bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating individual level plant traits at scale
Authors: Marconi Sergio , Graves Sarah J. , Weinstein Ben. G. , Bohlman Stephanie , White Ethan P. 
Published: February 2019

AbstractFunctional ecology has increasingly focused on describing ecological communities based on their traits (measurable features affecting individuals fitness and performance). Analyzing trait distributions within and among forests could significantly improve understanding of community composition and ecosystem function. Historically, data on trait distributions are generated by (1) collecting a small number of leaves from a small number of trees, which suffers from limited sampling but produces information at the fundamental ecological unit (the individual); or (2) using remote sensing images to infer traits, producing information continuously across large regions, but as plots (containing multiple trees of different species) or pixels, not individuals. Remote sensing methods that identify individual trees and estimate their traits would provide the benefits of both approaches, producing continuous large-scale data linked to biological individuals. We used data from the National Ecological Observatory Network (NEON) to develop a method to scale up functional traits from 160 trees to the millions of trees within the spatial extent of two NEON sites. The pipeline consists of three stages: 1) image segmentation, to identify individual trees and estimate structural traits; 2) ensemble of models to infer leaf mass area (LMA), nitrogen, carbon, and phosphorus content using hyperspectral signatures, and DBH from allometry; and 3) predictions for segmented crowns for the full remote sensing footprint at the NEON sites.The R2values on held out test data ranged from 0.41 to 0.75 on held out test data. The ensemble approach performed better than single partial least squares models. Carbon performed poorly compared to other traits (R2of 0.41). The crown segmentation step contributed the most uncertainty in the pipeline, due to over-segmentation. The pipeline produced good estimates of DBH (R2of 0.62 on held out data). Trait predictions for crowns performed significantly better than comparable predictions on pixels, resulting in improvement of R2on test data of between to 0.26. We used the pipeline to produce individual level trait data for ∼5 million individual crowns, covering a total extent of ∼360 km2. This large dataset allows testing ecological questions on landscape scales, revealing that foliar traits are correlated with structural traits and environmental conditions.
Maxdeletion destabilizes MYC protein and abrogates Eμ-Myclymphomagenesis
Authors: Mathsyaraja Haritha , Freie Brian , Cheng Pei-Feng , Babaeva Ekaterina , Janssens Derek , Henikoff Steven , Eisenman Robert N 
Published: February 2019

ABSTRACTAlthough MAX is widely regarded as an obligate dimerization partner for MYC, its function in normal development and neoplasia is not well defined. We show that B-cell specific deletion ofMaxhas a surprisingly modest effect on B-cell development but completely abrogates Eµ-Mycdriven lymphomagenesis. In both contexts, MAX loss leads to a significant reduction in MYC protein levels. This outcome is associated with the downregulation of numerous transcriptional targets of MAX including a subset that regulate MYC stability. Reduction in MYC protein levels is also observed in multiple cell lines treated with a MYC-MAX dimerization inhibitor. Our work uncovers a layer ofMycautoregulation critical for lymphomagenesis yet partly dispensable for normal lymphoid development.
Opportunistic interactions on Fe0 between methanogens and acetogens from a climate lake
Authors: Palacios Paola Andrea , Rotaru Amelia-Elena 
Published: February 2019

