bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuron collinearity differentiates human hippocampal subregions: a validated deep learning approach
Authors: Oltmer Jan , Williams Emily M , Groha Stefan , Rosenblum Emma W , Roy Jessica , Llamas-Rodriguez Josue , Perosa Valentina , Champion Samantha N , Frosch Matthew P , Augustinack Jean C 
Published: September 2024

Abstract
The hippocampus is heterogeneous in its architecture. It contributes to cognitive processes such as memory and spatial navigation and is susceptible to neurodegenerative disease. Cytoarchitectural features such as neuron size and neuronal collinearity have been used to parcellate the hippocampal subregions. Moreover, pyramidal neuron orientation (orientation of one individual neuron) and collinearity (how neurons align) have been investigated as a measure of disease in schizophrenia. However, a comprehensive quantitative study of pyramidal neuron orientation and collinearity within the hippocampal subregions has not yet been conducted. In this study, we present a high-throughput deep learning approach for the automated extraction of pyramidal neuron orientation in the hippocampal subregions. Based on the pretrained Cellpose algorithm for cellular segmentation, we measured 479 873 pyramidal neurons in 168 hippocampal partitions. We corrected the neuron orientation estimates to account for the curvature of the hippocampus and generated collinearity measures suitable for inter- and intra-individual comparisons. Our deep learning results were validated with manual orientation assessment. This study presents a quantitative metric of pyramidal neuron collinearity within the hippocampus. It reveals significant differences among the individual hippocampal subregions (P &lt; 0.001), with cornu ammonis 3 being the most collinear, followed by cornu ammonis 2, cornu ammonis 1, the medial/uncal subregions and subiculum. Our data establishes pyramidal neuron collinearity as a quantitative parameter for hippocampal subregion segmentation, including the differentiation of cornu ammonis 2 and cornu ammonis 3. This novel deep learning approach could facilitate large-scale multicentric analyses in subregion parcellation and lays groundwork for the investigation of mental illnesses at the cellular level.
A comprehensive review of rectangular duct solar air heaters featuring artificial roughness
Authors: Shankar Ravi , Kumar Rajeev , Pandey Arun Kumar , Thakur Deep Singh 
Published: September 2024

Abstract
Solar air heaters (SAHs) are widely used solar thermal systems with applications in diverse sectors. However, its effectiveness is restrained by low convective heat transfer (HT) coefficients at the absorber plate, leading to inefficient HT, and the elevated temperature of the absorber plate causes significant heat losses, reducing thermal efficiency. This study addresses these challenges by introducing ribs or roughness on the absorber plate creating turbulence in the airflow, resulting in significant improvements. The research investigates various rib configurations, the influence of rib parameters, performance methods, and arrangements to evaluate their HT and friction characteristics. Among these rib configurations, a comparative analysis is done on various factors such as the Nusselt number ratio, thermal enhancement factor, friction factor ratio, and thermal efficiency to optimize distinct roughness parameters and rib arrangement patterns. This study also provides valuable recommendations from existing literature, offering insights into the effective design, prospects, and implementation of SAH systems.
The role of TRPA1 and TRPV1 in the perception of astringency
Authors: Kim Min Sung , Simons Christopher T 
Published: September 2024

Abstract
Astringency, commonly described as a drying, roughening, and/or puckering sensation associated with polyphenol-rich foods affects their palatability. While the compounds eliciting astringency are known, its mechanism of action is debated. This study investigated the role of transient receptor potential (TRP) channels A1 and V1 in astringency perception. If TRP A1 or V1 have a functional role in astringency perception, then desensitizing these receptors should decrease perceived astringency. Thirty-seven panelists underwent unilateral lingual desensitization of TRP A1 and V1 channels using mustard oil and capsaicin, respectively. Panelists then evaluated four astringent stimuli: epicatechin (EC), epigallocatechin gallate (EGCG), tannic acid (TA), and potassium alum (Alum), via 2-AFC and intensity ratings. When TRPA1 receptors were desensitized on one half of the tongue via mustard oil, no significant differences were observed between the treated and untreated sides for both 2-AFC and intensity ratings. Similarly, when TRPV1 receptors were desensitized on one half of the tongue via capsaicin, no significant differences were observed between the treated and untreated sides for both 2-AFC and intensity ratings. These findings challenge the notion that TRP channels play a pivotal role in astringency perception.
Kidney re-transplantation in the ipsilateral iliac fossa: a surgeon's perspective on perioperative outcome
Authors: Tessmer Philipp , Weigle Clara A , Meyer Anna , Wiemann Bengt A , Gwinner Wilfried , Einecke Gunilla , Klempnauer Jürgen , Vondran Florian W R , Richter Nicolas , Oldhafer Felix , Beetz Oliver 
Published: September 2024

ABSTRACT

Background
Compared with primary transplantation, ipsilateral renal re-transplantation is associated with an increased risk of surgical complications and inferior graft outcomes. This study investigates whether an ipsilateral re-transplantation approach per se is an independent risk factor for surgical complications and early graft loss.

