bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invited commentary: influence of incomplete death information on cumulative risk estimates
Authors: Lok Judith J 
Published: July 2024

Abstract
Censoring at death is the only feasible option if death is not recorded and individuals who died simply no longer contribute visits, such as in the setting of Barberio et al (Am J Epidemiol. 2024;193(9):1281-1290) before they acquired access to mortality information. Censoring at death is known to lead to biased estimates of the probability of the event of interest before time $t$. Barberio et al showed through simulations that this bias increases with increasing mortality. However, when analyzing claims data it is often important to not exclude individuals with shorter life expectancies: An important strength of observational studies is that they allow estimation of treatment effects in more varied populations than are typically included in randomized clinical trials. In this commentary, I derive an analytical expression for the bias and provide 2 upper bounds for the bias. The bounds inform the usefulness of obtaining mortality information. If the probability of death before the event is known to be small, wider CIs can be created using the first bound on the bias; an algorithm is provided. If the bias is large, obtaining mortality information is important. Barberio et al show that obtaining mortality information can be essential in practice.
This article is part of a Special Collection on Pharmacoepidemiology.
Stability of extemporaneously prepared hydroxyurea solutions
Authors: Todd Hovey M , Patel Umesh S , Servos Mark A , Hovey Sara W , Van Haandel Leon 
Published: July 2024

Abstract

Purpose
To evaluate the stability of a new, more convenient (&lt;30 minutes for preparation), extemporaneously prepared hydroxyurea solution over 78 days.

Methods
A high-performance liquid chromatography (HPLC) method using a hydrophilic interaction chromatography (HILIC) column was developed and validated to accurately measure the concentration of hydroxyurea directly from solution without the need for chemical derivatization. Hydroxyurea was dissolved in sterile water in less than 5 minutes to yield a 100-mg/mL solution, which was then diluted by an equal volume of ORA-sweet vehicle to yield a 50-mg/mL extemporaneously prepared solution of hydroxyurea. The solution samples were kept at refrigeration (4 °C), room temperature (26 °C), and elevated temperature (40 °C) for 78 days.

Results
The 50-mg/mL solutions of hydroxyurea in a 1:1 mixture of water and ORA-sweet kept at 4 °C and 26 °C showed no significant loss of potency (&lt;2%) after 78 days. The solutions kept at 40 °C showed greater than 10% loss of potency after 28 days.

Conclusion
Extemporaneously compounded hydroxyurea 50-mg/mL solutions prepared in a 1:1 mixture of water and ORA-Sweet and stored in amber polypropylene plastic bottles were stable for at least 78 days at room temperature and under refrigeration.
Leaf functional trait evolution and its putative climatic drivers in African Coffea species
Authors: Hendrickx Aiden , Hatangi Yves , Honnay Olivier , Janssens Steven B , Stoffelen Piet , Vandelook Filip , Depecker Jonas 
Published: July 2024

Abstract

Background and Aims
Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships and evolutionary history of leaf functional traits in the genus Coffea, typically a rainforest understorey shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate.

Methods
We used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 African Coffea species. We added environmental data and data on maximum plant height for each species to test trait–environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification.

Key Results
Substantial leaf trait variation was detected across the genus Coffea in Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early-branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesize to be related to declining CO2 levels since the mid-Miocene. Brownian motion evolution was rejected in favor of white noise or Ornstein–Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in drier climates across the genus.

Conclusions
Generally, Coffea leaf traits appear to be evolutionarily labile and governed by stabilizing selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges.
Effectiveness of freezing temperatures on dormancy release of temperate woody species
Authors: Wang Huanjiong , Bai Wenrui , Hu Zhi , Lin Shaozhi , Ge Quansheng 
Published: July 2024

Abstract

Background and Aims
Spring phenological change of plants in response to global warming may affect many ecological processes and functions. Chilling temperature regulates budburst date by releasing dormancy. However, whether freezing temperatures (&lt;0 °C) contribute to dormancy release remains of debate. Our poor understanding of the role of chilling makes estimating shifts in budburst date difficult.

Methods
A 2-year chilling–forcing experiment was explicitly designed to test the effects of chilling temperatures on dormancy release of nine temperate woody species in Beijing, China. A total of 1620 twigs were first exposed to a wide range of temperatures (−10 to 10 °C) with different durations and then moved to growth chambers. Based on budburst data in experimental conditions, we examined whether freezing temperatures are effective on dormancy release. We also developed a new framework for constructing chilling functions based on the curve between chilling duration and forcing requirement (FR) of budburst. The chilling function derived from this framework was not affected by experimental forcing conditions.

