bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural network training with highly incomplete medical datasets
Authors: Chang Yu-Wei , Natali Laura , Jamialahmadi Oveis , Romeo Stefano , Pereira Joana B , Volpe Giovanni 
Published: June 2022

Abstract
Neural network training and validation rely on the availability of large high-quality datasets. However, in many cases only incomplete datasets are available, particularly in health care applications, where each patient typically undergoes different clinical procedures or can drop out of a study. Since the data to train the neural networks need to be complete, most studies discard the incomplete datapoints, which reduces the size of the training data, or impute the missing features, which can lead to artifacts. Alas, both approaches are inadequate when a large portion of the data is missing. Here, we introduce GapNet, an alternative deep-learning training approach that can use highly incomplete datasets without overfitting or introducing artefacts. First, the dataset is split into subsets of samples containing all values for a certain cluster of features. Then, these subsets are used to train individual neural networks. Finally, this ensemble of neural networks is combined into a single neural network whose training is fine-tuned using all complete datapoints. Using two highly incomplete real-world medical datasets, we show that GapNet improves the identification of patients with underlying Alzheimer’s disease pathology and of patients at risk of hospitalization due to Covid-19. Compared to commonly used imputation methods, this improvement suggests that GapNet can become a general tool to handle incomplete medical datasets.
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
Authors: Ye Cheng , Thornlow Bryan , Hinrichs Angie , Kramer Alexander , Mirchandani Cade , Torvi Devika , Lanfear Robert , Corbett-Detig Russell , Turakhia Yatish 
Published: June 2022

AbstractMotivationPhylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the coronavirus disease 2019 (COVID-19) pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic.ResultsHere, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. matOptimize is currently helping refine on a daily basis possibly the largest-ever phylogenetic tree, containing millions of SARS-CoV-2 sequences.Availability and implementationThe matOptimize code is freely available as part of the UShER package (https://github.com/yatisht/usher) and can also be installed via bioconda (https://bioconda.github.io/recipes/usher/README.html). All scripts we used to perform the experiments in this manuscript are available at https://github.com/yceh/matOptimize-experiments.Supplementary informationSupplementary data are available at Bioinformatics online.
Linking α-synuclein-induced synaptopathy and neural network dysfunction in early Parkinson’s disease
Authors: Kulkarni Aishwarya S , Burns Matthew R , Brundin Patrik , Wesson Daniel W 
Published: June 2022

AbstractThe prodromal phase of Parkinson’s disease is characterized by aggregation of the misfolded pathogenic protein α-synuclein in select neural centres, co-occurring with non-motor symptoms including sensory and cognitive loss, and emotional disturbances. It is unclear whether neuronal loss is significant during the prodrome. Underlying these symptoms are synaptic impairments and aberrant neural network activity. However, the relationships between synaptic defects and network-level perturbations are not established. In experimental models, pathological α-synuclein not only impacts neurotransmission at the synaptic level, but also leads to changes in brain network-level oscillatory dynamics—both of which likely contribute to non-motor deficits observed in Parkinson’s disease. Here we draw upon research from both human subjects and experimental models to propose a ‘synapse to network prodrome cascade’ wherein before overt cell death, pathological α-synuclein induces synaptic loss and contributes to aberrant network activity, which then gives rise to prodromal symptomology. As the disease progresses, abnormal patterns of neural activity ultimately lead to neuronal loss and clinical progression of disease. Finally, we outline goals and research needed to unravel the basis of functional impairments in Parkinson’s disease and other α-synucleinopathies.
From learners to users—errors, innovations, and universals
Authors: Ranta Elina 
Published: June 2022

Abstract
This paper looks into the dilemma of what counts as a grammatical ‘learner error’ in ELT on the basis of recent results from English variationist research and English as a lingua franca research. Examples from these studies show that features often perceived as ‘errors’ for EFL speakers also occur in ESL production—where they are called ‘innovations’—and even in English as a native language (ENL) production—where the term ‘spoken language universal’ would seem more appropriate. It is proposed that the traditional categorization of English speakers into EFL, ESL, and ENL actually hinders us from seeing the linguistic realities of the English-speaking world, disfavouring EFL speakers in particular. The paper calls for ELT to see EFL speakers as users of the language rather than learners in order to acknowledge their grammatical creativity as similar to that of other speakers of English.
Pandemic-Related Social Disruption and Well-Being in Pediatric Gastrointestinal Diseases
Authors: Robbertz Abigail S , Cohen Lindsey L , Armistead Lisa P , Reed Bonney 
Published: June 2022

Abstract

Objective
The coronavirus disease 2019 (COVID-19) pandemic has impacted everyone, but there are few data regarding how the pandemic has influenced the lives of children with gastrointestinal (GI) conditions. This cross-sectional study assessed pandemic-related social disruption (PRSD) in children with inflammatory bowel disease (IBD), celiac disease (CD), and irritable bowel syndrome (IBS), and the potential buffering effect of the parent–child relationship.