AbstractMicrobial-induced corrosion has been extensively studied in pure cultures. However, Fe0 corrosion by complex environmental communities, and especially the interplay between microbial physiological groups, is still poorly understood. In this study, we combined experimental physiology and metagenomics to explore Fe0-dependent microbial interactions between physiological groups enriched from anoxic climate lake sediments. Then, we investigated how each physiological group interacts with Fe0. We offer evidence for a new interspecies interaction during Fe0 corrosion. We showed that acetogens enhanced methanogenesis but were negatively impacted by methanogens (opportunistic microbial interaction). Methanogens were positively impacted by acetogens. In the metagenome of the corrosive community, the acetogens were mostly represented by Clostridium and Eubacterium, the methanogens by Methanosarcinales, Methanothermobacter and Methanobrevibacter. Within the corrosive community, acetogens and methanogens produced acetate and methane concurrently, however at rates that cannot be explained by abiotic H2-buildup at the Fe0 surface. Thus, microbial-induced corrosion might have occurred via a direct or enzymatically mediated electron uptake from Fe0. The shotgun metagenome of Clostridium within the corrosive community contained several H2-releasing enzymes including [FeFe]-hydrogenases, which could boost Fe0-dependent H2-formation as previously shown for pure culture acetogens. Outside the cell, acetogenic hydrogenases could become a common good for any H2/CO2-consuming member in the microbial community including methanogens that rely on Fe0 as a sole energy source. However, the exact electron uptake mechanism from Fe0 remains to be unraveled.
Aging alters the role of basolateral amygdala in intertemporal choice
Authors: Hernandez Caesar M. , Orsini Caitlin A. , Labiste Chase C. , Wheeler Alexa-Rae , Ten Eyck Tyler W. , Bruner Matthew M. , Sahagian Todd J. , Harden Scott W. , Frazier Charles J. , Setlow Barry , Bizon Jennifer L. 
Published: February 2019

AbstractAging is associated with an increased ability to delay gratification. Moreover, even when matched for performance, young and aged subjects recruit distinct brain circuitry to complete complex cognitive tasks. Experiments herein used an optogenetic approach to test whether altered recruitment of the basolateral amygdala (BLA), a brain region implicated in valuation of reward-cost contingencies, contributes to age-dependent changes in intertemporal decision making. BLA inactivation while rats deliberated prior to choices between options that yielded either small, immediate or large, delayed rewards rendered both young and aged rats less impulsive. In contrast, BLA inactivation after choices were made (during evaluation of choice outcomes) rendered young rats more impulsive but had no effect in aged rats. These data define multiple, temporally-discrete roles for BLA circuits in intertemporal decision making and implicate altered recruitment of BLA in the elevated preference for delayed rewards that is characteristic of advanced age.Impact StatementBasolateral amygdala (BLA) performs multiple, temporally-discrete functions during intertemporal decision making. Differential engagement of BLA contributes to the enhanced ability to delay gratification that is characteristic of advanced ages.
Developmental plasticity in metabolism but not in energy reserve accumulation in a seasonally polyphenic butterfly
Authors: Kivelä Sami M. , Gotthard Karl , Lehmann Philipp 
Published: February 2019

AbstractThe evolution of seasonal polyphenisms (discrete phenotypes in different annual generations) associated with alternative developmental pathways of diapause (overwintering) and direct development is favoured in temperate insects. Seasonal life history polyphenisms are common and include faster growth and development under direct development than diapause. However, the physiological underpinnings of this difference remain poorly known despite its significance for understanding the evolution of polyphenisms. We measured respiration and metabolic rates through the penultimate and final larval instars in the butterflyPieris napiand show that directly developing larvae grew and developed faster and had a higher metabolic rate than larvae entering pupal diapause. The metabolic divergence appeared only in the final instar, that is, after the induction of developmental pathway that takes place in the penultimate instar inP. napi. The accumulation of fat reserves during the final larval instar was similar under diapause and direct development, which was unexpected as diapause is predicted to select for exaggerated reserve accumulation. This suggests that overwinter survival may be more dependent on metabolic suppression during diapause than the size of energy reserves. The results, nevertheless, demonstrate that physiological changes coincide with the divergence of life histories between the alternative developmental pathways, thus elucidating the proximate basis of seasonal life history polyphenisms.Summary statementThe switch between diapause and direct development results in developmental pre-diapause plasticity in life history and metabolism but not in reserve accumulation in a seasonally polyphenic butterfly.
Using extracellular low frequency signals to improve the spike sorting of cerebellar complex spikes
Authors: Zur Gil , Joshua Mati 
Published: February 2019

