bluuebunny/crossref_metadata_2025_split huggingface dataset:
Over-the-counter medications encountered in the postmortem pediatric population from 2010–2020
Authors: Swatek Jennifer L , Marco Stephanie M , Midthun Kari M 
Published: May 2024

Abstract
In forensic toxicology, the pediatric population requires special focus when evaluating positive findings because of the many toxicokinetic and toxicodynamic differences (e.g., metabolic capabilities, body size, etc.) between the pediatric and adult populations. In particular, the administration of over-the-counter (OTC) medications needs careful consideration, as dosages given to the pediatric population (0 days–18 years), particularly those given to individuals &lt;5 years of age, tend to be lower than those given to individuals closer to adulthood. Postmortem pediatric data from 11 years (2010–2020) was compiled. A total of 1413 positive cases contained one or more of the following common OTC medications: antihistamines (brompheniramine, chlorpheniramine, diphenhydramine, doxylamine and pheniramine), pain relievers (acetaminophen, naproxen, ibuprofen and salicylates), cold/flu medications (dextro/levomethorphan, guaifenesin, ephedrine and pseudoephedrine), gastrointestinal aids (dicyclomine and loperamide) and/or sleep aids (melatonin). Antihistamines, cold/flu medications and pain relievers are the most common classes of drugs encountered in the postmortem pediatric population. To evaluate trends, three main age groups were created: ≤5 years old (5 U, birth-5 years old), middle childhood (MC, 6–11 years old), and early adolescence (EA, 12–18 years old). When considering the data, it must be noted that many of these drugs may be co-administered in single and/or multi-drug formulations. In addition, some drugs may have a variety of uses, e.g. antihistamines may also be used as sleep aids. Of note, the prevalence of cases involving those aged 6–11 years old was far less than their younger and older pediatric counterparts. With the widespread availability of OTC medications, unintentional overdoses, recreational misuse and suicidal overdoses can occur in the vulnerable, pediatric population.
Chlorophyll-α forecasting using LSTM, bidirectional LSTM and GRU networks in El Mar Menor (Spain)
Authors: González-Enrique Javier , RodrÍguez-GarcÍa María Inmaculada , Ruiz-Aguilar Juan Jesús , Carrasco-GarcÍa MarÍa Gema , Enguix Ivan Felis , Turias Ignacio J 
Published: May 2024

Abstract
The objective of this research is to develop accurate forecasting models for chlorophyll-α concentrations at various depths in El Mar Menor, Spain. Chlorophyll-α plays a crucial role in assessing eutrophication in this vulnerable ecosystem. To achieve this objective, various deep learning forecasting techniques, including long short-term memory, bidirectional long short-term memory and gated recurrent uni networks, were utilized. The models were designed to forecast the chlorophyll-α levels with a 2-week prediction horizon. To enhance the models’ accuracy, a sliding window method combined with a blocked cross-validation procedure for time series was also applied to these techniques. Two input strategies were also tested in this approach: using only chlorophyll-α time series and incorporating exogenous variables. The proposed approach significantly improved the accuracy of the predictive models, no matter the forecasting technique employed. Results were remarkable, with $\overline{\sigma}$ values reaching approximately 0.90 for the 0.5-m depth level and 0.80 for deeper levels. The proposed forecasting models and methodologies have great potential for predicting eutrophication episodes and acting as decision-making tools for environmental agencies. Accurate prediction of eutrophication episodes through these models could allow for proactive measures to be implemented, resulting in improved environmental management and the preservation of the ecosystem.
Protocol for a prospective multicenter randomized controlled trial to evaluate the efficacy of texture and color enhancement imaging (TXI) observation in the detection of colorectal lesions (deTXIon study)
Authors: Saito Yutaka , Toyoshima Naoya , Mizuguchi Yasuhiko , Sakamoto Taku , Uraoka Toshio , Ikematsu Hiroaki , Tamai Naoto , Matsuda Takahisa , Misawa Masashi , Hotta Kinichi , Shibata Taro 
Published: May 2024

