bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics
Authors: Castro Victor M , Gainer Vivian , Wattanasin Nich , Benoit Barbara , Cagan Andrew , Ghosh Bhaswati , Goryachev Sergey , Metta Reeta , Park Heekyong , Wang David , Mendis Michael , Rees Martin , Herrick Christopher , Murphy Shawn N 
Published: November 2021

AbstractObjectiveIntegrating and harmonizing disparate patient data sources into one consolidated data portal enables researchers to conduct analysis efficiently and effectively.Materials and MethodsWe describe an implementation of Informatics for Integrating Biology and the Bedside (i2b2) to create the Mass General Brigham (MGB) Biobank Portal data repository. The repository integrates data from primary and curated data sources and is updated weekly. The data are made readily available to investigators in a data portal where they can easily construct and export customized datasets for analysis.ResultsAs of July 2021, there are 125 645 consented patients enrolled in the MGB Biobank. 88 527 (70.5%) have a biospecimen, 55 121 (43.9%) have completed the health information survey, 43 552 (34.7%) have genomic data and 124 760 (99.3%) have EHR data. Twenty machine learning computed phenotypes are calculated on a weekly basis. There are currently 1220 active investigators who have run 58 793 patient queries and exported 10 257 analysis files.DiscussionThe Biobank Portal allows noninformatics researchers to conduct study feasibility by querying across many data sources and then extract data that are most useful to them for clinical studies. While institutions require substantial informatics resources to establish and maintain integrated data repositories, they yield significant research value to a wide range of investigators.ConclusionThe Biobank Portal and other patient data portals that integrate complex and simple datasets enable diverse research use cases. i2b2 tools to implement these registries and make the data interoperable are open source and freely available.
Multidisciplinary design optimization in design for additive manufacturing
Authors: Liu Guang , Xiong Yi , Rosen David W 
Published: November 2021

ABSTRACT
Design for additive manufacturing (AM) involves decision making in various design domains, including product design, material selection, and process planning. In practice, engineers typically adopt a sequential design process to optimize these design domains in consecutive order. However, coupling factors, e.g. shared variables, related constraints, and conflicting objectives, are not sufficiently considered within the sequential design process, resulting in an inefficient workflow and suboptimal design solutions. To address the above issues, this paper proposes a multidisciplinary design optimization framework to simultaneously optimize different domains, which enables rapid exploration and complete exploitation of the AM design space under complex constraints. More specifically, the proposed framework is based on the concurrent optimization method, which coordinates the optimization of different design domains by allowing an automated exchange of design information. Also, the framework utilizes the surrogate modeling approach to approximate high-fidelity simulations for facilitating the iterative process. The effectiveness of the proposed framework is validated with two examples, a plate with a hole design and a hook design, which involve multiple design objectives from both process and structure domains, i.e. the print time, print area, strain energy, and maximum von Mises stress.
The Influence of the Risk Reward Profile and of the Colour of Disclosure Documents on Attractiveness Perception of Mutual Fund Products
Authors: Bussoli Candida , Ceravolo Maria Gabriella , Fattobene Lucrezia , Raggetti GianMario 
Published: November 2021

ABSTRACT
This study investigates the influence of features of the mutual fund product and of the disclosure document on financial decision making. Using a laboratory setting, we show that the higher the risk and reward profile (RRP) of the product, the poorer the perception of the product. When the colour red (or blue) is applied to graphics (the RRP scale and the graph of the past performance) in the documents, the perception of the attractiveness of the product is lower (or higher) in comparison to a black and white document. Finally, longer visual processing as measured by means of eye-tracking is associated with a higher perception of attractiveness. This neurofinance study highlights the importance for regulators and supervisors of the financial industry to explore the influence of the different features of the product and of the disclosure document on consumers’ financial decision making.
Habitat selection by non-native masked palm civets in a Japanese rural landscape, incorporating individual differences
Authors: Toriyabe Ayaka , Enari Hiroto , Enari Haruka S , Saito Masayuki U 
Published: November 2021

