bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Argument from Neural Wiring
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
This chapter presents the fifth of our seven arguments for concept nativism—the argument from neural wiring. Considerations centred around the brain’s plasticity have been widely taken to argue for empiricist views of conceptual development and against rationalist views. The argument from neural wiring turns this traditional wisdom on its head, arguing that considerations centred around the brain’s plasticity can provide a powerful form of argument for concept nativism and against concept empiricism. As with the previous chapters in Part II, our discussion in this chapter has a dual focus. It aims both to clarify the logic of the argument from neural wiring and to use this argument to continue building the case for our version of concept nativism. The main case studies discussed focus on representations of space and motion, faces and individuals, living and non-living kinds, tools, action categories, and mental states.
The Argument from Cognitive and Behavioural Quirks
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
This chapter presents the seventh of our seven arguments for concept nativism—the argument from cognitive and behavioural quirks. This argument is another relatively unknown argument for concept nativism. The quirky phenomena referred to by this argument are surprising or unexpected facts about people’s minds or behaviour that are especially puzzling if it is assumed that concept acquisition is a purely domain-general process. As in the previous chapters in Part II, our discussion has a dual focus. It aims both to clarify the logic of the argument from cognitive and behavioural quirks and to use this argument to continue building the case for our version of concept nativism. The main case studies discussed focus on representations of route selection, social categorization, and physical reasoning.
Methodological Empiricism
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
In Part IV of the book we examine a representative sample of the most important and influential empiricist challenges and alternatives to concept nativism. In this chapter, we begin with the challenge stemming from what we call methodological empiricism. This widely held view contends that empiricist approaches should be considered the default position in the rationalism-empiricism debate about the origins of concepts and that rationalism should only be considered as a last resort if all possible empiricist alternatives have been ruled out. Our discussion of this challenge is centred around the origins of the concept of physical objects, but the morals of our discussion generalize. We show that there are no grounds for accepting methodological empiricism as a general position, and that consideration of the argument as applied to the case of the concept of physical objects only provides further support for concept nativism in this domain.
Neo-Associationism
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
This chapter examines what may be the most important and influential form of empiricism: associationism. It distinguishes and examines two ways in which processes of association play an important role in contemporary empiricist theorizing. The first of these focuses on evidence that rationalists have cited in favour of concept nativism, arguing that such data are better explained by deflationary accounts in terms of learned associations involving low-level perceptual properties. The second offers positive proposals for the origins of concepts that are exhausted by domain-general associative processes. To evaluate these two forms of associationism, we provide an in-depth analysis of their prospects regarding a domain that constitutes an ideal test case: the domain of sociomoral cognition. We show that neither form of associationism works in this domain and explain why this means that associationism is unable to provide a plausible general alternative to concept nativism.
The Argument from Prepared Learning
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
This chapter presents the sixth of our seven arguments for concept nativism—the argument from prepared learning. This argument was once a well-known argument for rationalist views of cognitive and conceptual development, but it has been neglected as a form of argument for rationalism in recent years. At the heart of the argument is the fact that learning often does not happen equally easily across different conceptual domains and that patterns in the relative ease or difficulty of learning across different conceptual domains can argue for the existence of rationalist learning mechanisms. As in the previous chapters in Part II, our discussion has a dual focus. It aims both to clarify the logic of the argument from prepared learning and to use this argument to continue building the case for our version of concept nativism. The main case studies discussed focus on representations of animals, danger, food, teleology, and emotion.
Urban Community Practice Realm
Authors: Delgado Melvin 
Published: July 2024

Abstract
Preserving an empty closed church for historical purposes is not always economically feasible. Thus, a fundamental decision will need to be made—tear the building down and erect a new structure, or keep the building and repurpose it for a new mission. If repurposing is the answer, will the new structure be considered a “respectful” and a “welcome” addition to be community, or will it have a purpose that is considered “disrespectful,” such as a bar or a music venue? Community practitioners can help communities in this deliberative process, looking to bring to fruition their desired goals for a former house of worship. This chapter provides a lens for understanding and responding to church repurposing. Community practice, however, will also be integrated throughout this book. Community practice must permeate our thinking and actions rather than being relegated to one time period or set of actions. Community practice is like the air we breathe—we cannot do without it! This worldview of practice emanates from a core belief system.
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems
Authors: Silberberg Mauro , Hermjakob Henning , Malik-Sheriff Rahuman S , Grecco Hernán E 
Published: July 2024

Abstract

Motivation
Chemical reaction networks (CRNs) play a pivotal role in diverse fields such as systems biology, biochemistry, chemical engineering, and epidemiology. High-level definitions of CRNs enables to use various simulation approaches, including deterministic and stochastic methods, from the same model. However, existing Python tools for simulation of CRN typically wrap external C/C++ libraries for model definition, translation into equations and/or numerically solving them, limiting their extensibility and integration with the broader Python ecosystem.

