bluuebunny/crossref_metadata_2025_split huggingface dataset:
Back to Basics in Measuring Lexical Diversity: Too Simple to Be True
Authors: Bestgen Yves 
Published: August 2024

Abstract
Measuring lexical diversity in texts that have different lengths is problematic because length has a significant effect on the number of types a text contains, thus hampering any comparison. Treffers-Daller et al. (2018) recommended a simple solution, namely counting the number of types in a section of a given length that was extracted from the middle of each of the texts to be analysed. By applying this approach to second language essays, the authors observed that using the number of types was slightly more effective for differentiating amongst the Common European Framework of Reference for Languages (CEFR) levels than were the Type-Token Ratio (TTR) and the Guiraud index and that these three indices were more effective than were mathematically more complex ones. However, their conclusions regarding these two points are incorrect, and a less basic approach should be used. The last section addresses two broader issues in applied linguistics that are highlighted by these problems.
A 360° Approach to Patient Care in Aesthetic Facial Rejuvenation
Authors: Humphrey Shannon , Bertucci Vince , Heydenrych Izolda , Ogilvie Patricia , Safa Marva , de la Guardia Carola 
Published: August 2024

Abstract

Background
Aesthetic medicine has traditionally focused on addressing perceived problem areas, with lack of long-term planning and engagement.

Objectives
This article describes a patient-centric model for nonsurgical aesthetic medical practice, termed the 360° approach to facial aesthetic rejuvenation.

Methods
The 360° approach was divided into 4 foundational pillars. Medical literature, the authors’ clinical experiences, and results from patient satisfaction surveys were used to support the approach.

Results
Pillar 1 describes the development of a complete understanding of the patient, based on the use of active listening principles, to characterize the patient's current aesthetic concerns, lifestyle, medical and treatment history, treatment goals, attitude toward aesthetic treatment, and financial resources. Pillar 2 involves conducting a comprehensive facial assessment in contrast to a feature-specific assessment, considering multiple facial tissues and structures and their interrelationships, thus helping to prevent the unanticipated consequences of narrowly focused treatment. Pillar 3 describes leveraging all available treatments and techniques in the development of an initial treatment plan arising from the facial assessment. Pillar 4 adds a time dimension to treatment planning, working toward the goal of a long-term modifiable treatment timeline, with full patient support and involvement; this is designed to facilitate a durable, sustained relationship between the patient and aesthetic healthcare professional (HCP).

Conclusions
Although implementation involves substantial commitment and time, the patient-oriented focus of the 360° approach can help achieve optimal patient outcomes and the development of enduring patient–HCP relationships.

Level of Evidence: 5
Microbial production of aromatic compounds and synthesis of high-performance bioplastics
Authors: Masuo Shunsuke 
Published: August 2024

ABSTRACT
Microbial fermentation has provided fermented foods and important chemicals such as antibiotics, amino acids, and vitamins. Metabolic engineering of synthetic microbes has expanded the range of compounds produced by fermentation. Petroleum-derived aromatic compounds are widely used in industry as raw materials for pharmaceuticals, dyes, and polymers and are in great demand. This review highlights the current efforts in the microbial production of various aromatic chemicals such as aromatic amines, cinnamic acid derivatives, and flavoring aromatics, including their biosynthesis pathways. In addition, the unique biosynthetic mechanism of pyrazine, a heterocyclic compound, from amino acids is described to expand the use of biomass-derived aromatic compounds. I also discuss our efforts to develop high-performance bioplastics superior to petroleum plastics from the aromatic compounds produced by microbial fermentation.
Galaxy Helm chart: a standardized method for deploying production Galaxy servers
Authors: Goonasekera Nuwan , Mahmoud Alexandru , Suderman Keith , Afgan Enis 
Published: August 2024

Abstract

Motivation
The Galaxy application is a popular open-source framework for data intensive sciences, counting thousands of monthly users across more than 100 public servers. To support a growing number of users and a greater variety of use cases, the complexity of a production-grade Galaxy installation has also grown, requiring more administration effort. There is a need for a rapid and reproducible Galaxy deployment method that can be maintained at high-availability with minimal maintenance.

