Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal monitoring and statistical modelling methods for feral cats and other mammalian predators in a pastoral landscape

Introduction. Mammalian predators have a global impact on biodiversity. Mammalian predator species often occur at low abundance and require efficient and non-invasive monitoring techniques, alongside reliable statistical modelling methods, to explain the probability of detection, presence and, when possible, abundance. Camera traps are a dynamic technology currently used around the world to monitor a wide range of species in a variety of ecological research programmes However, as camera traps continue to change and improve, there is a need for more standardisation for both camera settings and deployment methods, depending on the objective of the study. Aims. The aims of this study were to: 1) determine the optimal orientation for camera traps to detect mammalian pest species; 2) determine the optimal statistical method for modelling changes in a feral cat population pre-and post-predator control operation; 3) assess the effectiveness of a Bayesian abundance estimator at providing abundance estimates for a population of hedgehogs preand post-predator control; and 4) deploy camera traps on a wide scale to determine the baseline relative abundance and detection rate for feral cats prior to a predator control operation. Materials and methods. 1) I deployed 20 pairs of camera traps (one horizontal and one vertical) for 21 days across a pastoral landscape in Hawke’s Bay, North Island, New Zealand, and compared numbers of detections for target species (feral cats) and mustelids (M. furo, M. erminea, and M. nivalis); 2) I deployed 40 horizontally-oriented cameras on pre-determined grid sites across two pastoral properties in Hawke’s Bay, for two consecutive periods of 21 days, to monitor feral cats preand post-predator control. I compared four statistical modelling methods for gauging the success of the control operation: index manipulation
Immobilizing antibodies in pyelonephritis.

Type-Specific immobilizing antibodies were found in serum and urine in the course of retrograde experimental pyelonephritis due to Proteus mirabilis. Serum antibodies were detected 3 to 5 days after infection, reached high levels at 7 to 15 days and persisted until the animals were killed. Six-day serum contained both 2ME-resistant and 2ME-sensitive antibodies, but 13- or 19-day serum antibodies were not affected by 2ME. Upon gradient ultracentrifugation of 19-day sera, the highest immobilizing titer was found in 7 S fractions. Immobilizing antibodies were also demonstrated in dialyzed urine during infection, after infection had been suppressed or eradicated by antibiotics, and after immunization with formalin-treated bacteria by intravenous or intrarenal injection. Urinary immobilizing antibodies correlated well with the location and concentration of 7 S marker on the density gradient and appeared to be stable in infected urine.
Pancreas Injury in Shock

Background: The causes of acute pancreatitis are well known, and although enzymatic injury is the main factor in its development, pancreatic ischemia due to profound hypoperfusion in cardiogenic or hypovolemic shock patients can be an important etiological factor. The aim of our study was to analyse the histological alterations of the pancreas in patients dying after shock, to study the presence and severity of pancreatic injury. Material and methods: We studied the morphological alteration of the pancreas, in patients who died after cardiogenic or hypovolemic shock, hospitalized in intensive care units in the County Emergency Hospital Tîrgu Mureș, between 2007–2009. Results: We examined the structure of the pancreas of 117 patients, 20 showed acute hemorrhagic pancreatic necrosis on autopsy. None of the patients showed typical clinical and laboratory signs for acute pancreatitis. The common findings in these patients were prolonged and severe hypotension, leucocytosis, hyperglycemia and hypocalcemia. Conclusions: Pancreatitis can occur in patients with shock, due to ischemic injury of the pancreas. It is difficult to diagnose it because clinical signs are altered by the severity of the underlying disease or by analgo-sedation commonly used in intensive care units. We therefore recommend to consider the possible development of acute pancreatitis in patients with shock, in patients with prolonged hypotension, leucocytosis, hypocalcemia, even in the absence of characteristic clinical symptoms and hyperamylasemia.
Detecting bittorrent blocking

Recently, it has been reported that certain access ISPs are surreptitiously blocking their customers from uploading data using the popular BitTorrent file-sharing protocol. The reports have sparked an intense and wide-ranging policy debate on network neutrality and ISP traffic management practices. However, to date, end users lack access to measurement tools that can detect whether their access ISPs are blocking their BitTorrent traffic. And since ISPs do not voluntarily disclose their traffic management policies, no one knows how widely BitTorrent traffic blocking is deployed in the current Internet. In this paper, we address this problem by designing an easy-to-use tool to detect BitTorrent blocking and by presenting results from a widely used public deployment of the tool.
Natural Yeast Promoter Variants Reveal Epistasis in the Generation of Transcriptional-Mediated Noise and Its Potential Benefit in Stressful Conditions

