bluuebunny/crossref_metadata_2025_split huggingface dataset:
Therapeutic Hypothermia in Organ Donors: Follow-up and Safety Analysis
Authors: Malinoski Darren , Patel Madhukar S. , Axelrod David A. , Broglio Kristine , Lewis Roger J. , Groat Tahnee , Niemann Claus U. 
Published: July 2019

Background.
In a recent trial, targeted mild hypothermia in brain-dead organ donors significantly reduced the incidence of delayed graft function after kidney transplantation. This trial was stopped early for efficacy. Here, we report long-term graft survival for all organs along with donor critical care end points.

Methods.
We assessed graft survival through 1 year of all solid organs transplanted from 370 donors who had been randomly assigned to hypothermia (34–35°C) or normothermia (36.5–37.5°C) before donation. Additionally, changes in standardized critical care end points were compared between donors in each group.

Results.
Mild hypothermia was associated with a nonsignificant improvement in 1-year kidney transplant survival (95% versus 92%; hazard ratio, 0.61 [0.31–1.20]; P = 0.15). Mild hypothermia was associated with higher 1-year graft survival in the subgroup of standard criteria donors (97% versus 93%; hazard ratio, 0.39 [0.15 to −1.00]; P = 0.05). There were no significant differences in graft survival of extrarenal organs. There were no differences in critical care end points between groups.

Conclusions.
Mild hypothermia in the donor safely reduced the rate of delayed graft function in kidney transplant recipients without adversely affecting donor physiology or extrarenal graft survival. Kidneys from standard criteria donors who received targeted mild hypothermia had improved 1-year graft survival.
Assessing Predictors of Early and Late Hospital Readmission After Kidney Transplantation
Authors: Hogan Julien , Arenson Michael D. , Adhikary Sandesh M. , Li Kevin , Zhang Xingyu , Zhang Rebecca , Valdez Jeffrey N. , Lynch Raymond J. , Sun Jimeng , Adams Andrew B. , Patzer Rachel E. 
Published: July 2019

Background.
A better understanding of the risk factors of posttransplant hospital readmission is needed to develop accurate predictive models.

Methods.
We included 40 461 kidney transplant recipients from United States renal data system (USRDS) between 2005 and 2014. We used Prentice, Williams and Peterson Total time model to compare the importance of various risk factors in predicting posttransplant readmission based on the number of the readmissions (first vs subsequent) and a random forest model to compare risk factors based on the timing of readmission (early vs late).

Results.
Twelve thousand nine hundred eighty-five (31.8%) and 25 444 (62.9%) were readmitted within 30 days and 1 year postdischarge, respectively. Fifteen thousand eight hundred (39.0%) had multiple readmissions. Predictive accuracies of our models ranged from 0.61 to 0.63. Transplant factors remained the main predictors for early and late readmission but decreased with time. Although recipients’ demographics and socioeconomic factors only accounted for 2.5% and 11% of the prediction at 30 days, respectively, their contribution to the prediction of later readmission increased to 7% and 14%, respectively. Donor characteristics remained poor predictors at all times. The association between recipient characteristics and posttransplant readmission was consistent between the first and subsequent readmissions. Donor and transplant characteristics presented a stronger association with the first readmission compared with subsequent readmissions.

Conclusions.
These results may inform the development of future predictive models of hospital readmission that could be used to identify kidney transplant recipients at high risk for posttransplant hospitalization and design interventions to prevent readmission.
Behavioural valuation of landscapes using movement data
Authors: Wittemyer George , Northrup Joseph M. , Bastille-Rousseau Guillaume 
Published: July 2019

