bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a text messaging-based smoking cessation intervention for young smokers experiencing homelessness
Authors: Tucker Joan S. , Linnemayr Sebastian , Pedersen Eric R. , Shadel William G. , Zutshi Rushil , Mendoza-Graf Alexandra 
Published: November 2019

AbstractIntroductionCigarette smoking is highly prevalent among young people experiencing homelessness, and many of these smokers are motivated to quit. However, there is a lack of readily available cessation services for this population, which is highly mobile and can be challenging to engage in services.AimsWe describe the development of a smoking cessation text messaging intervention (TMI) for homeless youth who are interested in quitting smoking.MethodsParticipants were 18–25 years old and recruited from drop-in centers serving homeless youth. Three focus groups (N = 18) were conducted with smokers to refine the TMI content, and a separate sample of smokers (N = 8) provided feedback on the TMI after using it for 1 week. Survey data assessed the TMI's acceptability and feasibility.ResultsParticipants generally rated the TMI as helpful and relevant, and nearly all had cell phone plans that included unlimited texting and were able to view TMI content with few difficulties. Qualitative feedback on strengths/limitations of the TMI in terms of content, tone, and delivery parameters was used to finalize the TMI for a future evaluation.ConclusionsResults suggest that a TMI is a feasible and acceptable option for young people experiencing homelessness who are interested in quitting smoking.
How can we play together? Temporal inconsistencies in neural coding of music
Authors: Vickhoff Björn 
Published: November 2019

Abstract
If sensory organs encode environment, this code must be decoded to perception. The currently dominant theory of perception – predictive coding – assumes a “Bayesian decoder,” a probability function, which will present (to whom?) an optimal guess, given previous encodings of the environment – old codes testing new codes. Such a process would delay perception noticeably. This is inconsistent with the perception of music, which for several reasons must be direct.
Codes, functions, and causes: A critique of Brette's conceptual analysis of coding
Authors: Barack David , Jaegle Andrew 
Published: November 2019

AbstractBrette argues that coding as a concept is inappropriate for explanations of neurocognitive phenomena. Here, we argue that Brette's conceptual analysis mischaracterizes the structure of causal claims in coding and other forms of analysis-by-decomposition. We argue that analyses of this form are permissible and conceptually coherent and offer essential tools for building and developing models of neurocognitive systems like the brain.
Codes, communication and cognition
Authors: Harnad Stevan 
Published: November 2019

Abstract
Brette criticizes the notion of neural coding because it seems to entail that neural signals need to “decoded” by or for some receiver in the head. If that were so, then neural coding would indeed be homuncular (Brette calls it “dualistic”), requiring an entity to decipher the code. But I think Brette's plea to think instead in terms of complex, interactive causal throughput is preaching to the converted. Turing (not Shannon) has already shown the way. In any case, the metaphor of neural coding has little to do with the symbol grounding problem.
U.S. Food and Drug Administration anticancer drug approval trends from 2016 to 2018 for lung, colorectal, breast, and prostate cancer
Authors: Ribeiro Tatiane Bomfim , Ribeiro Adalton , Rodrigues Luíza de Oliveira , Harada Guilherme , Nobre Moacyr Roberto Cuce 
Published: November 2019

