bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleus Reuniens Is Required for Encoding and Retrieving Precise, Hippocampal-Dependent Contextual Fear Memories in Rats
Authors: Ramanathan Karthik R. , Ressler Reed L. , Jin Jingji , Maren Stephen 
Published: October 2018

The nucleus reuniens (RE) is a ventral midline thalamic nucleus that interconnects the medial prefrontal cortex (mPFC) and hippocampus (HPC). Considerable data indicate that HPC–mPFC circuits are involved in contextual and spatial memory; however, it is not clear whether the RE mediates the acquisition or retrieval of these memories. To examine this question, we inactivated the RE with muscimol before either the acquisition or retrieval of pavlovian fear conditioning in rats; freezing served as the index of fear. We found that RE inactivation before conditioning impaired the acquisition of contextual freezing, whereas inactivation of the RE before retrieval testing increased the generalization of freezing to a novel context; inactivation of the RE did not affect either the acquisition or expression of auditory fear conditioning. Interestingly, contextual conditioning impairments were absent when retrieval testing was also conducted after RE inactivation. Contextual memories acquired under RE inactivation were hippocampal independent, insofar as contextual freezing in rats conditioned under RE inactivation was insensitive to intrahippocampal infusions of the NMDA receptor antagonist aminophosphonovalerate. Together, these data reveal that the RE supports hippocampal-dependent encoding of precise contextual memories that allow discrimination of dangerous contexts from safe contexts. When the RE is inactive, however, alternate neural systems acquire an impoverished contextual memory that is expressed only when the RE is off-line.SIGNIFICANCE STATEMENTThe midline thalamic nucleus reuniens (RE) coordinates communication between the hippocampus and medial prefrontal cortex, brain areas that are critical for contextual and spatial memory. Here we show that temporary pharmacological inactivation of RE impairs the acquisition and precision of contextual fear memories after pavlovian fear conditioning in rats. However, inactivating the RE before retrieval testing restored contextual memory in rats conditioned after RE inactivation. Critically, we show that imprecise contextual memories acquired under RE inactivation are learned independently of the hippocampus. These data reveal that the RE is required for hippocampal-dependent encoding of precise contextual memories to support the discrimination of safe and dangerous contexts.
Birds of Brier Island
Authors: Mills Eric L. , Laviolette Lance 
Published: October 2018

Brier Island, Nova Scotia, Canada, at the southwestern entrance to the Bay of Fundy, has been known for years as a prime birding destination. It combines access to unusually rich gatherings of pelagic birds, the chance of seeing rarities in greater frequency than almost anywhere else in the province, and the spectacle of large volume land bird migrations. The island lies at the intersection of migratory routes along the east coast of North America. Because of intense oceanic turbulence in the adjacent shallow water, which is in close proximity to deeper water, rich feeding is available for nearshore seabirds and pelagic species. Of the 470+ species recorded from the Province of Nova Scotia as a whole, 355 have been recorded from Brier Island. Many of these are vagrants, mainly of western or southern origin in North America; others are common passage migrants that visit the island briefly in very large numbers, especially in autumn. Apart from possible vagrants in spring and fall, the island is noted for the abundance of passerine migrants in autumn, a striking hawk migration in September and October, late-summer gatherings of phalaropes, shearwaters, and storm petrels, and an abundance of overwintering alcids, loons, grebes, and sea ducks in winter. The island has been the site of bird-banding activity and of Christmas counts for more than 50 years. We provide an introduction to the physiography, geology, physical geography, oceanography, and ecology of the island, along with a list of the breeding birds, a comparison with Grand Manan, New Brunswick, an extensively annotated list of the birds plausibly reported from the island to the middle of 2011, describing occurrence, seasonality, and abundance of all species, and a checklist of the birds of the island. Species occurrence data available via the OBIS Canada data repository http://ipt.iobis.org/obiscanada/resource?r=brierisland_birds
Enabling high-accuracy, position monitoring of Sable Island through the Nova Scotia Coordinate Referencing System
Authors: Bond Jason 
Published: October 2018

