bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting Global Forest Reforestation Potential
Authors: Crowther Thomas W. , Glick Henry , Maynard Daniel , Ashley-Cantello Will , Evans Tom , Routh Devin 
Published: November 2017

Executive SummaryForests are important determinants of the carbon cycle, and they provide countless ecosystem services to support billions of people worldwide. Global-scale forest restoration is one of our most effective weapons in the fight against biodiversity loss, rural poverty and climate change. In this report, we generate a spatial map of tree density within the potential forest restoration areas delineated by the IUCN/WRI’s “Atlas of Forest Landscape Restoration Opportunities” to estimate the potential number of trees that could be restored at a global scale. We also estimate the number of trees that might be saved by avoiding deforestation in currently forested areas.We show that the restoration areas have the capacity to support a total of 1.33 trillion trees. However, given that a considerable proportion of these areas already contain forests, we estimate that 589 billion new trees (larger than 10 cm diameter) could be restored within these areas, which would have the potential to store 65–91 Gigatonnes of carbon after reaching forest maturation. These values will increase marginally over time, as deforestation is responsible for the removal of living trees within the restoration areas. However, if only 50% or 25% of the mosaic areas (the largest of the designated restoration types) are available for reforestation, this total number will fall to approximately 360, or 246 billion trees, respectively, with corresponding decreases in potential carbon storage. Given that anthropogenic carbon emissions are currently in the order of 9–12 Gigatonnes per year, effective global-scale restoration might potentially have a valuable impact on global-scale climate mitigation over the rest of this century.This report was produced with funding from WWF-UK as part of the Trillion Trees programme with the Wildlife Conservation Society and BirdLife International
Creating ethnicity-specific reference intervals for lab tests from EHR data
Authors: Rappoport Nadav , Paik Hyojung , Oskotsky Boris , Tor Ruth , Ziv Elad , Zaitlen Noah , Butte Atul J. 
Published: November 2017

AbstractThe results of clinical lab tests are an essential component of medical decision-making. To guide interpretation, test results are returned with reference intervals defined by the range in which 95% of values occur in healthy individuals. Clinical laboratories often set their own reference intervals to accommodate local population and instruments variations. This approach is costly and can be biased. We describe a novel data-driven method for using electronic health record data to extract healthy patients’ information to define reference intervals. We found that the distributions of many clinical lab tests differ among self-identified racial and ethnic groups (SIREs) in healthy patients. Finally, we derived SIRE-specific reference intervals and provide evidence that these intervals have clinical prognostic value. Specifically, we show that for two lab tests, serum creatinine level and hemoglobin A1C, SIRE-specific reference intervals are more predictive for need for dialysis and development type 2 diabetes than existing reference intervals.One Sentence SummaryA novel method for defining population-specific reference intervals of common clinical laboratory tests from electronical health records has better prognostic value than existing reference intervals.
A mid-level organization of the ventral stream
Authors: Long Bria , Yu Chen-Ping , Konkle Talia 
Published: November 2017

ABSTRACTHuman object-selective cortex shows a large-scale organization characterized by the high-level properties of both animacy and object-size. To what extent are these neural responses explained by primitive perceptual features that distinguish animals from objects and big objects from small objects? To address this question, we used a texture synthesis algorithm to create a novel class of stimuli—texforms—which preserve some mid-level texture and form information from objects while rendering them unrecognizable. We found that unrecognizable texforms were sufficient to elicit the large-scale organizations of object-selective cortex along the entire ventral pathway. Further, the structure in the neural patterns elicited by texforms was well predicted by curvature features and by intermediate layers of a deep convolutional neural network, supporting the mid-level nature of the representations. These results provide clear evidence that a substantial portion of ventral stream organization can be accounted for by coarse texture and form information, without requiring explicit recognition of intact objects.SIGNIFICANCE STATEMENTWhile neural responses to object categories are remarkably systematic across human visual cortex, the nature of these responses been hotly debated for the past 20 years. In this paper, a new class of stimuli (“texforms”) is used to examine how mid-level features contribute to the large-scale organization of the ventral visual stream. Despite their relatively primitive visual appearance, these unrecognizable texforms elicited the entire large-scale organizations of the ventral stream by animacy and object size. This work demonstrates that much of ventral stream organization can be explained by relatively primitive mid-level features, without requiring explicit recognition of the objects themselves.
CalR: A Web-based Analysis Tool for Indirect Calorimetry Experiments
Authors: Mina Amir I. , LeClair Raymond A. , LeClair Katherine B. , Cohen David E. , Lantier Louise , Banks Alexander S. 
Published: November 2017