ObjectiveThis paper aims to describe the clinical and regulatory aspects of new drugs and indications that were approved for lung, breast, prostate, and colorectal cancer, from 2016 to 2018, in order to provide health technology assessment trends in oncology.MethodsData were collected from the US Food and Drug Administration (FDA) online database for new medications and indications approved for the above-mentioned types of cancer. Data regarding clinical study characteristics and regulatory information were collected.ResultsFrom 2016 to 2018, 53 percent of the FDA approvals of new drugs and indications for the most incident cancers were for oral protein kinase inhibitor monotherapy for advanced lung cancer. Since 2018, four drugs were approved as tumor-agnostic therapies. A biomarker was included in 72 percent of indications, and 58 percent of approvals were for targeted therapies, potentially heralding an end to research into conventional cytotoxic agents. A special designation for faster approval was granted in 78 percent of new approvals. The majority of the studies were open label randomized controlled trials (RCTs) (44 percent), followed by blind RCTs, single-arm clinical trials, and cohort studies. Only 14 percent of studies used overall survival as the primary end point; the vast majority used surrogate end points, and did not use patient-important outcomes. Three biosimilars were approved in the period.ConclusionAdvanced lung cancer therapy, mainly targeted drugs, accounted for 53 percent of approvals. Special designations for faster approval were used in 78 percent of FDA approvals, and four drugs were approved for tumor-agnostic treatment—a new form of approval.
Food insecurity is associated with suboptimal sleep quality, but not sleep duration, among low-income Head Start children of pre-school age
Authors: Na Muzi , Eagleton Sally G , Jomaa Lamis , Lawton Kristen , Savage Jennifer S 
Published: November 2019

AbstractObjective:To examine the association between food insecurity and child sleep outcomes and to investigate whether parent psychosocial factors mediate such associations.Design:Cross-sectional study. Usual wake time and bedtime, bedtime routine and sleep quality were reported by parents using the adapted Brief Infant Sleep Questionnaire. Food insecurity was assessed using the eighteen-item US Department of Agriculture Household Food Security Module. Parent psychosocial factors, including perceived stress, parenting self-efficacy and depressive symptomology, were assessed using validated scales. Multivariable logistic regression models were performed to determine the association between food insecurity and sleep outcomes controlling for potential confounders. Mediation analyses and Sobel tests were applied to test the mediating effect of psychosocial factors.Setting:Head Start pre-school classrooms in four regions across central Pennsylvania, USA.Participants:Low-income children of pre-school age (n 362) and their caregivers.Results:Prevalence of household, adult and child food insecurity was 37·3, 31·8 and 17·7 %, respectively. Food security status at any level was not associated with child sleep duration or bedtime routine. Child food insecurity, but not household or adult food insecurity, was associated with 2·25 times increased odds (95 % CI 1·11, 4·55) of poor child sleep quality in the adjusted model. Perceived stress, self-efficacy and depressive symptomology mediated less than 2 % of the observed effect (all Sobel test P > 0·6).Conclusion:Food insecurity, particularly at the child level, is a potential modifiable risk factor for reducing sleep-related health disparities in early childhood. Future studies are needed to explore the plausible mechanisms underlying the associations between food insecurity and adverse child sleep outcomes.
Estuarine Responses to Long‐Term Changes in Inlets, Morphology, and Sea Level Rise
Authors: Mulligan Ryan P. , Mallinson David J. , Clunies Gregory J. , Rey Alexander , Culver Stephen J. , Zaremba Nick , Leorri Eduardo , Mitra Siddhartha 
Published: November 2019

AbstractPamlico Sound, a large back‐barrier estuary in North Carolina, is under threat of climate change due to increased storm activity and sea level rise. The response of this system is investigated by considering what has already happened during changes in sea level over the late Holocene epoch. The hydrodynamic changes that occurred in response to geomorphic evolution are simulated using a 3‐D numerical model for four distinct “time‐slice” scenarios. To accomplish this, the present‐day bathymetry was obtained from a high‐resolution digital elevation model, and paleobathymetric grids were developed from sediment cores and seismic observations. Using the same hydrodynamic forcing for each geomorphic scenario, the models are compared to assess the combined response to: different inlets connecting the back‐barrier estuary to the ocean, changes in basin geomorphology due to sedimentation, and sea level rise. The results indicate that these factors have a considerable effect on hydrodynamics, waves, and salinity in the estuary. The time‐averaged tidal ranges were up to 3 times as high for the past environments in comparison with present‐day water level elevations, and maximum current velocities were over 3 times higher in regions close to paleo‐inlets. The simulations for each time slice suggest that the salinity distribution in Pamlico Sound is strongly influenced by the hydraulic connectivity with other estuaries and the number and size of tidal inlets through the barrier island system. The results indicate that changes to barrier systems induce strong, nonuniform, and complex responses in back‐barrier estuaries with regime shifts in hydrodynamic energy and water mass properties.
Assessing Models for Pacific Absolute Plate and Plume Motions
Authors: Wessel Paul , Conrad Clinton P. 
Published: November 2019

