bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cosmological Reflections in Greek and Hebrew Texts
Authors: Najman Hindy 
Published: December 2024

Abstract
Texts in Hellenistic Judaism draw on both earlier biblical materials and Greek thinking to think philosophically in new and dynamic ways about nature, human essence, creation, and abstraction of time and history. The concept of the secret of being (raz nihyeh) reflects a kind of secrecy or hiding as linked to being or to nature as one tries to examine and investigate the workings of the world. Intellectual and spiritual work is about reflection and the pursuit of knowledge as a way of understanding human essence, and ultimately the pursuit of goodness. The subject is formed through discernment between good and evil and, as one aspires to apply this knowledge to the self, the process of repentance. To achieve this aspiration of becoming more ‘godlike’ and ‘human’, the notion of ‘paradigm’ functions in a liminal register between ‘heaven and earth’, accessible to God and the human mind. It is up to humanity to aspire toward perfection and actualize the potential of the unchanging heavenly paradigm for order and goodness that is already inscribed in the heavens.
Postscript
Authors: Najman Hindy 
Published: December 2024

Abstract
Hermeneutics is at the essence of the vitality of Judaism from its earliest inception until the present day. To understand vitality is to understand the various ways in which Judaism re-imagines itself through various expressions of writing, imagining, and performance. As such, philology must be situated within an account of what readers, writers, and editors are doing, of what they are trying to withstand, and of how they are trying to insist on the resistance and persistence of their language and culture. Philology needs to be grounded both philosophically and also literarily so that one does not lose sight of the text in its largest form as well as in its interrelatedness to itself. Reading is about understanding the interrelational dimensions of a work, not as a work only of the past, but rather one that is life-giving to itself through internal conversation and its afterlife as a read and interpreted text. Considering how texts are heard, read, performed, and experienced further builds a path between philology and philosophical hermeneutics. Continued integration of the contributions of literature and imagination during the Hellenistic period is necessary to overcome biases embedded in the field of biblical studies with respect to supersessionism, the privileging of an original and early expression of a tradition, and the dismissing of the Hellenistic period as late Judaism.
From Farm to Table
Authors: Kelly Alan , Fox Patrick , Cogan Tim 
Published: December 2024

Abstract
The consumption of dairy products, made from the milk of cows, sheep, goats, and buffalo, among other mammalian species, is almost as old as human civilization, with evidence of these products stretching back many millennia. The production of different kinds of dairy products originated as different ways to preserve the valuable nutritional goodness of milk components (lactose, fat, protein, vitamins, and minerals) and make the milk safe for consumption, using basic principles like fermentation, heating, separation, dehydration, acidification, smoking, and salting, which are the keys to producing products like cheese, butter, and yoghurt. Many dairy products today are still produced using the same basic principles, and in this book an introduction to the origins, constituents and properties of milk is given, alongside an outline of the ways in which dairy products are made, including the development of advanced products like infant formula and formulated nutritional products. The text introduces, at an introductory level, the chemistry and microbiology of milk, as well as the principles of the main processes used, such as spray-drying, fermentation, and pasteurization, to underpin understanding of how the properties of the main dairy products emerge. The book, which finishes with a discussion of the challenges and threats facing dairy today, is designed to be accessible to a wide range of non-specialist readers who may have an interest in milk and dairy products and want to learn more about this fascinating and ancient branch of the science of food.
Mammals and Milk Production
Authors: Kelly Alan , Fox Patrick , Cogan Tim 
Published: December 2024

Abstract
The key starting point for making dairy products is milk itself, and so this chapter begins the book with a description of the way in which milk is produced by mammals. The chapter begins with the introduction of the main milk producing species (cows, goats, sheep, buffalo) then goes on to describe the way in which milk is produced and synthesized, as well as the main factors that influence the composition of milk, such as the stage of the lactation cycle, diet, and illness. As the quality of milk and dairy products is very heavily dependent on what happens on the farm, this chapter is the logical place to open the discussion of the journey of milk from farm to table.
Pasteurized and Long-Life Milk
Authors: Kelly Alan , Fox Patrick , Cogan Tim 
Published: December 2024

Abstract
One of the main dairy products consumed on a daily basis is fluid milk in a carton or glass bottle. In most countries, this is pasteurized and refrigerated; in others, an ultra-high temperature (UHT) treated long-life product is preferred. This chapter explores the role of heat treatment in making milk safe for consumption and extending its shelf-life. It then describes (including simple explanatory diagrams) the building blocks of a modern dairy processing line for milk, covering the key operations of heat treatment (pasteurization or UHT), separation of fat and adjustment of fat content, and homogenization. The changes in milk during storage are then described, along with recent developments in the production of these products, such as production of fortified and flavored milk products.
Milk Chocolate
Authors: Kelly Alan , Fox Patrick , Cogan Tim 
Published: December 2024

