bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key performance indicators for monitoring of anemia management and iron status in children attending a pediatric dialysis unit: the experience of Ain Shams University
Authors: Khalil Mariam A. , Kasem Mohammed F. , El-Hakim Ihab Z. , Abd Elhafez Amany M. , El Farsy Mohamed S. , Said Ragia M. 
Published: July 2024

Abstract
Background
Anemia in children on maintenance hemodialysis (HD) leads to poor quality of life. Our study aimed to assess and monitor anemia and iron status management in children on maintenance HD over 18 months using key performance indicators.

Methods
Key performance indicators, formulated as the percentage of patients achieving the KDIGO (2012) guideline-recommended targets for hemoglobin (Hb) (11–12 g/dl), transferrin saturation (TSAT) (20–40%) and serum ferritin (200–500 ng/ml), were reported quarterly over the 18-month-period of this study.

Results
This study was carried out over an 18 month-period, from April 1st, 2020, till October 31st, 2021. A total of 78 patients (45 males and 33 females) were included; mean age 12.16 ± 3.3 years and HD duration range 3.0—140.88 months, median 16.51 months. The three most common primary causes of CKD were Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) (29.5%), unknown cause (24.4%), and chronic glomerular diseases (20.5%). The quarterly reported percentages of patients achieving the recommended targets for Hb, TSAT, and serum ferritin ranges were 18.2–35.7%, 38.8–57.1%, and 11.9–26.6%, respectively.

Conclusion
Although the mean Hb trend was nearing the KDIGO (2012) target, the key performance indicators showed that only a small percentage of our HD patients were achieving the targets for Hb, TSAT, & serum ferritin, thus alerting us to the need to revise our protocol for the management of anemia and iron status.

Graphical abstract
Mannan‑, VLP-, and flagellin-based adjuvants for allergen-specific immunotherapy: a review of the current literature
Authors: Pignard Clara , Schiller Hannah , Seyffer Alisa , Schülke Stefan 
Published: July 2024

AbstractCurrently, allergen-specific immunotherapy (AIT) with active ingredients derived from the causative allergen source is the only disease-modifying treatment for allergic patients. However, compared to, e.g., live-attenuated vaccines for the prevention of infectious diseases, purified allergens for AIT in many cases display only a low immunogenicity. This reduces treatment efficacy and prolongs treatment duration. Here, adjuvants may be a promising tool, allowing for dose reduction of the respective allergen while increasing immunogenicity of co-applied allergens and/or modulating allergen-specific immune responses toward T helper 1 (Th1) or regulatory phenotypes or the production of blocking antibody isotypes. Currently available adjuvants can be distinguished into first-generation adjuvants (promoting immune responses via aggregation and controlled release of co-applied allergens from a depot) and second-generation adjuvants (triggering immune responses via the activation of pattern recognition receptors expressed by immune cells). This review summarizes the mechanisms and effects of adjuvants currently or previously used for AIT (aluminum hydroxide, calcium phosphate, microcrystalline tyrosine, and monophosphoryl lipid A [MPLA]) and focuses on novel developments using mannan-, virus-like particle (VLP)-, and flagellin-based adjuvants and therapeutics for the treatment of allergic diseases.
„Sie dürfen sich nicht auf ihrer Muttersprache unterhalten und das finde ich tatsächlich auch gut“ – Sprachbezogene Diskriminierung in der Grundschule
Authors: Lange Sarah Désirée , Alhallak Zahia , Plohmer Anna 
Published: July 2024

ZusammenfassungMit der Studie wird bezweckt, ausgehend von Beschreibungen und Begründungen von Lehrkräften zu ihrem Umgang mit Mehrsprachigkeit potenziell linguizistische Überzeugungen aufzudecken, um Strukturen sichtbar zu machen, die sich möglicherweise benachteiligend auf mehrsprachige Kinder auswirken. Dazu wurden qualitative, vignettenbasierte Interviews der DFG-geförderten BLUME II-Vignettenstudie mit 43 berufstätigen Grundschullehrkräften ausgewertet. Die inhaltsanalytische Auswertung ergab acht zentrale Themen, die zu vier Legitimationen verdichtet wurden, mit denen das Exkludieren von Familiensprachen begründet wird: Die Lehrkräfte legitimieren den Ausschluss von Familiensprachen im Unterricht mit den eigenen begrenzten oder nicht vorhandenen sprachlichen Kompetenzen. Weiterhin legitimieren die Lehrkräfte mehrsprachige Kinder aus der Unterrichtsplanung auszuschließen mit der Vielfältigkeit der Familiensprachen innerhalb der Klasse und indem sie das Beherrschen des Deutschen als Voraussetzung für erfolgreiche, soziale Integration sehen. Als weitere Legitimation werden Sprachverbote benannt, denen sich die Lehrkräfte größtenteils verpflichtet fühlen. Auffällig sind bei der Beschreibung der Ergebnisse die vielen sprachbezogenen Defizitzuschreibungen und dass es sich bei allen Legitimierungen um Externalisierungen handelt. Die Ergebnisse verweisen auf die Schlüsselrolle von Grundschullehrkräften in der Reproduktion sprachbezogener Diskriminierung und regen dazu an, subjektive Begründungen und Argumentationsmuster für potenziell linguizistische Praktiken im Grundschulalltag kritisch zu hinterfragen, um besser zu verstehen, wie sprachbezogene Diskriminierung verhindert werden kann.
Inducers and Inhibitors of Pyroptotic Death of Granulosa Cells in Models of Premature Ovarian Insufficiency and Polycystic Ovary Syndrome
Authors: Berkel Caglar 
Published: July 2024

