bluuebunny/crossref_metadata_2025_split huggingface dataset:
Past, present and future approaches using computer vision for animal re‐identification from camera trap data
Authors: Schneider Stefan , Taylor Graham W. , Linquist Stefan , Kremer Stefan C. 
Published: December 2018

Abstract

The ability of a researcher to re‐identify (re‐ID) an individual animal upon re‐encounter is fundamental for addressing a broad range of questions in the study of ecosystem function, community and population dynamics and behavioural ecology. Tagging animals during mark and recapture studies is the most common method for reliable animal re‐ID; however, camera traps are a desirable alternative, requiring less labour, much less intrusion and prolonged and continuous monitoring into an environment. Despite these advantages, the analyses of camera traps and video for re‐ID by humans are criticized for their biases related to human judgement and inconsistencies between analyses.

In this review, we describe a brief history of camera traps for re‐ID, present a collection of computer vision feature engineering methodologies previously used for animal re‐ID, provide an introduction to the underlying mechanisms of deep learning relevant to animal re‐ID, highlight the success of deep learning methods for human re‐ID, describe the few ecological studies currently utilizing deep learning for camera trap analyses and our predictions for near future methodologies based on the rapid development of deep learning methods.

For decades, ecologists with expertise in computer vision have successfully utilized feature engineering to extract meaningful features from camera trap images to improve the statistical rigor of individual comparisons and remove human bias from their camera trap analyses. Recent years have witnessed the emergence of deep learning systems which have demonstrated the accurate re‐ID of humans based on image and video data with near perfect accuracy. Despite this success, ecologists have yet to utilize these approaches for animal re‐ID.

By utilizing novel deep learning methods for object detection and similarity comparisons, ecologists can extract animals from an image/video data and train deep learning classifiers to re‐ID animal individuals beyond the capabilities of a human observer. This methodology will allow ecologists with camera/video trap data to reidentify individuals that exit and re‐enter the camera frame. Our expectation is that this is just the beginning of a major trend that could stand to revolutionize the analysis of camera trap data and, ultimately, our approach to animal ecology.
Detecting Neurodevelopmental Effects of Early‐Gestation Ethanol Exposure: A Nonhuman Primate Model of Ethanol Drinking During Pregnancy
Authors: Jimenez Vanessa A. , Wang Xiaojie , Newman Natali , Walter Nicole A. R. , Gonzales Steven , Lo Jamie O. , Ford Mathew M. , Cuzon Carlson Verginia C. , Grant Kathleen A. , Kroenke Christopher D. 
Published: December 2018

BackgroundGestational ethanol (EtOH) exposure is associated with multiple developmental abnormalities, collectively termed fetal alcohol spectrum disorder (FASD). While the majority of women abstain from EtOH following knowledge of pregnancy, one contributing factor to the high FASD prevalence is that pregnancy is not detected until 4 to 6 weeks. Thus, EtOH consumption continues during the initial stages of fetal development.MethodsAn experimental protocol is described in which rhesus macaques self‐administer 1.5 g/kg/d EtOH (or isocaloric maltose dextrin) prior to pregnancy and through the first 60 days of a 168‐day gestation term. Menstrual cycles were monitored, including measurements of circulating estradiol and progesterone levels. The latency to consume 1.5 g/kg EtOH and blood EtOH concentration (BEC) was measured.ResultsTwenty‐eight fetuses (14 EtOH and 14 controls) were generated in this study. EtOH did not affect menstrual cycles or the probability of successful breeding. No EtOH‐induced gross adverse effects on pregnancy were observed. Individual variability in latency to complete drinking translated into variability in BEC, measured 90 minutes following session start. Drinking latencies in controls and EtOH drinkers were longer in the second gestational month than in the first. All pregnancies reached the planned experimental time point of G85, G110, or G135, when in utero MRIs were performed, fetuses were delivered by caesarean section, and brains were evaluated with ex vivo procedures, including slice electrophysiology. Fetal tissues have been deposited to the Monkey Alcohol Tissue Research Resource.ConclusionsThis FASD model takes advantage of the similarities between humans and rhesus macaques in gestational length relative to brain development, as well as similarities in EtOH self‐administration and metabolism. The daily 1.5 g/kg dose of EtOH through the first trimester does not influence pregnancy success rates. However, pregnancy influences drinking behavior during the second month of pregnancy. Future publications using this model will describe the effect of early‐gestation EtOH exposure on anatomical and functional brain development at subsequent gestational ages.
Review of rodent hypertensive glaucoma models
Authors: Biswas Sayantan , Wan Kelvin H. 
Published: December 2018

