bluuebunny/crossref_metadata_2025_split huggingface dataset:
A TCR mimic CAR T cell specific for NDC80 is broadly reactive with solid tumors and hematologic malignancies
Authors: Klatt Martin G. , Dao Tao , Yang Zhiyuan , Liu Jianying , Mun Sung Soo , Dacek Megan M. , Luo Hanzhi , Gardner Thomas J. , Bourne Christopher , Peraro Leila , Aretz Zita E. H. , Korontsvit Tanya , Lau Michael , Kharas Michael G. , Liu Cheng , Scheinberg David A. 
Published: April 2022

Abstract
Target identification for chimeric antigen receptor (CAR) T-cell therapies remains challenging due to the limited repertoire of tumor-specific surface proteins. Intracellular proteins presented in the context of cell surface HLA provide a wide pool of potential antigens targetable through T-cell receptor mimic antibodies. Mass spectrometry (MS) of HLA ligands from 8 hematologic and nonhematologic cancer cell lines identified a shared, non-immunogenic, HLA-A*02–restricted ligand (ALNEQIARL) derived from the kinetochore-associated NDC80 gene. CAR T cells directed against the ALNEQIARL:HLA-A*02 complex exhibited high sensitivity and specificity for recognition and killing of multiple cancer types, especially those of hematologic origin, and were efficacious in mouse models against a human leukemia and a solid tumor. In contrast, no toxicities toward resting or activated healthy leukocytes as well as hematopoietic stem cells were observed. This shows how MS can inform the design of broadly reactive therapeutic T-cell receptor mimic CAR T-cell therapies that can target multiple cancer types currently not druggable by small molecules, conventional CAR T cells, T cells, or antibodies.
LPInsider: a webserver for lncRNA–protein interaction extraction from the literature
Authors: Li Ying , Wei Lizheng , Wang Cankun , Zhao Jianing , Han Siyu , Zhang Yu , Du Wei 
Published: April 2022

Abstract
Background
Long non-coding RNA (LncRNA) plays important roles in physiological and pathological processes. Identifying LncRNA–protein interactions (LPIs) is essential to understand the molecular mechanism and infer the functions of lncRNAs. With the overwhelming size of the biomedical literature, extracting LPIs directly from the biomedical literature is essential, promising and challenging. However, there is no webserver of LPIs relationship extraction from literature.

Results
LPInsider is developed as the first webserver for extracting LPIs from biomedical literature texts based on multiple text features (semantic word vectors, syntactic structure vectors, distance vectors, and part of speech vectors) and logistic regression. LPInsider allows researchers to extract LPIs by uploading PMID, PMCID, PMID List, or biomedical text. A manually filtered and highly reliable LPI corpus is integrated in LPInsider. The performance of LPInsider is optimal by comprehensive experiment on different combinations of different feature and machine learning models.

Conclusions
LPInsider is an efficient analytical tool for LPIs that helps researchers to enhance their comprehension of lncRNAs from text mining, and also saving their time. In addition, LPInsider is freely accessible from http://www.csbg-jlu.info/LPInsider/ with no login requirement. The source code and LPIs corpus can be downloaded from https://github.com/qiufengdiewu/LPInsider.
Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means
Authors: Hadipour Hamid , Liu Chengyou , Davis Rebecca , Cardona Silvia T. , Hu Pingzhao 
Published: April 2022

Abstract
Background
Converting molecules into computer-interpretable features with rich molecular information is a core problem of data-driven machine learning applications in chemical and drug-related tasks. Generally speaking, there are global and local features to represent a given molecule. As most algorithms have been developed based on one type of feature, a remaining bottleneck is to combine both feature sets for advanced molecule-based machine learning analysis. Here, we explored a novel analytical framework to make embeddings of the molecular features and apply them in the clustering of a large number of small molecules.

Results
In this novel framework, we first introduced a principal component analysis method encoding the molecule-specific atom and bond information. We then used a variational autoencoder (AE)-based method to make embeddings of the global chemical properties and the local atom and bond features. Next, using the embeddings from the encoded local and global features, we implemented and compared several unsupervised clustering algorithms to group the molecule-specific embeddings. The number of clusters was treated as a hyper-parameter and determined by the Silhouette method. Finally, we evaluated the corresponding results using three internal indices. Applying the analysis framework to a large chemical library of more than 47,000 molecules, we successfully identified 50 molecular clusters using the K-means method with 32 embeddings based on the AE method. We visualized the clustering result via t-SNE for the overall distribution of molecules and the similarity maps for the structural analysis of randomly selected cluster-specific molecules.