AbstractGranulosa cells (GCs), the largest cell population and primary source of steroid hormones in the ovary, are the important somatic ovarian components. They have critical roles in folliculogenesis by supporting oocyte, facilitating its growth, and providing a microenvironment suitable for follicular development and oocyte maturation, thus having essential functions in maintaining female fertility and in reproductive health in general. Pyroptotic death of GCs and associated inflammation have been implicated in the pathogenesis of several reproductive disorders in females including Premature Ovarian Insufficiency (POI) and Polycystic Ovary Syndrome (PCOS). Here, I reviewed factors, either intrinsic or extrinsic, that induce or inhibit pyroptosis in GCs in various models of these disorders, both in vitro and in vivo, and also covered associated molecular mechanisms. Most of these studied factors influence NLRP3 inflammasome- and GSDMD (Gasdermin D)-mediated pyroptosis in GCs, compared to other inflammasomes and gasdermins (GSDMs). I conclude that a more complete mechanistic understanding of these factors in terms of GC pyroptosis is required to be able to develop novel strategies targeting inflammatory cell death in the ovary.
Global Distribution and Projected Variations of Compound Drought‐Extreme Precipitation Events
Authors: Deng Siqi , Zhao Dongsheng , Chen Ziwei , Liu Lei , Zhu Yu , Wang Ke , Gao Xuan , Wu Hanqian , Zheng Du 
Published: July 2024

AbstractThe compound drought‐extreme precipitation event (CDEP) is one of the most impactful successive compound events that shift from drought to extreme precipitation in the same location within a short period. Due to its dual characteristics of drought and flood, CDEP tends to be more destructive than the impact of individual drought or flood. Yet few studies have analyzed the likelihood of CDEP at different time intervals and their potential variations under global warming. In this study, we assessed the coincidence rate between droughts and extreme precipitation events at 1‐month (CDEP‐1), 2‐month (CDEP‐2), and 3‐month (CDEP‐3) intervals, as well as their potential changes in a 1.5 and 2°C warming world (under both SSP2‐4.5 and SSP5‐8.5 scenarios). Our results suggest that global droughts and extreme precipitation events have coincided more frequently at 1‐month interval than at 2‐ and 3‐month intervals during the period 1985–2014. The global average coincidence rates of CDEP‐1, CDEP‐2, and CDEP‐3 are 24%, 10%, and 7%, respectively. Notably, the coincidence rate of CDEP‐1 exceeded 40% in Eastern Asia, north‐eastern North America, and India, indicating that more than 40% of droughts have been followed by extreme precipitation events in the next month after drought termination. Under both SSP2‐4.5 and SSP5‐8.5 scenarios, climate warming will increase the coincidence rate of CDEP‐1, CDEP‐2, and CDEP‐3, especially will lead to higher values in the coincidence rate of CDEP‐1. This study contributes to a better understanding of the patterns of CDEP and helps to develop more targeted risk management strategies.
The Anthropocene Is More Than a Time Interval
Authors: Edgeworth Matthew , Bauer Andrew M. , Ellis Erle C. , Finney Stanley C. , Gill Jacquelyn L. , Gibbard Philip L. , Maslin Mark , Merritts Dorothy J. , Walker Michael J. C. 
Published: July 2024

