Miracle-dz/UniFAR-FTUs huggingface dataset:
Bringing replication and reproduction together with generalisability in NLP: Three reproduction studies for Target Dependent Sentiment Analysis

Lack of repeatability and generalisability are two significant threats to continuing scientific development in Natural Language Processing. Language models and learning methods are so complex that scientific conference papers no longer contain enough space for the technical depth required for replication or reproduction. Taking Target Dependent Sentiment Analysis as a case study, we show how recent work in the field has not consistently released code, or described settings for learning methods in enough detail, and lacks comparability and generalisability in train, test or validation data. To investigate generalisability and to enable state of the art comparative evaluations, we carry out the first reproduction studies of three groups of complementary methods and perform the first large-scale mass evaluation on six different English datasets. Reflecting on our experiences, we recommend that future replication or reproduction experiments should always consider a variety of datasets alongside documenting and releasing their methods and published code in order to minimise the barriers to both repeatability and generalisability. We have released our code with a model zoo on GitHub with Jupyter Notebooks to aid understanding and full documentation, and we recommend that others do the same with their papers at submission time through an anonymised GitHub account.
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

Abstract The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called ‘Clade Project’) to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.
A SPATIALLY EXPLICIT HABITAT SELECTION MODEL INCORPORATING HOME RANGE BEHAVIOR

Understanding habitat selection is of primary interest in theoretical and applied ecology. One approach is to infer habitat selection processes from differences in population densities between habitats using methods such as isodar and isoleg analysis. Another approach is to directly observe the movements of individuals. However, habitat selection models based on movement data often fail to adequately incorporate spatial processes. This is problematic if the probability of selecting a particular habitat is dependent upon its spatial context. This would occur, for example, where organisms exhibit home range behavior and the choice of habitat is dependent on its location relative to the home range. In this paper we present a spatially explicit habitat selection model for movement data that incorporates home range behavior as a spatial process. Our approach extends a previous model by formulating the probability of selecting a habitat as a function of its distance from the animal's current location and home range center. We demonstrate that these enhancements lead to more parsimonious models when applied to a koala radio-tracking data set from eastern Australia. This approach could also be applied to modeling other spatial habitat selection processes, leading to more biologically meaningful models for a range of species and applications.
Gill lesions and mortality in seawater pen-reared Atlantic salmon Salmo salar associated with a dense bloom of Skeletonema costatum and Thalassiosira species

Mortality and gill lesions in Atlantic salmon Salmo salar reared in a seawater netpen in British Columbia, Canada, were associated with a dense bloom of diatoms containing predominantly Skeletonema costatum, Thalassiosira aestivalis and T rotula. Other diatoms, present as minor components of the bloom, included Thalassionema nitzschiojdes, Coscinodiscus sp. and Pseudonitzschia sp. Gills of moribund and dead fish exhibited excessive mucus production. Histological examination revealed necrosis of the gill epithelium and edema at the base of secondary lamellae. The edematous spaces contained an inflammatory infiltrate. The mechanism of gill damage was not determined, but was likely due to physical irritation by the algae. None of these diatoms have previously been reported to cause disease in fish.
Costs of reproduction and carry-over effects in breeding albatrosses

Abstract We investigated the physiology of two closely related albatross species relative to their breeding strategy: black-browed albatrosses (Thalassarche melanophris) breed annually, while grey-headed albatrosses (T. chrysostoma) breed biennially. From observations of breeding fate and blood samples collected at the end of breeding in one season and feather corticosterone levels (fCort) sampled at the beginning of the next breeding season, we found that in both species some post-breeding physiological parameters differed according to breeding outcome (successful, failed, deferred). Correlations between post-breeding physiology and fCort, and links to future breeding decisions, were examined. In black-browed albatrosses, post-breeding physiology and fCort were not significantly correlated, but fCort independently predicted breeding decision the next year, which we interpret as a possible migratory carry-over effect. In grey-headed albatrosses, post-breeding triglyceride levels were negatively correlated with fCort, but only in females, which we interpret as a potential cost of reproduction. However, this potential cost did not carry-over to future breeding in the grey-headed albatrosses. None of the variables predicted future breeding decisions. We suggest that biennial breeding in the grey-headed albatrosses may have evolved as a strategy to buffer against the apparent susceptibility of females to negative physiological costs of reproduction. Future studies are needed to confirm this.
Curvelet-based multiscale denoising using non-local means & guided image filter