AbstractAbsolute plate motion (APM) models derived from hot spot trails must satisfy trail geometries, ages, and paleolatitudes, which requires modeling explicit plume motions. Models lacking plume motions or derived independently from seamounts must also fit these data, provided the implicit plume motions are geodynamically reasonable. We evaluate eight Pacific APM models; three have explicitly modeled plume motions. Seven derive from seamount age progressions; one is a geodynamic model driven by slab pull and ridge push. Using the long‐lived Hawaii‐Emperor and Louisville chains, we derive implicit motions of Hawaii and Louisville plumes for models lacking explicit estimates and compare them with observed paleolatitudes. Inferred plume motions are plausible given rheological constraints on mantle flow, but rates vary considerably and not all models fit the data well. One potential endmember model predicts no APM direction change at 50 Ma, which best explains trails and paleolatitudes, minimizes predicted rotation of Pacific‐Farallon ridge and assumes no true polar motion, yet its implicit plume drift is inconsistent with global circulation models. Alternatively, a global moving hot spot model yields acceptable fits to geometry and ages, implies a major APM change at 50 Ma, but requires significant true polar wander to explain observed paleolatitudes. The inherent inconsistency between age progressions and paleolatitudes may be reconciled by true polar wander, yet questions remain about the accuracy of age progressions for older sections of the Emperor and Louisville chains, the independent geologic evidence for an APM change at 50 Ma, and the uniqueness and relevance of true polar wander estimates.
Atmospheric Water Transport to the Endorheic Tibetan Plateau and Its Effect on the Hydrological Status in the Region
Authors: Li Ying , Su Fengge , Chen Deliang , Tang Qiuhong 
Published: November 2019

AbstractThe endorheic Tibetan Plateau (ETP), which consists of all the endorheic basins of the Tibetan Plateau (TP), has exhibited an overall mass gain in recent decades. However, the role played by atmospheric water (AW) transport on the hydrological status over the ETP is poorly understood. In this study, the AW source to the ETP was tracked with the Water Accounting Model‐2 layers (WAM‐2) and AW transport to the ETP through its boundaries was quantified, with three reanalysis products (ERA‐I, MERRA‐2, and JRA‐55) during 1979/1980–2015. It is found that total AW input to the ETP is about 13–25%, 59–71%, 10–13%, and 3–7% of mean annual totals in spring, summer, autumn, and winter, respectively. At annual scales, the AW source from land (52–54%) dominates the AW contribution to the ETP, while local recycling of AW over the ETP accounts for about 17–22% of the mean annual total AW contribution. Increased precipitation over the ETP during 1979–2015 was mostly attributed to the significantly increased AW contribution from the Indian Ocean, especially from increased AW inputs transported from the western and southern boundaries in summer. Comparisons between the AW budget and terrestrial water storage changes indicate that the AW budget change over the ETP modulated the variations of terrestrial water storage change during 2002–2014 and annual lake mass change during 1989–2015.
MATRIEX imaging: multiarea two-photon real-time in vivo explorer
Authors: Yang Mengke , Zhou Zhenqiao , Zhang Jianxiong , Jia Shanshan , Li Tong , Guan Jiangheng , Liao Xiang , Leng Bing , Lyu Jing , Zhang Kuan , Li Min , Gong Yan , Zhu Zhiming , Yan Junan , Zhou Yi , Liu Jian K , Varga Zsuzsanna , Konnerth Arthur , Tang Yuguo , Gao Jinsong , Chen Xiaowei , Jia Hongbo 
Published: November 2019