Abstract
This chapter describes another popular product, chocolate, the properties of which depend to a significant extent on milk. It begins with a short history of chocolate, from its first, primary use as a drink among the Maya and Aztec peoples, to the modern development of solid chocolate. The chapter goes on to describe the production of chocolate from cocoa beans, along with various innovations over the centuries to improve its production. It then describes the two main types of chocolate, milk and dark, as well as their varying constituents and production methods. Finally, a number of products containing chocolate are listed.
Packaging of Dairy Products
Authors: Kelly Alan , Fox Patrick , Cogan Tim 
Published: December 2024

Abstract
This chapter considers a key way in which dairy products are preserved and their quality maintained, which is through careful selection of packaging. It explains that this packaging is frequently more than an inert container in which food is contained and sold; it is a complex matrix that serves a range of functions. The chapter describes both the main types of packaging used for dairy products (card, metal, glass, and plastic) and the way packaging trends have changed over time (e.g., the switch from glass bottles to Tetra Paks for liquid milk products). Finally, it reviews the main considerations for selecting packaging for different dairy products, including the needs of different kinds of cheese.
Effectiveness of rasburicase 4.5 mg in the treatment of tumor lysis syndrome–related hyperuricemia
Authors: Schlueter Callahan , Stojova Emilija , Rozycki Elizabeth , Eisinger Gregory , Westfield Jaelyn , Shirk Mary Beth 
Published: December 2024

Abstract

Purpose
Optimal rasburicase dosing remains unknown. This study evaluated outcomes of single rasburicase 4.5 mg doses when treating moderate (12 to &lt;15 mg/dL) versus high (≥15 mg/dL) uric acid (UA) levels.

Methods
This retrospective observational cohort study included patients with an active malignancy and tumor lysis syndrome (TLS) who received rasburicase 4.5 mg. Patients were categorized by UA levels before administration of rasburicase. The primary outcome was UA normalization (&lt;8 mg/dL) 24 hours post rasburicase administration. Secondary outcomes included repeat rasburicase dose(s) within 72 hours and renal replacement therapy (RRT) within 7 days. Nominal and continuous data were analyzed using chi squared or Fisher’s exact and Wilcoxon rank-sum or Student’s t test, respectively. Multivariate regression analysis explored risk factors for continued hyperuricemia.

Results
After screening of 428 patients, 124 moderate and 95 high baseline UA values were included. Overall, baseline characteristics were similar between cohorts. The primary outcome was achieved more often in the moderate cohort (92.7% vs 67.4% [P &lt; 0.001]). More high cohort patients received repeat rasburicase doses (8.1% vs 21.1% [P = 0.009]) with no difference in RRT frequency. Risk factors for continued hyperuricemia included baseline UA, potassium and body mass index.

Conclusion
A single dose of rasburicase 4.5 mg was less effective in achieving UA normalization in patients with a baseline UA of ≥15 mg/dL vs 12 to &lt;15 mg/dL, without significant differences in patient-oriented outcomes such as RRT. Higher initial doses of rasburicase may be needed for patients with a baseline UA of ≥15 mg/dL. Additional studies are needed to determine optimal dosing for these patients.
Climatic and edaphic niche shifts during plant radiation in the Mediterranean biodiversity hotspot
Authors: Fernández-Mazuecos Mario , Glover Beverley J 
Published: December 2024

Abstract

Background and Aims
Ecological speciation is frequently invoked as a driver of plant radiation, but the behaviour of environmental niches during radiation is contentious, with patterns ranging from niche conservatism to niche divergence. Here, we investigated climatic and edaphic niche shifts during radiation in a western Mediterranean lineage of the genus Linaria (Plantaginaceae).

Methods
Detailed distributional, phylogenomic and environmental data were integrated to analyse changes in climatic and edaphic niches in a spatiotemporal context, including calculation of niche overlap, niche equivalency and similarity tests, maximum entropy modelling, phylogenetic comparative methods and biogeographical analyses.

Key Results
Active divergence of climatic and edaphic niches within a limited subset of available conditions was detected among the eight study species and particularly between sister species. Speciation and niche divergence are estimated to have happened in the southern Iberian Peninsula in Mediterranean conditions, followed by waxing and waning of distribution ranges resulting from the Quaternary climatic cycles.