Methods
A survey completed between September and December 2020 asked 146 children (ages 8–17) diagnosed with IBD (n = 44), CD (n = 81), or IBS (n = 51) and 185 parents how the pandemic has contributed to social disruption (i.e., financial stability, COVID-19 exposure, school changes, GI needs, and isolation) and their social–emotional well-being. Structural equation modeling was used to examine the role of social disruption on well-being, and the moderating effect of the parent–child relationship.

Results
Increased social disruption predicted worse parent, β = 0.24, p = .02, and child well-being, β = 0.38, p &lt; .01. The parent–child relationship moderated the relationship between parent and child well-being, β = 0.21, p = .03. Strong parent–child relationships predicted a positive association between parent and child well-being, β = 0.23, p = .003, whereas medium, β = 0.09, p = .14, and poor, β = −0.06, p = .52, relationships did not.

Conclusions
PRSD negatively impacted the well-being of children with GI conditions, and the parent–child relationship moderated this relationship. These findings are relevant to pediatric psychologists treating the physical and mental health needs of children with GI conditions and their parents.
Simplexviruses Successfully Adapt to Their Host by Fine-Tuning Immune Responses
Authors: Mozzi Alessandra , Cagliani Rachele , Pontremoli Chiara , Forni Diego , Saulle Irma , Saresella Marina , Pozzoli Uberto , Cappelletti Gioia , Vantaggiato Chiara , Clerici Mario , Biasin Mara , Sironi Manuela 
Published: June 2022

AbstractPrimate herpes simplex viruses are species-specific and relatively harmless to their natural hosts. However, cross-species transmission is often associated with severe disease, as exemplified by the virulence of macacine herpesvirus 1 (B virus) in humans. We performed a genome-wide scan for signals of adaptation of simplexviruses to their hominin hosts. Among core genes, we found evidence of episodic positive selection in three glycoproteins, with several selected sites located in antigenic determinants. Positively selected noncore genes were found to be involved in different immune-escape mechanisms. The herpes simplex virus (HSV)-1/HSV-2 encoded product (ICP47) of one of these genes is known to down-modulate major histocompatibility complex class I expression. This feature is not shared with B virus, which instead up-regulates Human Leukocyte Antigen (HLA)-G, an immunomodulatory molecule. By in vitro expression of different ICP47 mutants, we functionally characterized the selection signals. Results indicated that the selected sites do not represent the sole determinants of binding to the transporter associated with antigen processing (TAP). Conversely, the amino acid status at these sites was sufficient to determine HLA-G up-regulation. In fact, both HSV-1 and HSV-2 ICP47 induced HLA-G when mutated to recapitulate residues in B virus, whereas the mutated version of B virus ICP47 failed to determine HLA-G expression. These differences might contribute to the severity of B virus infection in humans. Importantly, they indicate that the evolution of ICP47 in HSV-1/HSV-2 led to the loss of an immunosuppressive effect. Thus, related simplexviruses finely tune the balance between immunosuppressive and immunostimulatory pathways to promote successful co-existence with their primate hosts.
Evaluation of anti-severe acute respiratory syndrome coronavirus 2 antibody levels in coronavirus disease breakthrough infection during immunosuppressive therapy in a patient with connective tissue disease-related interstitial lung disease
Authors: Wada Takuma Tsuzuki , Yokota Kazuhiro , Sakai Sakon , Soma Machika , Kajiyama Hiroshi , Tarumoto Norihito , Maesaki Shigefumi , Maeda Takuya , Nagata Makoto , Mimura Toshihide 
Published: June 2022

ABSTRACT
Herein, we report the case of a 67-year-old man with severe coronavirus disease (COVID-19) pneumonia and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccine breakthrough infection during immunosuppressive therapy for connective tissue disease-related interstitial lung disease (CTD-ILD). The patient received glucocorticoids combined with tacrolimus as maintenance therapy. His serum anti-SARS-CoV-2-immunoglobulin G (IgG) antibody levels were extremely low at the onset of COVID-19 pneumonia, even after the second dose of SARS-CoV-2 mRNA vaccine (BNT162b2). After treatment for COVID-19 pneumonia, the levels of anti-SARS-CoV-2-IgG antibodies increased. These results indicated a lack of the ability to produce neutralising antibodies from immune cells despite the booster vaccination. Therefore, we suggest that advanced-age patients with CTD-ILD receiving immunosuppressive therapy with polypharmacy require consistent personal protection, vaccination of close caregivers, increased awareness, and booster vaccination. Moreover, we recommend that tacrolimus should be withdrawn for a while after vaccination under controlled conditions.
Efficacy and toxicity with radiation field designs and concurrent temozolomide for CNS lymphoma
Authors: Laucis Anna M , Selwa Katherine , Sun Yilun , Kim Michelle M , Cuneo Kyle C , Lawrence Theodore S , Wahl Daniel R , Junck Larry , Umemura Yoshie 
Published: June 2022