Key Results
We demonstrated that freezing temperatures down to −10 °C were effective in dormancy release. The rate of dormancy release, indicated by the rate of decay in the chilling duration–FR curve, did not differ significantly between chilling temperatures in most cases, although it exhibited a maximum value at 0 or 5 °C. The chilling function-associated phenological models could simulate budburst date from independent experimental and observational data with a mean RMSE of 7.07 d.

Conclusions
The effective freezing temperatures found here are contrary to the well-known assumption of &lt;0 °C temperature generally not contributing to accumulated chilling in many previous chilling functions. A chilling function assuming that temperature below an upper temperature threshold has the same effects on dormancy release could be adopted to calculate chilling accumulation when using experiments to develop spring phenological models based on the chilling–forcing relationship.
Seasonal variation of vessel pits in sapwood: microscopical analyses of the morphology and chemical components of pit membrane encrustations in Fraxinus mandschurica
Authors: Yamagishi Shohei , Kojima Miho , Kuroda Katsushi , Abe Hisashi , Sano Yuzou 
Published: July 2024

Abstract

Background and Aims
Pit pairs and their filter-like partition, i.e. pit membranes, play important roles as water pathways, barriers and regulators in the water-conducting system of angiosperms. In Fraxinus species, the intervessel and vessel–parenchyma pit membranes in sapwood are normally encrusted during winter. Although these encrustations inevitably influence the performance of pits, their properties and functions remain unclear. This study aimed to reveal the morphological and chemical characteristics of encrustations in F. mandshurica in order to deepen understanding of the seasonal encrustation of pit membranes.

Methods
Seasonal and positional variations in the presence and morphology of encrustations were examined by field-emission scanning electron microscopy (FE-SEM). Cryo-FE-SEM for freeze-fixed greenwood samples was conducted to clarify whether encrustations were present in living trees. Chemical components were examined by histochemical staining using light and electron microscopy, immunofluorescence labelling and ultraviolet microspectroscopy.

Key Results
Encrustations began to deposit in autumn before leaf senescence and disappeared in spring before bud flushing. They infiltrated within the pit membranes, which suggested that they severely limit the permeation of pits. The encrustations differed in morphology among positions: they entirely filled the pit chambers in latewood, while they covered the pit membranes in earlywood. The encrustations were similarly observed in the samples that were freeze-fixed immediately after collection, indicating that they are present in living trees. The encrustations contained polysaccharides, including xyloglucan and homogalacturonan, and phenolic compounds, possibly including flavonoids and coumarins. These chemical components were also detected in droplets found in the latewood vessels with the encrustations, suggesting that the materials constituting encrustations were supplied through the vessel lumens.

Conclusions
Encrustations undoubtedly cover the pit membranes in living F. mandshurica trees in winter and their morphology and chemical composition indicate that they are impermeable, have positional differences in function and are characterized by elaborate deposition/removal processes.
Delineation of the impacts of varying 6-benzylaminopurine concentrations on physiological, biochemical and genetic traits of different olive cultivars under in vitro conditions
Authors: Zhao Ting , Khatoon Sadia , Matloob Javed Muhammad , Ghazy Abdel-Halim , Al-Doss Abdullah A , Rauf Muhammad , Khalid Taimoor , Ding Chuanbo , Shah Zahid Hussain 
Published: July 2024

Abstract
Abstract. The plant growth regulator 6-benzylaminopurine (BAP) is an important component of plant nutrient medium with tendency to accelerate physiological, biochemical and molecular processes in woody plants such as olive. To date, limited knowledge is available on the role of BAP in mediating physiological, biochemical and genetic activities in olives under in vitro conditions. To cover this research gap, the current study was conducted with the objective of studying the role of BAP in regulating physiological traits (chlorophyll, CO2 assimilation), antioxidant enzymes (superoxide dismutase, catalase and peroxidase), metabolic contents (starch, sucrose and flavonoids) and gene expression (OeRbcl, OePOD10, OeSOD10, OeCAT7, OeSS4, OeSuSY7, OeF3GT and OeChlH) under varying concentrations (0, 0.5, 1.5 and 2.5 mg L−1) within the provided in vitro conditions. The explants obtained from different olive cultivars (‘Leccino’, ‘Gemlik’, ‘Moraiolo’, ‘Arbosana’) were cultured on olive medium (OM) provided with different BAP concentrations using a two-factorial design, and data were analysed statistically. All traits increased significantly under in vitro conditions due to increasing concentrations of BAP; however, this increase was more dramatic at 2.5 mg L−1 and the least dramatic at 0.5 mg L−1. Moreover, correlation, principal component analysis and heatmap cluster analysis confirmed significant changes in the paired association and expression of traits with changing BAP concentration and type of olive cultivars. Likewise, the expression of all genes varied due to changes in BAP concentration in all cultivars, corresponding to variations in physiological and biochemical traits. Moreover, the spectrographs generated via scanning electron microscopy further indicated the variations in the distribution of elements in olive leaf samples due to varying BAP concentrations. Although all cultivars showed a significant response to in vitro varying concentrations of BAP, the response of Arbosana was statistically more significant. In conclusion, the current study proved the dynamic impact of the varying BAP concentrations on regulating the physiological, biochemical, and molecular attributes of olive cultivars.
Pearls of Wisdom: Expert Insights for Communicating With Aesthetic Patients
Authors: Martin Serena , Nugent Nora , Pacifico Marc D 
Published: July 2024