AbstractWe report a web-based tool for analysis of indirect calorimetry experiments which measure physiological energy balance. CalR easily imports raw data files, generates plots, and determines the most appropriate statistical tests for interpretation. Analysis with the general linear model (which includes ANOVA and ANCOVA) allows for flexibility to interpret experiments of obesity and thermogenesis. Users may also produce standardized output files of an experiment which can be shared and subsequently re-evaluated using CalR. This framework will provide the transparency necessary to enhance consistency and reproducibility in experiments of energy expenditure. CalR analysis software will greatly increase the speed and efficiency with which metabolic experiments can be organized, analyzed according to accepted norms, and reproduced—and will likely become a standard tool for the field. CalR is accessible at https://CalR.bwh.harvard.edu.Graphical Abstract
Chemical genomic guided engineering of gamma-valerolactone tolerant yeast
Authors: Bottoms Scott , Dickinson Quinn , McGee Mick , Hinchman Li , Higbee Alan , Hebert Alex , Serate Jose , Xie Dan , Zhang Yaoping , Coon Joshua J , Myers Chad L , Landick Robert , Piotrowski Jeff S 
Published: November 2017

AbstractBackgroundGamma valerolactone (GVL) is a promising technology for degradation of biomass for biofuel production; however, GVL has adverse toxicity effects on fermentative microbes. Using a combination of chemical genomics and chemical proteomics we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast.ResultsChemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate phenolic acids to vinyl derivatives, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain.ConclusionsWe found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol content in cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain. This strain represents a xylose fermenting yeast specifically tailored to GVL produced hydrolysates
Interdependent and separable functions ofC. elegansMRN-C complex members couple formation and repair of meiotic DSBs
Authors: Girard Chloe , Roelens Baptiste , Zawadzki Karl A. , Villeneuve Anne M. 
Published: November 2017

AbstractFaithful inheritance of genetic information through sexual reproduction relies on the formation of crossovers between homologous chromosomes during meiosis, which in turn relies on the formation and repair of numerous double-strand DNA breaks (DSBs). As DSBs pose a potential threat to the genome, mechanisms that ensure timely and error-free DSB repair are crucial for successful meiosis. Here we identify NBS-1, theCaenorhabditis elegansortholog of the NBS1 subunit of the conserved MRE11-RAD50-NBS1/Xrs2 (MRN) complex, as a key mediator of DSB repair via homologous recombination (HR) during meiosis. Loss ofnbs-1leads to: severely reduced loading of recombinase RAD-51, ssDNA binding protein RPA and pro-crossover factor COSA-1 during meiotic prophase progression; aggregated and fragmented chromosomes at the end of meiotic prophase; and 100% progeny lethality. These phenotypes reflect a role for NBS-1 in processing of meiotic DSBs for HR that is shared with its interacting partners MRE-11-RAD-50 and COM-1 (ortholog of Com1/Sae2/CtIP). Unexpectedly, in contrast to MRE-11 and RAD-50, NBS-1 is not required for meiotic DSB formation. Meiotic defects of thenbs-1mutant are partially suppressed by abrogation of the non-homologous end-joining (NHEJ) pathway, indicating a role for NBS-1 in antagonizing NHEJ during meiosis. Our data further reveal that NBS-1 and COM-1 play distinct roles in promoting HR and antagonizing NHEJ. We propose a model in which different components of the MRN-C complex work together to couple meiotic DSB formation with efficient and timely engagement of HR, thereby ensuring crossover formation and restoration of genome integrity prior to the meiotic divisions.Significance StatementDouble-strand breaks (DSBs) are deleterious DNA lesions, and impairment of the DSB repair machinery can lead to devastating diseases such as the Nijmegen Breakage Syndrome (NBS). During meiosis, DSBs represent a "necessary evil": they are required to promote formation of crossovers between homologous chromosomes. Crossovers in turn ensure correct chromosome inheritance during gamete formation, which is essential for viability and normal development of embryos. During meiosis, numerous DSBs are actively created, so meiotic cells must ensure that all breaks are properly repaired to ensure crossover formation and restore genomic integrity. Here we identifyC. elegansNBS-1 as essential to properly process meiotic DSBs, both to promote crossover formation and antagonize an error-prone DSB repair pathway, thereby ensuring faithful chromosome inheritance.
Enhanced deviant responses in patterned relative to random sound sequences
Authors: Southwell Rosy , Chait Maria 
Published: November 2017

