bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irony with a Point: Alan Turing and His Intelligent Machine Utopia
Authors: Gonçalves Bernardo 
Published: July 2023

AbstractTuring made strong statements about the future of machines in society. This article asks how they can be interpreted to advance our understanding of Turing’s philosophy. His irony has been largely caricatured or minimized by historians, philosophers, scientists, and others. Turing is often portrayed as an irresponsible scientist, or associated with childlike manners and polite humor. While these representations of Turing have been widely disseminated, another image suggested by one of his contemporaries, that of a nonconformist, utopian, and radically progressive thinker reminiscent of the English Romantic poet Percy B. Shelley, has remained largely underexplored. Following this image, I will reconstruct the argument underlying what Turing called (but denied being guilty of) his “Promethean irreverence” (1947–1951) as a utopian satire directed against chauvinists of all kinds, especially intellectuals who might sacrifice independent thought to maintain their power. These, Turing hoped, would eventually be rivaled and surpassed by intelligent machines and transformed into ordinary people, as work once considered “intellectual” would be transformed into non-intellectual, “mechanical” work. I study Turing’s irony in its historical context and follow the internal logic of his arguments to their limit. I suggest that Turing genuinely believed that the possibilities of the machines he envisioned were not utopian dreams, and yet he conceived them from a utopian frame of mind, aspiring to a different society. His ever-learning child machines, whose intelligence would grow out of their own individual experiences, would help distribute power.
Beyond Anatomy: The Role of Molecular Imaging in the Evaluation of Low Back Pain
Authors: Sweetwood Kevin , Junn Jacqueline C. , Qiao Yujie , Berven Sigurd , Shah Vinil , Pampaloni Miguel Hernandez , Flavell Robert R. , Dillon William , Talbott Jason , Lawhn-Heath Courtney 
Published: July 2023

AbstractPurpose of ReviewTo review the role of molecular imaging modalities in the evaluation of low back pain and identification of active pain generators.Recent FindingsLow back pain is a common condition associated with high utilization of imaging. Identification of a pain source in patients with nonspecific low back pain is an important clinical challenge. However, there is inadequate correlation between anatomic findings on CT and MRI with symptoms of back pain, or clinical response to therapeutic procedures including injection or surgery. In contrast, molecular imaging modalities including single-photon emission-computed tomography (SPECT) or positron emission tomography (PET) with bone-targeting radiotracers like Tc-99m methylene diphosphonate (MDP) and18F-NaF paired with CT or MRI demonstrate promise to improve test specificity in identification of pain generators in the spine. An accurate identification of pain source in patients with back pain is important in guiding therapeutic interventions including injection and surgery.SummaryMolecular imaging modalities have demonstrated improved diagnostic accuracy in identifying active pain generators and predicting response to therapeutic intervention compared to anatomic imaging alone.
A scalable physically consistent particle method for high-viscous incompressible flows
Authors: Kondo Masahiro , Matsumoto Junichi , Sawada Tomohiro 
Published: July 2023

AbstractA scalable matrix solver was developed for the moving particle hydrodynamics for incompressible flows (MPH-I) method. Since the MPH-I method can calculate both incompressible and highly viscous flows while ensuring stability through physical consistency, a wide range of industrial applications is expected. However, in its implicit calculation, both the pressure and velocity must be solved simultaneously via a linear equation with a nondefinite symmetric coefficient matrix. In this study, this nondefinite linear system was converted into a symmetric positive definite (SPD) system where only the velocity is unknown. This conversion enabled us to solve the system with well-known solvers such as the conjugated gradient (CG) and conjugated residual (CR) methods. For scalability, bucket-based multigrid preconditioned CG and CR solvers were developed for the SPD system. To handle multidimensionality during preconditioning, an extended Jacobi smoother that is even applicable in a nondiagonally dominant matrix system was proposed. The numerical efficiency was confirmed via a simple high-viscosity incompressible dam break calculation, and the scalability within the presented case was confirmed. In addition, the performance under shared memory parallel computations was studied.
Distribution and Disputation: Net Benefits, Equity, and Public Decision-Making
Authors: Banzhaf H. Spencer 
Published: July 2023