Abstract
Good communication with patients is essential in aesthetic surgery. In particular, the challenge of expectation management is crucial to optimizing patient satisfaction, which may be irrespective of objective outcomes. Experienced plastic surgeons inevitably refine their consultation process and hone their communication skills throughout years of practice. The invaluable “pearls” that expert surgeons develop would be beneficial to all surgeons, and particularly to those early in their practice. This prompted the authors to explore whether the communication skills acquired by a selected group of highly regarded plastic surgeons could be condensed and categorized in a way from which others could benefit. We seek to demonstrate that there are a select number of core messages that many plastic surgeons desire to communicate, particularly during the preoperative consultation process. Various phrases and aphorisms have been formulated within these subtopics that we hope will be positively incorporated into colleagues’ practices to improve the patient experience, and ultimately patients’ understanding of and satisfaction with their outcomes.
Genotype imputation in F2 crosses of inbred lines
Authors: Pierotti Saul , Welz Bettina , Osuna-López Mireia , Fitzgerald Tomas , Wittbrodt Joachim , Birney Ewan 
Published: July 2024

Abstract

Motivation
Crosses among inbred lines are a fundamental tool for the discovery of genetic loci associated with phenotypes of interest. In organisms for which large reference panels or SNP chips are not available, imputation from low-pass whole-genome sequencing is an effective method for obtaining genotype data from a large number of individuals. To date, a structured analysis of the conditions required for optimal genotype imputation has not been performed.

Results
We report a systematic exploration of the effect of several design variables on imputation performance in F2 crosses of inbred medaka lines using the imputation software STITCH. We determined that, depending on the number of samples, imputation performance reaches a plateau when increasing the per-sample sequencing coverage. We also systematically explored the trade-offs between cost, imputation accuracy, and sample numbers. We developed a computational pipeline to streamline the process, enabling other researchers to perform a similar cost–benefit analysis on their population of interest.

Availability and implementation
The source code for the pipeline is available at https://github.com/birneylab/stitchimpute. While our pipeline has been developed and tested for an F2 population, the software can also be used to analyse populations with a different structure.
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks
Authors: Gao Jiahao , Gerstein Mark 
Published: July 2024

Abstract

Motivation
Many types of networks, such as co-expression or ChIP-seq-based gene-regulatory networks, provide useful information for biomedical studies. However, they are often too full of connections and difficult to interpret, forming “indecipherable hairballs.”

Results
To address this issue, we propose that a Bayesian network can summarize the core relationships between gene expression activities. This network, which we call the LatentDAG, is substantially simpler than conventional co-expression network and ChIP-seq networks (by two orders of magnitude). It provides clearer clusters, without extraneous cross-cluster connections, and clear separators between modules. Moreover, one can find a number of clear examples showing how it bridges the connection between steps in the transcriptional regulatory network and other networks (e.g. RNA-binding protein). In conjunction with a graph neural network, the LatentDAG works better than other biological networks in a variety of tasks, including prediction of gene conservation and clustering genes.

Availability and implementation
Code is available at https://github.com/gersteinlab/LatentDAG
MetaHD: a multivariate meta-analysis model for metabolomics data
Authors: Liyanage Jayamini C , Prendergast Luke , Staudte Robert , De Livera Alysha M 
Published: July 2024

Abstract

Motivation
Meta-analysis methods widely used for combining metabolomics data do not account for correlation between metabolites or missing values. Within- and between-study variability are also often overlooked. These can give results with inferior statistical properties, leading to misidentification of biomarkers.