AbstractGlaucoma is a neurodegenerative disease characterized by the progressive loss of retinal ganglion cells (RGCs). Elevated intraocular pressure (IOP) is a primary risk factor for the development and progression of glaucoma. Rodent models of glaucoma have greatly improved our understanding of the pathophysiology of glaucoma and served as a useful tool to investigate neuroprotective agents. An ideal glaucoma animal model should be easy to induce, reproducible, biologically plausible and predictable. Of the available animal models of glaucoma, rodents are commonly studied because they have a relatively short life span and can be genetically altered. A successful hypertensive glaucoma model should induce structural glaucomatous changes: including loss of retinal nerve fibres, retinal ganglion cells and optic‐disc cupping along with IOP elevation. The level and duration of IOP elevation should be titratable depending on the targeted glaucomatous damage. This review summarizes the outcomes of induced rodent hypertensive glaucoma models including intracameral injection of microbeads, laser photocoagulation, episcleral vein cauterization, injection of hypertonic saline and hyaluronic acid. We aim to provide a detailed overview of each of the models with a focus on parameters that defines a successful glaucoma model. The induced IOP elevation and duration of elevation varied among the different models and strain of rodent; nonetheless, they all achieved a sustainable raised IOP with corresponding RGC loss. The limitations of each model are discussed.
Repeatability and reliability of quantitative fundus autofluorescence imaging in patients with early and intermediate age‐related macular degeneration
Authors: Reiter Gregor Sebastian , Told Reinhard , Baratsits Magdalena , Hecht Alexander , Schlanitz Ferdinand Georg , Sacu Stefan , Schmidt‐Erfurth Ursula 
Published: December 2018

AbstractPurposeQuantification of fundus autofluorescence has only recently become available. We report our findings on the evaluation of the repeatability and reliability of quantitative fundus autofluorescence (qAF) measurements in patients with early and intermediate age‐related macular degeneration (AMD), using the first approved and commercially available instrument.MethodsA total of 43 eyes of 22 patients (aged between 52 and 84 years) diagnosed with early and intermediate AMD were included. All eyes were imaged at day 1, 3 months and 6 months using a modified scanning laser ophthalmoscope, equipped with an internal fluorescent reference. Mean qAF values were calculated for the fovea and for each concentric ring of the Delori pattern. Repeatability and reliability were calculated using Bland–Altman analysis and intraclass correlation (ICC).ResultsThe mean patient age was 73.5 ± 7.9 years. Sixteen patients (73%) were female. qAF repeatability of the eight segments in the middle ring of the Delori pattern (qAFM8) for between sessions was ±8.2%. Agreement at 3‐ and 6‐month follow‐up in eyes without retinal changes was ±8.3% and ±9.8%, respectively. Reliability of qAFM8 was high for all images acquired [ICC = 0.98 (CI: 0.96–0.99), 0.97 (0.93–0.99) and 0.98 (0.92–0.99)]. Agreement at 3‐ and 6‐month follow‐up in eyes with retinal changes was ±18.1% and ±20.2%, respectively. Intraclass correlation (ICC) was slightly lower in eyes with retinal changes at 0.93 (0.84–0.97) and 0.96 (0.91–0.98), respectively.ConclusionsQuantitative autofluorescence shows excellent repeatability and reliability as well as follow‐up agreement in patients with early and intermediate AMD without retinal changes. This is relevant when conducting longitudinal studies using qAF.
Retinal metabolic and structural alterations in response to aflibercept treatment in neovascular age‐related macular degeneration
Authors: Jakobsen Ditte B. , Torp Thomas L. , Stefansson Einar , Peto Tunde , Grauslund Jakob 
Published: December 2018