Conclusions
This study developed a novel analytical framework that comprises a feature engineering scheme for molecule-specific atomic and bonding features and a deep learning-based embedding strategy for different molecular features. By applying the identified embeddings, we show their usefulness for clustering a large molecule dataset. Our novel analytic algorithms can be applied to any virtual library of chemical compounds with diverse molecular structures. Hence, these tools have the potential of optimizing drug discovery, as they can decrease the number of compounds to be screened in any drug screening campaign.
Construction of a high-density genetic map and identification of QTLs related to agronomic and physiological traits in an interspecific (Gossypium hirsutum × Gossypium barbadense) F2 population
Authors: Si Zhanfeng , Jin Shangkun , Chen Jiedan , Wang Sen , Fang Lei , Zhu Xiefei , Zhang Tianzhen , Hu Yan 
Published: April 2022

Abstract
Background
Advances in genome sequencing technology, particularly restriction-site associated DNA sequence (RAD-seq) and whole-genome resequencing, have greatly aided the construction of cotton interspecific genetic maps based on single nucleotide polymorphism (SNPs), Indels, and other types of markers. High-density genetic maps can improve accuracy of quantitative trait locus (QTL) mapping, narrow down location intervals, and facilitate identification of the candidate genes.

Result
In this study, 249 individuals from an interspecific F2 population (TM-1 and Hai7124) were re-sequenced, yielding 6303 high-confidence bin markers spanning 5057.13 cM across 26 cotton chromosomes. A total of 3380 recombination hot regions RHRs were identified which unevenly distributed on the 26 chromosomes. Based on this map, 112 QTLs relating to agronomic and physiological traits from seedling to boll opening stage were identified, including 15 loci associated with 14 traits that contained genes harboring nonsynonymous SNPs. We analyzed the sequence and expression of these ten candidate genes and discovered that GhRHD3 (GH_D10G0500) may affect fiber yield while GhGPAT6 (GH_D04G1426) may affect photosynthesis efficiency.

Conclusion
Our research illustrates the efficiency of constructing a genetic map using binmap and QTL mapping on the basis of a certain size of the early-generation population. High-density genetic map features high recombination exchanges in number and distribution. The QTLs and the candidate genes identified based on this high-density genetic map may provide important gene resources for the genetic improvement of cotton.
CRP levels are significantly associated with CRP genotype and estrogen use in The Lifestyle, Biomarker and Atherosclerosis (LBA) study
Authors: Fransén Karin , Pettersson Carolina , Hurtig-Wennlöf Anita 
Published: April 2022

Abstract
Background
The C-reactive protein (CRP) is an important biomarker for atherosclerosis and single nucleotide polymorphisms (SNPs) in the CRP locus have been associated with altered CRP levels and associated with risk for cardiovascular disease. However, the association between genetic variations in the CRP gene, estrogen use and CRP levels or early signs of atherosclerosis in young healthy individuals is not fully characterized. We aimed to evaluate the influence of five genetic variants on both plasma CRP levels and carotid intima-media thickness (cIMT) values, including aspects on estrogen containing contraceptive use in females.

Methods
Genotyping was performed with TaqMan real time PCR and compared with high sensitivity CRP serum levels in 780 Swedish young, self-reported healthy individuals. Haplotypes of the SNPs were estimated with the PHASE v 2.1. The cIMT was measured by 12 MHz ultrasound. The contraceptive use was self-reported.

Results
Strong associations between CRP and genotype were observed for rs3091244, rs1800947, rs1130864, and rs1205 in women (all p < 0.001). In men, only rs1800947 was associated with CRP (p = 0.029). The independent effect of genotypes on CRP remained significant also after adjustment for established risk factors. Female carriers of the H1/ATGTG haplotype had higher CRP than non-carriers. This was specifically pronounced in the estrogen-using group (p < 0.001), and they had also higher cIMT (p = 0.002) than non-carriers but with a small cIMT difference between the haplotype groups (0.02 mm). In parallel, a significant correlation between CRP and cIMT in the estrogen using group was observed (r = 0.194; p = 0.026).