Methods
In this retrospective, single-centre analysis, surgical complications and early graft outcomes of ipsilateral kidney re-transplantations from January 2007 to December 2017 were compared with primary transplantations and contralateral re-transplantations. Univariate and multivariate binary logistic regression analyses were performed to identify risk factors for surgical complications requiring surgical revision and graft loss within the first year after transplantation.

Results
Of the 1489 kidney transplantations, 51 were ipsilateral, 159 were contralateral re-transplantations and 1279 were primary transplantations. Baseline characteristics did not differ between the ipsilateral and contralateral re-transplant recipients except for current and highest panel reactive antibody levels. Major complications requiring surgical revision were significantly more frequent in ipsilateral re-transplantations (P = .010) than in primary transplantations but did not differ between ipsilateral and contralateral re-transplantations (P = .217). Graft loss within the first year after transplant was 15.7% in the ipsilateral versus 8.8% in the contralateral re-transplant group (P = .163) versus 6.4% in the primary transplantation group (P = .009). In a multivariate regression model, ipsilateral re-transplantation was not identified as an independent risk factor for complications requiring surgical revision or first-year graft loss.

Conclusions
Ipsilateral renal re-transplantation is not a risk factor for inferior outcomes. Graft implantation into a pre-transplanted iliac fossa is a feasible and valid therapeutic option.
Geohistorical insights into marine functional connectivity
Authors: Agiadi Konstantina , Caswell Bryony A , Almeida Rita , Becheker Ali , Blanco Andreu , Brito Cristina , León-Cobo Manuel Jesús , Cook Ellie-Mae E , Costantini Federica , Karakuş Merve , Leprieur Fabien , López Cataixa , López-López Lucía , O’Dea Aaron , Pallacks Sven , Rabanal Irene , Schultz Lotta , Tanner Susanne E , Theodoropoulou Tatiana , Thurstan Ruth H , Vieira Nina , Darnaude Audrey M 
Published: September 2024

Abstract
Marine functional connectivity (MFC) refers to the flows of organic matter, genes, and energy that are caused by the active and passive movements of marine organisms. Occurring at various temporal and spatial scales, MFC is a dynamic, constantly evolving global ecological process, part of overall ecological connectivity, but with its own distinct and specific patterns. Geological and historical archives of changes in the distributions, life histories, and migration of species can provide baselines for deciphering the long-term trends (decadal to millions of years) and variability of MFC. In this food-for-thought paper, we identify the different types of geohistorical data that can be used to study past MFC. We propose resources that are available for such work. Finally, we offer a roadmap outlining the most appropriate approaches for analysing and interpreting these data, the biases and limitations involved, and what we consider to be the primary themes for future research in this field. Overall, we demonstrate how, despite differences in norms and limitations between disciplines, valuable data on ecological and societal change can be extracted from geological and historical archives, and be used to understand changes of MFC through time.
A Positive Proportion of Monic Odd-Degree Hyperelliptic Curves of Genus g ≥ 4 Have no Unexpected Quadratic Points
Authors: Laga Jef , Swaminathan Ashvin A 
Published: September 2024

Abstract
Let $\mathcal{F}_{g}$ be the family of monic odd-degree hyperelliptic curves of genus $g$ over ${\mathbb{Q}}$. Poonen and Stoll have shown that for every $g \geq 3$, a positive proportion of curves in $\mathcal{F}_{g}$ have no rational points except the point at infinity. In this note, we prove the analogue for quadratic points: for each $g\geq 4$, a positive proportion of curves in $\mathcal{F}_{g}$ have no points defined over quadratic extensions except those that arise by pulling back rational points from $\mathbb{P}^{1}$.
ADLM Guidance Document on the Measurement and Reporting of Lipids and Lipoproteins
Authors: Cao Jing , Donato Leslie , El-Khoury Joe M , Goldberg Anne , Meeusen Jeffrey W , Remaley Alan T 
Published: September 2024

Abstract

Background
The accurate measurement of blood lipids and lipoproteins is crucial for the clinical management of atherosclerotic disease risk. Despite progress in standardization, there are still significant variations in pre-analytical requirements, methods, nomenclature, and reporting work flows.

