bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data
Authors: Yang Bin , Bao Wenzheng , Chen Baitong , Song Dan 
Published: June 2022

AbstractSingle-cell RNA-seq overcomes the shortcomings of conventional transcriptome sequencing technology and could provide a powerful tool for distinguishing the transcriptome characteristics of various cell types in biological tissues, and comprehensively revealing the heterogeneity of gene expression between cells. Many Intelligent Computing methods have been presented to infer gene regulatory network (GRN) with single-cell RNA-seq data. In this paper, we investigate the performances of seven classifiers including support vector machine (SVM), random forest (RF), Naive Bayesian (NB), GBDT, logical regression (LR), decision tree (DT) and K-Nearest Neighbor (KNN) for solving the binary classification problems of GRN inference with single-cell RNA-seq data (Single_cell_GRN). In SVM, three different kernel functions (linear, polynomial and radial basis function) are utilized, respectively. Three real single-cell RNA-seq datasets from mouse and human are utilized. The experiment results prove that in most cases supervised learning methods (SVM, RF, NB, GBDT, LR, DT and KNN) perform better than unsupervised learning method (GENIE3) in terms of AUC. SVM, RF and KNN have the better performances than other four classifiers. In SVM, linear and polynomial kernels are more fit to model single-cell RNA-seq data.
Preparation and application of FNAOSiPPEA/Cu(II) as a novel magnetite almondshell based Lewis acid-Bronsted base nano-catalyst for the synthesis of pyrimidobenzothiazoles
Authors: Mallah Dina , Mirjalili Bi Bi Fatemeh 
Published: June 2022

Abstract
Background
The magnetic nano-catalysts improve the contact between substrates and catalyst considerably and simple isolation of catalyst from reaction mixture. In this study, Fe3O4@nano-almondshell@OSi(CH2)3/2-(1-piperazinyl)ethylamine/Cu(II) abbreviated (FNAOSiPPEA/Cu(II)), was prepared, characterized and applied for the synthesis of 4H-pyrimido[2,1-b]benzothiazole.

Results
FNAOSiPPEA/Cu(II) as a bio-based nano-catalyst was prepared from the complexation of copper on 2-(1-piperazinyl)ethylamine, which was immobilized on Fe3O4@nano-almondshell@OSi(CH2)3 section. This new heterogeneous bifunctional Lewis acid/Bronsted base catalyst (FNAOSiPPEA/Cu(II)) was characterized by various techniques such as FT-IR, FESEM, TGA, EDS-MAP, XRD, VSM, BET, TEM, and XPS. So, the catalytic performance of this recyclable nano-catalyst was determined to promote the synthesis of 4H-pyrimido[2,1-b]benzothiazole derivatives at 100 °C under solvent-free conditions.

Conclusions
Magnetite nano-catalyst of (FNAOSiPPEA/Cu(II)) is easily separated by an external magnet and successfully reused up at least 3 times with a slight loss of yield of the desired product.
Psychosocial aspects of continuous subcutaneous insulin infusion in children with type 1 diabetes in Egypt; a limited resources country perspective
Authors: El Samahy Mona Hussein , Salah Nouran Yousef , Abdeen Mai Seifeldin , Falastin Batrishia Rafat Kamel 
Published: June 2022

AbstractBackgroundNovel innovations continue to emerge in type-1 diabetes (T1D) management aiming to improve glycemic control. Assessing the psychosocial outcomes of different treatment modalities is specifically crucial among children with T1D and differs from one population to another.ObjectivesTo compare the health related quality of life (HRQoL) and confidence in diabetes self-management (CIDS) among children with T1D on continuous subcutaneous insulin infusion (CSII) versus multiple daily injections (MDI) and to correlate them with the efficacy of glycemic control, Mini-International Neuropsychiatric Interview for Children and Adolescents(MINI-KID) depression module and socioeconomic-standard scale.MethodsThis real life study (ClinicalTrials.gov number NCT04756011) included 60 children with T1D (30 on CSII and 30 on MDI), aged 6–18 years. Disease duration, insulin therapy, average self-monitoring of blood glucose (SMBG) and HbA1C were assessed. CIDS, socioeconomic-standard, MINI-KID depression and HRQoL scales were applied.ResultsChildren with T1D on CSII have significantly higher HRQoL and CIDS than those on MDI (P < 0.001). A significant negative correlation is found between HRQoL and insulin daily dose(P = 0.022), HbA1C(P < 0.001), average SMBG(P < 0.001) and MINI-KID depression scale(P < 0.001). A significant positive correlation is found between HRQoL and CIDS(P < 0.001) and health care, home sanitation, family possessions and occupation socioeconomic scores(P = 0.033, P = 0.001, P < 0.001 and P = 0.006, respectively). Multivariate regression analysis revealed that HRQoL is most associated with MINI-KID depression scale (P = 0.004) and annual total cost(P < 0.001).ConclusionChildren with T1D on CSII have significantly better HRQoL, CIDS and HbA1C with less depression than those on MDI.
Comparison of landing kinematics and kinetics between experienced and novice volleyball players during block and spike jumps
Authors: Garcia Sébastien , Delattre N. , Berton E. , Divrechy G. , Rao G. 
Published: June 2022

Abstract
Background
The practice of volleyball requires many jumps. During landing, anterior cruciate ligament injuries may occur with high-risk lower limb kinematics and kinetics. Differences in landing strategies between experienced and novice volleyball players have not been fully explored. The purpose of the study was to compare lower limb kinematics and kinetics in experienced and novice volleyball players when performing volleyball specific jumps.