Conclusions
Estrogen use, genotypes and haplotypes in the CRP locus are significantly associated with CRP levels. Based on an observed interaction effect between sex/estrogen use and the H1/ATGTG haplotype on CRP, and a marginally thicker cIMT in the estrogen using group, our data suggest that both genotypes and estrogen usage could be involved in arterial wall structural differences. The causality between CRP levels and cIMT remains unclear, and the observed difference in cIMT is not clinically relevant in the present state. Future larger and longitudinal studies may shed further light on the role of more long-term estrogen use and early atherosclerosis.
Health-related quality of life in Italian children and adolescents with congenital heart diseases
Authors: Amodeo Giulia , Ragni Benedetta , Calcagni Giulio , Piga Simone , Giannico Salvatore , Yammine Marie Laure , Drago Fabrizio , Ciofi degli Atti Marta Luisa , Rossi Angela , De Stasio Simona , Grimaldi Capitello Teresa 
Published: April 2022

Abstract
Background
Congenital heart disease (CHD) is the most common congenital anomaly at birth, affecting approximately 1% of live births. In recent decades great medical and surgical advances have significantly increased life expectancy, shifting healthcare professionals' and researchers’ interests in patients' Quality of Life (QoL). The main aims of our study were to evaluate generic and condition-specific QoL in a group of Italian children and adolescents with CHD and their parents and examine the level of agreement and directional disagreement between child/adolescent and parents reports on generic and condition-specific QoL.

Methods
A cross-sectional study was designed with CHD children and adolescents and their parents referred to the Cardiology Department of “Bambino Gesù” Children’s Hospital. The PedsQL scale was used, including generic (PedsQL 4.0) and cardiac-specific modules (PedsQL 3.0) were administered to patients and caregivers. A Kruskal–Wallis test was used to compare generic and cardiac module scores between patients with different ages, CHD diagnoses, and between patients who underwent surgery interventions and/or are currently taking cardiac medications.

Results
498 families were enrolled in this study. On average, patients reported a good level of generic and condition-specific QoL, as well as their mothers and fathers. Children aged between 5–7 years old reported lower generic and cardiac-specific total QoL levels than children aged 8–12 years and adolescents (13–18 years). With regard to the agreement, patient-parent agreement on condition-specific QoL ranged from 25 to 75% while on generic QoL, it ranged from 19 to 76%. The highest percentage of disagreement between parents and children was found in patients aged 5–7 years old, both for condition-specific and generic QoL rates.

Conclusions
Our study contributed to the growing body of knowledge on QoL in CHD, emphasizing the need for these families to receive support from multidisciplinary standardized care, including psychological consultations and support.
Impact of the inspiratory oxygen fraction on the cardiac output during jugulo-femoral venoarterial extracorporeal membrane oxygenation in the rat
Authors: Edinger Fabian , Schneck Emmanuel , Schulte Charlotte , Schmidt Goetz , Gehron Johannes , Sander Michael , Koch Christian 
Published: April 2022

Abstract
Background
Venoarterial extracorporeal membrane oxygenation (V-A ECMO) with femoral access has gained wide acceptance in the treatment of critically ill patients. Since the patient´s cardiac output (CO) can compete with the retrograde aortic ECMO-flow, the aim of this study was to examine the impact of the inspiratory oxygen fraction on the cardiac function during V-A ECMO therapy.

Methods
Eighteen male Lewis rats (350–400 g) received V-A ECMO therapy. The inspiratory oxygen fraction on the ventilator was randomly set to 0.5 (group A), 0.21 (group B), or 0 in order to simulate apnea (group C), respectively. Each group consisted of six animals. Arterial blood pressure, central venous saturation (ScvO2), CO, stroke volume, left ventricular ejection fraction (LVEF), end diastolic volume, and pressure were measured. Cardiac injury was determined by analyzing the amount of lactate dehydrogenase (LDH).

