bluuebunny/crossref_metadata_2025_split huggingface dataset:
finFindR: Computer-assisted Recognition and Identification of Bottlenose Dolphin Photos in R
Authors: Thompson Jaime W. , Zero Victoria H. , Schwacke Lori H. , Speakman Todd R. , Quigley Brian M. , Morey Jeanine S. M. , McDonald Trent L. 
Published: October 2019

AbstractPhotographic identification is an essential research and management tool for studying population size and dynamics of common bottlenose dolphins (Tursiops truncatus). Photographic identification involves recognizing individuals based on unique dorsal fin markings. Manual identification of dolphins, while successful, is labor-intensive and time-consuming. To shorten processing times, we developed a series of neural networks that finds fins, assesses their unique characteristics, and matches them to an existing catalog.Our software, finFindR, shortens photo-ID processing times by autonomously finding and isolating (i.e., “cropping”) dolphin fins in raw field photographs, tracing the trailing edge of fins in cropped images, and producing a sorted list of likely identities from a catalog of known individuals. The program then presents users with the top 50 most likely matching identities, allowing users to view side-by-side image pairs and make final identity determinations.During testing on two sets of novel images, finFindR placed the correct individual in the first position of its ordered list in 88% (238/272 and 354/400) of test cases. finFindR placed the correct identity among the top 10 ranked images in 94% of test cases, and among the top 50 ranked images in 97% of test cases. Hence, if a match does not exist in the first 50 images of finFindR’s ordered list, researchers can be almost certain (~97%) that a match does not exist in the entire catalog.During a head-to-head blind test of the human-only and finFindR-assisted matching methods, two experienced photo-ID technicians both achieved 97% correct identification of identities when matched against a catalog containing over 2,000 known individuals. However, the manual-only technician examined 124 images on average before making a match, while the technician using finFindR examined only 10 images on average before finding a match.We conclude that finFindR will facilitate equal or improved match accuracy while greatly reducing the number of examined photos. The faster matches, automated detection, and automated cropping afforded by finFindR will greatly reduce typical photo-ID processing times.
Diversification of a cryptic radiation, a closer look at Madagascar’s recently recognized bird family
Authors: Younger Jane L. , Block Nicholas L. , Raherilalao Marie J. , Maddox J. Dylan , Wacker Kristen S. , Kyriazis Christopher C. , Goodman Steven M. , Reddy Sushma 
Published: October 2019

AbstractDespite its status as a global biodiversity hotspot there is still much to be discovered about the birds of Madagascar, including a full accounting of species-level diversity and the avifauna’s origins. The Bernieridae is a Malagasy endemic family that went unrecognized by science for decades and unnamed until 2010. This cryptic family has long represented a missing piece of the puzzle of the avian tree of life. We present the first comprehensive phylogeny of Bernieridae in order to examine its diversification history on Madagascar and its place within Passeriformes. In light of recent discoveries of cryptic species-level diversity in Madagascar’s vertebrate fauna, we used broad geographic sampling and integrative taxonomic methods to investigate the potential for cryptic lineages within every known species of the Bernieridae. Our approach combines phylogenomics using ∼4500 loci of ultraconserved elements (UCEs), genetic clustering of thousands of single nucleotide polymorphisms (SNPs), and statistical analysis of morphological variation. These methods yielded the discovery of two unrecognized species in the previously monotypic genusBernieria, along with new insights into patterns of fine-scale endemism in Madagascar’s humid forests. Our phylogenomic analyses provide conclusive support for Donacobiidae and Bernieridae as sister families, a biogeographically intriguing result given that the former is restricted to the Neotropics. We found a significant decline in the rate of speciation over time on Madagascar, consistent with a model of adaptive radiation. Bernieridae therefore joins the Vangidae as a second avian adaptive radiation on the island of Madagascar. These insights into the evolution of Bernieridae represent a step forward in understanding the origins and diversity of Madagascar’s endemic avifauna.
Polyjet 3D printing of tissue-mimicking materials: how well can 3D printed synthetic myocardium replicate mechanical properties of organic myocardium?
Authors: Severseike Leah , Lee Vania , Brandon Taycia , Bakken Chris , Bhatia Varun 
Published: October 2019