Conclusions
The results support the idea that the prevalence of niche conservatism or niche divergence patterns is a matter of phylogenetic scale. Habitat isolation pertaining to both climatic and soil conditions appears to have played a role in plant speciation in the western Mediterranean biodiversity hotspot, most probably in combination with pollinator isolation and some degree of geographical isolation. These findings are in agreement with an adaptive radiation scenario incorporating certain non-adaptive features.
Effect of coenzyme Q deficiency on ethanol fermentation in sake yeast
Authors: Nishida Ikuhisa , Nishihara Shogo , Kaino Tomohiro , Kawamukai Makoto , Hirata Dai 
Published: December 2024

Abstract
Coenzyme Q (CoQ), a component of the electron transport chain, participates in aerobic respiration to produce ATP. Little is known about the relationship between CoQ and ethanol fermentation. Herein, we revealed that the deficiency or the addition of CoQ in sake yeast led to an increase or a decrease, respectively, in ethanol production rate at the early stage of fermentation.
Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping
Authors: Ravishankar Shyamsundar , Perez Vilma , Davidson Roberta , Roca-Rada Xavier , Lan Divon , Souilmi Yassine , Llamas Bastien 
Published: December 2024

Abstract
Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments—including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.
Optimizing design of genomics studies for clonal evolution analysis
Authors: Srivatsa Arjun , Schwartz Russell 
Published: December 2024

Abstract

Motivation
Genomic biotechnology has rapidly advanced, allowing for the inference and modification of genetic and epigenetic information at the single-cell level. While these tools hold enormous potential for basic and clinical research, they also raise difficult issues of how to design studies to deploy them most effectively. In designing a genomic study, a modern researcher might combine many sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. This is especially relevant for studies of somatic variation, which may involve highly heterogeneous cell populations whose differences can be probed via an extensive set of biotechnological tools. Efficiently deploying genomic technologies in this space will require principled ways to create study designs that recover desired genomic information while minimizing various measures of cost.

Results
The central problem this paper attempts to address is how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation that occur most often with application to cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem. We introduce a Bayesian optimization framework that iteratively optimizes for an objective function using surrogate modeling combined with pattern and gradient search. We demonstrate our procedure on several test cases to derive resource and study design allocations optimized for various goals and criteria, demonstrating its ability to optimize study designs efficiently across diverse scenarios.

Availability and implementation
https://github.com/CMUSchwartzLab/StudyDesignOptimization
Exploring the role of the Rab network in epithelial-to-mesenchymal transition
Authors: Jaygude Unmani , Hughes Graham M , Simpson Jeremy C 
Published: December 2024

Abstract

Motivation
Rab GTPases (Rabs) are crucial for membrane trafficking within mammalian cells, and their dysfunction is implicated in many diseases. This gene family plays a role in several crucial cellular processes. Network analyses can uncover the complete repertoire of interaction patterns across the Rab network, informing disease research, opening new opportunities for therapeutic interventions.

Results
We examined Rabs and their interactors in the context of epithelial-to-mesenchymal transition (EMT), an indicator of cancer metastasizing to distant organs. A Rab network was first established from analysis of literature and was gradually expanded. Our Python module, resnet, assessed its network resilience and selected an optimally sized, resilient Rab network for further analyses. Pathway enrichment confirmed its role in EMT. We then identified 73 candidate genes showing a strong up-/down-regulation, across 10 cancer types, in patients with metastasized tumours compared to only primary-site tumours. We suggest that their encoded proteins might play a critical role in EMT, and further in vitro studies are needed to confirm their role as predictive markers of cancer metastasis. The use of resnet within the systematic analysis approach described here can be easily applied to assess other gene families and their role in biological events of interest.

Availability and implementation
Source code for resnet is freely available at https://github.com/Unmani199/resnet
Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiome
Authors: Monshizadeh Mahsa , Hong Yuhui , Ye Yuzhen 
Published: December 2024

Abstract

Motivation
Microbial signatures in the human microbiome are closely associated with various human diseases, driving the development of machine learning models for microbiome-based disease prediction. Despite progress, challenges remain in enhancing prediction accuracy, generalizability, and interpretability. Confounding factors, such as host’s gender, age, and body mass index, significantly influence the human microbiome, complicating microbiome-based predictions.

Results
To address these challenges, we developed MicroKPNN-MT, a unified model for predicting human phenotype based on microbiome data, as well as additional metadata like age and gender. This model builds on our earlier MicroKPNN framework, which incorporates prior knowledge of microbial species into neural networks to enhance prediction accuracy and interpretability. In MicroKPNN-MT, metadata, when available, serves as additional input features for prediction. Otherwise, the model predicts metadata from microbiome data using additional decoders. We applied MicroKPNN-MT to microbiome data collected in mBodyMap, covering healthy individuals and 25 different diseases, and demonstrated its potential as a predictive tool for multiple diseases, which at the same time provided predictions for the missing metadata. Our results showed that incorporating real or predicted metadata helped improve the accuracy of disease predictions, and more importantly, helped improve the generalizability of the predictive models.