Abstract
Colonoscopy is the gold standard for detecting and resecting adenomas or early stage cancers to reduce the incidence and mortality rates of colorectal cancer. In a recent observational study, texture and color enhancement imaging (TXI) was reported to improve polyp detection during colonoscopy. This randomized controlled trial involving six Japanese institutions aims to confirm the superiority of TXI over standard white-light imaging (WLI) in detecting colorectal lesions during colonoscopy. During the 1-year study period, 960 patients will be enrolled, with 480 patients in the TXI and WLI groups. The primary endpoint is the mean number of adenomas detected per procedure. The secondary endpoints include adenoma detection rate, advanced adenoma detection rate, polyp detection rate, flat polyp detection rate, depressed lesion detection rate, mean polyps detected per procedure, sessile serrated lesion (SSL) detection rate, mean SSLs detected per procedure and adverse events.
Early prediction of growth patterns after pediatric kidney transplantation based on height-related single-nucleotide polymorphisms
Authors: Feng Yi , Feng Yonghua , Hu Mingyao , Xu Hongen , Wang Zhigang , Xu Shicheng , Yan Yongchuang , Feng Chenghao , Li Zhou , Feng Guiwen , Shang Wenjun 
Published: May 2024

Abstract

Background:
Growth retardation is a common complication of chronic kidney disease in children, which can be partially relieved after renal transplantation. This study aimed to develop and validate a predictive model for growth patterns of children with end-stage renal disease (ESRD) after kidney transplantation using machine learning algorithms based on genomic and clinical variables.

Methods:
A retrospective cohort of 110 children who received kidney transplants between May 2013 and September 2021 at the First Affiliated Hospital of Zhengzhou University were recruited for whole-exome sequencing (WES), and another 39 children who underwent transplant from October 2021 to March 2022 were enrolled for external validation. Based on previous studies, we comprehensively collected 729 height-related single-nucleotide polymorphisms (SNPs) in exon regions. Seven machine learning algorithms and 10-fold cross-validation analysis were employed for model construction.

Results:
The 110 children were divided into two groups according to change in height-for-age Z-score. After univariate analysis, age and 19 SNPs were incorporated into the model and validated. The random forest model showed the best prediction efficacy with an accuracy of 0.8125 and an area under curve (AUC) of 0.924, and also performed well in the external validation cohort (accuracy, 0.7949; AUC, 0.796).

Conclusions:
A model with good performance for predicting post-transplant growth patterns in children based on SNPs and clinical variables was constructed and validated using machine learning algorithms. The model is expected to guide clinicians in the management of children after renal transplantation, including the use of growth hormone, glucocorticoid withdrawal, and nutritional supplementation, to alleviate growth retardation in children with ESRD.
CLINICAL CHARACTERIZATION OF AQUEOUS AND VITREOUS RETINOL-BINDING PROTEIN 3 CONCENTRATIONS IN RELATION TO DIABETIC RETINOPATHY SEVERITY, RETINAL STRUCTURES, AND SYSTEMIC COMPLICATIONS
Authors: Fickweiler Ward , Chokshi Tanvi , Jangolla Surya , Mitzner Margalit , Wu I-Hsien , Park Hyunseok , Park Kyoungmin , Aiello Lloyd Paul , Sun Jennifer , King George L. 
Published: May 2024

Purpose:
To evaluate Retinol-Binding Protein 3 (RBP3) from photoreceptors in aqueous and its association with vitreous concentrations, diabetic retinopathy (DR) severity, retinal layer thickness, and clinical characteristics in people with diabetes.

Methods:
RBP3 concentration was measured by custom-developed enzyme-linked immunosorbent assay in aqueous and correlated with vitreous concentrations in patients from the 50-Year Medalist study and Beetham Eye Institute at Joslin Diabetes Center.

Results:
Aqueous RBP3 concentration (N = 131) was elevated in eyes with no to mild DR (mean ± SD 0.7 nM ± 0.2) and decreased in eyes with moderate to severe DR (0.65 nM ± 0.3) and proliferative DR (0.5 nM ± 0.2, P < 0.001) compared to eyes without diabetes. Aqueous and vitreous RBP3 concentrations correlated with each other (r = 0.34, P = 0.001) and between fellow eyes (P < 0.0001). History of retinal surgery did not affect aqueous RBP3 concentrations, but cataract surgery affected both vitreous and aqueous levels. Elevated aqueous RBP3 concentration associated with increased thickness of the outer nuclear layer (P = 0.004) and correlated with hemoglobin A1c, whereas vitreous RBP3 concentrations correlated with diabetic systemic complications.