AbstractAs its practitioners know well, benefit-cost analysis (BCA) walks a fine line between the positive and normative, between the science of economics and the art of political economy. Missteps threaten to undermine its credibility as a value-free science, while overcaution risks irrelevance to the pressing questions of the day. As BCA adapts to give more weight to distributional concerns, while operating in a more highly charged political environment than ever before, these tensions will only grow. For perspective, I reexamine three prominent episodes in the history of economics where these issues were vigorously debated: (i) The founding of the NBER by Wesley Clair Mitchell, who insisted that the organization eschew all policy recommendations; (ii) the introduction of the modern definition of economics as the study of tradeoffs by Lionel Robbins, who insisted welfare effects could never be aggregated; and (iii) the origins of BCA as a measure of income, which to first-generation practitioners seemed to foreclose the possibility of measuring “intangible” benefits like recreation opportunities, mortality risks, and equity. These episodes, together with critiques of economics from philosophers of science, suggest we are best served by being as transparent as possible about the ways values influence BCA reasoning, without arrogating political decisions into it.
Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity
Authors: Houtkamp Isabel M. , van Zijll Langhout Martine , Bessem Mark , Pirovano Walter , Kort Remco 
Published: July 2023

Abstract
We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate-active and methanogenic potential of the zoo-housed gorilla (ZHG) microbiome through shotgun metagenomics and RNA sequencing. The ZHG microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fibre-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the ZHG gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.
Limited knowledge of national plastics policy effectiveness may hinder global progress
Authors: March Antaya , Karasik Rachel , Roberts Keiron , Evans Tegan 
Published: July 2023

Abstract
Policy effectiveness is a critical measure for assessing whether policies are working and determining necessary adjustments. However, understanding the effectiveness of plastic policies is a significant gap in the toolkit driving solutions to the plastics crisis. This review examines effectiveness evaluations and existing tools for assessing policy effectiveness. The review further identifies the barriers to understanding effectiveness before proposing ways forward. Most studies focus on plastic bag bans or taxes, neglecting other policy instruments. Additionally, these studies often employ simple attribution approaches, rather than causal inference methods, limiting our ability to determine the true impact of policies on desired outcomes. The lack of monitoring and evaluation of plastic policies further hampers knowledge acquisition. The global understanding of the plastics economy and measurable success metrics is insufficient, hindering the design of systemic interventions. These findings highlight the development and evaluation of plastic policies with limited information. A more nuanced understanding of effective plastic policies is necessary, including a harmonised approach to evaluations, a shared definition of effectiveness, the use of rapid assessment tools and the integration of monitoring and evaluation into policy instruments.
Atrial septal defect-associated pulmonary hypertension with decompensated heart failure: outcomes after fenestrated device closure
Authors: Deniwar Ahmed , Hernandez Jason , Aregullin Enrique O. , Khan Sana K. , Huang Sihong , Finn Michael T. , Vettukattil Joseph J. 
Published: July 2023

AbstractBackground:Up to 90% of adults with untreated atrial septal defect will be symptomatic by 4th decade, and 30-49% will develop heart failure. 8–10% of these patients have pulmonary arterial hypertension with a female predominance regardless of age. We aimed to demonstrate that fenestrated closure can be safely performed in patients with decompensated heart failure and atrial septal defect-associated pulmonary arterial hypertension with improved outcome.Methods:Transcatheter fenestrated atrial septal defect closures (Occlutech GmbH, Jena, Germany) were performed on a compassionate-use basis in 5 consecutive adult patients with atrial septal defect-associated pulmonary arterial hypertension and severe heart failure with prohibitive surgical mortality risks. Change in systemic oxygen saturation, 6-minute walk test, NYHA class, echocardiographic and haemodynamic parameters were used as parameters of outcome.Results:All patients were female, mean age 48.8 ± 13.5 years, followed up for a median of 29 months (max 64 months). Significant improvements observed in the 6-minute walk test, and oxygen saturation comparing day 0 time point to all other follow-up time points data (B = 1.32, SE = 0.28, t (22.7) = -4.77, p = 0.0001); and in the haemodynamic data (including pulmonary vascular resistance and pulmonary pressure) (B = –0.60, SE = 0.22, t (40.2) = 2.74, p = .009). All patients showed improved right ventricular size and function along with NYHA class. There were no procedure-related complications.Conclusion:Fenestrated atrial septal defect closure is feasible in adults with decompensated heart failure and atrial septal defect-associated pulmonary arterial hypertension. It results in sustained haemodynamic and functional improvement
A Comparison of Plasticity Regularization Approaches for Geodynamic Modeling
Authors: Duretz Thibault , Räss Ludovic , de Borst René , Hageman Tim 
Published: July 2023