Results
We describe the Galaxy Helm chart that codifies all elements of a production-grade Galaxy installation into a single package. Deployable on Kubernetes clusters, the chart encapsulates supporting software services and implements the best-practices model for running Galaxy. It is also the most rapid method available for deploying a scalable, production-grade Galaxy instance on one’s own infrastructure. The chart is highly configurable, allowing systems administrators to swap dependent services if desired. Notable uses of the chart include on-demand, fully-automated deployments on AnVIL, providing training infrastructure for the Bioconductor project, and as the AWS-recommended solution for running Galaxy on the Amazon cloud.

Availability and implementation
The source code for Galaxy Helm is available at https://github.com/galaxyproject/galaxy-helm, the corresponding Helm package at https://github.com/CloudVE/helm-charts, and the required Galaxy container image https://github.com/galaxyproject/galaxy-docker-k8s.
R2Dtool: integration and visualization of isoform-resolved RNA features
Authors: Sethi Aditya J , Acera Mateos Pablo , Hayashi Rippei , Shirokikh Nikolay E , Eyras Eduardo 
Published: August 2024

Abstract

Motivation
Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions.

Results
We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool’s capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms.

Availability and implementation
R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console
Authors: Nath Anindita , Mwesigwa Savannah , Dai Yulin , Jiang Xiaoqian , Zhao Zhongming 
Published: August 2024

Abstract

Summary
The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation and biomedical knowledge discovery. Leveraging generative AI, notably ChatGPT, it serves as a biologist’s “copilot.” It automates the analysis, retrieval, and visualization of customized domain-specific genetic information, and integrates functionalities to generate protein interaction networks, enrich gene sets, and search scientific literature from PubMed, Google Scholar, and arXiv, making it a comprehensive tool for biomedical research. In its pilot phase, GENEVIC is assessed using a curated database that ranks genetic variants associated with Alzheimer’s disease, schizophrenia, and cognition, based on their effect weights from the Polygenic Score (PGS) Catalog, thus enabling researchers to prioritize genetic variants in complex diseases. GENEVIC’s operation is user-friendly, accessible without any specialized training, secured by Azure OpenAI’s HIPAA-compliant infrastructure, and evaluated for its efficacy through real-time query testing. As a prototype, GENEVIC is set to advance genetic research, enabling informed biomedical decisions.

Availability and implementation
GENEVIC is publicly accessible at https://genevicanath2024.streamlit.app. The underlying code is open-source and available via GitHub at https://github.com/bsml320/GENEVIC.git (also at https://github.com/anath2110/GENEVIC.git).
Critical appraisal of the adequacy of surgical indications for non-functioning pancreatic neuroendocrine tumours
Authors: Partelli Stefano , Battistella Anna , Andreasi Valentina , Muffatti Francesca , Tamburrino Domenico , Pecorelli Nicolò , Crippa Stefano , Balzano Gianpaolo , Falconi Massimo 
Published: August 2024

Abstract

Background
The lack of preoperative prognostic factors to accurately predict tumour aggressiveness in non-functioning pancreatic neuroendocrine tumours may result in inappropriate management decisions. This study aimed to critically evaluate the adequacy of surgical treatment in patients with resectable non-functioning pancreatic neuroendocrine tumours and investigate preoperative features of surgical appropriateness.

Methods
A retrospective study was conducted on patients who underwent curative surgery for non-functioning pancreatic neuroendocrine tumours at San Raffaele Hospital (2002–2022). The appropriateness of surgical treatment was categorized as appropriate, potential overtreatment and potential undertreatment based on histologic features of aggressiveness and disease relapse within 1 year from surgery (early relapse).