Results
In response, we developed Poincaré and SimBio, two novel Python packages for simulation of dynamical systems and CRNs. Poincaré serves as a foundation for dynamical systems modeling, while SimBio extends this functionality to CRNs, including support for the Systems Biology Markup Language (SBML). Poincaré and SimBio are developed as pure Python packages enabling users to easily extend their simulation capabilities by writing new or leveraging other Python packages. Moreover, this does not compromise the performance, as code can be just-in-time compiled with Numba. Our benchmark tests using curated models from the BioModels repository demonstrate that these tools may provide a potentially superior performance advantage compared to other existing tools. In addition, to ensure a user-friendly experience, our packages use standard typed modern Python syntax that provides a seamless integration with integrated development environments. Our Python-centric approach significantly enhances code analysis, error detection, and refactoring capabilities, positioning Poincaré and SimBio as valuable tools for the modeling community.

Availability and implementation
Poincaré and SimBio are released under the MIT license. Their source code is available on GitHub (https://github.com/maurosilber/poincare and https://github.com/hgrecco/simbio) and can be installed from PyPI or conda-forge.
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization
Authors: Firtina Can , Soysal Melina , Lindegger Joël , Mutlu Onur 
Published: July 2024

Abstract

Summary
Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling the early stopping of the sequencing of a read or the entire sequencing run based on the analysis. The state-of-the-art mechanism, RawHash, offers the first hash-based efficient and accurate similarity identification between raw signals and a reference genome by quickly matching their hash values. In this work, we introduce RawHash2, which provides major improvements over RawHash, including more sensitive quantization and chaining algorithms, weighted mapping decisions, frequency filters to reduce ambiguous seed hits, minimizers for hash-based sketching, and support for the R10.4 flow cell version and POD5 and SLOW5 file formats. Compared to RawHash, RawHash2 provides better F1 accuracy (on average by 10.57% and up to 20.25%) and better throughput (on average by 4.0× and up to 9.9×) than RawHash.

Availability and implementation
RawHash2 is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.
GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies
Authors: Talwar James V , Klie Adam , Pagadala Meghana S , Carter Hannah 
Published: July 2024

Abstract

Summary
Harmonizing variant indexing and allele assignments across datasets is crucial for data integrity in cross-dataset studies such as multi-cohort genome-wide association studies, meta-analyses, and the development, validation, and application of polygenic risk scores. Ensuring this indexing and allele consistency is a laborious, time-consuming, and error-prone process requiring a certain degree of computational proficiency. Here, we introduce GRIEVOUS, a command-line tool for cross-dataset variant homogenization. By means of an internal database and a custom indexing methodology, GRIEVOUS identifies, formats, and aligns all biallelic single nucleotide polymorphisms (SNPs) across all summary statistic and genotype files of interest. Upon completion of dataset harmonization, GRIEVOUS can also be used to extract the maximal set of biallelic SNPs common to all datasets.

Availability and implementation
GRIEVOUS and all supporting documentation and tutorials can be found at https://github.com/jvtalwar/GRIEVOUS. It is freely and publicly available under the MIT license and can be installed via pip.
Determinants of invasive left atrial pressure in patients with atrial fibrillation
Authors: Bonelli Andrea , Degiovanni Anna , Cersosimo Angelica , Spinoni Enrico Guido , Bosco Manuel , Dell’Era Gabriele , Moreo Antonella , De Chiara Benedetta Carla , Gigli Lorenzo , Salghetti Francesca , Arabia Gianmarco , Lombardi Carlo Mario , Brangi Elisa , Giannattasio Cristina , Patti Giuseppe , Curnis Antonio , Metra Marco , Inciardi Riccardo M 
Published: July 2024

Abstract

Aims
Estimation of left ventricular (LV) filling pressures in patients with a history of atrial fibrillation (AF) is challenging due to lack of reliable parameters. This study investigates the association between cardiac structure and function and invasive mean left atrial pressure (LAP).