Wildlife tracking is one of the most frequently employed approaches to monitor and study wildlife populations. To date, the application of tracking data to applied objectives has focused largely on the intensity of use by an animal in a location or the type of habitat. While this has provided valuable insights and advanced spatial wildlife management, such interpretation of tracking data does not capture the complexity of spatio-temporal processes inherent to animal behaviour and represented in the movement path. Here, we discuss current and emerging approaches to estimate the behavioural value of spatial locations using movement data, focusing on the nexus of conservation behaviour and movement ecology that can amplify the application of animal tracking research to contemporary conservation challenges. We highlight the importance of applying behavioural ecological approaches to the analysis of tracking data and discuss the utility of comparative approaches, optimization theory and economic valuation to gain understanding of movement strategies and gauge population-level processes. First, we discuss innovations in the most fundamental movement-based valuation of landscapes, the intensity of use of a location, namely dissecting temporal dynamics in and means by which to weight the intensity of use. We then expand our discussion to three less common currencies for behavioural valuation of landscapes, namely the assessment of the functional (i.e. what an individual is doing at a location), structural (i.e. how a location relates to use of the broader landscape) and fitness (i.e. the return from using a location) value of a location. Strengthening the behavioural theoretical underpinnings of movement ecology research promises to provide a deeper, mechanistic understanding of animal movement that can lead to unprecedented insights into the interaction between landscapes and animal behaviour and advance the application of movement research to conservation challenges.
This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
Mechanisms driving phenological and range change in migratory species
Authors: Gill Jennifer A. , Alves José A. , Gunnarsson Tómas G. 
Published: July 2019

Many migratory systems are changing rapidly in space and time, and these changes present challenges for conservation. Changes in local abundance and site occupancy across species' ranges have raised concerns over the efficacy of the existing protected area networks, while changes in phenology can potentially create mismatches in the timing of annual events with the availability of key resources. These changes could arise either through individuals shifting in space and time or through generational shifts in the frequency of individuals using different locations or on differing migratory schedules. Using a long-term study of a migratory shorebird in which individuals have been tracked through a period of range expansion and phenological change, we show that these changes occur through generational shifts in spatial and phenological distributions, and that individuals are highly consistent in space and time. Predictions of future rates of changes in range size and phenology, and their implications for species conservation, will require an understanding of the processes that can drive generational shifts. We therefore explore the developmental, demographic and environmental processes that could influence generational shifts in phenology and distribution, and the studies that will be needed to distinguish among these mechanisms of change.
This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
Invisible barriers: anthropogenic impacts on inter- and intra-specific interactions as drivers of landscape-independent fragmentation
Authors: Berger-Tal Oded , Saltz David 
Published: July 2019

Anthropogenically induced fragmentation constitutes a major threat to biodiversity. Presently, conservation research and actions focus predominantly on fragmentation caused directly by physical transformation of the landscape (e.g. deforestation, agriculture, urbanization, roads, etc.). While there is no doubt that landscape features play a key role in fragmenting populations or enhancing connectivity, fragmentation may also come about by processes other than the transformation of the landscape and which may not be readily visible. Such landscape-independent fragmentation (LIF) usually comes about when anthropogenic disturbance alters the inter- and intra-specific interactions among and within species. LIF and its drivers have received little attention in the scientific literature and in the management of wildlife populations. We discuss three major classes of LIF processes and their relevance for the conservation and management of species and habitats: (i) interspecific dispersal dependency, in which populations of species that rely on other species for transport and propagation become fragmented as the transporting species declines; (ii) interspecific avoidance induction, where species are excluded from habitats and corridors owing to interspecific interactions resulting from anthropogenically induced changes in community structure (e.g. exclusions by increased predation pressure); and (iii) intraspecific behavioural divergence, where populations become segregated owing to anthropogenically induced behavioural differentiation among them.
This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.
Animal learning may contribute to both problems and solutions for wildlife–train collisions
Authors: St. Clair Colleen Cassady , Backs Jonathan , Friesen Alyssa , Gangadharan Aditya , Gilhooly Patrick , Murray Maureen , Pollock Sonya 
Published: July 2019

Transportation infrastructure can cause an ecological trap if it attracts wildlife for foraging and travel opportunities, while increasing the risk of mortality from collisions. This situation occurs for a vulnerable population of grizzly bears (Ursus arctos) in Banff National Park, Canada, where train strikes have become a leading cause of mortality. We explored this problem with analyses of rail-associated food attractants, habitat use of GPS-collared bears and patterns of past mortality. Bears appeared to be attracted to grain spilled from rail cars, enhanced growth of adjacent vegetation and train-killed ungulates with rail use that increased in spring and autumn, and in areas where trains slowed, topography was rugged, and human density was low. However, areas with higher grain deposits or greater use by bears did not predict sites of past mortality. The onset of reported train strikes occurred amid several other interacting changes in this landscape, including the cessation of lethal bear management, changes in the distribution and abundance of ungulates, increasing human use and new anthropogenic features. We posit that rapid learning by bears is critical to their persistence in this landscape and that this capacity might be enhanced to prevent train strikes in future with simple warning devices, such as the one we invented, that signal approaching trains.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
Can hyena behaviour provide information on population trends of sympatric carnivores?
Authors: Green David S. , Farr Matthew T. , Holekamp Kay E. , Strauss Eli D. , Zipkin Elise F. 
Published: July 2019