Results
A total of 384 patients were included. Among them, 230 (60%) received appropriate surgical treatment, whereas the remaining 154 (40%) underwent potentially inadequate treatment: 129 (34%) experienced potential overtreatment and 25 (6%) received potential undertreatment. The appropriateness of surgical treatment was significantly associated with radiological tumour size (P &lt; 0.001), tumour site (P = 0.012), surgical technique (P &lt; 0.001) and year of surgical resection (P &lt; 0.001). Surgery performed before 2015 (OR 2.580, 95% c.i. 1.570 to 4.242; P &lt; 0.001), radiological tumour diameter &lt; 25.5 mm (OR 6.566, 95% c.i. 4.010 to 10.751; P &lt; 0.001) and pancreatic body/tail localization (OR 1.908, 95% c.i. 1.119 to 3.253; P = 0.018) were identified as independent predictors of potential overtreatment. Radiological tumour size was the only independent determinant of potential undertreatment (OR 0.291, 95% c.i. 0.107 to 0.791; P = 0.016). Patients subjected to potential undertreatment exhibited significantly poorer disease-free survival (P &lt; 0.001), overall survival (P &lt; 0.001) and disease-specific survival (P &lt; 0.001).

Conclusions
Potential overtreatment occurs in nearly one-third of patients undergoing surgery for non-functioning pancreatic neuroendocrine tumours. Tumour diameter emerges as the sole variable capable of predicting the risk of both potential surgical overtreatment and undertreatment.
Nuclear factor of activated T-cells 5 is indispensable for a balanced adaptive transcriptional response of lung endothelial cells to hypoxia
Authors: Laban Hebatullah , Siegmund Sophia , Schlereth Katharina , Trogisch Felix A , Ablieh Alia , Brandenburg Lennart , Weigert Andreas , De La Torre Carolina , Mogler Carolin , Hecker Markus , Kuebler Wolfgang M , Korff Thomas 
Published: August 2024

Abstract

Aims
Chronic hypoxia causes detrimental structural alterations in the lung, which may cause pulmonary hypertension and are partially mediated by the endothelium. While its relevance for the development of hypoxia-associated lung diseases is well known, determinants controlling the initial adaptation of the lung endothelium to hypoxia remain largely unexplored.

Methods and results
We revealed that hypoxia activates the transcription factor nuclear factor of activated T-cells 5 (NFAT5) and studied its regulatory function in murine lung endothelial cells (MLECs). EC-specific knockout of Nfat5 (Nfat5(EC)−/−) in mice exposed to normobaric hypoxia (10% O2) for 21 days promoted vascular fibrosis and aggravated the increase in pulmonary right ventricular systolic pressure as well as right ventricular dysfunction as compared with control mice. Microarray- and single-cell RNA-sequencing-based analyses revealed an impaired growth factor-, energy-, and protein–metabolism-associated gene expression in Nfat5-deficient MLEC after exposure to hypoxia for 7 days. Specifically, loss of NFAT5 boosted the expression and release of platelet-derived growth factor B (Pdgfb)—a hypoxia-inducible factor 1 alpha (HIF1α)-regulated driver of vascular smooth muscle cell (VSMC) growth—in capillary MLEC of hypoxia-exposed Nfat5(EC)−/− mice, which was accompanied by intensified VSMC coverage of distal pulmonary arteries.

Conclusion
Collectively, our study shows that early and transient subpopulation-specific responses of MLEC to hypoxia may determine the degree of organ dysfunction in later stages. In this context, NFAT5 acts as a protective transcription factor required to rapidly adjust the endothelial transcriptome to cope with hypoxia. Specifically, NFAT5 restricts HIF1α-mediated Pdgfb expression and consequently limits muscularization and resistance of the pulmonary vasculature.
Sudden cardiac death after early-onset myocardial infarction: a multicentre longitudinal cohort study with a 20-year follow-up
Authors: Bricoli Serena , Magnani Giulia , Ardissino Maddalena , Maglietta Giuseppe , Celli Patrizia , Ferrario Maurizio , Canosi Umberto , Cernetti Carlo , Negri Francesco , Merlini Piera Angelica , Tubaro Marco , Berzuini Carlo , Manzalini Chiara , Moschini Luigi , Ponte Elisabetta , Pozzi Roberto , Buratti Silvia , Botti Andrea , Barocelli Federico , Biagi Andrea , Bonura Rosario , Bearzot Luca , Moccetti Tiziano , Crocamo Antonio , Notarangelo Maria Francesca , Moscarella Elisabetta , Calabrò Paolo , Niccoli Giampaolo , Ardissino Diego 
Published: August 2024