This study presents an image denoising technique using multiscale non-local means (NLM) filtering combined with hard thresholding in curvelet domain. The inevitable ringing artefacts in the reconstructed image - due to thresholding - is further processed using a guided image filter for better preservation of local structures like edges, textures and small details. The authors decomposed the image into three different curvelet scales including the approximation and the fine scale. The low-frequency noise in the approximation sub-band and the edges with small textural details in the fine scale are processed independently using a multiscale NLM filter. On the other hand, the hard thresholding in the remaining coarser scale is applied to separate the signal and the noise subspace. Experimental results on both greyscale and colour images indicate that the proposed approach is competitive at lower noise strength with respect to peak signal to noise ratio and structural similarity index measure and excels in performance at higher noise strength compared with several state-of-the-art algorithms.
Three-dimensional hydrodynamic model of New York Harbor region

Three-dimensional simulations of estuarine circulation in the New York Harbor complex, Long Island Sound, and the New York Bight have been conducted using the Estuarine, Coastal and Ocean Model (ECOM) within the framework of a single grid system. The model grid is curvilinear and orthogonal, with resolution from 100 m in rivers to approximately 50 km in the bight. The model forcing functions consist of meteorological data, water level elevation and temperature and salinity fields along the open boundary, and freshwater inflows from 30 rivers, 110 wastewater treatment plants, and 268 point sources from combined sewer overflows and surface runoffs. Because the goal of this study is to maximize, to the extent possible, the predictive skill of the modeling system, the motivation for and a detailed description of the construction of these boundary forcing functions are presented. Two 12-month periods are considered: October 1988 to September 1989 for model calibration and October 1994 to September 1995 for model validation. For model calibration, the results are compared with water levels at 14 stations, currents at six stations, and temperature and salinity at 35 stations. Model validation is accomplished using data from an extensive hydrodynamic monitoring program. Mean errors in predicted elevations and currents are less than 10% and 15%, respectively. Correlation coefficients for salinity and temperature are as high as 0.86 and 1.0, respectively. The level of skill shown by these statistical measures suggests that the model is capable of describing the entire spectrum of time scales for the computed quantities, from the semidiurnal to the annual scales.
Opioid Doses and Acute Care Utilization Outcomes for Adults with Sickle Cell Disease: Emergency Department versus Acute Care Unit

Background: Acute care units (ACUs) with focused sickle cell disease (SCD) care have been shown to effectively address pain and limit hospitalizations compared to emergency departments (ED), the reason for differences in admission rates is understudied. Our aim was compare effects of usual care for adult SCD pain in ACU and ED on opioid doses and discharge pain ratings, hospital admission rates and lengths of stay. Methods: In a retrospective, comparative cohort, single academic tertiary center study, 148 adults with sickle cell pain received care in the ED, ACU or both. From the medical records we documented opioid doses, unit discharge pain ratings, hospital admission rates, and lengths of stay. ACCEPTED MANUSCRIPT
Exploiting Repetitions for Image‐Based Rendering of Facades

Street‐level imagery is now abundant but does not have sufficient capture density to be usable for Image‐Based Rendering (IBR) of facades. We present a method that exploits repetitive elements in facades ‐ such as windows ‐ to perform data augmentation, in turn improving camera calibration, reconstructed geometry and overall rendering quality for IBR. The main intuition behind our approach is that a few views of several instances of an element provide similar information to many views of a single instance of that element. We first select similar instances of an element from 3–4 views of a facade and transform them into a common coordinate system, creating a “platonic” element. We use this common space to refine the camera calibration of each view of each instance and to reconstruct a 3D mesh of the element with multi‐view stereo, that we regularize to obtain a piecewise‐planar mesh aligned with dominant image contours. Observing the same element under multiple views also allows us to identify reflective areas ‐ such as glass panels ‐ which we use at rendering time to generate plausible reflections using an environment map. Our detailed 3D mesh, augmented set of views, and reflection mask enable image‐based rendering of much higher quality than results obtained using the input images directly.
Thin Structures in Image Based Rendering