AbstractAnatomical 3-D printing has potential for many uses in education, research and development, implant training, and procedure planning. Conventionally, the material properties of 3D printed anatomical models have often been similar only in form and not in mechanical response compared to biological tissue. The new Digital Anatomy material from Stratasys utilizes composite printed materials to more closely mimic the mechanical properties of tissue. Work was done to evaluate Digital Anatomy myocardium under axial loading for comparison with porcine myocardium regarding puncture, compliance, suturing, and cutting performance.In general, the Digital Anatomy myocardium showed promising comparisons to porcine myocardium. For compliance testing, the Digital Anatomy was either within the same range as the porcine myocardium or stiffer. Specifically, for use conditions involving higher stress concentrations or smaller displacements, Digital Anatomy was stiffer. Digital Anatomy did not perform as strongly as porcine myocardium when evaluating suture and cutting properties. The suture tore through the printed material more easily and had higher friction forces both during needle insertion and cutting. Despite these differences, the new Digital Anatomy myocardium material was much closer to the compliance of real tissue than other 3D printed materials. Furthermore, unlike biological tissue, Digital Anatomy provided repeatability of results. For tests such as cyclic compression, the material showed less than two percent variation in results between trials and between parts, resulting in lower variability than tissue. Despite some limitations, the myocardium Digital Anatomy material can be used to configure structures with similar mechanical properties to porcine myocardium in a repeatable manner, making this a valuable research tool.
Rod-cone signal interference in the retina shapes perception in primates
Authors: Songco-Aguas Adree , Grimes William N , Rieke Fred 
Published: October 2019

AbstractLinking the activity of neurons, circuits and synapses to human behavior is a fundamental goal of neuroscience. Meeting this goal is challenging, in part because behavior, particularly perception, often masks the complexity of the underlying neural circuits, and in part because of the significant behavioral differences between primates and animals like mice and flies in which genetic manipulations are relatively common. Here we relate circuit-level processing of rod and cone signals in the non-human primate retina to a known break in the normal seamlessness of human vision – a surprising inability to see high contrast flickering lights under specific conditions. We use electrophysiological recordings and perceptual experiments to identify key mechanisms that shape the retinal integration of rod- and cone-generated retinal signals. We incorporate these mechanistic insights into a predictive model that accurately captures the cancellation of rod- and cone-mediated responses and can explain the perceptual insensitivity to flicker.
CO2intensity and GDP per capita
Authors: Hannesson Rögnvaldur 
Published: October 2019

PurposeTo investigate whether CO2intensity falls at a diminishing rate as countries grow richer.Design/methodology/approachRegression of CO2intensity on the gross domestic product (GDP) per capita, including squared and cubic terms, for a panel of countries and individual countries.FindingsCO2intensity falls at a diminishing rate as countries grow richer.Originality/valueMany studies have found that CO2intensity falls with GDP per capita, but whether it does so at a diminishing rate has not been investigated. This result suggests that structural changes in GDP (more services) as countries get richer will provide little or no help toward decarbonization. It is shown that the extraction of minerals critical for industrial production has increased on par with real GDP. This could explain why CO2emissions fall at a diminishing rate.
Interdisciplinary treatment of family violence in traumatized refugee families
Authors: Dalgaard Nina Thorup , Thøgersen Marie Høgh , Montgomery Edith 
Published: October 2019