Conclusion:
These findings suggest that aqueous RBP3 concentration may be an important endogenous clinical retinal protective factor, a biomarker for DR severity, and a promising VEGF-independent clinical intervention target in DR.
Comparison of Different Intraocular Lens Power Calculation Formulas in Eyes With Primary Angle Closure
Authors: Liu Jinkun , Wang Yuhong , Huang Weiyi , Wang Fei , Xu Yazhang , Xue Yingying , Zhao Zhimin , Huang Luping , Gao Ruxin 
Published: May 2024

Study Design:
Prospective case series.

Précis:
This prospective study determines which formulas can best predict the refractive outcome in patients with primary angle closure disease (PACD) after cataract surgery.

Objective:
To compare the accuracy of 6 intraocular lens power calculation formulas, Barrett Universal II (BU II), Haigis, Hoffer Q, Holladay I, Kane and SRK/T, in eyes with PACD.

Patients and Methods:
Patients diagnosed with PACD and cataracts and who met the indication for cataract surgery were enrolled in the study. Six intraocular lens power calculation formulas were used to calculate the refractive diopter. The percentage of eyes with prediction error (PE) within ±0.50 D and the median absolute PE were compared to determine the accuracy of different formulas in patients with PACD. Subgroup analysis was performed according to axial length (AL). The accuracy of BU II was compared between patients with PACD and patients with age-related cataracts.

Results:
One hundred five patients (105 eyes) with PACD and 35 patients (35 eyes) with age-related cataracts were enrolled in the study. Haigis, Kane, and BU II formula achieved a comparable outcome and outperformed over the other 3 formulas in patients with PACD. Subgroup analysis showed that the group with long AL has lower values of median absolute PE. PE was significantly positively correlated with AL and negatively correlated with relative lens position when calculated using BU II and Kane.

Conclusions:
Haigis, Kane, and BU II formula achieved a comparable outcome and outperformed over the other 3 formulas in patients with PACD.
Impact of Peripheral Anterior Synechiae on the Outcome of Combined Phacoemulsification, Goniosynechialysis, and Goniotomy for Primary Angle Closure Glaucoma and Cataract: A Multicenter Observational Study
Authors: Lin Fengbin , Zhang Yingzhe , Zhu Xiaomin , Yu Ping , Fan Sujie , Lv Aiguo , Li Xiaoyan , Tang Li , Zhang Yao , Tang Guangxian , Yan Xiaowei , Lu Lan , Xiao Meichun , Yuan Huiping , Song Wulian , Zhou Minwen , Zhao Xiaohuan , Nie Xin , Liao Mengfei , Song Yunhe , Wang Zhenyu , Chen Weirong , Barton Keith , Park Ki Ho , Aung Tin , Lam Dennis S.C. , Weinreb Robert N. , Tham Clement C. , Zeng Liuzhi , Xie Lin , Wang Ningli , Zhang Xiulan ,   for the PVP study group
Published: May 2024

Précis:
The combination of phacoemulsification, goniosynechialysis and goniotomy is an effective treatment for primary angle closure glaucoma patients with cataract, and this is not linked to the extent of preoperative peripheral anterior synechiae.

Purpose:
To evaluate the impact of the extent of peripheral anterior synechiae (PAS) on the effectiveness and safety of combined phacoemulsification (PEI), goniosynechialysis (GSL), and goniotomy (GT) in eyes with primary angle closure glaucoma (PACG) and cataract.

Patients and Methods:
This study included patients diagnosed with PACG and cataracts who underwent combined PEI and 120 degrees GSL plus GT (PEI+GSL+GT) between April 2020 and October 2022 at 10 ophthalmic institutes. Eligible patients were divided into 3 groups based on the extent of PAS: 180°≤PAS<270°, 270°≤PAS<360°, and PAS=360°. Data on intraocular pressure (IOP), the number of ocular hypotensive medications, and complications were collected and compared. The study defined complete success as postoperative IOP within the 6–18 mm Hg range and a 20% reduction from baseline without the use of topical medications. Qualified success was defined in the same way as complete success, but it allowed for the use of ocular hypotensive medications.