Mammalian carnivores are declining worldwide owing to human activities. Behavioural indicators have the potential to help identify population trends and inform conservation actions, although this area of research is understudied. We investigate whether behaviour is linked to abundance in a community of carnivores in the Masai Mara National Reserve, Kenya. Anthropogenic disturbance increased exponentially in parts of the Reserve between 1988 and 2017, mainly owing to daily incursions by large numbers of livestock and tourists. Previous research showed that hyena behaviour changed markedly during this period. Through a series of vignettes, we inquire whether hyena behaviours correlate with changes in abundance of hyenas themselves, or those of other carnivore species in the region. We find that changes in spotted hyena behaviour in disturbed areas, but not in undisturbed areas, can be linked to changes in their demography (vignette 1). We also find that declines in observed lion–hyena interactions, as well as increases in spotted hyena abundance, are probably caused by competitive release of hyenas from declining lion abundance (vignette 2). Finally, we demonstrate that in some cases, hyena behaviour and demography is linked to the density and distribution of sympatric carnivores, and that behavioural changes in hyenas can provide information on shifts within the carnivore community (vignettes 3 and 4). Our vignettes reveal intriguing relationships between behaviour and demography that should be explored in future research. Pairing behavioural studies with more traditional monitoring efforts can yield useful insights regarding population and community trends, and aid wildlife conservation and management.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.
Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation
Authors: Bro-Jørgensen Jakob , Franks Daniel W. , Meise Kristine 
Published: July 2019

The impact of environmental change on the reproduction and survival of wildlife is often behaviourally mediated, placing behavioural ecology in a central position to quantify population- and community-level consequences of anthropogenic threats to biodiversity. This theme issue demonstrates how recent conceptual and methodological advances in the discipline are applied to inform conservation. The issue highlights how the focus in behavioural ecology on understanding variation in behaviour between individuals, rather than just measuring the population mean, is critical to explaining demographic stochasticity and thereby reducing fuzziness of population models. The contributions also show the importance of knowing the mechanisms by which behaviour is achieved, i.e. the role of learning, reasoning and instincts, in order to understand how behaviours change in human-modified environments, where their function is less likely to be adaptive. More recent work has thus abandoned the ‘adaptationist’ paradigm of early behavioural ecology and increasingly measures evolutionary processes directly by quantifying selection gradients and phenotypic plasticity. To support quantitative predictions at the population and community levels, a rich arsenal of modelling techniques has developed, and interdisciplinary approaches show promising prospects for predicting the effectiveness of alternative management options, with the social sciences, movement ecology and epidemiology particularly pertinent. The theme issue furthermore explores the relevance of behaviour for global threat assessment, and practical advice is given as to how behavioural ecologists can augment their conservation impact by carefully selecting and promoting their study systems, and increasing their engagement with local communities, natural resource managers and policy-makers. Its aim to uncover the nuts and bolts of how natural systems work positions behavioural ecology squarely in the heart of conservation biology, where its perspective offers an all-important complement to more descriptive ‘big-picture’ approaches to priority setting.
This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
Toward Automated Classification of Pathological Transcranial Doppler Waveform Morphology via Spectral Clustering
Authors: Thorpe Samuel G. , Thibeault Corey M. , Canac Nicolas , Jalaleddini Kian , Dorn Amber , Wilk Seth J. , Devlin Thomas , Scalzo Fabien , Hamilton Robert B. 
Published: July 2019

