bluuebunny/crossref_metadata_2025_split huggingface dataset:
REPEATABILITY OF A DIGITAL IMAGING TECHNOLOGY FOR DENTAL PLAQUE QUANTITATION (QRAYCAM™ PRO) IN CURRENT, FORMER AND NEVER SMOKERS – STUDY PROTOCOL
Authors: Conte Gianluca , Pacino Sebastiano Antonio , Urso Toti , Emma Rosalia , Caponnetto Pasquale , Cibella Fabio , Polosa Riccardo 
Published: January 2021

ABSTRACTAlthough the detrimental health effects of smoking on human health are well described, the impact of smoking on dental plaque build-up lacks consistent records. This is because dental research on periodontal health has primarily relied on subjective indices with poor discriminatory power. Novel digital imaging techniques for the objective quantitation of dental plaque are now available. Quantitative Light-Induced Fluorescence (QLF) technology has been used in several studies for digital quantification and monitoring of dental plaque.The objective of the study is to quantitate and compare short- and long-term repeatability of dental plaque among current, former, and never smokers by using a high resolution, auto-focus, hand-held QLF scanner (QRayCam™ Pro; Inspektor Research Systems BV, Amsterdam, NL).Demonstration of good reproducibility of QLF technology with clear discrimination for dental plaque quantitation among current, former, and never smokers will pave the way to future application of this test for both medical and regulatory research applied not only to combustion-free tobacco products (e.g. e-cigarettes, heated tobacco products, oral tobacco/nicotine products, etc.) and smoking cessation medications, but also to consume care product for oral hygiene.
Toward Assessing Clinical Trial Publications for Reporting Transparency
Authors: Kilicoglu Halil , Rosemblat Graciela , Hoang Linh , Wadhwa Sahil , Peng Zeshan , Malički Mario , Schneider Jodi , Riet Gerben ter 
Published: January 2021

AbstractObjectiveTo annotate a corpus of randomized controlled trial (RCT) publications with the checklist items of CONSORT reporting guidelines and using the corpus to develop text mining methods for RCT appraisal.MethodsWe annotated a corpus of 50 RCT articles at the sentence level using 37 fine-grained CONSORT checklist items. A subset (31 articles) was double-annotated and adjudicated, while 19 were annotated by a single annotator and reconciled by another. We calculated inter-annotator agreement at the article and section level using MASI (Measuring Agreement on Set-Valued Items) and at the CONSORT item level using Krippendorff’s α. We experimented with two rule-based methods (phrase-based and section header-based) and two supervised learning approaches (support vector machine and BioBERT-based neural network classifiers), for recognizing 17 methodology-related items in the RCT Methods sections.ResultsWe created CONSORT-TM consisting of 10,709 sentences, 4,845 (45%) of which were annotated with 5,246 labels. A median of 28 CONSORT items (out of possible 37) were annotated per article. Agreement was moderate at the article and section levels (average MASI: 0.60 and 0.64, respectively). Agreement varied considerably among individual checklist items (Krippendorff’s α= 0.06-0.96). The model based on BioBERT performed best overall for recognizing methodology-related items (micro-precision: 0.82, micro-recall: 0.63, micro-F1: 0.71). Combining models using majority vote and label aggregation further improved precision and recall, respectively.ConclusionOur annotated corpus, CONSORT-TM, contains more fine-grained information than earlier RCT corpora. Low frequency of some CONSORT items made it difficult to train effective text mining models to recognize them. For the items commonly reported, CONSORT-TM can serve as a testbed for text mining methods that assess RCT transparency, rigor, and reliability, and support methods for peer review and authoring assistance. Minor modifications to the annotation scheme and a larger corpus could facilitate improved text mining models. CONSORT-TM is publicly available at https://github.com/kilicogluh/CONSORT-TM.Graphical abstractHighlightsWe constructed a corpus of RCT publications annotated with CONSORT checklist items.We developed text mining methods to identify methodology-related check-list items.A BioBERT-based model performs best in recognizing adequately reported items.A phrase-based method performs best in recognizing infrequently reported items.The corpus and the text mining methods can be used to address reporting transparency.
Phylogenomics of plant-associatedBotryosphaeriaceaespecies
Authors: Garcia Jadran , Lawrence Daniel P. , Morales-Cruz Abraham , Travadon Renaud , Minio Andrea , Hernandez-Martinez Rufina , Rolshausen Philippe E. , Baumgartner Kendra , Cantu Dario 
Published: January 2021