Results
We propose a multivariate meta-analysis model for high-dimensional metabolomics data (MetaHD), which accommodates the correlation between metabolites, within- and between-study variances, and missing values. MetaHD can be used for integrating and collectively analysing individual-level metabolomics data generated from multiple studies as well as for combining summary estimates. We show that MetaHD leads to lower root mean square error compared to the existing approaches. Furthermore, we demonstrate that MetaHD, which exploits the borrowing strength between metabolites, could be particularly useful in the presence of missing data compared with univariate meta-analysis methods, which can return biased estimates in the presence of data missing at random.

Availability and implementation
The MetaHD R package can be downloaded through Comprehensive R Archive Network (CRAN) repository. A detailed vignette with example datasets and code to prepare data and analyses are available on https://bookdown.org/a2delivera/MetaHD/.
TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data
Authors: Kim Ha Young , Kim Sungsik , Park Woong-Yang , Kim Dongsup 
Published: July 2024

Abstract

Motivation
Prediction of T-cell receptor (TCR)–epitope interactions is important for many applications in biomedical research, such as cancer immunotherapy and vaccine design. The prediction of TCR–epitope interactions remains challenging especially for novel epitopes, due to the scarcity of available data.

Results
We propose TSpred, a new deep learning approach for the pan-specific prediction of TCR binding specificity based on paired chain TCR data. We develop a robust model that generalizes well to unseen epitopes by combining the predictive power of CNN and the attention mechanism. In particular, we design a reciprocal attention mechanism which focuses on extracting the patterns underlying TCR–epitope interactions. Upon a comprehensive evaluation of our model, we find that TSpred achieves state-of-the-art performances in both seen and unseen epitope specificity prediction tasks. Also, compared to other predictors, TSpred is more robust to bias related to peptide imbalance in the dataset. In addition, the reciprocal attention component of our model allows for model interpretability by capturing structurally important binding regions. Results indicate that TSpred is a robust and reliable method for the task of TCR–epitope binding prediction.

Availability and implementation
Source code is available at https://github.com/ha01994/TSpred.
Contrasting interspecific hybridization patterns in two goby groups radiating in divergent freshwater habitats
Authors: Ito Ryosuke K , Mishina Tappei , Hashiguchi Yasuyuki , Watanabe Katsutoshi 
Published: July 2024

Abstract
Hybridization and introgression between closely related species significantly affect their evolutionary and ecological processes. Understanding the ecological, environmental, and geographical conditions that promote their occurrence is imperative. It is hypothesized that species inhabiting geologically unstable habitats or with life-history constraints that prevent evasion from such environments are more prone to interspecific hybridization, due to limited development of prezygotic isolation. To test this hypothesis, we conducted a comparative analysis of genome-wide hybridization patterns in two freshwater goby groups of Gymnogobius: the castaneus- and urotaenia-groups. Utilizing the newly determined draft genome of G. isaza and single nucleotide variants identified by RNA sequencing, we first established the species phylogeny and then examined genetic signatures of interspecific hybridization in each group. The results revealed that all castaneus-group species, which primarily inhabit unstable habitats such as ponds, have undergone interspecific hybridization. Conversely, no species of the urotaenia-group showed clear evidence of hybridization over a period of more than 1 million years. These species inhabit an ancient lake (one species) or rivers (three amphidromous species), the latter possessing potential dispersal abilities in early life to evade geological disturbances. These ecology–geology relationships have remarkable implications for the intricate processes of adaptation and speciation.
Writing as Social Work: Thematic Review of the Literature
Authors: Rai Lucy , Ferguson Gillian , Giddings Lindsay 
Published: July 2024

Abstract
This article offers a thematic review of research and analysis of academic and practice-based social work writing. It aims to highlight specific challenges, arguing that support is needed in the development of writing as a core element of professional practice. Social work writing in the United Kingdom has been framed as a ‘problematic’, time-intensive activity [Lillis, T. (2023) ‘Professional written voice “in flux”: The case of social work’, Applied Linguistics Review, 14(3), pp. 615–41]. It records practice, but is also a vital tool for undertaking assessments, formulating professional judgements, decision making and multi-agency collaboration. However, the centrality of writing to social work practice is not reflected in the regulatory frameworks for the profession in the United Kingdom where it only appears in the context of ‘report writing’ and loosely ‘communication’. The discussion is contextualised within a theoretical framing of social work writing followed by a discussion of student writing and then writing in professional practice. The article addresses the themes related to academic writing of concerns about the quality of writing; disciplinarity; conventions and implicit codes; and challenges to teach professional writing. In relation to practice-based writing, the article addresses the themes of social work as a ‘writing intensive’ profession; writing as enacting practice; and the challenges and experience of social work writers.