PurposeThe purpose of this paper is to explore the defining characteristics of an interdisciplinary culturally sensitive approach to family therapy with traumatized refugee families affected by family violence. Furthermore, the paper aims to explore the mechanisms of change as seen from the perspective of the therapists.Design/methodology/approachBased on qualitative analysis of semi-structured interviews with therapists working in an interdisciplinary team as well as observations of treatment conferences, the study identified the ways in which therapists perceive the challenges faced by their patients, the ways in which positive change is facilitated within therapy and the characteristics of a culturally sensitive interdisciplinary approach to family therapy with traumatized refugee families.FindingsThe study identified a number of defining characteristics of the treatment model, which includes the interdisciplinary approach, treatment objectives and concrete interventions targeting these objectives.Originality/valueThrough a theoretically informed critical analysis of the data, the present study examined the defining characteristics of the treatment model as well as the mechanisms of change as perceived by the therapists.
Comparison of STL skull models produced using open-source software versus commercial software
Authors: Abdullah Johari Yap , Abdullah Abdul Manaf , Hadi Helmi , Husein Adam , Rajion Zainul Ahmad 
Published: October 2019

Purpose
This paper aims to compare the automatic segmentation of medical data and conversion to stereolithography (STL) skull models using open-source software versus commercial software.

Design/methodology/approach
Both open-source and commercial software used automatic segmentation and post-processing of the data without user intervention, thus avoiding human error. Detailed steps were provided for comparisons and easier to be repeated by other researchers. The results of segmentation, which were converted to STL format were compared using geometric analysis.

Findings
STL skull models produced using open-source software are comparable with the one produced using commercial software. A comparison of STL skull model produced using InVesalius with STL skull model produced using MIMICS resulted in an average dice similarity coefficient (DSC) of 97.6 ± 0.04 per cent and Hausdorff distance (HD) of 0.01 ± 0.005 mm. Inter-rater study for repeatability on MIMICS software yielded an average DSC of 100 per cent and HD of 0.

Social implications
The application of open-source software will benefit the small research institutions or hospitals to produce and virtualise three-dimensional model of the skulls for teaching or clinical purposes without having to purchase expensive commercial software. It is also easily reproduceable by other researchers.

Originality/value
This study is one of the first comparative evaluations of an open-source software with propriety commercial software in producing accurate STL skull models. Inaccurate STL models can lead to inaccurate pre-operative planning or unfit implant.
Gametophytic competition games among relatives: When does spatial structure select for facilitativeness or competitiveness in pollination?
Authors: Iritani Ryosuke 
Published: October 2019

AbstractDetermining whether pollination occurs competitively or rather facilitatively among co‐flowering plants is a central question in plant reproductive ecology. Kobayashi [2018;Journal of Ecology107: 1433–1438] theoretically investigated the scenario in which intraspecific pollen tube competition (male–male competition) can lead to regulation of population growth due to reduced female success.Kobayashi (2018) showed that evolutionary dynamics in intraspecific pollen tube competition can reduce female success and consequently generate negative density‐dependence of population growth, which allows for numerous species to coexist in a spatially subdivided metacommunity. Kobayashi (2018) hypothesized that trait evolution driven by sexual selection may maintain biodiversity.However, the models proposed by Kobayashi (2018) allow for the assumptions to be relaxed; he assumed: (i) fully global seed dispersal (instead of limited dispersal, albeit the spatial subdivision), (ii) fully local pollination (i.e., pollination occurred exclusively within patches), (iii) selfing rate was exactly proportionate (i.e., pollen grains distributed equally among all individuals within a patch, irrespective of their parental origins), (iv) haploid mode of inheritance, and most importantly, (v) each individual was mutually competitive, rather than facilitative for pollination.Here, I extend the models of Kobayashi (2018) and show that when I relax assumptions (i)–(v), facilitativeness, as opposed to competitiveness, is more likely to be favoured by selection. The present results are attributed to kin selection in gametopythic competition among relatives in spatially subdivided populations.If facilitativeness for pollination is favoured by kin selection, then the premise that the evolution of pollen traits can generate negative density‐dependence does not necessarily follow. I also discuss the potential mechanisms by which pollen phenotypes can either strengthen or attenuate intraspecific and interspecific competition.
Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest
Authors: Ushio Masayuki , Osada Yutaka , Kumagai Tomo'omi , Kume Tomonori , Pungga Runi anak Sylvester , Nakashizuka Tohru , Itioka Takao , Sakai Shoko 
Published: October 2019