Since 1968, the Province of Nova Scotia has carried out a mandate of providing coordinate referencing infrastructure for its citizens. The current infrastructure is known as the Nova Scotia Coordinate Referencing System (NSCRS) and allows property boundaries, engineering works, and natural features to be spatially related within the Province, including Sable Island. Traditionally, thousands of survey monuments across the Province provided access to the coordinate referencing system for surveying and engineering work. Of the original 23,000 monuments installed in the 1970s and 1980s, many have been destroyed by natural occurrences or human activities. In the case of Sable Island, most have been enveloped by sand or the sea. In 2013, the Province began implementing a modernized strategy for delivering coordinate referencing services to its citizens using permanent GPS stations. This technology was installed at Main Station on Sable Island in June of 2014. This GPS infrastructure has already had a positive impact by:a)Allowing, for the first time, the three dimensional position of Sable Island (specifically Main Station) to be monitored with millimeter level accuracy b)Enabling Light Detection and Ranging (LiDAR) and aerial photography surveys to be consistently referenced within a global reference frame; andc)Providing quick and accurate positioning of natural features around the island with millimeter level accuracy and consequently enabling long term, position trends of these features (e.g., Bald Dune) to be determined.Each of these topics is discussed and a history of the NSCRS on Sable Island is presented.
Using laser photogrammetry to measure long-finned pilot whales (Globicephala melas)
Authors: Wong Joanna B. , Auger-Méthé Marie 
Published: October 2018

Knowledge of animal morphometry is important to understanding their ecology. By attaching two parallel lasers to a camera, known as laser photogrammetry (LP), a scale is projected onto photographed animals, allowing measurement of their body. Our primary aims were to test LP precision, and to estimate body length from dorsal-fin dimensions of Globicephala melas. Secondary aims involved demonstrating applications of LP, such as sex and leader determination. Using photographs taken over two-months, we measured dorsal base lengths (DBL) of 194 individuals individually-identified with natural markings. Results indicated 33 individuals were photographed in multiple encounters and eight matched previously-sexed whales. A mean difference of <2.1% between DBL’s of 58% of repeatedly-sighted individuals was found, and whales closer to the boat (<22m) produced more precise measures. The length from the blowhole to anterior insertion of the dorsal fin (BAID) was a better predictor of total body length in stranded whales than DBL, and laser-estimated lengths fell almost all within known pilot whale size. Despite our small sample size, we showed two examples of how LP could be applied in research: (1) males and females had similar DBL (n=8), but large males could be distinguished using DBL; (2) leaders were not necessarily bigger than other individuals in the same cluster (n=4). The ease of use of LP makes it a valuable tool in collecting measurements of body features, especially when coupled with photo-identification. Keywords: laser photogrammetry, morphometrics, measurement, length, Globicephala melas
Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices
Authors: Garcia Victor , Zoller Stefan , Anisimova Maria 
Published: October 2018

AbstractExperimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes’ true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy.
Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato
Authors: Sharma Sanjeev Kumar , MacKenzie Katrin , McLean Karen , Dale Finlay , Daniels Steve , Bryan Glenn J 
Published: October 2018

AbstractGenome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a ‘one model fits all traits’ approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a ‘trait-specific’ fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
Estimating Genetic Relatedness in Admixed Populations
Authors: Sethuraman Arun 
Published: October 2018

AbstractEstimating genetic relatedness, and inbreeding coefficients is important to the fields of quantitative genetics, conservation, genome-wide association studies (GWAS), and population genetics. Traditional estimators of genetic relatedness assume an underlying model of population structure. Each individual is assigned to a population, depending on a priori assumptions about geographical location of sampling, proximity, or genetic similarity. But often, this population assignment is unknown and assumptions about assignment can lead to erroneous estimates of genetic relatedness. I develop a generalized method of estimating relatedness in admixed populations, to account for (1) multi-allelic genomic data, (2) including all nine Identity By Descent (IBD) states, and implement a maximum likelihood based estimator of pairwise genetic relatedness in structured populations, part of the software, InRelate. Replicated estimations of genetic relatedness between admixed full sib (FS), half sib (HS), first cousin (FC), parent-offspring (PO) and unrelated (UR) dyads in simulated and empirical data from the HGDP-CEPH panel show considerably low bias and error while using InRelate, compared to several previously developed methods. I also propose a bootstrap scheme, and a series of Wald Tests to assign relatedness categories to pairs of individuals.
Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies
Authors: Wojcik Genevieve L , Fuchsberger Christian , Taliun Daniel , Welch Ryan , Martin Alicia R , Shringarpure Suyash , Carlson Christopher S , Abecasis Goncalo , Kang Hyun Min , Boehnke Michael , Bustamante Carlos D , Gignoux Christopher R , Kenny Eimear E 
Published: October 2018