We propose a novel method to handle thin structures in Image‐Based Rendering (IBR), and specifically structures supported by simple geometric shapes such as planes, cylinders, etc. These structures, e.g. railings, fences, oven grills etc, are present in many man‐made environments and are extremely challenging for multi‐view 3D reconstruction, representing a major limitation of existing IBR methods. Our key insight is to exploit multi‐view information. After a handful of user clicks to specify the supporting geometry, we compute multi‐view and multi‐layer alpha mattes to extract the thin structures. We use two multi‐view terms in a graph‐cut segmentation, the first based on multi‐view foreground color prediction and the second ensuring multiview consistency of labels. Occlusion of the background can challenge reprojection error calculation and we use multiview median images and variance, with multiple layers of thin structures. Our end‐to‐end solution uses the multi‐layer segmentation to create per‐view mattes and the median colors and variance to create a clean background. We introduce a new multi‐pass IBR algorithm based on depth‐peeling to allow free‐viewpoint navigation of multi‐layer semi‐transparent thin structures. Our results show significant improvement in rendering quality for thin structures compared to previous image‐based rendering solutions.
Ramanauskaite and Tervonen The Efficacy of Supportive Peri-Implant Therapies in Preventing Peri-Implantitis and Implant Loss : a Systematic Review of the Literature

Objectives: To study the efficacy of supportive peri-implant therapies in preventing clinical and radiological signs of periimplantitis and implant loss. Material and Methods: Longitudinal human studies published in 2006 2016 in the English language were included based on an electronic search using MEDLINE and EMBASE databases and complemented by a manual search. Articles were included only if 1) they comprised a group of patients involved in/adhering to regular supportive peri-implant therapies (SPTs) and a control group without such therapies or with poor adherence to them, 2) the protocol of the SPTs was clearly described and 3) the outcome was indicated by means of clinical/radiological changes or implant loss. Results: After initially identifying a total of 710 titles and abstracts, 12 full text articles were selected for eligibility assessment. Seven studies, three prospective and four retrospective, fulfilled the inclusion criteria for this review. The frequency of recall visits varied between the studies from a minimum of one visit every three months to an individually tailored regimen. In all the studies a lack of SPTs or poor adherence to them resulted in significantly higher frequencies of sites with mucosal bleeding, deepened peri-implant pockets or alveolar bone loss. In line with the above, a lack of/poor adherence to SPTs was associated with higher implant loss. Conclusions: To prevent peri-implantitis, an individually tailored supportive programme based on patient motivation and reinstruction in oral hygiene measures combined with professional implant cleaning seem to be crucial.
Laboratory demonstrations of multi-object adaptive optics in the visible on a 10 meter telescope

We have demonstrated MOAO-type atmospheric compensation on a 10 meter telescope at visible wavelengths with the UCO/Lick MCAO/MOAO testbed in the Laboratory for Adaptive Optics at UCSC. We report Strehls of ~20% in R band (658 nm) on-axis and Strehls of ~15% off-axis 25" for a 3D Mauna Kea-type atmosphere with r0 = 15 cm and &Tgr;0 = 3.5". We show that a tomographic MOAO approach with 5 LGS's in a 50" constellation is sufficient to realize good correction in the visible. Two major improvements to the testbed realized this gain: (1) An upgrade to 64x64 subapertures across a 10 meter pupil (2) and a predictor-corrector wind model. We discuss limitations to wide-field visible light AO on 8-10 meter class telescopes and stress that the tomographic error due to blind modes is frequently the largest field-dependent error. We use a predictor-corrector wind model (Wiberg et al. 2006) to take advantage of windlayer shearing in the atmosphere to reduce the tomographic error over a 50" diameter field. Depending on the validity of the Taylor frozen flow model for individual layers in the real atmosphere, this approach could be more effective than increasing the number of LGS's.
Classification for DGA-Based Malicious Domain Names with Deep Learning Architectures

The preemptive defenses against various malware created by domain generation algorithms (DGAs) have traditionally been solved using manually-crafted domain features obtained by heuristic process. However, it is difficult to achieve real-world deployment with most research on detecting DGA-based malicious domain names due to poor performance and time consuming. Based on the recent overwhelming success of deep learning networks in a broad range of applications, this article transfers five advanced learned ImageNet models from Alex Net, VGG, Squeeze Net, Inception, Res Net to classify DGA domains and non-DGA domains, which: (i) is suited to automate feature extraction from raw inputs; (ii) has fast inference speed and good accuracy performance; and (iii) is capable of handling large-scale data. The results show that the proposed approach is effective and efficient.
Data-driven discovery of Koopman eigenfunctions for control