Abstract

Aims
Sudden cardiac death (SCD) is a serious consequence of a myocardial infarction (MI), but identifying patients at risk of developing SCD remains a major clinical challenge, especially in the case of juvenile MI. The aim of this study is to identify predictors of SCD after early-onset MI using long-term follow-up data relating to a large nationwide patient cohort.

Methods and results
The Italian Genetic Study on Early-onset MI enrolled 2000 patients experiencing a first MI before the age of 45 years, who were followed up for a median of 19.9 years. Fine–Gray proportional hazard models were used to assess the associations between their clinical, demographic, and index event data and the occurrence of SCD. Sudden cardiac death occurred in 195 patients, who were more frequently males, were hypertensive and/or diabetic, had a history of previous thrombo-embolic events with a greater atherosclerotic burden, and had a lower left ventricular ejection fraction (LVEF) after the index event. A multivariable analysis showed that the independent predictors of SCD were diabetes, hypertension, previous thrombo-embolic events, a higher SYNTAX score, and a lower LVEF. There was no clear evidence of the clustering of SCD events during the follow-up. Sudden cardiac death was the first post-MI clinical event in 101 patients; the remaining 94 experienced SCD after a non-fatal MI or hospitalization for coronary revascularization.

Conclusion
Sudden cardiac death frequently occurs during the 20 years after early-onset MI. The nature of the identified predictors and the absence of clustering suggest that the pathophysiological basis of SCD may be related to progressive coronary atherosclerosis.
Steep right anterior oblique view of self-expandable transcatheter aortic valve to timely detect stent under-expansion or non-uniform expansion before final release: a case series
Authors: Kaneko Umihiko , Hachinohe Daisuke , Kobayashi Ken , Shitan Hidemasa , Horita Ryo , Ootake Ryo , Fujita Tsutomu 
Published: August 2024

Abstract

Background
Severely calcified aortic valves are a major limitation of transcatheter aortic valve replacement, because eccentric and heavy calcification of the aortic valve occasionally inhibits self-expansion of the valve frame, resulting in stent under-expansion, including non-uniform expansion or infolding. Nevertheless, the two-dimensional nature of fluoroscopic projection imaging can limit detection of stent under-expansion prior to the final release.

Case summary
We present two cases demonstrating the importance of the steep right anterior oblique (RAO) view (&gt;50°) in detecting significant stent under-expansion of a self-expanding valve prior to the final release. In Case 1, despite enough pre-dilatation, the partially deployed transcatheter heart valve (THV) appeared to be a substantial under-expansion, which was detected only in steep RAO view. Immediately after the final release, the THV was spontaneously embolized into the ascending aorta (the so-called ‘pop-up’ phenomenon). Emergent implantation of balloon-expandable valve proved to be successful as a bailout. In Case 2, significant stent distortion and infolding, especially on the non-coronary cusp side, was successfully diagnosed only in a steep RAO view prior to the final release. This finding allowed THV recapture and replacement with a new THV.