Content
The guidance document aims to improve standardization of clinical lipid testing work flows. It provides recommendations for the components of the lipid panel, fasting requirements, reporting of results, and specific recommendations for non-high-density lipoprotein cholesterol (non-HDL-C), low-density lipoprotein cholesterol (LDL-C), lipoprotein(a) [Lp(a)], apolipoprotein B (apo B), point-of-care lipid testing, and LDL subfraction testing.

Summary
Lipid panels should always report non-HDL-C and LDL-C calculations if possible. Fasting is not routinely required except in specific cases. Modern equations should be utilized for LDL-C calculation. These equations allow for LDL-C reporting at elevated concentrations of triglycerides and obviate the need for direct measured LDL-C in most cases.
Implementation and delivery of electronic health records training programs for nurses working in inpatient settings: a scoping review
Authors: Nguyen Oliver T , Vo Steven D , Lee Taeheon , Cato Kenrick D , Cho Hwayoung 
Published: September 2024

Abstract

Objectives
Well-designed electronic health records (EHRs) training programs for clinical practice are known to be valuable. Training programs should be role-specific and there is a need to identify key implementation factors of EHR training programs for nurses. This scoping review (1) characterizes the EHR training programs used and (2) identifies their implementation facilitators and barriers.

Materials and Methods
We searched MEDLINE, CINAHL, PsycINFO, and Web of Science on September 3, 2023, for peer-reviewed articles that described EHR training program implementation or delivery to nurses in inpatient settings without any date restrictions. We mapped implementation factors to the Consolidated Framework for Implementation Research. Additional themes were inductively identified by reviewing these findings.

Results
This review included 30 articles. Healthcare systems’ approaches to implementing and delivering EHR training programs were highly varied. For implementation factors, we observed themes in innovation (eg, ability to practice EHR skills after training is over, personalizing training, training pace), inner setting (eg, availability of computers, clear documentation requirements and expectations), individual (eg, computer literacy, learning preferences), and implementation process (eg, trainers and support staff hold nursing backgrounds, establishing process for dissemination of EHR updates). No themes in the outer setting were observed.

Discussion
We found that multilevel factors can influence the implementation and delivery of EHR training programs for inpatient nurses. Several areas for future research were identified, such as evaluating nurse preceptorship models and developing training programs for ongoing EHR training (eg, in response to new EHR workflows or features).

Conclusions
This scoping review highlighted numerous factors pertaining to training interventions, healthcare systems, and implementation approaches. Meanwhile, it is unclear how external factors outside of a healthcare system influence EHR training programs. Additional studies are needed that focus on EHR retraining programs, comparing outcomes of different training models, and how to effectively disseminate updates with the EHR to nurses.
CACER: Clinical concept Annotations for Cancer Events and Relations
Authors: Fu Yujuan Velvin , Ramachandran Giridhar Kaushik , Halwani Ahmad , McInnes Bridget T , Xia Fei , Lybarger Kevin , Yetisgen Meliha , Uzuner Özlem 
Published: September 2024

Abstract

Objective
Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes.

Materials and Methods
We present Clinical concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48 000 medical problems and drug events and 10 000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction models such as Bidirectional Encoder Representations from Transformers (BERT), Fine-tuned Language Net Text-To-Text Transfer Transformer (Flan-T5), Large Language Model Meta AI (Llama3), and Generative Pre-trained Transformers-4 (GPT-4) using fine-tuning and in-context learning (ICL).

Results
In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks.

Discussion
The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, large language models offer no performance advantage over the smaller BERT models.

Conclusions
We introduce CACER, a novel corpus with fine-grained annotations for medical problems, drugs, and their relationships in clinical narratives of oncology notes. State-of-the-art transformer models achieved performance comparable to IAA for several extraction tasks.
Measuring the impact of new risk factors within survival models
Authors: Heller Glenn , Devlin Sean M 
Published: September 2024

Abstract
Survival is poor for patients with metastatic cancer, and it is vital to examine new biomarkers that can improve patient prognostication and identify those who would benefit from more aggressive therapy. In metastatic prostate cancer, 2 new assays have become available: one that quantifies the number of cancer cells circulating in the peripheral blood, and the other a marker of the aggressiveness of the disease. It is critical to determine the magnitude of the effect of these biomarkers on the discrimination of a model-based risk score. To do so, most analysts frequently consider the discrimination of 2 separate survival models: one that includes both the new and standard factors and a second that includes the standard factors alone. However, this analysis is ultimately incorrect for many of the scale-transformation models ubiquitous in survival, as the reduced model is misspecified if the full model is specified correctly. To circumvent this issue, we developed a projection-based approach to estimate the impact of the 2 prostate cancer biomarkers. The results indicate that the new biomarkers can influence model discrimination and justify their inclusion in the risk model; however, the hunt remains for an applicable model to risk-stratify patients with metastatic prostate cancer.
ASPECT: Answer Set rePresentation as vEctor graphiCs in laTex
Authors: Bertagnon Alessandro , Gavanelli Marco 
Published: September 2024