Results
During anoxic ventilation the systolic, mean and diastolic arterial pressure, CO, stroke volume, LVEF and ScvO2 were significantly impaired compared to group A and B. The course of LDH values revealed no significant differences between the groups.

Conclusion
Anoxic ventilation during V-A ECMO with femoral cannulation leads to cardiogenic shock in rats. Therefore, awake V-A ECMO patients might be at risk for hypoxia-induced complications.
MicroRNA profile of circulating CD4+ T cells in aged patients with atherosclerosis obliterans
Authors: Wang Siwen , Jiang Suiting , Feng Ruijia , Liu Jiawei , Liu Longshan , Cui Jin , Shi Yi , Ning Junjie , Jia Benyuan , Hu Zuojun , Wang Shenming 
Published: April 2022

Abstract
Background
To evaluate the specificity of the expression patterns of microRNAs (miRNAs) in circulating CD4+ T cells in aged patients with atherosclerosis obliterans (ASO).

Methods
A comprehensive miRNA expression study was conducted using a miRNA microarray of CD4+ T cells isolated from peripheral blood mononuclear cells (PBMCs) of 33 patients with ASO and 24 healthy donors. A t test was used for statistical analysis, and the average linkage method was used for hierarchical clustering. The results were validated by qRT–PCR. Putative targeted pathways associated with validated miRNAs were predicted with the online software DIANA miRPath.

Results
We identified 44 miRNAs based on a cutoff value of a 1.3-fold change in expression between the two groups, with 18 miRNAs showing a false discovery rate (FDR) p value < 0.05. The qRT–PCR analysis validated differences in 12 miRNAs, and 6 miRNAs were proven to be differentially expressed among three age groups (age: 35–55 years; 56–75 years; 76–95 years): the miRNAs miR-21 (p: 0.0008; 0.0009; 0.0022), miR-29b (p: 0.453; < 0.0001; < 0.0001), and miR-374b (p: < 0.0001; < 0.0001; 0.2493) showed upregulated expression in patients with ASO, while miR-142-3p (p: < 0.0001; < 0.0001; < 0.0001), miR-142-5p (p: < 0.0001; < 0.0001; < 0.0001), and miR-150 (p: < 0.0001; < 0.0001; 0.0001) showed downregulated expression in patients with ASO. The validated miRNAs participated in CD4+ T cell activation, proliferation, and migration pathways.

Conclusions
Circulating CD4+ T cells in aged patients with ASO may show a distinct molecular signature. This is the first time that a distinctive, validated miRNA profile from circulating CD4+ T cells in atherosclerosis has been presented. This miRNA signature may be used to help elucidate the underlying mechanism of atherosclerosis. Further clinical studies and in-depth reports will contribute to identifying predictive and therapeutic targets in these patients with atherosclerosis.
External validation of a new predictive model for falls among inpatients using the official Japanese ADL scale, Bedriddenness ranks: a double-centered prospective cohort study
Authors: Tago Masaki , Katsuki Naoko E. , Nakatani Eiji , Tokushima Midori , Dogomori Akiko , Mori Kazumi , Yamashita Shun , Oda Yoshimasa , Yamashita Shu-ichi 
Published: April 2022

AbstractBackgroundSeveral reliable predictive models for falls have been reported, but are too complicated and time-consuming to evaluate. We recently developed a new predictive model using just eight easily-available parameters including the official Japanese activities of daily living scale, Bedriddenness ranks, from the Ministry of Health, Labour and Welfare. This model has not yet been prospectively validated. This study aims to prospectively validate our new predictive model for falls among inpatients admitted to two different hospitals.MethodsA double-centered prospective cohort study was performed from October 1, 2018, to September 30, 2019 in an acute care hospital and a chronic care hospital. We analyzed data from all adult inpatients, for whom all data required by the predictive model were evaluated and recorded. The eight items required by the predictive model were age, gender, emergency admission, department of admission, use of hypnotic medications, previous falls, independence of eating, and Bedriddenness ranks. The main outcome is in-hospital falls among adult inpatients, and the model was assessed by area under the curve.ResultsA total of 3,551 adult participants were available, who experienced 125 falls (3.5%). The median age (interquartile range) was 78 (66–87) years, 1,701 (47.9%) were men, and the incidence of falls was 2.25 per 1,000 patient-days and 2.06 per 1,000 occupied bed days. The area under the curve of the model was 0.793 (95% confidence interval: 0.761–0.825). The cutoff value was set as − 2.18, making the specificity 90% with the positive predictive value and negative predictive value at 11.4% and 97%.ConclusionsThis double-centered prospective cohort external validation study showed that the new predictive model had excellent validity for falls among inpatients. This reliable and easy-to-use model is therefore recommended for prediction of falls among inpatients, to improve preventive interventions.Trial registrationUMIN000040103(2020/04/08)
Preoperative clinical-radiomics nomogram for microvascular invasion prediction in hepatocellular carcinoma using $$^{18}$$F-FDG PET/CT
Authors: Wang Yutao , Luo Shuying , Jin Gehui , Fu Randi , Yu Zhongfei , Zhang Jian 
Published: April 2022