Abstract
Animals that succeed as non-native species may have highly plastic characteristics. We conducted a radio telemetry survey for introduced masked palm civets (Paguma larvata), which inhabit rural landscapes in almost all of Japan, to clarify their habitat selection and intraspecific variation. We compared two generalized linear mixed models, one that did not consider individual differences and another that did, which indicated the importance of incorporating individual differences for evaluating habitat selection by this species. We obtained results of habitat selectivity for all individuals (i.e., common effect on the species) and for each individual using coefficients of fixed effects or fixed effects with random effects. Masked palm civets significantly selected deciduous broad-leaved forests, artificial structures, rice fields, and orchards as a common effect for all individuals. However, these habitats were not necessarily selected as a significant effect for each individual. Deciduous broad-leaved forests and artificial structures were more important than other habitats. The wide range of possible environments and the plasticity of habitat selection shown in this study may partly explain the success of this species in expanding its distribution in Japan.
Morphological integration and cranial modularity in six genera of echimyid rodents (Rodentia: Echimyidae)
Authors: Raidan Carolline , de Andrade Costa Bárbara Maria , Marroig Gabriel , Aprígio Assis Ana Paula , Paresque Roberta 
Published: November 2021

Abstract
Rodents of the family Echimyidae present a wide variety of life histories and ecomorphological adaptations. This study evaluated morphological integration patterns, modularity, and evolutionary flexibility in six Echimyid genera representing ecomorphological extremes within the family. The relationships between traits were evaluated by comparing estimated covariance and correlations matrices of populations. The presence of modules was investigated by comparing the patterns of integration between traits and using hypothetical matrices based on shared development/function and masticatory stress. The results point to a common covariance and correlation pattern among the six echimyid genera, suggesting a conserved pattern of covariation (associations among traits) throughout the evolution of this group. The overall magnitude of integration, however, varied greatly. We also found a high degree of modularity in all six echimyid genera. Finally, we observed a clear association between flexibility, i.e., the ability of a species to respond to the direction of selection, with the overall magnitude of integration and degree of modularization. The results of this study provide hypotheses concerning the underlying effects of the association among traits, which may have facilitated or constrained the evolution of morphological variation in the diverse family Echimyidae.
Inference from Nonrandom Samples Using Bayesian Machine Learning
Authors: Liu Yutao , Gelman Andrew , Chen Qixuan 
Published: November 2021

AbstractWe consider inference from nonrandom samples in data-rich settings where high-dimensional auxiliary information is available both in the sample and the target population, with survey inference being a special case. We propose a regularized prediction approach that predicts the outcomes in the population using a large number of auxiliary variables such that the ignorability assumption is reasonable and the Bayesian framework is straightforward for quantification of uncertainty. Besides the auxiliary variables, we also extend the approach by estimating the propensity score for a unit to be included in the sample and also including it as a predictor in the machine learning models. We find in simulation studies that the regularized predictions using soft Bayesian additive regression trees yield valid inference for the population means and coverage rates close to the nominal levels. We demonstrate the application of the proposed methods using two different real data applications, one in a survey and one in an epidemiologic study.
The dust-continuum size of TNG50 galaxies at z = 1–5: a comparison with the distribution of stellar light, stars, dust, and H2
Authors: Popping Gergö , Pillepich Annalisa , Calistro Rivera Gabriela , Schulz Sebastian , Hernquist Lars , Kaasinen Melanie , Marinacci Federico , Nelson Dylan , Vogelsberger Mark 
Published: November 2021