AbstractThe emergence, geometry and activation of faults are intrinsically linked to frictional rheology. The latter is thus a central element in geodynamic simulations which aim at modeling the generation and evolution of fault zones and plate boundaries. However, resolving frictional strain localization in geodynamic models is problematic. In simulations, equilibrium cannot always be attained and results can depend on mesh resolution. Spatial and temporal regularization techniques have been developed to alleviate these issues. Herein, we investigate three popular regularization techniques, namely viscoplasticity, gradient plasticity and the use of a Cosserat continuum. These techniques have been implemented in a single framework based on an accelerated pseudo‐transient solution strategy. The latter allows to explore the effects of regularization on shear banding using the same code and model configuration. We have used model configurations that involve three levels of complexity: from the emergence of a single isolated shear band to the visco‐elasto‐plastic stress buildup of a crust. All considered approaches allow to resolve shear banding, provide convergence upon mesh refinement and satisfaction of equilibrium. Viscoplastic regularization is straightforward to implement in geodynamic codes. Nevertheless, more stable shear banding patterns and strength estimates are achieved with computationally more expensive gradient and Cosserat‐type regularizations. We discuss the relative benefits of these techniques and their combinations for geodynamic modeling. Emphasis is put on the potential of Cosserat‐type media for geodynamic applications.
Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease
Authors: Mullari Meeli , Fossat Nicolas , Skotte Niels H. , Asenjo-Martinez Andrea , Humphreys David T. , Bukh Jens , Kirkeby Agnete , Scheel Troels K. H. , Nielsen Michael L. 
Published: July 2023

AbstractRNA-binding proteins (RBPs) are key players regulating RNA processing and are associated with disorders ranging from cancer to neurodegeneration. Here, we present a proteomics workflow for large-scale identification of RBPs and their RNA-binding regions in the mammalian brain identifying 526 RBPs. Analysing brain tissue from males of the Huntington’s disease (HD) R6/2 mouse model uncovered differential RNA-binding of the alternative splicing regulator RBM5. Combining several omics workflows, we show that RBM5 binds differentially to transcripts enriched in pathways of neurodegeneration in R6/2 brain tissue. We further find these transcripts to undergo changes in splicing and demonstrate that RBM5 directly regulates these changes in human neurons derived from embryonic stem cells. Finally, we reveal that RBM5 interacts differently with several known huntingtin interactors and components of huntingtin aggregates. Collectively, we demonstrate the applicability of our method for capturing RNA interactor dynamics in the contexts of tissue and disease.
An unconventional proanthocyanidin pathway in maize
Authors: Lu Nan , Jun Ji Hyung , Li Ying , Dixon Richard A. 
Published: July 2023

AbstractProanthocyanidins (PAs), flavonoid polymers involved in plant defense, are also beneficial to human health and ruminant nutrition. To date, there is little evidence for accumulation of PAs in maize (Zea mays), although maize makes anthocyanins and possesses the key enzyme of the PA pathway, anthocyanidin reductase (ANR). Here, we explore whether there is a functional PA biosynthesis pathway in maize using a combination of analytical chemistry and genetic approaches. The endogenous PA biosynthetic machinery in maize preferentially produces the unusual PA precursor (+)-epicatechin, as well as 4β-(S-cysteinyl)-catechin, as potential PA starter and extension units. Uncommon procyanidin dimers with (+)-epicatechin as starter unit are also found. Expression of soybean (Glycine max) anthocyanidin reductase 1 (ANR1) in maize seeds increases the levels of 4β-(S-cysteinyl)-epicatechin and procyanidin dimers mainly using (-)-epicatechin as starter units. Introducing a Sorghum bicolor transcription factor (SbTT2) specifically regulating PA biosynthesis into a maize inbred deficient in anthocyanin biosynthesis activates both anthocyanin and PA biosynthesis pathways, suggesting conservation of the PA regulatory machinery across species. Our data support the divergence of PA biosynthesis across plant species and offer perspectives for future agricultrural applications in maize.
Tuning electronic and phononic states with hidden order in disordered crystals
Authors: Roth Nikolaj , Goodwin Andrew L. 
Published: July 2023