AbstractHow are brain responses to deviant events affected by the statistics of the preceding context? We recorded electroencephalography (EEG) brain responses to frequency deviants in matched, regularly-patterned (REG) versus random (RAND) tone-pip sequences. Listeners were naïve and distracted by an incidental visual task. Stimuli were very rapid so as to limit conscious reasoning about the sequence order and tap automatic processing of regularity.Deviants within REG sequences evoked a substantially larger response (by 71%) than matched deviants in RAND sequences from 80 ms after deviant onset. This effect was underpinned by distinct sources in right temporal pole and orbitofrontal cortex in addition to the standard bilateral temporal and right pre-frontal network for generic frequency deviance-detection. These findings demonstrate that the human brain rapidly acquires a detailed representation of regularities within the sensory input and evaluates incoming information according to the context established by the specific pattern.
Prediction error induced motor contagions in human behaviors
Authors: Ikegami Tsuyoshi , Ganesh Gowrishankar , Takeuchi Tatsuya , Nakamoto Hiroki 
Published: November 2017

AbstractMotor contagions refer to implicit effects on one’s actions induced by observation of other’s actions. Motor contagions are believed to be induced simply by action observation and cause an observer’s action to become similar to the observed action. In contrast, here we report a new motor contagion that is induced only when the observation is accompanied by prediction errors-differences between actions one observes and those he/she predicts or expects. Moreover, this contagion may not manifest as a similarity between one’s own and observed actions. In our experiment, observation of the same action induced distinct motor contagions, depending on whether prediction errors are present or not. In the absence of prediction errors, similarly to previous reports, participants’ actions changed to become similar to the observed action, while in the presence of prediction errors, their actions changed to diverge away from it. Our results suggest distinct effects of action observation and action prediction on human actions.
Sporulation-specific cell division defects inylmEmutants ofStreptomyces coelicolorare rescued by additional deletion ofylmD
Authors: Zhang Le , Willemse Joost , Hoskisson Paul A. , van Wezel Gilles P. 
Published: November 2017

ABSTRACTCell division during the reproductive phase of theStreptomyceslife-cycle requires tight coordination between synchronous formation of multiple septa and DNA segregation. One remarkable difference with most other bacterial systems is that cell division inStreptomycesis positively controlled by the recruitment of FtsZ by SsgB. Here we show that deletion ofylmD(SCO2081) orylmE(SCO2080), which lie in operon withftsZin thedcwcluster of actinomycetes, has major consequences for sporulation-specific cell division inStreptomyces coelicolor. Electron and fluorescence microscopy demonstrated thatylmEmutants have a highly aberrant phenotype with defective septum synthesis, and produce very few spores with low viability and high heat sensitivity. FtsZ-ring formation was also highly disturbed inylmEmutants. Deletion ofylmDhad a far less severe effect on sporulation. Interestingly, the additional deletion ofylmDrestored sporulation to theylmEnull mutant. YlmD and YlmE are not part of the divisome, but instead localize diffusely in aerial hyphae, with differential intensity throughout the sporogenic part of the hyphae. Taken together, our work reveals a function for YlmD and YlmE in the control of sporulation-specific cell division inS. coelicolor, whereby the presence of YlmD alone results in major developmental defects.
Percent amplitude of fluctuation: a simple measure for resting-state fMRI signal at single voxel level
Authors: Jia Xi-Ze , Ji Gong-Jun , Liao Wei , Lv Ya-Ting , Wang Jue , Wang Ze , Zhang Han , Liu Dong-Qiang , Zang Yu-Feng 
Published: November 2017

AbstractThe amplitude of low-frequency fluctuation (ALFF) measures resting-state functional magnetic resonance imaging (RS-fMRI) signal of each voxel. However, the unit of blood oxygenation level-dependent (BOLD) signal is arbitrary and hence ALFF is sensitive to the scale of raw signal. A well-accepted standardization procedure is to divide each voxel’s ALFF by the global mean ALFF. However, this makes the individual voxel’s ALFF dependent on the global mean. Although Fractional ALFF (fALFF), proposed as a ratio of the ALFF to the total amplitude within the full frequency band, offers possible solution of the standardization, it actually mixes with the fluctuation power within the full frequency band and thus cannot reveal the true amplitude characteristics of a given frequency band. We proposed a new standardized, stand-alone, single-voxel metrics for RS-fMRI, namely percent amplitude of fluctuation (PerAF). PerAF is an analog to the percent signal change that has been widely used in the task fMRI communities, which allows it to be a straightforward measurement of BOLD signal fluctuations during resting state. We further conducted a test-retest reliability analysis comparing the relevant metrics, which indicated that PerAF was generally more reliable than the ALFF and fALFF. In a real RS-fMRI application, we further demonstrated that with and without standardization by global mean PerAF yielded prominently different results when comparing eyes open with eyes closed resting conditions, suggesting that future study should provide both with and without global mean standardization. The above results suggest that PerAF is a more reliable, straightforward and promising measurement for voxelwise brain activity-based RS-fMRI studies. For prompting future application of PerAF, we also implemented this method into a user-friendly toolbox REST-PerAF.
Squid Ring Teeth Coated Mesh Improves Abdominal Wall Repair
Authors: Leberfinger Ashley N. , Hospodiuk Monika , Pena-Francesch Abdon , Ayan Bugra , Ozbolat Veli , Koduru Srinivas , Ozbolat Ibrahim T. , Demirel Melik C. , Ravnic, DO Dino J. 
Published: November 2017