Abstract
The emergence of very large cohorts in genomic research has facilitated a focus on genotype-imputation strategies to power rare variant association. These strategies have benefited from improvements in imputation methods and association tests, however little attention has been paid to ways in which array design can increase rare variant association power. Therefore, we developed a novel framework to select tag SNPs using the reference panel of 26 populations from Phase 3 of the 1000 Genomes Project. We evaluate tag SNP performance via mean imputed r2 at untyped sites using leave-one-out internal validation and standard imputation methods, rather than pairwise linkage disequilibrium. Moving beyond pairwise metrics allows us to account for haplotype diversity across the genome for improve imputation accuracy and demonstrates population-specific biases from pairwise estimates. We also examine array design strategies that contrast multi-ethnic cohorts vs. single populations, and show a boost in performance for the former can be obtained by prioritizing tag SNPs that contribute information across multiple populations simultaneously. Using our framework, we demonstrate increased imputation accuracy for rare variants (frequency &lt; 1%) by 0.5–3.1% for an array of one million sites and 0.7–7.1% for an array of 500,000 sites, depending on the population. Finally, we show how recent explosive growth in non-African populations means tag SNPs capture on average 30% fewer other variants than in African populations. The unified framework presented here will enable investigators to make informed decisions for the design of new arrays, and help empower the next phase of rare variant association for global health.
Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea (Vigna unguiculata[L.] Walp)
Authors: Herniter Ira A , Muñoz-Amatriaín María , Lo Sassoum , Guo Yi-Ning , Close Timothy J 
Published: October 2018

AbstractSeed coat color is an important part of consumer preferences for cowpea (Vigna unguiculata [L.] Walp). Color has been studied in numerous crop species and has often been linked to loci controlling the anthocyanin biosynthesis pathway. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits, with the gene symbol Bl, in cowpea. Several gene models encoding MYB domain protein 113 were identified as candidate genes. MYB domain proteins have been shown in other species to control expression of genes encoding enzymes for the final steps in the anthocyanin biosynthesis pathway. PCR analysis indicated that a presence/absence variation of one or more MYB113 genes may control the presence or absence of black pigment. A PCR marker has been developed for the MYB113 gene Vigun05g039500, a candidate gene for black seed coat color in cowpea.
An Electronic Referral and Social Work Protocol to Improve Access to Mental Health Services
Authors: Peters Kara M. , Sadler Gary , Miller Elizabeth , Radovic Ana 
Published: October 2018

BACKGROUND AND OBJECTIVES:
The prevalence of mental health problems among adolescents in the United States is a major public health concern. However, the uptake of mental health treatment is low. Integrating behavioral health into primary care is 1 research-informed strategy to increase engagement in treatment. Facilitators of and barriers to implementation of integrated behavioral health in a pediatric primary care setting are not well delineated.

METHODS:
We examined the effectiveness of 2 mental health quality improvement strategies: an electronic referral and a social work follow-up protocol. We analyzed the following measures: uptake rate of first mental health appointments, overall use of mental health appointments, and first and overall mental health appointment show rate.

RESULTS:
Overall use rate improved after implementation of electronic referral, with 13 consecutive points above the median. First appointment show rates improved with a special cause run occurring after adding social work students to the mental health quality improvement team. First appointment show rate improved from a monthly average of 51% (November 2014 to March 2016) to 78% (April 2016 to December 2016). Use rate improved initially with increased efforts in assisting patients with scheduling; show rate improved more slowly after an emphasis on scheduling patients exhibiting treatment readiness.

CONCLUSIONS:
Findings suggest that a number of facilitators can increase the effective use of mental health services in an integrated adolescent clinical setting. These include an electronic referral through a shared electronic health record, multidisciplinary collaboration, and care management by social workers equipped with a variety of clinical and care coordination skills.
Non-motorised transport prioritisation model using spatial intelligence
Authors: Poyil Rohith P. , Rojas Lopez Maria Cecilia , Wong Yiik Diew 
Published: October 2018