AbstractTwo-photon laser scanning microscopy has been extensively applied to study in vivo neuronal activity at cellular and subcellular resolutions in mammalian brains. However, the extent of such studies is typically confined to a single functional region of the brain. Here, we demonstrate a novel technique, termed the multiarea two-photon real-time in vivo explorer (MATRIEX), that allows the user to target multiple functional brain regions distributed within a zone of up to 12 mm in diameter, each with a field of view (FOV) of ~200 μm in diameter, thus performing two-photon Ca2+ imaging with single-cell resolution in all of the regions simultaneously. For example, we demonstrate real-time functional imaging of single-neuron activities in the primary visual cortex, primary motor cortex and hippocampal CA1 region of mice in both anesthetized and awake states. A unique advantage of the MATRIEX technique is the configuration of multiple microscopic FOVs that are distributed in three-dimensional space over macroscopic distances (>1 mm) both laterally and axially but that are imaged by a single conventional laser scanning device. In particular, the MATRIEX technique can be effectively implemented as an add-on optical module for an existing conventional single-beam-scanning two-photon microscope without requiring any modification to the microscope itself. Thus, the MATRIEX technique can be readily applied to substantially facilitate the exploration of multiarea neuronal activity in vivo for studies of brain-wide neural circuit function with single-cell resolution.
Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
Authors: Belkina Anna C. , Ciccolella Christopher O. , Anno Rina , Halpert Richard , Spidlen Josef , Snyder-Cappione Jennifer E. 
Published: November 2019

AbstractAccurate and comprehensive extraction of information from high-dimensional single cell datasets necessitates faithful visualizations to assess biological populations. A state-of-the-art algorithm for non-linear dimension reduction, t-SNE, requires multiple heuristics and fails to produce clear representations of datasets when millions of cells are projected. We develop opt-SNE, an automated toolkit for t-SNE parameter selection that utilizes Kullback-Leibler divergence evaluation in real time to tailor the early exaggeration and overall number of gradient descent iterations in a dataset-specific manner. The precise calibration of early exaggeration together with opt-SNE adjustment of gradient descent learning rate dramatically improves computation time and enables high-quality visualization of large cytometry and transcriptomics datasets, overcoming limitations of analysis tools with hard-coded parameters that often produce poorly resolved or misleading maps of fluorescent and mass cytometry data. In summary, opt-SNE enables superior data resolution in t-SNE space and thereby more accurate data interpretation.
The art of using t-SNE for single-cell transcriptomics
Authors: Kobak Dmitry , Berens Philipp 
Published: November 2019

AbstractSingle-cell transcriptomics yields ever growing data sets containing RNA expression levels for thousands of genes from up to millions of cells. Common data analysis pipelines include a dimensionality reduction step for visualising the data in two dimensions, most frequently performed using t-distributed stochastic neighbour embedding (t-SNE). It excels at revealing local structure in high-dimensional data, but naive applications often suffer from severe shortcomings, e.g. the global structure of the data is not represented accurately. Here we describe how to circumvent such pitfalls, and develop a protocol for creating more faithful t-SNE visualisations. It includes PCA initialisation, a high learning rate, and multi-scale similarity kernels; for very large data sets, we additionally use exaggeration and downsampling-based initialisation. We use published single-cell RNA-seq data sets to demonstrate that this protocol yields superior results compared to the naive application of t-SNE.
Automated sequence design of 2D wireframe DNA origami with honeycomb edges
Authors: Jun Hyungmin , Wang Xiao , Bricker William P. , Bathe Mark 
Published: November 2019

AbstractWireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.
Two-tiered enforcement of high-fidelity DNA ligation
Authors: Tumbale Percy P. , Jurkiw Thomas J. , Schellenberg Matthew J. , Riccio Amanda A. , O’Brien Patrick J , Williams R. Scott 
Published: November 2019

AbstractDNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3′-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg2+-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg2+, and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.
Simulating quantum many-body dynamics on a current digital quantum computer
Authors: Smith Adam , Kim M. S. , Pollmann Frank , Knolle Johannes 
Published: November 2019

AbstractUniversal quantum computers are potentially an ideal setting for simulating many-body quantum dynamics that is out of reach for classical digital computers. We use state-of-the-art IBM quantum computers to study paradigmatic examples of condensed matter physics—we simulate the effects of disorder and interactions on quantum particle transport, as well as correlation and entanglement spreading. Our benchmark results show that the quality of the current machines is below what is necessary for quantitatively accurate continuous-time dynamics of observables and reachable system sizes are small comparable to exact diagonalization. Despite this, we are successfully able to demonstrate clear qualitative behaviour associated with localization physics and many-body interaction effects.
Production of recombinant soluble dimeric C-type lectin-like receptors of rat natural killer cells
Authors: Vaněk Ondřej , Celadova Petra , Skořepa Ondřej , Bláha Jan , Kalousková Barbora , Dvorská Anna , Poláchová Edita , Pucholtová Helena , Kavan Daniel , Pompach Petr , Hofbauerová Kateřina , Kopecký Vladimír , Mesci Aruz , Voigt Sebastian , Carlyle James R. 
Published: November 2019

AbstractWorking at the border between innate and adaptive immunity, natural killer (NK) cells play a key role in the immune system by protecting healthy cells and by eliminating malignantly transformed, stressed or virally infected cells. NK cell recognition of a target cell is mediated by a receptor “zipper” consisting of various activating and inhibitory receptors, including C-type lectin-like receptors. Among this major group of receptors, two of the largest rodent receptor families are the NKR-P1 and the Clr receptor families. Although these families have been shown to encode receptor-ligand pairs involved in MHC-independent self-nonself discrimination and are a target for immune evasion by tumour cells and viruses, structural mechanisms of their mutual recognition remain less well characterized. Therefore, we developed a non-viral eukaryotic expression system based on transient transfection of suspension-adapted human embryonic kidney 293 cells to produce soluble native disulphide dimers of NK cell C-type lectin-like receptor ectodomains. The expression system was optimized using green fluorescent protein and secreted alkaline phosphatase, easily quantifiable markers of recombinant protein production. We describe an application of this approach to the recombinant protein production and characterization of native rat NKR-P1B and Clr-11 proteins suitable for further structural and functional studies.
Holocene Critical Zone dynamics in an Alpine catchment inferred from a speleothem multiproxy record: disentangling climate and human influences
Authors: Regattieri Eleonora , Zanchetta Giovanni , Isola Ilaria , Zanella Elena , Drysdale Russell N. , Hellstrom John C. , Zerboni Andrea , Dallai Luigi , Tema Evdokia , Lanci Luca , Costa Emanuele , Magrì Federico 
Published: November 2019

AbstractDisentangling the effects of climate and human impact on the long-term evolution of the Earth Critical Zone is crucial to understand the array of its potential responses to the ongoing Global Change. This task requires natural archives from which local information about soil and vegetation can be linked directly to climate parameters. Here we present a high-resolution, well-dated, speleothem multiproxy record from the SW Italian Alps, spanning the last ~10,000 years of the present interglacial (Holocene). We correlate magnetic properties and the carbon stable isotope ratio to soil stability and pedogenesis, whereas the oxygen isotope composition is interpreted as primarily related to precipitation amount, modulated at different timescales by changes in precipitation source and seasonality. During the 9.7-2.8 ka period, when anthropic pressure over the catchment was scarce, intervals of enhanced soil erosion are related to climate-driven vegetation contractions and occurred during drier periods. Immediately following the onset of the Iron Age (ca. 2.8 ka), by contrast, periods of enhanced soil erosion coincided with a wetter climate. We propose that the observed changes in the soil response to climate forcing were related to early anthropogenic manipulations of Earth’s surface, which made the ECZ more sensitive to climate oscillations.