The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast.
Measuring Access to Eye Care: A Public Health Perspective

Purpose: To examine the different dimensions of access to eye care from a public health perspective. Methods: We substantively review the theoretical and empirical literature on access to eye care and summarize the major considerations in measuring access to eye care using a modified behavioral framework. Results: We found that progress has been made, but some gaps still remain in measuring access to eye care. Most studies have focused on individual characteristics and use of eye care services. Only a very few studies have touched on contextual characteristics, such as demographic make-up of the area in which the patient lives, and their impact on the use of eye care services. Few studies have explored the linkage between the use of eye care services and outcomes or between the use of such services and patient satisfaction. Conclusions: To address a variety of demands from patients, providers, and policy makers, it is necessary to account for potential access and realized access measures. We need to adopt new methods in assessing the relationship between contextual characteristics and use of eye care services. Moreover, we need to better understand patients' satisfaction and their relationship with utilization and health outcomes.
Proximal muscle rehabilitation is effective for patellofemoral pain: a systematic review with meta-analysis

Background Proximal muscle rehabilitation is commonly prescribed to address muscle strength and function deficits in individuals with patellofemoral pain (PFP). This review (1) evaluates the efficacy of proximal musculature rehabilitation for patients with PFP; (2) compares the efficacy of various rehabilitation protocols; and (3) identifies potential biomechanical mechanisms of effect in order to optimise outcomes from proximal rehabilitation in this problematic patient group. Methods Web of Knowledge, CINAHL, EMBASE and Medline databases were searched in December 2014 for randomised clinical trials and cohort studies evaluating proximal rehabilitation for PFP. Quality assessment was performed by two independent reviewers. Effect size calculations using standard mean differences and 95% CIs were calculated for each comparison. Results 14 studies were identified, seven of high quality. Strong evidence indicated proximal combined with quadriceps rehabilitation decreased pain and improved function in the short term, with moderate evidence for medium-term outcomes. Moderate evidence indicated that proximal when compared with quadriceps rehabilitation decreased pain in the short-term and medium-term, and improved function in the medium term. Limited evidence indicated proximal combined with quadriceps rehabilitation decreased pain more than quadriceps rehabilitation in the long term. Very limited short-term mechanistic evidence indicated proximal rehabilitation compared with no intervention decreased pain, improved function, increased isometric hip strength and decreased knee valgum variability while running. Conclusions A robust body of work shows proximal rehabilitation for PFP should be included in conservative management. Importantly, greater pain reduction and improved function at 1 year highlight the long-term value of proximal combined with quadriceps rehabilitation for PFP.
Appears in Seventh Eurographics Workshop on Rendering Conservative Interpolants for Ray Tracing Conservative Interpolants for Ray Tracing Conservative Radiance Interpolants for Ray Tracing

Classical ray-tracing algorithms compute radiance returning to the eye along one or more sample rays through each pixel of an image. The output of a ray-tracing algorithm, although potentially photoreal-istic, is a two-dimensional quantity { an image array of radiance values { and is not directly useful from any viewpoint other than the one for which it was computed. This paper makes several contributions. First, it directly incorporates the notion of radiometric error into classical ray-tracing, by lazy construction of conservative radiance interpolants in ray space. For any relative error tolerance , we show how to construct interpolants which return radiance values within of those that would be computed by classical (e.g., Whitted) ray-tracing. The second contribution of the paper is an explication of the four sources of aliasing inherent in classical ray tracing { termed gaps, blockers, funnels, and peaks { and an adaptive subdivision algorithm for identifying ray space regions guaranteed to be free of these phenomena. Finally, we describe a novel data structure that exploits object-space coherence in the radiance function to accelerate not only the generation of single images, but of image sequences arising from a smoothly varying sequence of eyepoints. We describe a preliminary implementation incorporating each of these ideas.
Infantile Nystagmus and Visual Deprivation: Foveal Instability and Refractive Development in a Low Vision Register Series