Abstract
Logic programming is a declarative programming paradigm that finds extensive use in the field of Artificial Intelligence (AI). As a result, it has become a valuable tool used in university courses for teaching students AI techniques. Besides Prolog language, the more recent Answer Set Programming (ASP) language turns out to be a powerful tool for developing advanced applications due to the expressiveness of the language and the availability of efficient solving systems. Unfortunately, the output of ASP solvers can be difficult to interpret, since it is a set of atoms, often long and verbose. This is most true in the case of students learning the language or in the case of experts developing applications for complex real-world problems. For these reasons, the ability to produce, when possible, a graphical representation of the solver output becomes useful to ensure easier interpretation of the results. In this paper we present ASPECT, a sub-language of ASP in which the user can directly define, in an intuitive and declarative way, a graphical representation of the answer set. The ASPECT atoms can be converted into the popular LaTeX markup language to produce vector graphics. The documents produced by ASPECT are easy to embed in documents such as scientific articles, course handouts and presentations. Also, the development of user-friendly interfaces is critical for wider use of similar technologies in the industrial sector as well. Moreover, ASPECT is also extended to deal with temporal information, and provide graphical animations of answer sets that enclose the temporal dimension, such as in planning problems. Finally, we advocate the use of ASPECT to create complex and animated presentations starting from a declarative specification.
Simulating the impact of a carbon tax on food in four European countries
Authors: Varacca Alessandro , Castellari Elena , Moro Daniele , Tiboldo Giulia , Dogbe Wisdom , Gil Jose Maria , Revoredo-Giha Cesar , Akaichi Faical , Irz Xavier , Surry Yves , Amuakwa-Mensah Franklin , Sckokai Paolo 
Published: September 2024

Abstract
Since agriculture is responsible for a considerable share of anthropogenic greenhouse gas emissions (GHGE), this paper examines the impact of various carbon taxes designed to incentivize environmentally friendly food consumption patterns in four European countries: Finland, Italy, Sweden, and the UK. As the proposed fiscal policies are likely to affect food consumption patterns, the study also assesses the consequent changes in diet quality and welfare. The results from this analysis reveal considerable variations in the reduction of GHGE across countries and tax schemes. While most taxation schemes have only a modest impact on dietary quality, these effects differ among nations. Additionally, the welfare cost of the compensated scheme is relatively small but not insignificant. These findings raise questions about the efficacy of a common European fiscal policy for climate mitigation compared to a more flexible approach where each member state calibrates the tax according to its unique circumstances.
Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Authors: Melo Bruno F , Ota Rafaela P , Benine Ricardo C , Carvalho Fernando R , Lima Flavio C T , Mattox George M T , Souza Camila S , Faria Tiago C , Reia Lais , Roxo Fabio F , Valdez-Moreno Martha , Near Thomas J , Oliveira Claudio 
Published: September 2024

Abstract
Neotropical tetras of the family Characidae form the largest and most taxonomically complex clade within the order Characiformes. Previous phylogenetic relationships concur on the recognition of four major subclades, whereas knowledge on intergeneric and interspecific relationships remains largely incomplete or nonexistent. We sampled 575 specimens of 494 species and 123 genera classified in Characidae, generated new molecular data of ultraconserved elements (UCEs), and used likelihood and Bayesian analyses. The phylogeny (1348 UCE loci: 538 472 bp) yielded clades with unprecedented resolution at species- and genus-levels, allowing us to propose a new classification of former Characidae into four families: Spintherobolidae, Stevardiidae, Characidae, and Acestrorhamphidae. The family Stevardiidae includes nine subfamilies: Landoninae, Xenurobryconinae, Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, and Diapominae. The family Characidae includes five subfamilies: Aphyocharacinae, Cheirodontinae, Exodontinae, Tetragonopterinae, and Characinae. The family Acestrorhamphidae congregates 15 subfamilies: Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, Stichonodontinae, unnamed subfamily, Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, Hyphessobryconinae, Thayeriinae, Rhoadsiinae, Grundulinae, and Acestrorhamphinae. The phylogeny resolves intergeneric relationships and supports revalidation of Myxiops, Megalamphodus, Ramirezella, Holopristis, and Astyanacinus, synonymy of Aphyodite, Genycharax, and Psellogrammus, and expansion of Cyanogaster, Makunaima, Deuterodon, Hasemania, Hemigrammus, Bario, Ctenobrycon, and Psalidodon. The phylogeny opens avenues for new systematic reviews and redefinitions of included genera.