Data-driven transformations that reformulate nonlinear systems in a linear framework have the potential to enable the prediction, estimation, and control of strongly nonlinear dynamics using linear systems theory. The Koopman operator has emerged as a principled linear embedding of nonlinear dynamics, and its eigenfunctions establish intrinsic coordinates along which the dynamics behave linearly. Previous studies have used finite-dimensional approximations of the Koopman operator for model-predictive control approaches. In this work, we illustrate a fundamental closure issue of this approach and argue that it is beneficial to first validate eigenfunctions and then construct reduced-order models in these validated eigenfunctions. These coordinates form a Koopman-invariant subspace by design and, thus, have improved predictive power. We show then how the control can be formulated directly in these intrinsic coordinates and discuss potential benefits and caveats of this perspective. The resulting control architecture is termed Koopman Reduced Order Nonlinear Identification and Control (KRONIC). It is further demonstrated that these eigenfunctions can be approximated with data-driven regression and power series expansions, based on the partial differential equation governing the infinitesimal generator of the Koopman operator. Validating discovered eigenfunctions is crucial and we show that lightly damped eigenfunctions may be faithfully extracted from EDMD or an implicit formulation. These lightly damped eigenfunctions are particularly relevant for control, as they correspond to nearly conserved quantities that are associated with persistent dynamics, such as the Hamiltonian. KRONIC is then demonstrated on a number of relevant examples, including (a) a nonlinear system with a known linear embedding, (b) a variety of Hamiltonian systems, and (c) a high-dimensional double-gyre model for ocean mixing.
A New Approach to the -Genvalue Equation

We show that the eigenvalues and eigenfunctions of the star-genvalue equation can be completely expressed in terms of the corresponding eigenvalue problem for the quantum Hamiltonian. Our methods make use of a Weyl-type representation of the star- product and of the properties of the cross-Wigner transform, which appears as an inter- twining operator. Mathematics Subject Classification (2000). 47G30, 81S10.
Straight gaze facilitates face processing but does not cause involuntary attentional capture

ABSTRACT This study aimed to investigate the conditions under which eyes with a straight gaze capture attention more than eyes with an averted gaze, a phenomenon called the stare-in-the-crowd effect. In Experiment 1, we measured attentional capture by distractor faces with either straight or averted gaze that were shown among faces with closed eyes. Gaze direction of the distractor face was irrelevant because participants searched for a tilted face and indicated its gender. The presence of the distractor face with open eyes resulted in slower reaction times, but gaze direction had no effect, suggesting that straight gaze does not result in more involuntary attentional capture than averted gaze. In three further experiments with the same stimuli, the gaze direction of the target, and not the distractor, was varied. Better performance with straight than averted gaze of the target face was observed when the gaze direction or gender of the target face had to be discriminated. However, no difference between straight and averted was observed when only the presence of a face with open eyes had to be detected. Thus, the stare-in-the crowd effect is only observed when eye gaze is selected as part of the target and only when features of the face have to be discriminated. Our findings suggest that preference for straight gaze bears on target-related processes rather than on attentional capture per se.
Analysis of the Contact Zone between the Dusky Salamanders Desmognathus fuscus fuscus and Desmognathus fuscus conanti(Caudata: Plethodontidae)

Abstract Two most widely distributed “subspecies” of the Desmognathus fuscus complex are the northern dusky salamander (Desmognathus fuscus fuscus) and the spotted dusky salamander (Desmognathus fuscus conanti). Previous mitochondrial DNA and allozyme studies of this complex have suggested that these two forms should be granted species-level recognition. However, detailed examination of populations inhabiting the region where the two taxa come into contact have not been performed to corroborate this taxonomic change. In this study, specimens were collected from four transects that traverse the putative contact zone. Allozyme and color pattern analysis were employed to determine the nature of variation across the area and evaluate the taxonomic status of D. f. conanti. Phylogenetic analyses of allozyme data divide the populations sampled into at least four major groups, two of which are referable to Desmognathus fuscus (groups A and C) and two referable to D. conanti (groups B and D). This study supports the distinctiveness of D. conanti by revealing parapatry between populations of groups A and B in western Kentucky with only a minor amount of hybridization between them and identifies color pattern differences that are effective for characterizing most group B individuals. The data presented here suggest that a longitudinal division may exist within D. conanti in central Alabama. Group C occurs primarily on the Piedmont of North Carolina and Virginia and appears to hybridize with group A in central Virginia. Groups C and D are treated, conservatively, as D. fuscus and D. conanti, respectively; but further study may reveal that each is a distinct species.