The aim of the work reported in this paper was to develop a non-motorised transport (NMT, covering walking and cycling) prioritisation model using a geographic information system that can be used for planning as well as auditing existing NMT infrastructure. ArcGIS 10.1 ModelBuilder software was used to design NMT prioritisation using the cases of Sembawang and Yishun residential townships in Singapore. The concept of spatial intelligence was used to predict the NMT prioritisation scheme; spatial intelligence is the ability to visualise spatial features and apply spatial judgement for mobility problems involving navigation or to identify fine details or patterns. The NMT prioritisation model was developed based on NMT movements in relation to spatial features such as residential buildings, community centres, schools and hospitals, recreation and sports centres, economic zones, transport hubs, bus stops and green spaces. The designed NMT prioritisation map is the weighted sum of Euclidean distance rasters of eight spatial layers. The results were subsequently used to assess the existing NMT facilities in the Sembawang and Yishun townships.
A Clinical Trial of The Evaluation of Environmental Exposure in Yttrium 90 Radioembolization
Authors: TANYİLDİZİ Handan , ÇAVDAR İffet , DEMİR Mustafa 
Published: October 2018

Aim: The aim of this study is to measure the dose rate of two
different forms of Y-90 microsphere used for radioembolization and to evaluate
the results according to radiation safety regularities. Material and Methods:
19 patients were enrolled in study (Age:61±1.5, F/M:12/7). As a result of the
evaluation of the physicians, 7 patients were treated with TheraSphere and 12
patients were treated with SIR-Sphere. Dose rate measurements were taken at the
stage of activity preparation, injection, radioactive wastes and discharge of
patients via electronic dosimeter (ED). Results: The staff was exposed to dose
rate of 1,3.10-4 μSv/MBq.h during activity preparation stage, 2,4.10-4 μSv/MBq.h in injection
stage for Therapshere application. For SIR-spheres application, the staff was
exposed to dose rate of 24,5.10-4 μSv/MBq.h during activity preparation
stage, 10,1.10-4 μSv/MBq.h in injection stage. The average amount of
dose received per operation was calculated 0.92±0.48 μSv in TheraSphere and
3.22±0.89 μSv in SIR-Spheres. For discharge of the patients, the average dose
rate recorded from 1 m was found 4±0.28 μGy.h-1 for TheraSphere and
3.2±0.15 μGy.h-1 for SIR-Spheres. The dose rate of radioactive
wastes measured from the surface of the container which contained the
radioactive wastes generated after the application was 0.5±0.1 μSv.h-1
for TheraSphere and 1.1±0.08 μSv.h-1 for SIR-Spheres. Conclusion: It
is emphasized that Y-90 Therasphere application provides radiation safety more
than SIR-Spheres because of its closed system, even so both applications shows
low dose rate around the patient and short-term storage of radioactive wastes
after application would be sufficient.
Влияние чувствительности к человеку на принятие позиций взаимодействия студентами
Authors: Маралов Владимир Георгиевич , Романюк Лариса Валерьевна 
Published: October 2018

<p>В статье анализируются психологические особенности влияния чувствительности к человеку на принятие студентами позиций взаимодействия: принуждения, манипулирования, ненасилия, невмешательства. Актуальность проблемы обусловлена значимостью выявления факторов, механизмов и условий формирования у студентов — будущих специалистов сферы психолого-педагогического сопровождения способности к ненасильственному взаимодействию с людьми. </p><p>Материалами анализа выступили результаты опроса на выявление уровней выраженности позиций взаимодействия и чувствительности к людям. Были применены методы математической обработки данных, в т. ч. критерий φ* — угловое преобразование Фишера.</p><p> В исследовании 2018 г. приняли участие 118 студентов психолого-педагогических специальностей Московского гуманитарного университета и Череповецкого государственного университета. Средний возраст испытуемых — 19,5 года.</p><p>Было установлено, что студенты с высоким уровнем чувствительности к человеку чаще принимают позицию ненасилия (63%), реже — позиции принуждения (25%) и невмешательства (19%). Студенты же с низким уровнем чувствительности к человеку чаще принимают позиции невмешательства (59%) и позицию принуждения (52%) и практически не используют позицию ненасилия (3%). Позиция манипулирования не обнаружила существенной связи с уровнями чувствительности к человеку.</p><p>Делается вывод о значимости формирования у студентов чувствительности к человеку как фактора, способствующего принятию личностью позиции ненасилия. Полученные результаты могут быть использованы в процессе разработки специальных программ по целенаправленному формированию у студентов — будущих специалистов сферы психолого-педагогического сопровождения способности к ненасильственному взаимодействию.</p>