any segment, including obstruents, to be a syllable nucleus. The most striking and controversial examples taken as arguments in favour of this analysis involve series of words claimed to contain only obstruents. This claim is disputed in some recent work, where it is argued that these consonant sequences contain schwas that can be syllable nuclei. This article presents arguments showing that vowelless syllables do exist in Tashlhiyt, both at the phonetic and phonological levels. Acoustic, ﬁbrescopic and photoelectroglottographic examination of voiceless words (e.g. [tkkststt]) provide evidence that such items lack syllabic vocalic elements. In addition, two types of phonological data, metrics and a spirantisation process, are presented to show that in this language schwa is not a segment which can be independently manipulated by phonological grammar and which can be referred to the syllable structure.
MONITORING THE ENVIRONMENTAL AND ECOLOGICAL IMPACTS OF CLIMATE CHANGE ON BYLOT ISLAND, SIRMILIK NATIONAL PARK

Our ecological and environmental program has been monitoring the climate, the reproduction and the abundance of several key species of birds, mammals and plants on Bylot Island, Sirmilik National Park, Nunavut for the past 19 years. The main goal of our project is to measure changes occurring in the Arctic ecosystems, analyse temporal trends, and evaluate to what extent these changes may be driven by climate change. Our results showed that the region surrounding Bylot Island has been experiencing a strong warming trend over the past three decades. These trends were mostly detectable during the spring, summer and fall (from 2.1 to 4.5C for that period), which is contradictory to GCM models that forecast changes to be more intense during the winter months. Nonetheless, our long-term dataset on ecological monitoring of several birds, mammals and plants already show some signs of change on Bylot Island, which could be due in part to climate change. Plant production in wetlands has increased by 84% over the last 18 years, most likely a consequence of climate warming. Climatic variations also appear to be the most important driver of the annual production of several migratory birds such as Greater Snow Geese, as warm spring temperature increases their breeding effort and advances their breeding phenology. The two lemming species found on Bylot Island play a key role in the food web as they are the primary prey of most tundra predators. Their large cyclical fluctuations in annual abundance not only affect their main predators (Snowy Owls and foxes) but also indirectly affect other species like geese through shared-predator interactions. Other bird species such as shorebirds, longspurs, gulls and jaegers are likely to be influenced by fluctuating abundance of lemmings but further studies are needed to investigate this relationship. We found evidence that lemming cycles have dampened in recent years and that their abundance during peak years of the cycle is much lower than in the past. Although this could be linked to the strong warming trend observed in the fall, which could lead to poor snow conditions and low overwinter lemming survival, more data are needed to test this hypothesis. The proportion of fox dens with reproductive activity has decreased over the years, possibly a consequence of the low abundance of lemmings recorded recently during peak years of abundance. Our Traditional Ecological Knowledge study pertaining to snow geese and foxes has shown that Elders knowledge can provide complementary information to our monitoring program. Indeed, we found that traditional knowledge on foxes expanded the spatial and temporal scales of our current scientific knowledge. Our community workshops and public presentations proved to be valuable tools to foster communications and exchanges with the community of Pond Inlet on ecological studies carried out on Bylot Island. Finally, we contributed to increase the capacity building of the community through the hiring of several northerners during our field activities.
2019) Cybercrime Investigators are Users Too! Understanding the Socio-Technical Challenges Faced by Law Enforcement. In: Proceedings of the 2019 Workshop on Usable Security (USEC) at Network and Distributed System Security

—Cybercrime investigators face numerous challenges when policing online crimes. Firstly, the methods and processes they use when dealing with traditional crimes do not necessarily apply in the cyber-world. Additionally, cyber criminals are usually technologically-aware and constantly adapting and developing new tools that allow them to stay ahead of law enforcement investigations. In order to provide adequate support for cybercrime investigators, there needs to be a better understanding of the challenges they face at both technical and socio-technical levels. In this paper, we investigate this problem through an analysis of current practices and workﬂows of investigators. We use interviews with experts from government and private sectors who investigate cybercrimes as our main data gathering process. From an analysis of the collected data, we identify several outstanding challenges faced by investigators. These pertain to practical, technical, and social issues such as systems availability, usability, and in computer-supported collaborative work. Importantly, we use our ﬁndings to highlight research areas where user-centric workﬂows and tools are desirable. We also deﬁne a set of recommendations that can aid in providing a better foundation for future research in the ﬁeld and allow more effective combating of cybercrimes.
The Polygon-Ellipse Method of Data Compression of Weather Maps

Abstract : Providing an accurate picture of the weather conditions in the pilot's area of interest could be a highly useful application for ground-to-air data links. The problem with using data links to transmit weather pictures is the large number of bits required to exactly specify a weather image. To make transmission of weather maps practical, a means must be found to compress this image. The Polygon-Ellipse (PE) encoding algorithm developed in this report represents weather regions as ellipses, polygons, and exact patterns. The actual ellipse and polygon parameters are encoded and transmitted; the decoder algorithm redraws the shape from their encoded parameter values and fills in the included weather pixels. Special coding techniques are used in PE to compress the encoding of the shape parameters to achieve further overall compression. The PE algorithm contains procedures for gracefully degrading the fidelity of the transmitted image when necessary to meet a specified bit limit. Pictorial examples of the operation of this algorithm on both Terminal Doppler Weather Radar (TDWR) and ASR-9 radar-generated weather images are presented. Data compression, Weather images, Weather transmission, Data link
Validation of ISCCP Cloud Detections

Abstract The International Satellite Cloud Climatology Project (ISCCP) began in 1983 to collect and analyze weather satellite datasets to produce a new global cloud climatology as part of the World Climate Research Programme. The first step of the analysis is detection of the presence of clouds at each location and time by a series of tests on the space / time variations of infrared and visible radiances. This paper describes the validation of the ISCCP cloud detections by verifying the accuracy of the inferred clear-sky radiance. Comparison of retrieved surface temperatures to other measurements shows that bias errors are <2 K and random errors are about 2 K for sea surface (monthly means at 280-km scales) and that bias errors are <2 K and random errors are about 4 K for land surfaces (3 hourly at 280-km scale). Bias errors over a few persistently cloudy locations are sometimes −(2–4) K and over winter sea ice may be about +2 K. Surface reflectances are confirmed to be within 3% of other measurements and.