ABSTRACT
We present predictions for the extent of the dust-continuum emission of main-sequence galaxies drawn from the TNG50 simulation in the range z = 1–5. We couple the radiative transfer code SKIRT to the output of the TNG50 simulation and measure the dust-continuum half-light radius of the modelled galaxies, assuming a Milky Way dust type and a metallicity-dependent dust-to-metal ratio. The dust-continuum half-light radius at observed-frame 850 $\mu$m is up to ∼75 per cent larger than the stellar half-mass radius, but significantly more compact than the observed-frame 1.6 $\mu$m (roughly corresponding to H band) half-light radius, particularly towards high redshifts: the compactness compared to the 1.6 $\mu$m emission increases with redshift. This is driven by obscuration of stellar light from the galaxy centres, which increases the apparent extent of 1.6 $\mu$m disc sizes relative to that at 850 $\mu$m. The difference in relative extents increases with redshift because the observed-frame 1.6 $\mu$m emission stems from ever shorter wavelength stellar emission. These results suggest that the compact dust-continuum emission observed in z &gt; 1 galaxies is not (necessarily) evidence of the build-up of a dense central stellar component. We find that the dust-continuum half-light radius closely follows the radius containing half the star formation and half the dust mass in galaxies and is ∼80 per cent of the radius containing half the H2 mass. The presented results are a common feature of main-sequence galaxies.
How robust are the inferred density and metallicity of the circumgalactic medium?
Authors: Acharya Anshuman , Khaire Vikram 
Published: November 2021

ABSTRACT
Quantitative estimates of the basic properties of the circumgalactic medium (CGM), such as its density and metallicity, depend on the spectrum of incident UV background radiation. Models of UV background are known to have large variations, mainly because they are synthesized using poorly constrained parameters, which introduce uncertainty in the inferred properties of the CGM. Here, we quantify this uncertainty using a large set of new UV background models with physically motivated toy models of metal-enriched CGM. We find that the inferred density and metallicity of low-density (10−5 cm−3) gas is uncertain by factors of 6.3 and 3.2, whereas high-density (10−3 cm−3) gas by factors of 4 and 1.6, respectively. The variation in the shape of the UV background models is entirely responsible for such a variation in the metallicity, while variation in the density arises from both normalization and shape of the UV background. Moreover, we find a harder (softer) UV background infers higher (lower) density and metallicity. We also study warm-hot gas at T = 105.5 K and find that metallicity is robustly estimated but the inferred density is uncertain by a factor of 3 to 5.4 for low to high-density gas. Such large uncertainties in density and metallicity may severely limit the studies of the CGM and demand better observational constraints on the input parameters used in synthesizing UV background.
A connection between spectral sharpness and energies as well as flux in fermi gamma-ray bursts
Authors: Wang Dao-Zhou , Peng Zhao-Yang , Chen Jia-Ming , Yin Yue 
Published: November 2021

ABSTRACT
We revisit the sharpness angle (θ) under the peak or break of gamma-ray burst (GRB) spectra with the best peak flux P and time-integrated F spectral data provided by the Fermi GBM Burst Catalogue. We compute the sharpness angles of best-fit model spectra and check some interesting relations between θ and physics quantities. It is found that (i) a positive correlations between θ and the observed fluence as well as the isotropic radiated energy holds among GRBs, especially for the F spectra; (ii) when checking the correlation between θ and energy flux a weaker anti-correlation holds among GRBs and a tighter anti-correlation holds within GRBs, especially in single pulses. Our results further show that the spectral shape is related to the energy and flux by cross-checking other measures of spectral curvature. The correlated relationship between spectral sharpness and energy flux can be well explained as a thermal origin for GRB prompt emission: A large entropy around the peak of the light curve makes the photosphere approach the saturation radius, resulting in an intense emission with a narrow spectrum; as the entropy decreases, the photosphere deviates from the saturation radius, resulting in weaker emission with a broader spectrum.
Noninsect-Based Diet Leads to Structural and Functional Changes of Acidic Chitinase in Carnivora
Authors: Tabata Eri , Itoigawa Akihiro , Koinuma Takumi , Tayama Hiroshi , Kashimura Akinori , Sakaguchi Masayoshi , Matoska Vaclav , Bauer Peter O , Oyama Fumitaka 
Published: November 2021