Methods and results
This is a multi-centre prospective study enrolling patients undergoing transcatheter ablation for AF. The invasive measurement of LAP was performed at the time of the procedure while the echocardiography within the previous 24 h. A mean LAP ≥ 15 mmHg was considered as increased. Overall, 101 patients were included (mean age 65.8 ± 8.5 years, 68% male, mean LV ejection fraction 56.6 ± 8.0%). No significant differences regarding clinical characteristics were detected between the group of patients with normal (n = 47) or increased LAP (n = 54). The latter showed lower values of LV global longitudinal strain, larger left atrial volumes (LAVs) and worse right ventricular (RV) function. After multivariable adjustment, higher E/e′ ratio (P = 0.041) and minimal LAV index (LAVI min) (P = 0.031), lower peak atrial longitudinal strain (P = 0.030), and RV free wall longitudinal strain (P = 0.037), but not maximal LAV index (LAVI max) (P = 0.137), were significantly associated with mean LAP. The associations were not modified by cardiac rhythm. Overall, LAVI min showed the best diagnostic accuracy to predict elevated LAP (area under the curve 0.703).

Conclusion
LA structure and function assessment well correlates with mean LAP in patients with a history of AF. These measures may be used in the assessment of filling pressure in these patients.
Multiple recurrences of a left ventricular pseudoaneurysm: a case report
Authors: Umer Muhammad , Peters Matthew , Dholiya Hardeep , Sagheer Usman , Bhandari Sagar , Ghafghazi Shahab , Slaughter Mark S , Kalra Dinesh K 
Published: July 2024

Abstract

Background
Takotsubo syndrome (TTS) is being diagnosed more often with its increased recognition over the past 2 decades and with the availability of imaging such as point-of-care echocardiography and tissue characterization by cardiovascular magnetic resonance (CMR).

Case summary
A young man developed pericarditis and was treated with steroids. A few weeks later, he suffered classic TTS and then presented a week later with the rare complication of apical myocardial rupture and a left ventricular (LV) pseudoaneurysm. He subsequently sustained two recurrences, likely secondary to the poor tensile strength of the repair in the region of necrotic myocardium.

Discussion
Various features of both syndromes are discussed herein (myopericarditis and TTS) as well as their classic imaging findings with an emphasis on the echocardiographic diagnosis of an LV pseudoaneurysm and differentiating it from an aneurysm. Furthermore, we elucidate the classic imaging findings of CMR in myocarditis, myocardial infarction with non-obstructive coronary arteries, and TTS. Lastly, we discuss treatment options for LV pseudoaneurysms and strategies to prevent recurrence.
Cardiac troponin T associates with left ventricular function and synchrony assessed by CMR in the general population: results from the Akershus Cardiac Examination 1950 Study
Authors: Sulkowska Joanna , Melles Aikilu Woldegabriel , Skranes Julia Brox , Berge Trygve , Tveit Arnljot , Røsjø Helge , Lyngbakken Magnus Nakrem , Omland Torbjørn , Heck Siri Lagethon 
Published: July 2024

Abstract

Background and aim
Cardiac troponin T (cTnT) is a blood biomarker of myocardial injury that is associated with future adverse cardiovascular events in the general population. Left ventricular (LV) global longitudinal strain (GLS) and mechanical dispersion (MD) are metrics of systolic function and synchrony that can be obtained from cardiac imaging. Studies suggest an association between cTnT and echocardiographically assessed GLS and MD, but it is unknown whether cTnT relates to these metrics when assessed by cardiac magnetic resonance (CMR). We hypothesized that cTnT associates with GLS and with MD assessed by CMR feature tracking (CMR-FT) in the general population.

Methods and results
cTnT and CMR-FT measurements were performed in 186 community dwellers from the Akershus Cardiac Examination 1950 Study. The participants’ age ranged from 68 to 70 years. Median cTnT concentration was 7.0 ng/L (interquartile interval 5.0–12.6 ng/L), median absolute value of GLS was 17.3% (interquartile interval 15.7–18.8%), and median MD was 80.7 milliseconds (interquartile interval 61.8–105.0 milliseconds). In multivariable linear regression models adjusted for common clinical risk factors of cardiovascular disease, with GLS and MD as outcome and cTnT as the predictor variable of interest, log10 transformed cTnT was significantly associated with both absolute GLS [β-coefficient −1.65, confidence interval (−2.84, −0.46)] and MD [β-coefficient 28.56, confidence interval (12.14, 44.92)].

Conclusion
In older adults from the general population, higher cTnT concentrations are associated with worse systolic function and synchrony assessed by CMR-FT LV GLS and MD, adding information about myocardial function to traditional risk factors.
Myocardial calcification: case reports and a systematic review
Authors: Kido Takashi , Tanimoto Kazuki , Watanabe Takuji , Taira Masaki , Narita Jun , Ishida Hidekazu , Ishii Ryo , Ueno Takayoshi , Miyagawa Shigeru 
Published: July 2024

Abstract

Aims
Myocardial calcification is an unusual condition in which excess calcium is deposited in the myocardium. Herein, we report two cases of myocardial calcification from our clinical experience. Furthermore, we conduct a systematic review to examine the clinical course and associated pathologies of myocardial calcification.