Purpose To evaluate whether effects of early foveal motor instability due to infantile nystagmus might compare to those of experimental visual deprivation on refraction in a childhood series. Methods This was a retrospective analysis of data from the Danish Register for Blind and Weak-sighted Children with infantile nystagmus recorded as prime diagnosis. We perused 90 records of children now aged 10–17 years, some of whom eventually exceeded the register borderline of 0.3 as best-corrected visual acuity. Spherical equivalent refraction was the primary outcome parameter, but visual acuity, astigmatism, and age were further considered. The series comprised 48 children with nystagmus as single diagnosis, whereas 42 had clinical colabels (Down syndrome [13], dysmaturity [9], and mental retardation, encephalopathy [20]). Results Median binocular visual acuity was 0.3 in the full series, and median refraction was emmetropia in all subgroups. Compared with Danish control data, myopia was over-represented, and generally of juvenile onset. The Down syndrome subgroup was separated from the remainder by an even higher myopia prevalence. Astigmatism above 1 D cylinder value was recorded in 52% of all cases. Conclusions The prevalence of myopia and astigmatism was higher among children with nystagmus than in controls. Myopia was mainly juvenile, and not related to the period of infancy when the motor foveal smear is considered most disturbing and possibly influencing visual development.
Quantity and Quality of Dispersed Fine Particles after the Low-Energy Water-Dispersible Soil Test: Impact of the Initial Soil Matrix Potential

Transfer of <2-µm soil particles is a key process in the dispersion of pollutants and the textural differentiation of soil. Dispersion tests involving low-energy water-dispersible clay (LeWDC) are commonly used to indicate the stock of particles <2-µm that can be mobilized. However, notable differences in LeWDC protocols exist. We discuss the impact of the initial soil matrix potential on the dispersion sensitivity of <2-µm particles and the nature (mineralogy and particle size) of the dispersed particles. The dispersion sensitivity was more differentiated among soils with a high initial water content, which allows better soil discrimination. The nature of dispersed <2-µm particles was closer to that of the bulk <2-µm soil when moist initial conditions were considered, whereas enrichment in coarse clay minerals (with a particle-size mode of around 2 µm) was observed with dry initial conditions. Performing the LeWDC test under both moist and dry initial conditions can be used to interpret soil functioning. Abbreviations: CEC, cation exchange capacity; LEWDC: low-energy water-dispersible clay; OC, organic C; pF, log of soil water suction; XRD, x-ray diffraction.
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules

SUMMARY Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the first step in T-cell mediated immune response. To understand the structural principles governing MHC-specific peptide recognition and binding, we have developed the MHC-Peptide Interaction Database (MPID), containing sequence-structure-function information. MPID (version 1.2) contains curated x-ray crystallographic data on 86 MHC peptide complexes, with precomputed interaction parameters (solvent accessibility, hydrogen bonds, gap volume and gap index). A user-friendly web interface and query tools will facilitate the development of predictive algorithms for MHC-peptide binding from a structural viewpoint. AVAILABILITY Freely accessible from http://surya.bic. nus.edu. sg/mpid.
Fundamental techniques for order optimization

Decision support applications are growing in popularity as more business data is kept on-line. Such applications typically include complex SQL queries that can test a query optimizer's ability to produce an efficient access plan. Many access plan strategies exploit the physical ordering of data provided by indexes or sorting. Sorting is an expensive operation, however. Therefore, it is imperative that sorting is optimized in some way or avoided all together. Toward that goal, this paper describes novel optimization techniques for pushing down sorts in joins, minimizing the number of sorting columns, and detecting when sorting can be avoided because of predicates, keys, or indexes. A set of fundamental operations is described that provide the foundation for implementing such techniques. The operations exploit data properties that arise from predicate application, uniqueness, and functional dependencies. These operations and techniques have been implemented in IBM's DB2/CS.
Memoization aspects: a case study

Mondrian, an open-source visualization engine, uses a number of caches to avoid redundant computation. These caches are structured along Mondrian purpose: generating static two-dimensional visualizations. We have noticed that the caches are meaningless for the evolution being made on Mondrian. Using aspect-oriented programming, we have refactored these caches into well defined aspects to address the evolution problem. We have achieved it without paying the price of runtime problems.
Standard conjectures for the arithmetic Grassmannian G(2,N) and Racah polynomials

We prove the arithmetic Hodge index and hard Lefschetz conjectures for the Grassmannian G = G(2,N) parametrizing lines in projective space, for the natural arithmetic Lefschetz operator defined via the Plucker embedding of G in projective space. The analysis of the Hodge index inequality involves estimates on values of certain Racah polynomials.
Continuous monitoring of heart rate using accelerometric sensors

The results of application of differential geometry in the processing of human biosignals are presented. Using accelerometric sensors placed under the mattress the ballistocardiogram was measured together with the related ECG signal. The R-R intervals were calculated and compared with the accelerometric data. We shown, that the accelerometric sensors acquire sufficient accuracy to acquire the heart rate with an accuracy comparable to the classical ECG devices.
Role Based Access Control and OWL