AbstractAcidic chitinase (Chia) digests the chitin of insects in the omnivorous stomach and the chitinase activity in carnivorous Chia is significantly lower than that of the omnivorous enzyme. However, mechanistic and evolutionary insights into the functional changes in Chia remain unclear. Here we show that a noninsect-based diet has caused structural and functional changes in Chia during the course of evolution in Carnivora. By creating mouse-dog chimeric Chia proteins and modifying the amino acid sequences, we revealed that F214L and A216G substitutions led to the dog enzyme activation. In 31 Carnivora, Chia was present as a pseudogene with stop codons in the open reading frame (ORF) region. Importantly, the Chia proteins of skunk, meerkat, mongoose, and hyena, which are insect-eating species, showed high chitinolytic activity. The cat Chia pseudogene product was still inactive even after ORF restoration. However, the enzyme was activated by matching the number and position of Cys residues to an active form and by introducing five meerkat Chia residues. Mutations affecting the Chia conformation and activity after pseudogenization have accumulated in the common ancestor of Felidae due to functional constraints. Evolutionary analysis indicates that Chia genes are under relaxed selective constraint in species with noninsect-based diets except for Canidae. These results suggest that there are two types of inactivating processes in Carnivora and that dietary changes affect the structure and activity of Chia.
Functional Dysconnectivity in Ventral Striatocortical Systems in 22q11.2 Deletion Syndrome
Authors: Tepper Ángeles , Cuiza Analía , Alliende Luz María , Mena Carlos , Ramirez-Mahaluf Juan Pablo , Iruretagoyena Barbara , Ornstein Claudia , Fritsch Rosemarie , Nachar Ruben , González-Valderrama Alfonso , Undurraga Juan , Cruz Juan Pablo , Tejos Cristian , Fornito Alex , Repetto Gabriela , Crossley Nicolas 
Published: November 2021

Abstract
22q11.2 deletion syndrome (22q11.2DS) is a genetic neurodevelopmental disorder that represents one of the greatest known risk factors for psychosis. Previous studies in psychotic subjects without the deletion have identified a dopaminergic dysfunction in striatal regions, and dysconnectivity of striatocortical systems, as an important mechanism in the emergence of psychosis. Here, we used resting-state functional MRI to examine striatocortical functional connectivity in 22q11.2DS patients. We used a 2 × 2 factorial design including 125 subjects (55 healthy controls, 28 22q11.2DS patients without a history of psychosis, 10 22q11.2DS patients with a history of psychosis, and 32 subjects with a history of psychosis without the deletion), allowing us to identify network effects related to the deletion and to the presence of psychosis. In line with previous results from psychotic patients without 22q11.2DS, we found that there was a dorsal to ventral gradient of hypo- to hyperstriatocortical connectivity related to psychosis across both patient groups. The 22q11.2DS was additionally associated with abnormal functional connectivity in ventral striatocortical networks, with no significant differences identified in the dorsal system. Abnormalities in the ventral striatocortical system observed in these individuals with high genetic risk to psychosis may thus reflect a marker of illness risk.
Characterization of Hemodynamic Alterations in Schizophrenia and Bipolar Disorder and Their Effect on Resting-State fMRI Functional Connectivity
Authors: Yan Wenjing , Palaniyappan Lena , Liddle Peter F , Rangaprakash D , Wei Wei , Deshpande Gopikrishna 
Published: November 2021

Abstract
Common and distinct neural bases of Schizophrenia (SZ) and bipolar disorder (BP) have been explored using resting-state fMRI (rs-fMRI) functional connectivity (FC). However, fMRI is an indirect measure of neural activity, which is a convolution of the hemodynamic response function (HRF) and latent neural activity. The HRF, which models neurovascular coupling, varies across the brain within and across individuals, and is altered in many psychiatric disorders. Given this background, this study had three aims: quantifying HRF aberrations in SZ and BP, measuring the impact of such HRF aberrations on FC group differences, and exploring the genetic basis of HRF aberrations. We estimated voxel-level HRFs by deconvolving rs-fMRI data obtained from SZ (N = 38), BP (N = 19), and matched healthy controls (N = 35). We identified HRF group differences (P &lt; .05, FDR corrected) in many regions previously implicated in SZ/BP, with mediodorsal, habenular, and central lateral nuclei of the thalamus exhibiting HRF differences in all pairwise group comparisons. Thalamus seed-based FC analysis revealed that ignoring HRF variability results in false-positive and false-negative FC group differences, especially in insula, superior frontal, and lingual gyri. HRF was associated with DRD2 gene expression (P &lt; .05, 1.62 &lt; |Z| &lt; 2.0), as well as with medication dose (P &lt; .05, 1.75 &lt; |Z| &lt; 3.25). In this first study to report HRF aberrations in SZ and BP, we report the possible modulatory effect of dopaminergic signalling on HRF, and the impact that HRF variability can have on FC studies in clinical samples. To mitigate the impact of HRF variability on FC group differences, we suggest deconvolution during data preprocessing.
Mapping Personal Geographies in Psychosis: From Space to Place
Authors: Baumann Philipp S , Söderström Ola , Abrahamyan Empson Lilith , Duc Marwood Alessandra , Conus Philippe 
Published: November 2021