AbstractFollowing the recent rejection of a formal Anthropocene series/epoch by the Subcommission on Quaternary Stratigraphy (SQS) of the International Commission on Stratigraphy (ICS), and its subsequent confirmation by the International Union of Geological Sciences (IUGS), the opportunity arises to reset the definition of the Anthropocene. The case for informally recognizing the Anthropocene to be a major planetary event of Earth system transformation offers a promising way forward, but this has been criticized by proponents of an Anthropocene series/epoch. In order to move on from the assumption that it must be a time interval, and to foster a more transdisciplinary and inclusive approach, the main points of the critique must be directly addressed.
A Contiguous Taltson‐Thelon Margin Revisited
Authors: Cutts J. A. , Dyck B. V. , Perrot M. G. , Davies J. H. F. L. , Osinchuk A. M. , Šilerová D. , Stern R. A. , Chiaradia M. , Canam R. 
Published: July 2024

AbstractThe amalgamation of Laurentia was initiated along the western margin of the Rae craton. However, the tectonic setting that generated magmatic rocks along this margin has long been debated, with the Thelon tectonic zone in the north having formed in an arc setting, and the Taltson magmatic zone in the south variably attributed to either continental arc or intracratonic magmatism. The magmatic rocks of the Great Slave Lake shear zone (GSLsz) lie between these two tectonic belts and, thus, may be critical to the interpretation of the evolution of the western Rae margin. To understand the origin of the rocks in the GSLsz, we have applied U‐Pb geochronology, trace‐element geochemistry, and O and Hf isotope analyses to zircons from a suite of samples that transect the La Loche River fault (LRf)—a major structure that bisects the GSLsz. Samples collected to the north of the LRf are Neoarchean in age, have mantle‐like δ18O (4.7–5.8‰) and chondritic to juvenile εHf values (0–4.5), whereas those to the south are exclusively Paleoproterozoic in age and have more elevated δ18O (6.3–7‰) and much more evolved εHf values (−12 to −6); these results indicate that the LRf marks a crustal‐scale suture between the Slave craton and the Taltson magmatic zone. Our isotopic data, together with other regional constraints from the area, are most consistent with the Taltson magmatic zone having formed in a continental arc setting emplaced into ca. 2.3 Ga juvenile basement crust.
Association study of GBA1 variants with MSA based on comprehensive sequence analysis -Pitfalls in short-read sequence analysis depending on the human reference genome-
Authors: Orimo Kenta , Mitsui Jun , Matsukawa Takashi , Tanaka Masaki , Nomoto Junko , Ishiura Hiroyuki , Omae Yosuke , Kawai Yosuke , Tokunaga Katsushi ,   NCBN Controls WGS Consortium, Ishibashi-Ueda Hatsue , Tomita Tsutomu , Noguchi Michio , Takahashi Ayako , Goto Yu-ichi , Yoshida Sumiko , Hattori Kotaro , Matsumura Ryo , Iida Aritoshi , Maruoka Yutaka , Gatanaga Hiroyuki , Shimomura Akihiko , Sugiyama Masaya , Suzuki Satoshi , Miyo Kengo , Matsubara Yoichi , Umezawa Akihiro , Hata Kenichiro , Kaname Tadashi , Ozaki Kouichi , Tokuda Haruhiko , Watanabe Hiroshi , Niida Shumpei , Noiri Eisei , Kitajima Koji , Omae Yosuke , Miyahara Reiko , Shimanuki Hideyuki , Kawai Yosuke , Tokunaga Katsushi , Toda Tatsushi , Tsuji Shoji 
Published: July 2024

AbstractMultiple system atrophy (MSA) is a neurodegenerative disorder characterized by various combinations of autonomic failure, parkinsonism, and cerebellar ataxia. To elucidate variants associated with MSA, we have been conducting short-read-based whole-genome sequence analysis. In the process of the association studies, we initially focused on GBA1, a previously proposed susceptibility gene for MSA, to evaluate whether GBA1 variants can be efficiently identified despite its extraordinarily high homology with its pseudogene, GBA1LP. To accomplish this, we conducted a short-read whole-genome sequence analysis with alignment to GRCh38 as well as Sanger sequence analysis and compared the results. We identified five variants with inconsistencies between the two pipelines, of which three variants (p.L483P, p.A495P–p.V499V, p.L483_M489delinsW) were the results of misalignment due to minor alleles in GBA1P1 registered in GRCh38. The miscalling events in these variants were resolved by alignment to GRCh37 as the reference genome, where the major alleles are registered. In addition, a structural variant was not properly identified either by short-read or by Sanger sequence analyses. Having accomplished correct variant calling, we identified three variants pathogenic for Gaucher disease (p.S310G, p.L483P, and p.L483_M489delinsW). Of these variants, the allele frequency of p.L483P (0.003) in the MSA cases was higher than that (0.0011) in controls. The meta-analysis incorporating a previous report demonstrated a significant association of p.L483P with MSA with an odds ratio of 2.85 (95% CI; 1.05 – 7.76, p = 0.0400).
Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices
Authors: Basinski Jade J. , Bone Sharon E. , Klein Annaleise R. , Thongsomboon Wiriya , Mitchell Valerie , Shukle John T. , Druschel Gregory K. , Thompson Aaron , Aristilde Ludmilla 
Published: July 2024