Methods and results
This systematic review was registered in PROSPERO (CRD42023463285). PubMed and Scopus were searched according to the following inclusion criteria: (i) case reports or case series describing patients with myocardial calcification; (ii) diagnosis of myocardial calcification by computed tomography (CT); (iii) adequate description of patients, including their chief complaint, medical history, evaluations, and treatments; and (iv) publication in English. Among the 75 patients, 24 had sepsis, 14 had myocarditis, and 37 had other pathologies. The mortality rate was 33% for patients with sepsis, 14% for patients with myocarditis, and 11% for patients with other pathologies. Follow-up CT findings beyond 2 years were reported in six patients, showing that the CT findings of myocardial calcification persisted but subsided over time. Autopsy was performed in seven patients, and extensive interstitial fibrosis and collection of inflammatory cells were observed in patients with myocarditis, sepsis, and ischaemic heart disease.

Conclusion
While various medical conditions can cause myocardial calcification, accompanying conditions commonly reported with myocardial calcification were sepsis and myocarditis. The CT findings of myocardial calcification tend to regress over time if the underlying disease can be treated.
Acute Metabolic Stress Induces Lymphatic Dysfunction Through KATP Channel Activation
Authors: Kim Hae Jin , Norton Charles E , Zawieja Scott D , Castorena-Gonzalez Jorge A , Davis Michael J 
Published: July 2024

Abstract
Lymphatic dysfunction is an underlying component of multiple metabolic diseases, including diabetes, obesity, and metabolic syndrome. We investigated the roles of KATP channels in lymphatic contractile dysfunction in response to acute metabolic stress induced by inhibition of the mitochondrial electron transport chain. Ex vivo popliteal lymphatic vessels from mice were exposed to the electron transport chain inhibitors antimycin A and rotenone, or the oxidative phosphorylation inhibitor/protonophore, CCCP. Each inhibitor led to a significant reduction in the frequency of spontaneous lymphatic contractions and calculated pump flow, without a significant change in contraction amplitude. Contraction frequency was restored by the KATP channel inhibitor, glibenclamide. Lymphatic vessels from mice with global Kir6.1 deficiency or expressing a smooth muscle-specific dominant negative Kir6.1 channel were resistant to inhibition. Antimycin A inhibited the spontaneous action potentials generated in lymphatic muscle and this effect was reversed by glibenclamide, confirming the role of KATP channels. Antimycin A, but not rotenone or CCCP, increased dihydrorhodamine fluorescence in lymphatic muscle, indicating ROS production. Pretreatment with tiron or catalase prevented the effect of antimycin A on wild-type lymphatic vessels, consistent with its action being mediated by ROS. Our results support the conclusion that KATP channels in lymphatic muscle can be directly activated by reduced mitochondrial ATP production or ROS generation, consequent to acute metabolic stress, leading to contractile dysfunction through inhibition of the ionic pacemaker controlling spontaneous lymphatic contractions. We propose that a similar activation of KATP channels contributes to lymphatic dysfunction in metabolic disease.
Association Between Falls and Social Frailty in Community-Dwelling Older Japanese Adults
Authors: Sawa Ryuichi , Doi Takehiko , Tsutsumimoto Kota , Nakakubo Sho , Sakimoto Fumio , Matsuda Soichiro , Shimada Hiroyuki 
Published: July 2024

Abstract

Objectives
This study aimed to investigate the association between falls and social frailty and its components among older Japanese adults.

Methods
This is a cross-sectional study. Participants were categorized into 3 groups based on the number of falls in the past year: no fall (none), a single fall (occasional), and more than one fall (recurrent). The participants who met 2 or more of the following criteria were defined as socially frail: living alone, going out less frequently compared with the previous year, rarely visiting friends, feeling unhelpful to friends or family, and not talking with someone daily.

Results
A total of 4,495 older Japanese adults living in a community analyzed in this study (51.0% women). Of the participants in this study, 3,851 (85.7%) were categorized as none, 443 (9.9%) as occasional, and 201 (4.5%) as recurrent. The proportion of participants considered socially frail was 11.5% in this study. Recurrent falls were associated with social frailty, even after adjusting for covariates (odds ratio [OR]: 1.49; 95% confidence interval [CI]: 1.01–2.19). The experience of recurrent falls was associated with the following components: “feeling unhelpful to friends and family” (OR: 1.62; 95% CI: 1.14–2.31) and “going outside less frequently compared with last year” (OR: 1.57; 95% CI: 1.06–2.31).

Discussion
Among older Japanese adults, recurrent falls were associated with social frailty and with 2 of its components in particular: social roles and social participation. Future longitudinal studies should be conducted to gain insight into any causal relationships between these variables.