AbstractThe challenge of spike sorting has been addressed by numerous electrophysiological studies. These methods tend to focus on the information conveyed by the high frequencies, but ignore the potentially informative signals at lower frequencies. Activation of Purkinje cells in the cerebellum by input from the climbing fibers results in a large amplitude dendritic spike concurrent with a high frequency burst known as a complex spike. Due to the variability in the high frequency component of complex spikes, previous methods have struggled to sort these complex spikes in an accurate and reliable way. However, complex spikes have a prominent extracellular low frequency signal generated by the input from the climbing fibers. We exploited this to improve complex spike sorting by applying Principal Component Analysis (PCA) on the low frequencies of the signal and show that the low frequency first PC achieves a better separation of the complex spikes from noise. The low frequency data are more effective in detecting events entering into the analysis, and therefore can be harnessed to analyze the data with a larger signal to noise ratio. These two advantages make our method more effective for complex spike sorting. Our characterization of the dendritic low frequency components of complex spikes can be applied in other studies to gain insights into processing in the cerebellum.
TGFβ signaling curbs cell fusion and muscle regeneration
Authors: Girardi Francesco , Taleb Anissa , Giordani Lorenzo , Cadot Bruno , Datye Asiman , Ebrahimi Majid , Gamage Dilani G. , Millay Douglas P. , Gilbert Penney M , Grand Fabien Le 
Published: February 2019

SummaryFusion of muscle progenitor cells is necessary for skeletal muscle development and repair. Cell fusion is a multistep process involving cell migration, adhesion, membrane remodeling and actin-nucleation pathways to generate multinucleated myotubes. While the cellular and molecular mechanisms promoting muscle cell fusion have been intensely investigated in recent years, molecular brakes restraining cell–cell fusion events to control syncytia formation have remained elusive. Here, we show that transforming growth factor beta (TGFβ) signaling is active in adult muscle cells throughout the fusion process and reduce muscle cell fusion independently of the differentiation step. In contrast, inhibition of TGFβ signaling enhances cell fusion and promotes branching between myotubes. Pharmacological modulation of the pathway in vivo perturbs muscle regeneration after injury. Exogenous addition of TGFβ protein results in a loss of muscle function while inhibition of the TGFβ pathway induces the formation of giant myofibres. Transcriptome analyses and functional assays revealed that TGFβ acts on actin dynamics and reduce cell spreading through modulation of actin-based protrusions. Together our results reveal a signaling pathway that limits mammalian myoblast fusion and add a new level of understanding to the molecular regulation of myogenesis.
The effect of environmental enrichment on behavioral variability depends on genotype, behavior, and type of enrichment
Authors: Akhund-Zade Jamilla , Ho Sandra , O’Leary Chelsea , de Bivort Benjamin 
Published: February 2019

AbstractNon-genetic individuality in behavior, also termed intragenotypic variability, has been observed across many different organisms. A potential cause of intragenotypic variability is sensitivity to minute environmental differences during development, even as major environmental parameters are kept constant. Animal enrichment paradigms often include the addition of environmental diversity, whether in the form of social interaction, novel objects, or exploratory opportunities. Enrichment could plausibly affect intragenotypic variability in opposing ways: it could cause an increase in variability due to the increase in microenvironmental variation, or a decrease in variability due to elimination of aberrant behavior as animals are taken out of impoverished laboratory conditions. In order to test our hypothesis, we assayed five isogenic Drosophila melanogaster lines raised in control and mild enrichment conditions, and one isogenic line under both mild and intense enrichment conditions. We compared the mean and variability of six behavioral metrics between our enriched fly populations and the laboratory housing control. We found that enrichment often caused a small increase in variability across most of our behaviors, but that the ultimate effect of enrichment on both behavioral means and variabilities was highly dependent on genotype and its interaction with the particular enrichment treatment. Our results support previous work on enrichment that presents a highly variable picture of its effects on both behavior and physiology.
Effect of Maxillary Expansion and Protraction on the Oropharyngeal Airway in Individuals with Non-syndromic Cleft Palate with or without Cleft Lip
Authors: Alrejaye Najla , Gao Jonathan , Oberoi Snehlata 
Published: February 2019