AbstractSupra‐annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are “spectacular and mysterious” forest events. Recently, studies that combined novel molecular techniques and model‐based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Although these advanced our understanding of GF, it is still difficult to know whether the individual‐based molecular measurements and model‐based mathematical representations reasonably well capture the complex and dynamic GF processes at the community level. In the present study, we collected a 17‐year set of community‐wide phenology data from Lambir Hills National Park in Borneo, Malaysia, and analyzed it using a model‐free approach, empirical dynamic modeling (EDM), which does not rely on specific assumptions about the underlying mechanisms, to overcome and complement the previous limitations. We found that GF in the region is driven synergistically, not independently, by cool air temperature and drought, which is consistent with the previous studies. More importantly, our model‐free approach showed for the first time that effects of cumulative meteorological variables on GF changed over time. The time‐varying influences of meteorological variables on GF imply that the relationship between GF and meteorological variables might be influenced by other factors such as plant/soil nutrient resource dynamics. Our study provides a novel insight about the mechanism underlying the spectacular tropical forest event GF, and future studies integrating advanced mathematical/statistical frameworks, long‐term and large spatial scale ecosystem monitoring and molecular phenology data are promising for achieving better understanding and forecasting of GF events in Southeast Asia.
Preferential catabolism of the (S)‐enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in Sphingobium sp. strain B2
Authors: Huang Junwei , Chen Dian , Jiang Jiandong 
Published: October 2019

SummaryThe (R)‐ and (S)‐enantiomers of the chiral herbicide napropamide (NAP) show different biological activities and ecotoxicities. These two enantiomers behave differently in the environment due to enantioselective catabolism by microorganisms. However, the molecular mechanisms underlying this enantioselective catabolism remain largely unknown. In this study, the genes (snaH and snpd) involved in the catabolism of NAP were cloned from Sphingobium sp. B2, which was capable of catabolizing both NAP enantiomers. Compared with (R)‐NAP, (S)‐NAP was much more rapidly transformed by the amidase SnaH, which initially cleaved the amide bonds of (S)/(R)‐NAP to form (S)/(R)‐2‐(1‐naphthalenyloxy)‐propanoic acid [(S)/(R)‐NP] and diethylamine. The α‐ketoglutarate‐dependent dioxygenase Snpd, showing strict stereoselectivity for (S)‐NP, further transformed (S)‐NP to 1‐naphthol and pyruvate. Molecular docking and site‐directed mutagenesis analyses revealed that when the (S)‐enantiomers of NAP and NP occupied the active sites, the distance between the ligand molecule and the coordination atom was shorter than that when the (R)‐enantiomers occupied the active sites, which facilitated formation of the transition state complex. This study enhances our understanding of the preferential catabolism of the (S)‐enantiomer of NAP on the molecular level.
Beyond trade creation: Preferential trade agreements and trade disputes
Authors: Li Tan , Qiu Larry D. 
Published: October 2019

AbstractThis study investigates the effects of preferential trade agreements (PTA) on bilateral trade disputes. We construct a unique and comprehensive dataset on inter‐country trade disputes from 1995 to 2007. The dataset covers 110 countries and 1,162 bilateral country‐pair trade disputes. Using this dataset in a gravity‐type model of trade dispute analysis, we find that countries belonging to the same PTA tend to experience fewer trade conflicts among themselves than with non‐member countries. By studying various types of PTA with different dispute settlement mechanisms, we further find that the dispute‐reducing effect only comes from PTA with specific provisions on dispute settlement mechanisms. Moreover, the effect is stronger if those PTA explicitly stipulate that members can also resolve their disputes via the WTO Dispute Settlement Body. However, having PTA that do not address how members should resolve their disputes may lead to more dispute initiations than in cases without PTA.
Discrimination in the United States: Experiences of Latinos
Authors: Findling Mary G. , Bleich Sara N. , Casey Logan S. , Blendon Robert J. , Benson John M. , Sayde Justin M. , Miller Carolyn 
Published: October 2019