Abstract

Background
There is no consensus on the treatment of central nervous system (CNS) lymphoma refractory to first-line methotrexate-based chemotherapy. Whole brain radiotherapy (WBRT) is sometimes used but may result in unacceptable neurocognitive dysfunction. We examined the efficacy and toxicities of WBRT with or without concurrent temozolomide in CNS lymphoma treatment.

Methods
This single-institution IRB-approved retrospective study included adults with CNS lymphoma who received WBRT, either consolidative low-dose WBRT alone or low-dose WBRT with a focal boost to residual disease and were previously treated with high-dose methotrexate. The relationships between the WBRT regimen, concurrent temozolomide, and clinical outcomes and toxicities were assessed using proportional hazards and logistic regression models.

Results
A total of 45 patients with a median age of 64 years (range 24–74) treated from 2004 to 2019 were included. In total, 20 patients received concurrent temozolomide. In the WBRT + Boost cohort (n = 32), concurrent temozolomide resulted in better 2-year overall survival (OS) and progression free survival (PFS) (73% OS and 66% PFS) compared to patients treated without concurrent temozolomide (44% OS and 24% PFS). On multivariate analysis, concurrent temozolomide was associated with significantly better PFS (HR 0.28, P = .02). There were no significant differences between the two radiation groups or between those treated with or without concurrent temozolomide, with respect to significant acute hematologic, non-hematologic, and long-term neurocognitive toxicities (P &gt; .05).

Conclusions
In this study, concurrent temozolomide with radiotherapy in CNS lymphoma was associated with better PFS and was well tolerated. Low-dose WBRT with a boost is a safe and reasonable treatment approach for focal refractory disease. Prospective research that includes rigorous neurocognitive assessments is now warranted.
Three Problems
Authors: Dove Guy 
Published: June 2022

Abstract
This chapter examines the ways in which abstract concepts threaten grounded cognition. The author argues that abstract concepts pose at least three distinct theoretical challenges: the problems of generalization, disembodiment, and flexibility. The problem of generalization emerges in the context of conceptual hierarchies where higher-level concepts are more abstract than lower-level concepts. It is hard to see how such abstractions can be captured solely by means of primary sensorimotor representations. The problem of disembodiment arises because some abstract concepts lack any clear connections to our immediate experiences. Such concepts are not likely to arise from merely abstracting away from experiential particulars. Finally, the problem of flexibility arises because the content of abstract concepts tends to vary more in response to context than the content of concrete concepts. Each of these imperils the hypothesis that conceptual processing depends entirely on simulations of experience. Any successful account of grounded cognition must address all of them.
Hierarchies and Hubs
Authors: Dove Guy 
Published: June 2022

Abstract
This chapter focuses on the problem generalization raised by abstract concepts. After demonstrating that multimodal and multilevel structure are common design features of human action, emotion, and perception systems, the author proposes that higher-level representations help us generalize and abstract away from experiential particulars. This hypothesis is supported by neuroimaging and neuropsychological evidence implicating these sorts of representations in conceptual processing. Evidence from neuropsychological case studies also suggests that conceptual content is encoded through the interaction of higher-level heteromodal “hubs” with lower-level experiential “spokes.” It concludes that an account of grounded cognition that posits hierarchical organization is well-positioned to address the problem of generalization.
Heterogeneity
Authors: Dove Guy 
Published: June 2022

Abstract
This chapter defends the claim that abstract concepts are heterogeneous. It reviews the emerging body of evidence suggesting that different types of abstract concepts are grounded in different ways. Abstract concepts can be distinguished in terms of the degree to which they evoke action, emotion, exteroceptive, interoceptive, and linguistic systems. Some appear to rely more on sensorimotor features, others appear to rely more on emotions or inner experiences, and others still appear to rely more on verbal associations. The author discusses how our ability to process abstract concepts of various stripes is dependent on the multidimensional nature of our conceptual system.
Gendered History of Immigration and Political Socialization in the Election of Asians
Authors: Lien Pei-te , Filler Nicole 
Published: June 2022