Current access control research follows two parallel themes: many efforts focus on developing novel access control models meeting the policy needs of real world application domains while others are exploring new policy languages. This paper is motivated by the desire to develop a synergy between these themes facilitated by OWL. Our vision for the future is a world where advanced access control concepts are embodied in models that are supported by policy languages in a natural intuitive manner, while allowing for details beyond the models to be further speciﬁed in the policy language. In this paper we speciﬁcally study the relationship between the Web Ontology Language (OWL) and the Role Based Access Control (RBAC) model. Although OWL is a web ontology language and not speciﬁcally designed for expressing authorization policies, it has been used successfully for this purpose in previous work such as KAoS and Rei. We show two different ways to support the NIST Standard RBAC model in OWL and then discuss how the OWL constructions can be extended to model attribute-based RBAC or more generally attribute-based access control.
Computerized Planning of Prostate Cryosurgery and Shape Considerations

The current study aims to explore possible relationships between various prostate shapes and the difficulty in creating a computer-based plan for cryosurgery. This research effort is a part of an ongoing study to develop computational means in order to improve cryosurgery training and education. This study uses a computerized planner—a key building block of a recently developed prototype for cryosurgery training. The quality of planning is measured by the overall defect volume, a proprietary concept which refers to undercooled areas internal to the target region and overcooled areas external to it. Results of this study numerically confirm that the overall defect volume decreases with an increasing number of cryoprobes, regardless of the geometry of the prostate. However, the number of cryoprobes required to achieve the smallest possible defect may be unrealistically high (<30). Results of this study also demonstrate that the optimal cryoprobe layout is associated with a smaller defect for symmetric prostate geometries and, independently, for prostate models that better resemble a sphere. Furthermore, a smaller defect is typically achieved when the urethra passes through the center of the prostate model. This study proposes to create a cryoprobe convex hull for the purpose of initial planning, which is a subdomain similar in shape to the prostate but at a reduced size. Parametric studies indicate that a cryoprobe convex hull contracted by 7 to 9 mm in all directions from the prostate capsule serves as a quasi-optimal initial condition for planning, that is, a preselected number of cryoprobes placed in the cryoprobe convex hull yields favorable results for optimization. The cryoprobe convex hull could accelerate computer-based planning, while also being adopted as a concept for traditional cryosurgery training, when computerized means are absent.
Robust voicing estimation with dynamic time warping

This paper presents a robust voicing estimation algorithm for low bit rate harmonic speech coding. The algorithm is based on waveform time-warping followed by spectral matching based on voiced and unvoiced local spectral models. The objective of time warping is to reduce the effect of pitch variations on the voicing decision. Several adaptive techniques are used to improve the flexibility and robustness of the conventional spectral matching algorithm. An objective evaluation of the new voicing algorithm is obtained by comparing to manually estimated voicing values. Subjective tests of a sinusoidal coder using the new voicing algorithm show significantly better performance than the standard spectral matching under both clean and noisy environment.
The Primacy of Cognition in the Manifestations of Substance Use Disorders

Drug addiction is a serious public healthproblem that consists of a compulsivedrive to take drugs despite repeated severeadverse consequences (1). Factors thatinﬂuence the development and mainte-nance of addiction include access to drugs,socialenvironment,geneticpredisposition,and psychiatric comorbidities (2). Even inthe absence of speciﬁc psychiatric diag-noses, certain psychological vulnerabili-ties may serve as substrates compound-ing the initiation of drug use and thedevelopment of substance use disorders.For example,individual who are sensation-seekers, impulsive, or behavioral disinhib-ited appear more prone to develop addic-tion to both licit and illicit substances (3–6). In this context, it is to be noted that notall individuals who try these drugs becomeaddicted as about only 20% of people whohave tried drugs become addicts (7). It isalso worth mentioning that repeated expo-sure to moderate to large doses of someof these illicit drugs may be associatedwith well-known neuropathological con-sequences (8, 9) that might not be eithernecessary or sufﬁcient for the developmentand the maintenance of addicted states.The accumulated evidence supports theview that a large number of substanceusers suffer from signiﬁcant neuropsy-chological impairments (10). Neuroimag-ing studies in drug-dependent individu-als have also documented signiﬁcant func-tional and structural alterations in severalbrain regions (1). These regions includemesocortical, mesolimbic, and mesostri-atal brain regions that are known to beimpacted by administration of licit andillicit drugs in both clinical and preclinicalstudies (2). In what follows, we discuss thepotential impact of illicit drugs on thesebrain regions and the associated cogni-tive consequences of these drugs. We thensuggest that these cognitive consequencesplay primary roles in the maintenance ofaddiction across several classes of abusedsubstances.