AbstractPurposeNon‐invasive retinal markers of disease activity could pave the way for individualized treatment in neovascular age‐related macular degeneration (nAMD). We aimed to evaluate if retinal vascular oxygen saturation and calibres could predict the initial treatment response after a loading phase of intravitreal aflibercept in nAMD.MethodA total of 149 eyes were included (nAMD, n = 76; dry AMD, n = 30; normal eyes n = 43). Of these, 57 treatment‐naïve eyes with nAMD received three monthly injections with 2.0 mg aflibercept and were subsequently stratified according to functional and structural response according to development in best‐corrected visual acuity and macular retinal thickness. The retinal vascular oxygen saturation and calibres were measured prior to treatment and 1 month after the third injection.ResultsPatients with nAMD and dry AMD had higher retinal arteriolar oxygen saturation as compared to normal eyes (94.3% versus 95.2% versus 92.6%, p = 0.04). Thirty‐nine (68.4%) and 12 (21.1%) eyes with nAMD were functional and structural responders. After the loading phase, structural nonresponders developed a higher retinal arteriolar (95.3% versus 93.3%, p = 0.03) and venular (64.7% versus 59.4%, p = 0.02) oxygen saturation, and responders developed a lower retinal arteriolar calibre (118.0 versus 114.3 μm, p < 0.01). In a multiple logistic regression model, increasing retinal venular oxygen saturation associated with a negative structural treatment outcome (odds ratio 1.17 for each 1% increment after the loading phase, 95% confidence interval 1.01–1.36, p = 0.03).ConclusionChanges in the retinal venular oxygen saturation associate independently with initial treatment response in nAMD, but functional and structural retinal measurements prior to treatment could not predict the treatment response.
Dependence Modeling for Recurrent Event Times Subject to Right-Censoring With D-Vine Copulas
Authors: Barthel Nicole , Geerdens Candida , Czado Claudia , Janssen Paul 
Published: December 2018

Abstract
In many time-to-event studies, the event of interest is recurrent. Here, the data for each sample unit correspond to a series of gap times between the subsequent events. Given a limited follow-up period, the last gap time might be right-censored. In contrast to classical analysis, gap times and censoring times cannot be assumed independent, i.e., the sequential nature of the data induces dependent censoring. Also, the number of recurrences typically varies among sample units leading to unbalanced data. To model the association pattern between gap times, so far only parametric margins combined with the restrictive class of Archimedean copulas have been considered. Here, taking the specific data features into account, we extend existing work in several directions: we allow for nonparametric margins and consider the flexible class of D-vine copulas. A global and sequential (one- and two-stage) likelihood approach are suggested. We discuss the computational efficiency of each estimation strategy. Extensive simulations show good finite sample performance of the proposed methodology. It is used to analyze the association of recurrent asthma attacks in children. The analysis reveals that a D-vine copula detects relevant insights, on how dependence changes in strength and type over time.
Distribution-Free Estimation of Local Growth Rates Around Interval Censored Anchoring Events
Authors: Chu Chenghao , Zhang Ying , Tu Wanzhu 
Published: December 2018