Abstract
This chapter opens with a brief review of the gendered history of immigration and settlement patterns of the Asian population by major ethnic or national origins. This historical account helps contextualize the significance of international migration in the political socialization of pioneering women and men in elective offices and other trailblazers in each Asian ethnic community. The narration follows chronological order by the year of winning the first office, segmented by geographic state, ethnicity, and gender. The information presented is salvaged from scarce and scattered accounts of these pioneers regarding their family background, political socialization, and motivation to run for the first office. The chapter interprets the impacts of immigration generation, traumatic political events, ethnic and gender identities, and family class background on the socialization and politicization of those individuals elected to office after the political “firsts,” all of which have played a significant role in the development of political incorporation in each major Asian ethnic community to the present day.
Conclusion
Authors: Lien Pei-te , Filler Nicole 
Published: June 2022

Abstract
The chapter summarizes the political trajectories of APAEOs through the stories of two pioneering male California state legislators. Their encounters of racism are compared to what happened to a group of mostly female APAEOs serving in different offices and localities during the Covid-19 era. The chapter then contrasts the assimilationist with the proactive reactions of APAEOs to anti-Asian hate. It highlights the specific ways of advancing justice by APAEOs serving at national, state, and local levels of office in 2020–21. Through case studies of Hmong Americans, the chapter showcases a new generation of APAEOs who achieved subnational incorporation by engaging local nonethnic, ethnic, women-centered, and/or partisan organizations and groups. It then presents a systematic analysis of the growing roles of nonpartisan ethnic and nonethnic but women-centered and mostly partisan organizations in building the political infrastructure for APA incorporation and empowerment. In closing, the chapter reminds readers of the heritage of advancing justice by APAEOs.
Dark Satanic Mills
Authors: Whittaker Jason 
Published: June 2022

Abstract
During the 1920s and 1930s, ‘Jerusalem’ became more widely known and performed among various communities, helping to build up a sense of national identity after the devastation caused by the First World War. This chapter describes its various uses—in church congregations, in anthologies produced for various Christian organizations as well as for secular collections, and by the Women’s Institute—as well as how the poem and song (which assumed the status of a hymn for some, for others that of an anthem) represented conflicting imperial and socialist visions of British society in the lead up to the Second World War.
The Background
Authors: Wilson Catherine 
Published: June 2022

Abstract
Atomism and mechanism were reintroduced into European natural philosophy by Galileo and Descartes. Opposing the ‘mechanical philosophy’ as both atheistic and inadequate to the explanation of many phenomena, especially generation, biological functions, and chemistry, some theorists demanded a greater range of active powers and/or a more active role for God in maintaining the universe. Newton’s work legitimised reference to both. A different tack was taken by Leibniz, who retained a conservative form of mechanism but at the same time dematerialised the atom and proposed a form of panvitalism. Kant’s own largely unsuccessful struggles with the problems of life and matter are to be understood against this challenging background.
Civilization, Extinction, and Moral Effort
Authors: Wilson Catherine 
Published: June 2022

Abstract
Enlightenment pessimism was the dialectical complement to the more familiar Enlightenment optimism based in signs of technological progress and faith in the guiding hand of Providence. Eighteenth century Europeans were disheartened by unremitting warfare, the immiseration of the peasantry, the mania for conquest, and the stumbling blocks to reform posed by autocratic rulers. New threats to complacency—and incentives to Epicurean hedonism—emerged in palaeological evidence for the extinction of entire species and widening scepticism over the immortality of the soul and the joys and compensations of heaven. Kant’s view of human nature became increasingly dark, but he strongly resisted the arguments of Rousseau and Herder regarding the corrupting influence of civilisation and the European domination of the globe.
Political Settlements and Development
Authors: Kelsall Tim , Schulz Nicolai , Ferguson William D. , vom Hau Matthias , Hickey Sam , Levy Brian 
Published: June 2022

Abstract
Few concepts have captured the imagination of the conflict and development communities in recent years as powerfully as the idea of a ‘political settlement’. At its most ambitious, ‘political settlements analysis’ (PSA) promises to explain why conflicts occur and states collapse, the conditions for their successful rehabilitation, different developmental pathways from peace, and how to better fit development policy to country context. Yet despite the meteoric rise of the term and its tremendous promise, not all is well in the world of PSA. Rival definitions of the concept abound; there are disagreements about its scope and the way it should be used; a growing schism between conflict specialists and economists; basic concepts are ambiguous; and little progress has been made on measurement. This book consequently has three main aims. The first is to argue for a revised definition of a political settlement, capable of unifying its diverse strands. The second is to put the concept on a more solid theoretical and scientific footing, providing a method for measuring and categorizing political settlements, using both qualitative case studies and a large-n statistical analysis to illustrate its potential. And the third is to examine the implications of the findings for mainstream social science analysis and for policymakers.