AbstractTheBotryosphaeriaceaeis a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the generaBotryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, andNeoscytalidiumattack a range of horticultural crops, but they vary in virulence and in their abilities to infect their hosts via different infection courts (flowers, green shoots, woody twigs). Isolates of seventeen species, originating from symptomatic apricot, grape, pistachio, and walnut were tested for pathogenicity to grapevine wood after four months of incubation in potted plants in the greenhouse. Results revealed significant variation in virulence in terms of the length of the internal wood lesions caused by these seventeen species. Phylogenomic comparisons of the seventeen species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors involved in toxin production and mobilization, wood degradation, and nutrient uptake. Statistical analyses of the evolution of the size of gene families revealed expansions of secondary metabolism and transporter gene families inLasiodiplodiaand of secreted cell wall degrading enzymes (CAZymes) inBotryosphaeriaandNeofusicoccumgenomes. In contrast,Diplodia, Dothiorella, andNeoscytalidiumgenerally showed a contraction in the number of members of these gene families. Overall, species with expansions of gene families, such as secreted CAZymes, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of theBotryosphaeriaceae.
A simple method for comparing peripheral and central color vision by means of two smartphones
Authors: Rozhkova Galina I. , Belokopytov Alexander V. , Gracheva Maria A. , Ershov Egor I. , Nikolaev Petr P. 
Published: January 2021

AbstractInformation on peripheral color perception is far from being sufficient since it was predominantly obtained using small stimuli, limited ranges of eccentricities, and sophisticated experimental conditions. Our purpose was to consider a possibility of facilitating technical realization of the classical method of asymmetric color matching (ACM) developed by Moreland and Cruz (1959) for assessing appearance of color stimuli in the peripheral visual field (VF). We adopted the ACM method by employing two smartphones to implement matching procedure at various eccentricities. Although smartphones were successfully employed in vision studies, we are aware that some photometric parameters of smartphone displays are not sufficiently precise to ensure accurate color matching in foveal vision; moreover, certain technical characteristics of commercially available devices are variable. In the present study we provide evidence that, despite these shortages, smartphones can be applied for general and wide investigations of the peripheral vision. In our experiments, the smartphones were mounted on a mechanical perimeter to simultaneously present colored stimuli foveally and peripherally. Trying to reduce essential discomfort and fatigue experienced by most observers in peripheral vision studies, we did not apply bite bars, pupil dilatation, and Maxwellian view. The ACM measurements were performed without prior training of observers and in a wide range of eccentricities, varying between 0 and 95°. Color appearance was measured in the HSV color space coordinates as a function of eccentricity and stimulus luminance. We demonstrate that our easy-to-conduct method provides a reliable means to estimate color appearance in the peripheral vision and to assess inter-individual differences.
Somatic Depolarization Enhances Hippocampal CA1 Dendritic Spike Propagation and Distal Input Driven Synaptic Plasticity
Authors: Bock Tobias , Siegelbaum Steven A. 
Published: January 2021

AbstractSynaptic inputs that target distal regions of neuronal dendrites can often generate local dendritic spikes that can amplify synaptic depolarization, induce synaptic plasticity, and enhance neuronal output. However, distal dendritic spikes are subject to significant attenuation by dendritic cable properties, and often produce only a weak subthreshold depolarization of the soma. Nonetheless, such spikes have been implicated in memory storage, sensory perception and place field formation. How can such a weak somatic response produce such powerful behavioral effects? Here we use dual dendritic and somatic recordings in acute hippocampal slices to reveal that dendritic spike propagation, but not spike initiation, is strongly enhanced when the somatic resting potential is depolarized, likely as a result of increased inactivation of A-type K+channels. Somatic depolarization also facilitates the induction of a form of dendritic spike driven heterosynaptic plasticity that enhances memory specificity. Thus, the effect of somatic membrane depolarization to enhance dendritic spike propagation and long-term synaptic plasticity is likely to play an important role in hippocampal-dependent spatial representations as well as learning and memory.
A simple explanation for declining temperature sensitivity with warming
Authors: Wolkovich E. M. , Auerbach J. L. , Chamberlain C. J. , Buonaiuto D. M. , Ettinger A. K. , Morales-Castilla I. , Gelman A. 
Published: January 2021