Availability and implementation
https://github.com/mgtools/MicroKPNN-MT.
MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD
Authors: Cadman Tim , Slofstra Mariska K , van der Geest Marije A , Avraam Demetris , Bishop Tom R P , de Boer Tommy , Duijts Liesbeth , Haakma Sido , Hyde Eleanor , Jaddoe Vincent , Karramass Tarik , Kelpin Fleur , Marcon Yannick , Pinot de Moira Angela , Postma Dick , Tolboom Clemens , Veenstra Ruben L , Wheater Stuart , Welten Marieke , Wilson Rebecca C , Zwart Erik , Swertz Morris 
Published: December 2024

Abstract

Summary
Extensive human health data from cohort studies, national registries, and biobanks can reveal lifecourse risk factors impacting health. Combining these sources offers increased statistical power, rare outcome detection, replication of findings, and extended study periods. Traditionally, this required data transfer to a central location or separate partner analyses with pooled summary statistics, posing ethical, legal, and time constraints. Federated analysis—which involves remote data analysis without sharing individual-level data—is a promising alternative. One promising solution is DataSHIELD (https://datashield.org/), an open-source R based implementation. To enable federated analysis, data owners need a user-friendly way to install the federated infrastructure and manage users and data. Here, we present MOLGENIS Armadillo: a lightweight server for federated analysis solutions such as DataSHIELD.

Availability and implementation
Armadillo is implemented as a collection of three packages freely available under the open source licence LGPLv3: two R packages downloadable from the Comprehensive R Archive Network (CRAN) (“MolgenisArmadillo” and “DSMolgenisArmdillo”) and one Java application (“ArmadilloService”) as jar and docker images via Github (https://github.com/molgenis/molgenis-service-armadillo).
Protocol for obtaining doubled haploids in isolated microspore culture in vitro for poorly responsive genotypes of brassicaceae family
Authors: Kozar Elena V , Domblides Elena A 
Published: December 2024

Abstract
In this protocol for obtaining doubled haploids plants (DH), we propose a new method for microspore isolation. This method is useful for genotypes of the Brassicaceae family with low responsiveness to DH technology. For such crops, it allows increasing the embryo yield several times and sometimes obtaining embryos for the first time. This method of microspore isolation reduces the mechanical impact on the bud tissue, which minimizes somatic cell destruction and reduces to get it into the preparation through the filter, thus increasing its purity. The new isolation method also increases the relative concentration of embryogenic microspores in the preparation. This is possible because the anther tissues are not destroyed during the isolation process. Therefore, the anther retains its structure and microspores of early and late stages are trapped by the anther tissue, thus the anther acts as a sieve. Late stages are trapped because of their larger size, while early stages are trapped because they are even more tightly bound to the anther tissue. Together, these factors increase the efficiency of the technology for DH production in vitro microspore culture. This protocol article provides a detailed experimental protocol to the method presented in the experimental article (E.V. Kozar, E.G. Kozar, E.A. Domblides. Effect of the Method of Microspore Isolation on the Efficiency of Isolated Microspore Culture In Vitro for Brassicaceae Family. Horticulturae. 2022. Vol. 8, No. 10. P. 864. DOI 10.3390/horticulturae8100864) but does not repeat all the results documenting the efficacy of the actual method.
BAMITA: Bayesian multiple imputation for tensor arrays
Authors: Jiang Ziren , Li Gen , Lock Eric F 
Published: December 2024

Abstract
Data increasingly take the form of a multi-way array, or tensor, in several biomedical domains. Such tensors are often incompletely observed. For example, we are motivated by longitudinal microbiome studies in which several timepoints are missing for several subjects. There is a growing literature on missing data imputation for tensors. However, existing methods give a point estimate for missing values without capturing uncertainty. We propose a multiple imputation approach for tensors in a flexible Bayesian framework, that yields realistic simulated values for missing entries and can propagate uncertainty through subsequent analyses. Our model uses efficient and widely applicable conjugate priors for a CANDECOMP/PARAFAC (CP) factorization, with a separable residual covariance structure. This approach is shown to perform well with respect to both imputation accuracy and uncertainty calibration, for scenarios in which either single entries or entire fibers of the tensor are missing. For two microbiome applications, it is shown to accurately capture uncertainty in the full microbiome profile at missing timepoints and used to infer trends in species diversity for the population. Documented R code to perform our multiple imputation approach is available at https://github.com/lockEF/MultiwayImputation.