Abstract
Recently, there has been a growing interest in the interaction between the urban milieu and the development of psychosis. While growing up in an urban environment constitutes a risk factor for developing psychosis, patients who develop a first episode of psychosis tend to avoid city centers and suffer from isolation. These observations have fostered emerging interest in ways of developing contexts in cities that are favorable to mental health and that may help service users in their paths to recovery. Building on work on place attachment as well as systemic therapy, we present a new approach to map the urban spaces experienced by service users. We propose two tools, the “place attachment diagram” and “life space network,” to situate emotional bond and spatial dimension respectively at their center and help service users to map meaningful places in the city. We also suggest that different facets of the illness such as epidemiological risk factors (residential mobility, migration, urban living, trauma), early place attachment and abnormal space experience, may shape individual space and place experience in psychosis. Psychotherapeutic process with patients should aim at turning urban “spaces” into “places” characterized by a sense of familiarity, security and opportunity. Finally, we argue that the “spatial” is a forgotten dimension in psychotherapy and should be taken into account when treating individuals with psychosis.
Guiding Chemically Synthesized Peptide Drug Lead Optimization by Derisking Mast Cell Degranulation-Related Toxicities of a NaV1.7 Peptide Inhibitor
Authors: Morissette Pierre , Li Nianyu , Ballard Jeanine E , Vavrek Marissa , Adams Gregory L , Regan Chris , Regan Hillary , Lee K J , Wang Weixun , Burton Aimee , Chen Feifei , Gerenser Pamela , Li Yuxing , Kraus Richard L , Tellers David , Palani Anand , Zhu Yuping , Sun Chengzao , Bianchi Elisabetta , Colarusso Stefania , De Simone Daniele , Frattarelli Tommaso , Pasquini Nicolo’ Maria , Amin Rupesh P 
Published: November 2021

AbstractStudies have shown that some peptides and small molecules can induce non IgE-mediated anaphylactoid reactions through mast cell activation. Upon activation, mast cells degranulate and release vasoactive and proinflammatory mediators, from cytoplasmic granules into the extracellular environment which can induce a cascade of severe adverse reactions. This study describes a lead optimization strategy to select NaV1.7 inhibitor peptides that minimize acute mast cell degranulation (MCD) toxicities. Various in vitro, in vivo, and PKPD models were used to screen candidates and guide peptide chemical modifications to mitigate this risk. Anesthetized rats dosed with peptides demonstrated treatment-related decreases in blood pressure and increases in plasma histamine concentrations which were reversible with a mast cell stabilizer, supporting the MCD mechanism. In vitro testing in rat mast cells with NaV1.7 peptides demonstrated a concentration-dependent increase in histamine. Pharmacodynamic modeling facilitated establishing an in vitro to in vivo correlation for histamine as a biomarker for blood pressure decline via the MCD mechanism. These models enabled assessment of structure-activity relationship (SAR) to identify substructures that contribute to peptide-mediated MCD. Peptides with hydrophobic and cationic characteristics were determined to have an elevated risk for MCD, which could be reduced or avoided by incorporating anionic residues into the protoxin II scaffold. Our analyses support that in vitro MCD assessment in combination with PKPD modeling can guide SAR to improve peptide lead optimization and ensure an acceptable early in vivo tolerability profile with reduced resources, cycle time, and animal use.