Abstract
Biological processes are usually defined on timelines that are anchored by specific events. For example, cancer growth is typically measured by the change in tumor size from the time of oncogenesis. In the absence of such anchoring events, longitudinal assessments of the outcome lose their temporal reference. In this paper, we considered the estimation of local change rates in the outcomes when the anchoring events are interval-censored. Viewing the subject-specific anchoring event times as random variables from an unspecified distribution, we proposed a distribution-free estimation method for the local growth rates around the unobserved anchoring events. We expressed the rate parameters as stochastic functionals of the anchoring time distribution and showed that under mild regularity conditions, consistent and asymptotically normal estimates of the rate parameters could be achieved, with a convergence rate. We conducted a carefully designed simulation study to evaluate the finite sample performance of the method. To motivate and illustrate the use of the proposed method, we estimated the skeletal growth rates of male and female adolescents, before and after the unobserved pubertal growth spurt (PGS) times.
Pressure pain sensitivity is associated with dental fear in adults in middle age: Findings from the Northern Finland 1966 birth cohort study
Authors: Kankaanpää Rami , Auvinen Juha , Rantavuori Kari , Jokelainen Jari , Karppinen Jaro , Lahti Satu 
Published: December 2018

AbstractIntroductionDental fear is a prevalent problem leading to severe deterioration of oral health and health‐related quality of life. Despite the knowledge that dental fear is closely linked to painful experience, the association between pain sensitivity and dental fear remains unclear. This study was designed to evaluate this association with validated measures of dental fear and pressure pain sensitivity in a cohort population.MethodsThe study population consisted of a subpopulation of the Northern Finland Birth Cohort 1966. At the age of 46 years, 1736 participants completed the valid and reliable Modified Dental Anxiety Scale (MDAS) and participated in a clinical examination, where their nonorofacial pressure pain sensitivity was evaluated by validated pressure pain threshold (PPT) and tolerance (PPTo) measurements. Gender‐specific Tobit regressions were performed to analyse this association adjusted for smoking and depressive and anxiety symptoms.ResultsWomen with moderate dental fear had 5% (31.3 kPa; P < 0.05), and women with high dental fear had 7% (42.9 kPa; n.s.) lower pressure pain threshold than women with low dental fear. Women with moderate dental fear had 4% (35.4 kPa; P < 0.05) and women with high dental fear had 9% (82.7 kPa; P < 0.01) lower pressure pain tolerance than women with low dental fear. Men with moderate and high dental fear had 3% lower pressure pain tolerance (35.4 kPa; P < 0.05 and 29.6 kPa; n.s., respectively) than men with low dental fear, whereas the associations with pain threshold were not statistically significant. Among women, both anticipatory and treatment‐related dental fears were associated with pain threshold and pain tolerance. Among men, pain threshold was associated with treatment‐related dental fear only and the associations with pain tolerance were not statistically significant.ConclusionsNonorofacial pressure pain threshold and tolerance appeared to be lower in participants with dental fear, which emphasizes the role of pain sensitivity in dental fear.
Changes in Australian practice patterns for glaucoma management
Authors: Newman Alexander R. , Andrew Nicholas H. 
Published: December 2018

AbstractImportanceThe demand for glaucoma care is projected to increase significantly with the ageing population.BackgroundTo characterize trends in Australian practice patterns for glaucoma management over the 15‐y period between 2003 and 2017.DesignRetrospective audit.SamplesThe Medicare eligible population.MethodsAudit of Medicare Benefits Schedule item number reimbursements in the private healthcare sector, and dispensed Pharmaceutical Benefits Scheme (PBS) prescriptions.Main Outcome MeasuresNumber, unadjusted cost and services per capita in the enrolled population.ResultsThe number of medication prescriptions peaked in 2015, but then declined by 14.9%. PBS expenditure on glaucoma medications has been falling since 2012. There was a 9.2‐fold increase in fixed‐combination prescriptions and 281‐fold increase in unpreserved medication prescriptions. In 2017, optometrists generated 1.86% of glaucoma prescriptions. Reimbursements for computerized perimetry increased dramatically for optometrists, and in 2017 optometrist‐initiated perimetry exceeded ophthalmologist‐initiated perimetry by 35.3%. There were significant increases in laser procedure rates, including laser trabeculoplasty (4.61‐fold), laser iridotomy (2.55‐fold) and cyclodestructive procedures (2.33‐fold). There was a 3.83‐fold increase in glaucoma drainage device insertions. Ab interno trabecular microbypass procedures increased 715% from 2014 to 2017. Adjusted for Medicare population, trabecular microbypass is performed at more than twice the rate of primary filtering operations.Conclusions and RelevanceThis is the first time that glaucoma medication use and expenditure have declined since auditing began in 1992. Glaucoma laser procedures, drainage device implantation and trabecular microbypass increased substantially over the study period. In contrast, the rate of primary filtering operations increased in proportion to population growth. The increase in overall cost of glaucoma care has primarily been driven by computerized perimetry; however, this has been partially offset by a decline in medication expenditure.
Survey on the status of teledermatology in Austria
Authors: Eber Elena Lucia , Janda Monika , Arzberger Edith , Hofmann‐Wellenhof Rainer 
Published: December 2018