AbstractIntroductionThe aim of this study was to evaluate three dimensionally the effect of the combined maxillary expansion and protraction treatment on oropharyngeal airway in children with non-syndromic cleft palate with or without cleft lip (CP/L).MethodsCBCT data of 18 preadolescent individuals (ages, 8.4 ± 1.7 years) with CP/L, who underwent Phase I orthodontic maxillary expansion with protraction, were compared before and after treatment. The average length of treatment was 24.1± 7.6 months. The airway volume and minimal cross-sectional area (MCA) were determined using 3DMD Vultus imaging software with cross-sectional areas calculated for each 2-mm over the entire length of the airway. A control group of 9 preadolescent individuals (ages, 8.7 ± 2.6 years) with CP/L was used for comparison.ResultsThere was a statistically significant increase in pharyngeal airway volume after phase I orthodontic treatment in both groups, however, there was no statistically significant change in minimal cross-sectional area in neither study nor control group.ConclusionThe findings showed that maxillary expansion and protraction did not have a significant effect on increasing oropharyngeal volume and MCA in patients with CP/L.
Evolution of interface binding strengths in simplified model of protein quaternary structure
Authors: Leonard Alexander S. , Ahnert Sebastian E. 
Published: February 2019

AbstractThe self-assembly of proteins into protein quaternary structures is of fundamental importance to many biological processes, and protein misassembly is responsible for a wide range of proteopathic diseases. In recent years, abstract lattice models of protein self-assembly have been used to simulate the evolution and assembly of protein quaternary structure, and to provide a tractable way to study the genotype-phenotype map of such systems. Here we generalize these models by representing the interfaces as mutable binary strings. This simple change enables us to model the evolution of interface strengths, interface symmetry, and deterministic assembly pathways. Using the generalized model we are able to reproduce two important results established for real protein complexes: The first is that protein assembly pathways are under evolutionary selection to minimize misassembly. The second is that the assembly pathway of a complex mirrors its evolutionary history, and that both can be derived from the relative strengths of interfaces. These results demonstrate that the generalized lattice model offers a powerful new framework for the study of protein self-assembly processes and their evolution.
Can early assessment of hand grip strength in elderly hip fracture patients predict functional outcome?
Authors: Selakovic Ivan , Dubljanin-Raspopovic Emilija , Markovic-Denic Ljiljana , Marusic Vuk , Cirkovic Andja , Kadija Marko , Tomanovic-Vujadinovic Sanja , Tulic Goran 
Published: February 2019

AbstractDecreased muscle strength is not only a risk factor for hip fracture in elderly patients, but plays a role in recovery of physical function. Our aim was to assess the role of grip strength measured early after hip fracture, and classified according to the EWGSOP2 criteria in predicting short- and long-term functional recovery. One hundred ninety-one patients with acute hip fracture consecutively admitted to an orthopaedic hospital have been selected. A multidimensional geriatric assessment evaluating sociodemographic variables, cognitive status, functional status and quality of life prior to fracture, as well as perioperative variables were performed. Follow-ups at 3 and 6 months after surgery were carried out to evaluate functional recovery. Multivariate regression models were used to assess the predictive role of handgrip strength. The mean age of the participants was 80.3 ±6.8 years. Thirty-five percent of our patients with clinically relevant hand grip strength weakness were significantly older, more often female, had a lower BMI, and were of worse physical health. They also had a lower cognitive level, lower Barthel index, and lower EQ5D scores before fracture. Multivariate regression analysis adjusted for age and gender revealed that hand grip weakness was an independent predictor of worse functional outcome at 3 and 6 months after hip fracture for both genders and in all age populations. Our study supports the prognostic role of hand grip strength assessed at hospital admission in patients with hip fracture. Thus, clinicians should be encouraged to include hand grip assessment in their evaluation of hip fracture patients in the acute setting in order to optimize treatment of high-risk individuals.
Knowledge Gaps of STIs in Africa; Systematic review
Authors: Badawi M M , Salah-Eldin M A , Idris A B , Hasabo E A , Osman Z H , Osman W M 
Published: February 2019