Results:
Three hundred four eyes of 283 patients were included. The mean follow-up was 12.50±1.24 months. All groups experienced a significant reduction in IOP after the surgery (P<0.05). There were no significant differences in final IOP, number of medications, and cumulative complete and qualified success rates among the 3 groups (P>0.05). The groups with 270°≤PAS<360°had a higher frequency of hyphema compared with 180°≤PAS<270° (P = 0.044).

Conclusions:
PEI+GSL+GT has proven to be an effective treatment for PACG with cataracts over a 1 year period. However, the outcome was not correlated with the preoperative extent of PAS.
Advancing Standardization in Fat Graft Survival Studies
Authors: Cinar Fatih , Okyay Mehmet Fatih 
Published: May 2024

Background
There is currently no standardization in the field of research on fat grafts in rats, which is one of the most popular topics in plastic surgery. The aim of our study was to demonstrate the effects of selecting paraepididymal fat grafts as the donor area on enhancing the reliability of fat graft studies.

Methods
In this study, 12 male Sprague-Dawley rats were used to obtain adipose grafts from both inguinal and paraepididymal regions. After measuring the graft weights, they were subjected to histological examination using hematoxylin-eosin staining, as well as immunohistochemical staining with antiperilipin antibody. Purity of the samples, viability of adipose cells, and the presence of lymph nodes within the grafts were analyzed.

Results
The purity of adipose cells in graft samples obtained from the paraepididymal region was found to be 98.1% compared with the total sample. In contrast, the purity of adipose cells in graft samples obtained from the inguinal region was 58.37%. Hematoxylin-eosin staining revealed significantly higher adipocyte viability and vascularity in the paraepididymal region compared with the inguinal region (P = 0.0134). Conversely, lymphatic tissue content in samples obtained from the inguinal region was significantly higher compared with paraepididymal adipose tissue samples (P < 0.0001). Immunohistochemical staining with antiperilipin antibody showed a denser and more uniform staining pattern in paraepididymal adipose grafts (P < 0.0001).

Conclusions
Using paraepididymal fat, devoid of lymphatic tissue, naturally eliminates 2 critical biases (estrogen and lymphatic tissue), enhancing the standardization and reliability of fat graft survival studies.
Feeding Rates in Sessile versus Motile Ciliates are Hydrodynamically Equivalent
Authors: Liu Jingyi , Man Yi , Costello John H. , Kanso Eva 
Published: May 2024

AbstractMotility endows microorganisms with the ability to swim to nutrient-rich environments, but many species are sessile. Existing hydrodynamic arguments in support of either strategy, to swim or to attach and generate feeding currents, are often built on a limited set of experimental or modeling assumptions. Here, to assess the hydrodynamics of these “swim” or “stay” strategies, we propose a comprehensive methodology that combines mechanistic modeling with a survey of published shape and flow data in ciliates. Model predictions and empirical observations show small variations in feeding rates in favor of either motile or sessile cells. Case-specific variations notwithstanding, our overarching analysis shows that flow physics imposes no constraint on the feeding rates that are achievable by the swimming versus sessile strategies – they can both be equally competitive in transporting nutrients and wastes to and from the cell surface within flow regimes typically experienced by ciliates. Our findings help resolve a long-standing dilemma of which strategy is hydrodynamically optimal and explain patterns occurring in natural communities that alternate between free swimming and temporary attachments. Importantly, our findings indicate that the evolutionary pressures that shaped these strategies acted in concert with, not against, flow physics.
The ancient evolution of far-red light photoacclimation in cyanobacteria
Authors: Antonaru Laura A. , Rad-Menéndez Cecilia , Mbedi Susan , Sparmann Sarah , Pope Matthew , Oliver Thomas , Wu Shujie , Green David , Gugger Muriel , Nürnberg Dennis J. 
Published: May 2024

SummaryCyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes, and involves the synthesis of red-shifted chlorophyllsfandd, together with paralogues of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to clarify this issue; sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 52 new gene clusters. These data enable high-resolution phylogenetics and - by relying on multiple gene trees, together with gene arrangement conservation - support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and the process may have been associated with microbial mats and stromatolite formation in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing a conserved intergenic regulatory sequence that has been maintained for billions of years. Taken together, our results indicate that oxygenic photosynthesis using far-red light may have played a significant role in Earth’s early history.
Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases
Authors: Pesesky Mitchell , Bharanikumar Ramit , Le Bourhis Lionel , ElAbd Hesham , Rosati Elisa , Carty Cara L. , Singh Namita , Bokemeyer Bernd , Schreiber Stefan , Görg Siegfried , Noceda Marco Garcia , Chapfuwa Paidamoyo , Gittelman Rachel M. , May Damon , Dines Jennifer N. , Zhou Wenyu , Kaplan Ian M. , Snyder Thomas M. , Zahid H. Jabran , Greissl Julia , Chen-Harris Haiyin , Howie Bryan , Franke Andre , Robins Harlan S. , Allez Matthieu 
Published: May 2024

ABSTRACTBackgroundInflammatory Bowel Diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are known to involve shifts in the T-cell repertoires of affected individuals. These include a reduction in regulatory T cells in both diseases, increase in TNFα production in CD, expansion of an unconventional T-cell population in CD, and clonal expansion of abundant T-cell populations in CD mucosal tissue. There are also differential HLA risk and protective alleles between CD and UC, implying CD- and UC-specific repertoire changes that have not yet been identified.MethodsWe performed ImmunoSequencing on blood samples from 3,853 CD cases, 1,803 UC cases, and 5,596 healthy controls. For each sample we imputed HLA type and cytomegalovirus (CMV) infection status based on public T-cell receptor β (TCRB) usage and identified public TCRBs enriched in CD or UC cases.FindingsWe determine that there is more expansion across clonotypes in CD, but not UC, compared with healthy controls. We also identify novel interactive effects of HLA-DQ heterodimers with CD and UC risk. Strikingly, from blood we identify public TCRBs specifically expanded in CD or UC. These sequences are more abundant in intestinal mucosal samples, form groups of similar CDR3 sequences, and can be associated to specific HLA alleles. Although the prevalence of these sequences is higher in ileal and ileocolonic CD than colonic CD or UC, the TCRB sequences themselves are shared across CD and not between CD and UC.InterpretationThere are peptide antigens that commonly evoke immune reactions in IBD cases and rarely in non-IBD controls. These antigens differ between CD and UC. CD, particularly ileal CD, also seems to involve more substantial changes in clonal population structure than UC, compared to healthy controls.
MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database bias
Authors: Pipart Julian , Holstein Tanja , Martens Lennart , Muth Thilo 
Published: May 2024

AbstractThe recent years, with the global SARS-Cov-2 pandemic, have shown the importance of strain level identification of viral pathogens. While the gold-standard approach for unkown viral sample identification remains genomics, studies have shown the necessity and advantages of orthogonal experimental approaches such as proteomics, based on proteomic database search methods. The databases required as references for both proteins and genome sequences are known to be biased towards certain taxa, such as pathogenic strains or species, or common model organisms. Aditionally, the proteomic databases are not as comprehensive as the genomic databases.We present MultiStageSearch, an iterative database search approach for the taxonomic identification of viral samples combining proteomic and genomic databases. The potentially present species and strains are inferred using a generalist proteomic reference database. MultiStageSearch then automatically creates a proteogenomic database. This database is further pre-processed byfiltering for duplicates as well as clustering of identical ORFs to address potential bias present in the genomic database. Furthermore, the workflow is independent of the strain level NCBI taxonomy, enabling the inference of strains that are not present in the NCBI taxonomy.We performed a benchmark on several viral samples to demonstrate the performance of the strain level taxonomic inference. The benchmark shows superior performance compared to state of the art methods for untargeted strain level inference using proteomic data while being independent of the NCBI taxonomy at strain level.