AbstractTemperature sensitivity—the magnitude of a biological response per °C—is a fundamental concept across scientific disciplines, especially biology, where temperature determines the rate of many plant, animal and ecosystem processes. Recently, a growing body of literature in global change biology has found temperature sensitivities decline as temperatures rise (Fuet al., 2015; Güsewell et al., 2017; Piao et al., 2017; Chen et al., 2019; Dai et al., 2019). Such observations have been used to suggest climate change is reshaping biological processes, with major implications for forecasts of future change. Here we present a simple alternative explanation for observed declining sensitivities: the use of linear models to estimate non-linear temperature responses. We show how linear estimates of sensitivities will appear to decline with warming for events that occur after a cumulative thermal threshold is met—a common model for many biological events. Corrections for the non-linearity of temperature response in simulated data and long-term phenological data from Europe remove the apparent decline. Our results show that rising temperatures combined with linear estimates based on calendar time produce observations of declining sensitivity—without any shift in the underlying biology. Current methods may thus undermine efforts to identify when and how warming will reshape biological processes.Significance statementRecently a growing body of literature has observed declining temperature sensitivities of plant leafout and other events with higher temperatures. Such results suggest that climate change is already reshaping fundamental biological processes. These temperature sensitivities are often estimated as the magnitude of a biological response per °C from linear regression. The underlying model for many events—that a critical threshold of warmth must be reached to trigger the event—however, is non-linear. We show that this mismatch between the statistical and biological models can produce the illusion of declining sensitivities with warming using current methods. We suggest simple alternative approaches that can better identify when and how warming will reshape biological processes.
Dominant and nondominant distal radius microstructure: predictors of asymmetry and effects of a unilateral mechanical loading intervention
Authors: Troy Karen L. , Mancuso Megan E. , Johnson Joshua E. , Butler Tiffiny A. , Ngo Bao Han , Schnitzer Thomas J. 
Published: January 2021

AbstractMost information about distal radius microstructure is based on the non-dominant forearm, with little known about the factors that contribute to bilateral asymmetries in the general population, or what factors may influence bilateral changes over time. Here, we analyzed bilateral longitudinal high resolution peripheral quantitative computed tomography (HRpQCT) data collected over a 12-month period as part of a clinical trial that prescribed a well-controlled, compressive loading task to the nondominant forearm. Baseline data from 102 women age 21-40, and longitudinal data from 66 women who completed the 12-month trial, were examined to determine factors responsible for side-to-side asymmetries in bone structure and change in structure over time. Cross-sectionally, the dominant radius had 2.4%-2.7% larger cross-sectional area, trabecular area, and bone mineral content than the nondominant radius, but no other differences were noted. Those who more strongly favored their dominant arm had significantly more, thinner, closely spaced trabecular struts in their dominant versus nondominant radius. Individuals assigned to a loading intervention had significant bilateral gains in total bone mineral density (2.0% and 1.2% in the nondominant versus dominan sides), and unilateral gains in cortical area (3.1%), thickness (3.0%), bone mineral density (1.7%) and inner trabecular density (1.3%). Each of these gains were significantly predicted by loading dose, a metric that included bone strain, number of cycles, and strain rate. Within individuals, change was negatively associated with age, meaning that women closer to age 40 experienced less of a gain in bone versus those closer to age 21. We believe that dominant/nondominant asymmetries in bone structure reflect differences in habitual loads during growth and past ability to adapt, while response to loading reflects current individual physiologic capacity to adapt.
Diversification dynamics and (non-)parallel evolution along an ecological gradient in African cichlid fishes
Authors: Weber A. A.-T. , Rajkov J. , Smailus K. , Egger B. , Salzburger W. 
Published: January 2021

AbstractUnderstanding the drivers and dynamics of diversification is a central topic in evolutionary biology. Here, we investigated the dynamics of diversification in the cichlid fishAstatotilapia burtonithat diverged along a lake-stream environmental gradient. Whole-genome and morphometric analyses revealed that divergent selection was essential at the early stages of diversification, but that periods in allopatry were likely involved towards the completion of speciation. While morphological differentiation was continuous, genomic differentiation was not, as shown by two clearly separated categories of genomic differentiation. Reproductive isolation increased along a continuum of genomic divergence, with a “grey zone” of speciation at ∼0.1% net nucleotide divergence. The quantification of the extent of (non-)parallelism in nine lake-stream population pairs from four cichlid species by means of multivariate analyses revealed one parallel axis of genomic and morphological differentiation among seven lake-stream systems. Finally, we found that parallelism was higher when ancestral lake populations were more similar.
Identification of a Pathway for Electron Uptake in Shewanella oneidensis
Authors: Rowe Annette R. , Salimijazi Farshid , Trutschel Leah , Sackett Joshua , Adesina Oluwakemi , Anzai Isao , Kugelmass Liat H. , Baym Michael H. , Barstow Buz 
Published: January 2021

AbstractExtracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO2 and renewable electricity1-6 . EET could do this with an efficiency comparable to H2 -oxidation7,8 but without the need for a volatile intermediate and the problems it causes for scale up9. However, naturally occurring electroactive organisms suffer from a number of technical drawbacks. Correcting these will require extensive knowledge of the genetics and mechanisms of electron uptake. To date, studies of electron uptake in electroactive microbes have focused on shared molecular machinery also used for anaerobic mineral reduction, like the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-110-14. However, this shared machinery cannot explain all features of electron uptake, hindering efforts to engineer electron uptake. To address this, we screened gene disruption mutants for 3,667 genes, representing ≈ 99% of all non-essential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay as a proxy for electron uptake. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in 4 of the 5 cases produces no significant defect in electron donation to an anode, highlighting a distinct role for these loci in electron uptake vs. donation. This result highlights an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Furthermore, we find homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be a widespread phenomenon. These gene discoveries provide a foundation for studying this phenotype in exotic metal-oxidizing autotrophic microbes. Additionally, we anticipate that the characterization of these genes will allow for the genetic improvement of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation15.
Informative neural representations of unseen contents during higher-order processing in human brains and deep artificial networks
Authors: Mei Ning , Santana Roberto , Soto David 
Published: January 2021

AbstractA framework to pinpoint the scope of unconscious processing is critical to improve our models of visual consciousness. Previous research observed brain signatures of unconscious processing in visual cortex but these were not reliably identified. Further, whether unconscious content is represented in high-level stages of the ventral visual stream and linked parieto-frontal areas remains unknown. Using a within-subject, high-precision fMRI approach, we show that unconscious contents can be decoded from multivoxel patterns that are highly distributed alongside the ventral visual pathway and also involving parieto-frontal substrates. Classifiers trained with multivoxel patterns of conscious items generalised to predict the unconscious counterparts, indicating that their neural representations overlap. These findings suggest revisions to models of consciousness such as the neuronal global workspace. We then provide a computational simulation of visual processing/representation without perceptual sensitivity by using deep neural networks performing a similar visual task. The work provides a framework for pinpointing the representation of unconscious knowledge across different task domains.
Super-Resolution Cryo-EM Maps With 3D Deep Generative Networks
Authors: Venkata Subramaniya Sai Raghavendra Maddhuri , Terashi Genki , Kihara Daisuke 
Published: January 2021

AbstractAn increasing number of biological macromolecules have been solved with cryo-electron microscopy (cryo-EM). Over the past few years, the resolutions of density maps determined by cryo-EM have largely improved in general. However, there are still many cases where the resolution is not high enough to model molecular structures with standard computational tools. If the resolution obtained is near the empirical border line (3-4 Å), a small improvement of resolution will significantly facilitate structure modeling. Here, we report SuperEM, a novel deep learning-based method that uses a three-dimensional generative adversarial network for generating an improved-resolution EM map from an experimental EM map. SuperEM is designed to work with EM maps in the resolution range of 3 Å to 6 Å and has shown an average resolution improvement of 1.0 Å on a test dataset of 36 experimental maps. The generated super-resolution maps are shown to result in better structure modelling of proteins.
Microtubule associated proteins and motors required for ectopic microtubule array formation inS. cerevisiae
Authors: King Brianna R. , Meehl Janet B. , Vojnar Tamira , Winey Mark , Muller Eric G. , Davis Trisha N. 
Published: January 2021

AbstractThe mitotic spindle is resilient to perturbation due to the concerted, and sometimes redundant, action of motors and microtubule-associated proteins. Here we utilize an inducible ectopic microtubule nucleation site in the nucleus ofSaccharomyces cerevisiaeto study three necessary steps in the formation of a bipolar array: the recruitment of the γ-tubulin complex, nucleation and elongation of microtubules, and the organization of microtubules relative to each other. This novel tool, an Spc110 chimera, reveals previously unreported roles of the microtubule-associated proteins Stu2, Bim1, and Bik1, and the motors Vik1 and Kip3. We report that Stu2 and Bim1 are required for nucleation and that Bik1 and Kip3 promote nucleation at the ectopic site. Stu2, Bim1, and Kip3 join their homologs XMAP215, EB1 and kinesin-8 as promoters of microtubule nucleation, while Bik1 promotes MT nucleation indirectly via its role in SPB positioning. Further, we find that the nucleation activity of Stu2in vivocorrelates with its polymerase activityin vitro. Finally, we provide the first evidence that Vik1, a subunit of Kar3/Vik1 kinesin-14, promotes microtubule minus end focusing at the ectopic site.