AbstractIn biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to twenty-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylation rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.
Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen
Authors: Nowell Reuben W. , Rodriguez Fernando , Hecox-Lea Bette J. , Mark Welch David B. , Arkhipova Irina R. , Barraclough Timothy G. , Wilson Christopher G. 
Published: July 2024

AbstractCoevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes — a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.
Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales
Authors: Lax Carlos , Mondo Stephen J. , Osorio-Concepción Macario , Muszewska Anna , Corrochano-Luque María , Gutiérrez Gabriel , Riley Robert , Lipzen Anna , Guo Jie , Hundley Hope , Amirebrahimi Mojgan , Ng Vivian , Lorenzo-Gutiérrez Damaris , Binder Ulrike , Yang Junhuan , Song Yuanda , Cánovas David , Navarro Eusebio , Freitag Michael , Gabaldón Toni , Grigoriev Igor V. , Corrochano Luis M. , Nicolás Francisco E. , Garre Victoriano 
Published: July 2024

AbstractDNA N6-adenine methylation (6mA) has recently gained importance as an epigenetic modification in eukaryotes. Its function in lineages with high levels, such as early-diverging fungi (EDF), is of particular interest. Here, we investigated the biological significance and evolutionary implications of 6mA in EDF, which exhibit divergent evolutionary patterns in 6mA usage. The analysis of two Mucorales species displaying extreme 6mA usage reveals that species with high 6mA levels show symmetric methylation enriched in highly expressed genes. In contrast, species with low 6mA levels show mostly asymmetric 6mA. Interestingly, transcriptomic regulation throughout development and in response to environmental cues is associated with changes in the 6mA landscape. Furthermore, we identify an EDF-specific methyltransferase, likely originated from endosymbiotic bacteria, as responsible for asymmetric methylation, while an MTA-70 methylation complex performs symmetric methylation. The distinct phenotypes observed in the corresponding mutants reinforced the critical role of both types of 6mA in EDF.
Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk
Authors: Yang Yaohua , Chen Yaxin , Xu Shuai , Guo Xingyi , Jia Guochong , Ping Jie , Shu Xiang , Zhao Tianying , Yuan Fangcheng , Wang Gang , Xie Yufang , Ci Hang , Liu Hongmo , Qi Yawen , Liu Yongjun , Liu Dan , Li Weimin , Ye Fei , Shu Xiao-Ou , Zheng Wei , Li Li , Cai Qiuyin , Long Jirong 
Published: July 2024

AbstractThe relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
Cartesian atomic cluster expansion for machine learning interatomic potentials
Authors: Cheng Bingqing 
Published: July 2024

AbstractMachine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys.
Single-cell EpiChem jointly measures drug–chromatin binding and multimodal epigenome
Authors: Dong Chao , Meng Xiaoxuan , Zhang Tong , Guo Zhifang , Liu Yaxi , Wu Peihuang , Chen Shiwei , Zhou Fanqi , Ma Yanni , Xiong Haiqing , Shu Shaokun , He Aibin 
Published: July 2024

AbstractStudies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.
A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg
Authors: Huang Tianqing , Liu Enhui , Cao Baorui , Li Wenwen , Wang Gaochao , Gu Wei , Ma Haibing , Dong Fulin , Wang Bingqian , Xu Gefeng 
Published: July 2024

AbstractCoregonus ussuriensis Berg, distributed widely in cold waters above 45° N latitude, is a savored freshwater whitefish that has been included in the list of endangered animals as a consequence of overfishing. Lack of genomic information seriously hampers evolutionary and genetic research on C. ussuriensis warranting the need to assemble a high-quality reference genome to promote its genetic breeding. We assembled and constructed a reference chromosome-level C. ussuriensis genome (sequence length, 2.51 Gb; contig N50 length, 4.27 Mb) using PacBio sequencing and Hi-C assembly technology, 3,109 contigs were assembled into scaffolds, resulting in a genome assembly with 40 chromosomes and a scaffold N50 length of 62.20 Mb. In addition, 43,320 protein-coding genes were annotated. The peak Ks position in the species comparison reflects the whole-genome replication event of C. ussuriensis. This chromosome-level genome provides reference data for further studies on the molecular breeding of C. ussuriensis.