SummaryBackgroundThe use of digital communication media is becoming increasingly important, with the primary aim of improving both treatment quality and patients' quality of life. In an effort to optimize telemedicine in the field of dermatology, we conducted a survey among dermatologists in Austria.MethodsStatistical analysis of a questionnaire that was developed by a working group and sent to 769 Austrian dermatologists.ResultsOverall, 243 dermatologists (132 women/111 men) participated in the survey. Forty‐seven percent of male respondents and 55 % of female respondents had already received requests for teledermatology consultations. Seventy‐three percent felt that telemedicine was able to contribute to relieving the economic burden on the health care system. Telecommunication between dermatologists and experts (in a given field of dermatology) was deemed to be particularly useful. While telemedicine was also considered to be appropriate for patient follow‐up, it was viewed to be less useful for initial consultations. Roughly 50 % of respondents used telemedicine to get a second opinion; one‐third used it for initial consultations.ConclusionsOur survey shows that the majority of participants consider teledermatology to be a useful supplement to the current practice of dermatology. Given its particular usefulness for triage purposes, teledermatology can help reduce the number of trips to the hospital and subsequent waiting times. This in turn leads to cost reduction and saves time for both patients and doctors. Legal regulations that include provisions for appropriate reimbursement of physicians would make using teledermatology more attractive.
Biotic resistance or introduction bias? Immigrant plant performance decreases with residence times over millennia
Authors: Sheppard Christine S. , Schurr Frank M. 
Published: December 2018

AbstractAimInvasions are dynamic processes. Invasive spread causes the geographical range size of alien species to increase with residence time. However, with time native competitors and antagonists can adapt to invaders. This build‐up of biotic resistance may eventually limit the invader’s performance and reduce its range size. Using a species‐for‐time approach, we test (a) whether native communities more strongly reduce the fitness of immigrants with longer residence times, and (b) whether the range size of immigrant species shows a unimodal response to residence time.LocationGermany.Time period18,000 years BP to present.Major taxa studied352 plant species in the Asteraceae family.MethodsFor plant species with a wide range of minimum residence times in Germany (6–18,000 years), we combined a common garden experiment with historical and macroecological analyses. In a multi‐species experiment, we quantified the effect of native communities on fitness components of 30 annual Asteraceae. For these and other species, we then analysed how current range size depends on minimum residence time and other covariates.ResultsNative communities reduced survival, reproductive output and fitness of Asteraceae. This fitness reduction was stronger for immigrant species with long residence times. We found a unimodal relationship between range size and residence time of Asteraceae in Germany, when including natives that immigrated after the last glaciation.Main conclusionsBiotic resistance may limit the performance and geographical ranges of immigrant species over long time‐scales. The initial advantages invaders have over natives thus may not persist over millennia, supporting the concept of an alien–native species continuum defined by gradual changes in eco‐evolutionary processes. While our analysis controlled for major ecological, evolutionary and biogeographical factors, it is conceivable that the detected patterns are influenced by additional differences between natives and aliens. Experimental macroecology has great potential to disentangle these processes and predict long‐term invasion dynamics.