Abstract
Purpose
To develop a clinical-radiomics nomogram by incorporating radiomics score and clinical predictors for preoperative prediction of microvascular invasion in hepatocellular carcinoma.

Methods
A total of 97 HCC patients were retrospectively enrolled from Shanghai Universal Medical Imaging Diagnostic Center and Changhai Hospital Affiliated to the Second Military Medical University. 909 CT and 909 PET slicers from 97 HCC patients were divided into a training cohort (N = 637) and a validation cohort (N = 272). Radiomics features were extracted from each CT or PET slicer, and features selection was performed with least absolute shrinkage and selection operator regression and radiomics score was also generated. The clinical-radiomics nomogram was established by integrating radiomics score and clinical predictors, and the performance of the models were evaluated from its discrimination ability, calibration ability, and clinical usefulness.

Results
The radiomics score consisted of 45 selected features, and age, the ratio of maximum to minimum tumor diameter, and $$^{18}$$

18

F-FDG uptake status were independent predictors of microvascular invasion. The clinical-radiomics nomogram showed better performance for MVI detection (0.890 [0.854, 0.927]) than the clinical nomogram (0.849 [0.804, 0.893]) ($$p<0.05$$

p
<
0.05

). Both nomograms showed good calibration and the clinical-radiomics nomogram’s clinical practicability outperformed the clinical nomogram.

Conclusions
With the combination of radiomics score and clinical predictors, the clinical-radiomics nomogram can significantly improve the predictive efficacy of microvascular invasion in hepatocellular carcinoma ($$p<0.05$$

p
<
0.05

) compared with clinical nomogram.
Corticomedullary shunting after ischaemia and reperfusion in the porcine kidney?
Authors: Rehling Michael , Skjøth Stine Gram , Frøkiær Jørgen , Nielsen Lene Elsebeth , Flø Christian , Jespersen Bente , Keller Anna Krarup 
Published: April 2022

Abstract
Background
Renal perfusion may redistribute from cortex to medulla during systemic hypovolaemia and after renal ischaemia for other reasons, but there is no consensus on this matter. We studied renal perfusion after renal ischaemia and reperfusion.

Methods
Renal perfusion distribution was examined by use of 153Gadolinium-labeled microspheres (MS) after 2 h (hrs) and 4 h ischaemia of the pig kidney followed by 4 h of reperfusion. Intra-arterial injected MS are trapped in the glomeruli in renal cortex, which means that MS are not present in the medulla under normal physiological conditions.

Results
Visual evaluation after reperfusion demonstrated that MS redistributed from the renal cortex to the medulla in 6 out of 16 pigs (38%) subjected to 4 h ischaemia and in one out of 18 pigs subjected to 2 h ischaemia. Central renal uptake of MS covering the medullary/total renal uptake was significantly higher in kidneys subjected to 4 h ischaemia compared with pigs subjected to 2 h ischaemia (69 ± 5% vs. 63 ± 1%, p < 0.001), and also significantly higher than in the contralateral kidney (69 ± 5% vs. 63 ± 2%, p < 0.001). Analysis of blood and urine demonstrated no presence of radioactivity.

Conclusion
The study demonstrated the presence of MS in the renal medulla in response to renal ischaemia and reperfusion suggesting that severe ischaemia and reperfusion of the pig kidney leads to opening of functional shunts bypassing glomeruli.