Discussion
Notably, the steep RAO view can visualize the THV from its short axis while eliminating parallax, allowing for accurate diagnosis of THV under-expansion particularly in patients with severe calcification in the non- or right-coronary cusp. Therefore, the steep RAO view allows timely detection of THV under-expansion before the final release, enabling THV recapture and the adoption of several management strategies.
Hypothyroidism due to biallelic variants in IYD: description of 4 families and a novel variant
Authors: Boros Emese , Vilain Catheline , Driessens Natacha , Heinrichs Claudine , Van Vliet Guy , Brachet Cécile 
Published: August 2024

Abstract
Biallelic loss-of-function variants in the IYD gene cause hypothyroidism resulting from iodine wasting. We describe 8 patients (from 4 families in which the parents are first cousins) who are homozygous for a variant in IYD (including a novel missense deleterious variant, c.791C&gt;T [P264L], in 1 family). Seven patients presented between 5 and 16 years of age with a large goiter, overt hypothyroidism, and a high serum thyroglobulin. The goiter subsided with levothyroxine therapy in most. Upon stopping levothyroxine in 5 patients, goiter and hypothyroidism reappeared in 3. In these 3 patients, a rising serum thyroglobulin concentration preceded hypothyroidism and goiter and urinary iodine excretion was low. In patients who remained euthyroid, urinary iodine was normal. In conclusion, these patients bearing biallelic pathogenic variants in IYD developed a large goiter, a high serum thyroglobulin, and overt hypothyroidism when their iodine intake was low.
The simple macroeconomics of AI
Authors: Acemoglu Daron 
Published: August 2024

SUMMARY
This paper evaluates claims about the large macroeconomic implications of new advances in Artificial intelligence (AI). It starts from a task-based model of AI’s effects, working through automation and task complementarities. So long as AI’s microeconomic effects are driven by cost savings/productivity improvements at the task level, its macroeconomic consequences will be given by a version of Hulten’s theorem: Gross Domestic Product (GDP) and aggregate productivity gains can be estimated by what fraction of tasks are impacted and average task-level cost savings. Using existing estimates on exposure to AI and productivity improvements at the task level, these macroeconomic effects appear non-trivial but modest – no more than a 0.66% increase in total factor productivity (TFP) over 10 years. The paper then argues that even these estimates could be exaggerated, because early evidence is from easy-to-learn tasks, whereas some of the future effects will come from hard-to-learn tasks, where there are many context-dependent factors affecting decision-making and no objective outcome measures from which to learn successful performance. Consequently, predicted TFP gains over the next 10 years are even more modest and are predicted to be less than 0.53%. I also explore AI’s wage and inequality effects. I show theoretically that even when AI improves the productivity of low-skill workers in certain tasks (without creating new tasks for them), this may increase rather than reduce inequality. Empirically, I find that AI advances are unlikely to increase inequality as much as previous automation technologies because their impact is more equally distributed across demographic groups, but there is also no evidence that AI will reduce labour income inequality. Instead, AI is predicted to widen the gap between capital and labour income. Finally, some of the new tasks created by AI may have negative social value (such as the design of algorithms for online manipulation), and I discuss how to incorporate the macroeconomic effects of new tasks that may have negative social value.
Multilateral tax treaty revision to combat tax avoidance: on the merits and limits of BEPS’s multilateral instrument
Authors: Hohmann Antonia , Merlo Valeria , Riedel Nadine 
Published: August 2024

Summary
Since 2015, more than 140 countries have cooperated in the OECD’s ‘Base Erosion and Profit Shifting’ (BEPS) project to combat multinational tax avoidance. Several of the key actions, most importantly measures against tax treaty shopping, require changes to double taxation treaties. The OECD designed a special instrument – the ‘multilateral instrument’ (MLI) – to allow for a swift implementation of BEPS-related tax treaty changes. In this paper, we show that MLI take-up is incomplete, and we present (partly surprising) correlates of the take-up decision and develop a simple theoretical model to rationalize the observed take-up behaviour. A key insight is that conduit countries, which are the beneficiaries of tax treaty shopping, can benefit from anti-treaty shopping laws as firms have incentives to scale-up real activity in conduit nations in order to be exempted from the new anti-treaty shopping rules. Empirical findings are consistent with these considerations: MLI adoption rates of conduit countries are high. Treaty shopping has, to date, not significantly dropped. And there is indeed indication that firms have scaled up their real economic activity in conduit nations. Overall, our findings reject that treaty shopping has been ‘killed’ as envisaged by the OECD.