AbstractDisorder in crystals is rarely random, and instead involves local correlations whose presence and nature are hidden from conventional crystallographic probes. This hidden order can sometimes be controlled, but its importance for physical properties of materials is not well understood. Using simple models for electronic and interatomic interactions, we show how crystals with identical average structures but different types of hidden order can have very different electronic and phononic band structures. Increasing the strength of local correlations within hidden-order states can open band gaps and tune mode (de)localisation—both mechanisms allowing for fundamental changes in physical properties without long-range symmetry breaking. Taken together, our results demonstrate how control over hidden order offers a new mechanism for tuning material properties, orthogonal to the conventional principles of (ordered) structure/property relationships.
Organization of the human intestine at single-cell resolution
Authors: Hickey John W. , Becker Winston R. , Nevins Stephanie A. , Horning Aaron , Perez Almudena Espin , Zhu Chenchen , Zhu Bokai , Wei Bei , Chiu Roxanne , Chen Derek C. , Cotter Daniel L. , Esplin Edward D. , Weimer Annika K. , Caraccio Chiara , Venkataraaman Vishal , Schürch Christian M. , Black Sarah , Brbić Maria , Cao Kaidi , Chen Shuxiao , Zhang Weiruo , Monte Emma , Zhang Nancy R. , Ma Zongming , Leskovec Jure , Zhang Zhengyan , Lin Shin , Longacre Teri , Plevritis Sylvia K. , Lin Yiing , Nolan Garry P. , Greenleaf William J. , Snyder Michael 
Published: July 2023

AbstractThe intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function. Here, to better understand these differences, we evaluated the organization of single cells using multiplexed imaging and single-nucleus RNA and open chromatin assays across eight different intestinal sites from nine donors. Through systematic analyses, we find cell compositions that differ substantially across regions of the intestine and demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighbourhoods and communities, highlighting distinct immunological niches that are present in the intestine. We also map gene regulatory differences in these cells that are suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation and organization for this organ, and serve as an important reference map for understanding human biology and disease.
Chromosome-level genome assembly of watershield (Brasenia schreberi)
Authors: Lu Bei , Shi Tao , Chen Jinming 
Published: July 2023

AbstractWatershield (Brasenia schreberi) is an aquatic plant that belongs to the basal angiosperm family Cabombaceae. This species has been cultivated as an aquatic vegetable for more than 3000 years in East Asia, but the natural populations have greatly declined in recent decades and have become endangered in several countries of East Asia. In this study, by using PacBio long reads, Illumina short reads, and Hi-C sequencing data, we assembled the genome of B. schreberi, which was approximately 1170.4 Mb in size with a contig N50 of 7.1 Mb. Of the total assembled sequences, 93.6% were anchored to 36 pseudochromosomes with a scaffold N50 of 28.9 Mb. A total of 74,699 protein-coding genes were predicted in the B. schreberi genome, and 558 Mb of repetitive elements occupying 47.69% of the genome were identified. BUSCO analysis yielded a completeness score of 95.8%. The assembled high-quality genome of B. schreberi will be a valuable reference for the study of conservation, evolution and molecular breeding in this species.
Biobank-scale methods and projections for sparse polygenic prediction from machine learning
Authors: Raben Timothy G. , Lello Louis , Widen Erik , Hsu Stephen D. H. 
Published: July 2023

AbstractIn this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of $$0.63_{(0.02)}$$

0
.

63

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and for height a correlation of $$0.648_{(0.009)}$$

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.

648

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0.009
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for a Taiwanese population. This is above the measured values of $$0.61_{(0.01)}$$

0
.

61

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0.01
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and $$0.631_{(0.008)}$$

0
.

631

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, respectively, for UK Biobank trained predictors applied to a European population.
Occipital and parietal cortex participate in a cortical network for transsaccadic discrimination of object shape and orientation
Authors: Baltaretu B. R. , Stevens W. Dale , Freud E. , Crawford J. D. 
Published: July 2023

AbstractSaccades change eye position and interrupt vision several times per second, necessitating neural mechanisms for continuous perception of object identity, orientation, and location. Neuroimaging studies suggest that occipital and parietal cortex play complementary roles for transsaccadic perception of intrinsic versus extrinsic spatial properties, e.g., dorsomedial occipital cortex (cuneus) is sensitive to changes in spatial frequency, whereas the supramarginal gyrus (SMG) is modulated by changes in object orientation. Based on this, we hypothesized that both structures would be recruited to simultaneously monitor object identity and orientation across saccades. To test this, we merged two previous neuroimaging protocols: 21 participants viewed a 2D object and then, after sustained fixation or a saccade, judged whether the shape or orientation of the re-presented object changed. We, then, performed a bilateral region-of-interest analysis on identified cuneus and SMG sites. As hypothesized, cuneus showed both saccade and feature (i.e., object orientation vs. shape change) modulations, and right SMG showed saccade-feature interactions. Further, the cuneus activity time course correlated with several other cortical saccade/visual areas, suggesting a ‘functional network’ for feature discrimination. These results confirm the involvement of occipital/parietal cortex in transsaccadic vision and support complementary roles in spatial versus identity updating.