AbstractCerebral Blood Flow Velocity waveforms acquired via Transcranial Doppler (TCD) can provide evidence for cerebrovascular occlusion and stenosis. Thrombolysis in Brain Ischemia (TIBI) flow grades are widely used for this purpose, but require subjective assessment by expert evaluators to be reliable. In this work we seek to determine whether TCD morphology can be objectively assessed using an unsupervised machine learning approach to waveform categorization. TCD beat waveforms were recorded at multiple depths from the Middle Cerebral Arteries of 106 subjects; 33 with CTA-confirmed Large Vessel Occlusion (LVO). From each waveform, three morphological variables were extracted, quantifying absolute peak onset, number/prominence of auxiliary peaks, and systolic canopy length. Spectral clustering identified groups implicit in the resultant three-dimensional feature space, with gap-statistic criteria establishing the optimal cluster number. We found that gap-statistic disparity was maximized at four clusters, referred to as flow types I, II, III, and IV. Types I and II were primarily composed of control subject waveforms, whereas types III and IV derived mainly from LVO patients. Cluster morphologies for types I and IV aligned clearly with Normal and Blunted TIBI flows, respectively. Types II and III represented commonly observed flow-types not delineated by TIBI, which nonetheless deviate quantifiably from normal and blunted flows. We conclude that important morphological variability exists beyond that currently quantified by TIBI in populations experiencing or at-risk for acute ischemic stroke, and posit that the observed flow-types provide the foundation for objective methods of real-time automated flow type classification.
The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms
Authors: Veenstra Jan A. 
Published: July 2019

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.
MicrobComp – graphical user interface enables an in-silico comparison of taxonomic differences between two amplicon datasets
Authors: Nussbaumer Thomas 
Published: July 2019

ABSTRACTThe experimental and computational analysis of microbes is in the focus of basic and applied research for several decades already and has massively extended our knowledge of role and impact of microbes during that time.Amplicon sequencing is still widely adapted and standard procedure to determine key species in a biological sample and despite a high number of different datasets being steadily generated and fed into current data archives, there is a shortcoming in data interpretation. Furthermore, more computational tools are still required to guide the researcher towards an in-depth understanding of an experiment in a more systematic way. Towards that aim, MicrobComp was created as a graphical user interface which allows to compare two separate species frequency tables that contain the relative or absolute abundance of microbial species in an experiment. Therefore, this tool can be of great help when studying different amplicon experiments where studies were originally performed in different experimental labs.
Lentivirus-mediated long-term overexpression of specific microRNA for complementary miRNA pairs in mammalian cells
Authors: Qiao Shupei , Zhao Yufang , Li Kai , Sun Yulu , Sun Liuke , Hou Xiaolu , Tian Hui , Ye Kangruo , Nie Yongzhan , Tian Weiming 
Published: July 2019

AbstractThe establishment of a method that would overexpress or suppress of specific microRNA activity is essential for the functional analysis of these molecules and for the development of miRNA therapeutic applications. There already exist excellent ways to inhibit miRNA function in vitro and in vivo by overexpressing miRNA target sequences, which include miRNA ‘decoys’, ‘sponges’, or ‘antagomirs’ that are complementary to an miRNA seed region. Conversely, no methods to induce stable gain-of-function phenotypes for specific miRNAs have, as yet, been reported. Furthermore, the discovery of complementary miRNA pairs raises suspicion regarding the existing methods used for miRNA overexpression. In our study, we will study whether the traditional methods for miRNA overexpression can be used for specific miRNA overexpression while complementary miRNA pairs exist. In addition, we test various miRNA-expression cassettes that were designed to efficiently overexpress specific miRNA through the shRNA lentivirus expression system. We report the optimal conditions that were established for the design of such miRNA-expression cassettes. We finally demonstrate that the miRNA-expression cassettes achieve efficient and long-term overexpression of specific miRNAs. Meanwhile, our results also support the notion that miRNA–miRNA interactions are implicated in potential, mutual regulatory patterns and beyond the seed sequence of miRNA, extensive pairing interactions between a miRNA and its target also lead to target-directed miRNA degradation. Our results indicate that our method offers a simple and efficient means to over-express the specific miRNA with long-term which will be very useful for future studies in miRNA biology, as well as contributed to the development of miRNA-based therapy for clinical applications.