ABSTRACTBackgroundHernia repair is a common surgical procedure with mesh often used. Current mesh materials have a high incidence of repair failures, due to poor tissue integration, and complications such as seroma and pain. Polypropylene (PP) mesh is the standard material in hernia repair secondary to its material durability; however, failures still approach 15%. In this first time animal study, we hypothesized that squid ring teeth (SRT), a biologically-derived high strength protein, coated polypropylene (SRT-PP) mesh, would offer enhanced tissue integration and strength compared to standard PP mesh, while proving biocompatibility for in vivo use.Materials and methodsPolypropylene mesh was coated with SRT. Mechanical properties and cell proliferation studies of the composite mesh were performed in vitro. Rats underwent inlay mesh implantation in an anterior abdominal wall defect model. Repair was assessed clinically and radiographically, with integration evaluated by histology and mechanical testing.ResultsCell proliferation was enhanced on SRT-PP composite mesh. This was corroborated by abdominal wall histology, dramatically diminished cranio-caudal mesh contraction, improved strength testing, and higher tissue failure strain following in vivo implantation. There was no increase in complications with SRT, with regard to seroma or visceral adhesion. No foreign body reactions were noted on liver histology.ConclusionSRT-PP mesh showed better tissue integration than PP mesh. SRT is a high strength protein that is applied as a coating to augment mesh-tissue integration leading to improvements in abdominal wall stability with potential to reduce re-intervention for failures.
Two-stage adaptation of inhibition mediates predictive sensitization in the retina
Authors: Kastner David B. , Ozuysal Yusuf , Panagiotakos Georgia , Baccus Stephen A. 
Published: November 2017

AbstractA critical function of the nervous system is the prediction of future sensory input. One such predictive computation is retinal sensitization, a form of short-term plasticity seen in multiple species that elevates local sensitivity following strong local stimulation. Here we perform a causal circuit analysis of retinal sensitization using simultaneous intracellular and multielectrode recording in the salamander. We show, using direct current injection into inhibitory sustained amacrine cells that a decrease in amacrine transmission is necessary, sufficient and occurs at the right time and manner to cause sensitization in ganglion cells. Because of neural dynamics and nonlinear pathways, a computational model is essential to explain how a change in steady inhibitory transmission causes sensitization. Whereas adaptation of excitation removes an expected result in order to transmit novelty, adaptation of inhibition provides a general mechanism to enhance the sensitivity to the sensory feature conveyed by an inhibitory pathway, creating a prediction of future input.
Using Biogeography to Assess Key Adaptation Strength in Two Bird Families
Authors: Halloway Abdel H. , Whelan Christopher J. , Şekercioğlu Çağan H. , Brown Joel S. 
Published: November 2017

AbstractAdaptations can be thought of as evolutionary technologies which allow an organism to exploit environments. Among convergent taxa, adaptations may be largely equivalent with the taxa operating in a similar set of environmental conditions, divergent with the taxa operating in different sets of environmental conditions, or superior with one taxon operating within an extended range of environmental conditions than the other. With this framework in mind, we sought to characterize the adaptations of two convergent nectarivorous bird families, the New World hummingbirds (Trochilidae) and Old World sunbirds (Nectariniidae), by comparing their biogeography. Looking at their elevational and latitudinal gradients, hummingbirds not only extend into but also maintain species richness in more extreme environments. We suspect that hummingbirds have a superior key adaptation that sunbirds lack, namely a musculoskeletal architecture that allows for hovering. Through biogeographic comparisons, we have been able to assess and understand adaptations as evolutionary technologies among two convergent bird families, a process that should work for most taxa.
Fractional Dynamics in Bioscience and Biomedicine and the Physics of Cancer
Authors: Nasrolahpour Hosein 
Published: November 2017

AbstractAlmost all phenomena and structures in nature exhibit some degrees of fractionality or fractality. Fractional calculus and fractal theory are two interrelated concepts. In this article we study the memory effects in nature and particularly in biological structures. Based on this fact that natural way to incorporate memory effects in the modeling of various phenomena and dealing with complexities is using of fractional calculus, in this article we present different examples in various branch of science from cosmology to biology and we investigate this idea that are we able to describe all of such these phenomena using the well-know and powerful tool of fractional calculus. In particular we focus on fractional calculus approach as an effective tool for better understanding of physics of living systems and organism and especially physics of cancer.