AbstractObjectiveTo examine experiences of racial/ethnic discrimination among Latinos in the United States, which broadly contribute to their poor health outcomes.Data Source and Study DesignData come from a nationally representative, probability‐based telephone survey including 803 Latinos and a comparison group of 902 non‐Hispanic white US adults, conducted January—April 2017.MethodsWe calculated the percent of Latinos reporting discrimination in several domains, including health care. We used logistic regression to compare the Latino‐white difference in odds of discrimination, and among Latinos only to examine variation by socioeconomic status and country of birth.Principal FindingsOne in five Latinos (20 percent) reported experiencing discrimination in clinical encounters, while 17 percent avoided seeking health care for themselves or family members due to anticipated discrimination. A notable share of Latinos also reported experiencing discrimination with employment (33 percent applying for jobs; 32 percent obtaining equal pay/promotions), housing (31 percent), and police interactions (27 percent). In adjusted models, Latinos had significantly higher odds than whites for reporting discrimination in health care visits (OR: 3.18, 95% CI: 1.61, 6.26) and across several other domains. Latinos with college degrees had significantly higher odds of reporting discrimination in multiple domains than those without college degrees, with few differences between foreign‐born and US‐born Latinos.ConclusionsLatinos in the United States report experiencing widespread discrimination in health care and other areas of their lives, at significantly higher levels than whites. Being born in the United States and earning a college degree are not protective against discrimination, suggesting that further health and social policy efforts to eliminate discrimination are needed.
The Evolving Structure of Chinese R&D Funding and its Implications for the Productivity of Agricultural Biotechnology Research
Authors: Cai Jinyang , Chen Weiqiong , Huang Jikun , Hu Ruifa , Pray Carl E. 
Published: October 2019

AbstractChina’s research and development (R&D) policy has changed considerably over recent decades, and great changes occurred in 2006 when the main programme objective of China’s R&D changed from the 863 Programme and 973 Programme to the National Science and Technology Major Project. One topic that has drawn extensive attention is whether the investment reform improved R&D productivity in China. Using a unique panel dataset from 160 universities, this paper examines the effect of the investment reform on productivity improvement in China’s agricultural biotechnology sector. We use a panel count data model with a dynamic feedback mechanism to model the knowledge production process. Strong evidence indicates that the investment reform greatly contributes to knowledge output production in China’s agricultural biotechnology sector. We also find that the input quality is more important than the absolute quantity; human research capacity exhibits the greatest contribution to the output of patents; past knowledge accumulation helps produce more patents; and entry barriers to patent production exist in China’s agricultural biotechnology sector. Moreover, the patent explosion in China may have been largely caused by improvements in the human capital input quality.
Nonfatal Bites by a Sicklefin Lemon Shark Negaprion acutidens on a Surfer in Makemo Atoll (French Polynesia)
Authors: Clua Eric E. G. , Haguenauer Anne 
Published: October 2019

AbstractIdentifying the species and size of sharks responsible for biting humans is essential for developing strategies to prevent these incidents. Here, we use bite wound characteristics and genetic analysis of a tooth fragment extracted from the wounds to identify a sicklefin lemon shark Negaprion acutidens as the perpetrator of nonfatal bites on the legs of an adult male surfer at Makemo atoll (French Polynesia) in January 2018. The bite was superficial, and N. acutidens are fish predators not known to feed on large prey; hence, foraging is an unlikely explanation for this incident rather linked to territoriality. Lemon sharks are occasionally aggressive toward humans and are site attached with relatively small home ranges; hence, avoiding surfing in the area of a previous bite incident is recommended to decrease the risk of future injuries.