AbstractSexually Transmitted Infections (STIs) are ambiguous burden of tremendous health, social and economic consequences, The current systematic review was conducted in order to determine awareness and knowledge of Africans of sexually transmitted infections, not only concerning HIV/AIDS, but also other STIs such as, gonorrhea, syphilis, HBV, HCV and HPV. A systematic review of the literature was conducted, studies were retrieved and selected after they fulfilled the inclusion criteria and passed the assessment procedure. related data was extracted, quantitative analysis was conducted among participants who responded to questions related to HIV, HBV, HCV, HPV or STIs knowledge, sensitivity analysis as well as subgroup analysis were also conducted. Seventy four articles addressing knowledge among 35 African countries were included and 136 questions were analyzed and synthesized. The question Using condom will reduce HIV transmission?” was answered by 1,799,374 Africans in 35 countries, 66.82% [95% Cl; 62.65, 70.98] answered yes. While the question “Is sexual contact a possible route of HBV transmission?” was answered by 7,490 participants in 5 countries; 42.58% [95% Cl; 20.45, 64.71] answered yes. The differences observed among populations are highlighting the possibility for containment and control by directing light toward specific populations or countries as well as addressing specific awareness knowledge to ensure that the general as well as the related specific preventive awareness knowledge is improved.
Association Between The Posterior Part Of The Circle Of Willis And Vertebral Artery Hypoplasia
Authors: Gaigalaite Virginija , Dementaviciene Jurate , Vilimas Augenijus , Kalibatiene Danute 
Published: February 2019

AbstractBackgroundIt is not clear whether the configuration of the posterior part of the circle of Willis (CW) depends on the proximal part of the vertebrobasilar system. Our aim is to evaluate the posterior part of CW in association with different size of vertebral arteries (VA) in subjects free from stroke and TIA.Materials and methodsThe present study was based on a sample of 923 subjects free from stroke and TIA who were examined from 2013 through 2018. All the participants underwent MRA examination. The duplex ultrasonographic examination of the extracranial arteries (vertebral and carotid) was performed. VA was defined as hypoplastic (VAH) when VA diameter in the entire course was less than 2.5 mm. We classified the posterior communicating arteries (PCoA) as presence PCoA, absence/hypoplastic PCoA and fetal CW (FCW). The comparison of the posterior part of CW was made in subjects with normal VA and VAH of a different degree (communicating with basilar artery (VAH-BA) and not communicating with the basilar artery and terminating in PICA, neck or aplasia (VAH-PICA)).ResultsFCW was found in 15.9% of subjects, bilaterally – in 2.3 %. The coexisting VAH was more common in subjects with FCW rather than in those with adult CW (respectively, 28.6% and 13.4%, p<0.001). Aplasia of A1 of the anterior cerebral artery, i.e. blood flow redistribution in the anterior part of anterior circulation in the majority of cases (in 6 of 7 cases) was found ipsilaterally to FCW. FCW was recorded in 50% of the subjects with VA - PICA in comparison with 13.5% of those with normal VA and 22.8% with VAH - BA, p<0.005. On the contrary, absence/hypoplasia of both PCoA was mostly found in the group with normal VA in comparison with VAH-BA and VAH-PICA (accordingly, 50.7%, 38.6% and 12.5%, p<0.01).ConclusionIndividuals with VAH have a different pattern of the posterior part of CW in comparison with those with normal VA. With the increasing degree of VAH, the proportion of FCW increases, while the proportion of absence/hypoplastic of both PCoA decreases.
A Machine Learning Approach for Long-Term Prognosis of Bladder Cancer based on Clinical and Molecular Features
Authors: Song Qingyuan , Seigne John D. , Schned Alan R. , Kelsey Karl T. , Karagas Margaret R. , Hassanpour Saeed 
Published: February 2019

AbstractImproving the consistency and reproducibility of bladder cancer prognoses necessitates the development of accurate, predictive prognostic models. Current methods of determining the prognosis of bladder cancer patients rely on manual decision-making, including factors with high intra- and inter-observer variability, such as tumor grade. To advance the long-term prediction of bladder cancer prognoses, we developed and tested a computational model to predict the 10-year overall survival outcome using population-based bladder cancer data, without considering tumor grade classification. The resulted predictive model demonstrated promising performance using a combination of clinical and molecular features, and was also strongly related to patient overall survival in Cox models. Our study suggests that machine learning methods can provide reliable long-term prognoses for bladder cancer patients, without relying on the less consistent tumor grade. If validated in clinical trials, this automated approach could guide and improve personalized management and treatment for bladder cancer patients.