Methods
A total of 30 healthy males, 15 experienced and 15 novice volleyball players, participated in the study. Participants performed block and spike jumps at a controlled jump height. Hip, knee and ankle joints angles at initial ground contact and ranges of motion in the sagittal plane, knee joint angles and moments in the frontal plane, vertical ground reaction force peak and loading rate were analyzed to investigate the expertise effect.

Results
Experienced volleyball players landed with larger ankle dorsiflexion range of motion compared to novices. For the spike jump, experienced players landed with larger ankle plantarflexion angles at initial contact and larger ankle dorsiflexion ranges of motion, and for the block jump, they landed with larger knee flexion ranges of motion. Experienced players jumped significantly higher than novices. No difference was found in vertical ground reaction force peaks and loading rates.

Conclusions
Although the experienced group jumped higher than the novice group, no difference was found in ground reaction force parameters. These findings highlight that the experience of volleyball players acquired during regular trainings and competitions may play an important role in landing kinematics and kinetics to reduce the injury risk.
Is the future of peer review automated?
Authors: Schulz Robert , Barnett Adrian , Bernard René , Brown Nicholas J. L. , Byrne Jennifer A. , Eckmann Peter , Gazda Małgorzata A. , Kilicoglu Halil , Prager Eric M. , Salholz-Hillel Maia , ter Riet Gerben , Vines Timothy , Vorland Colby J. , Zhuang Han , Bandrowski Anita , Weissgerber Tracey L. 
Published: June 2022

AbstractThe rising rate of preprints and publications, combined with persistent inadequate reporting practices and problems with study design and execution, have strained the traditional peer review system. Automated screening tools could potentially enhance peer review by helping authors, journal editors, and reviewers to identify beneficial practices and common problems in preprints or submitted manuscripts. Tools can screen many papers quickly, and may be particularly helpful in assessing compliance with journal policies and with straightforward items in reporting guidelines. However, existing tools cannot understand or interpret the paper in the context of the scientific literature. Tools cannot yet determine whether the methods used are suitable to answer the research question, or whether the data support the authors’ conclusions. Editors and peer reviewers are essential for assessing journal fit and the overall quality of a paper, including the experimental design, the soundness of the study’s conclusions, potential impact and innovation. Automated screening tools cannot replace peer review, but may aid authors, reviewers, and editors in improving scientific papers. Strategies for responsible use of automated tools in peer review may include setting performance criteria for tools, transparently reporting tool performance and use, and training users to interpret reports.
Intramyocardial injected human umbilical cord-derived mesenchymal stem cells (HucMSCs) contribute to the recovery of cardiac function and the migration of CD4+ T cells into the infarcted heart via CCL5/CCR5 signaling
Authors: Liu Jing , Liang Xiaoting , Li Mimi , Lin Fang , Ma Xiaoxue , Xin Yuanfeng , Meng Qingshu , Zhuang Rulin , Zhang Qingliu , Han Wei , Gao Ling , He Zhiying , Zhou Xiaohui , Liu Zhongmin 
Published: June 2022

AbstractBackgroundHuman umbilical cord-derived mesenchymal stem cells (HucMSCs) have been recognized as a promising cell for treating myocardial infarction (MI). Inflammatory response post MI is critical in determining the cardiac function and subsequent adverse left ventricular remodeling. However, the local inflammatory effect of HucMSCs after intramyocardial injection in murine remains unclear.MethodsHucMSCs were cultured and transplanted into the mice after MI surgery. Cardiac function of mice were analyzed among MI-N.S, MI-HucMSC and MI-HucMSC-C–C Motif Chemokine receptor 5 (CCR5) antagonist groups, and angiogenesis, fibrosis and hypertrophy, and immune cells infiltration of murine hearts were evaluated between MI-N.S and MI-HucMSC groups. We detected the expression of inflammatory cytokines and their effects on CD4+T cells migration.ResultsHucMSCs treatment can significantly improve the cardiac function and some cells can survive at least 28 days after MI. Intramyocardial administration of HucMSCs also improved angiogenesis and alleviated cardiac fibrosis and hypertrophy. Moreover, we found the much higher numbers of CD4+T cells and CD4+FoxP3+regulatory T cells (Tregs) in the heart with HucMSCs than that with N.S treatment on day 7 post MI. In addition, the protein level of C–C Motif Chemokine Ligand 5 (CCL5) greatly increased in HucMSCs treated heart compared to MI-N.S group. In vitro, HucMSCs inhibited CD4+T cells migration and addition of CCL5 antibody or CCR5 antagonist significantly reversed this effect. In vivo results further showed that addition of CCR5 antagonist can reduce the cardioprotective effect of HucMSCs administration on day 7 post MI injury.ConclusionThese findings indicated that HucMSCs contributed to cardiac functional recovery and attenuated cardiac remodeling post MI. Intramyocardial injection of HucMSCs upregulated the CD4+FoxP3+Tregs and contributed to the migration of CD4+T cells into the injured heart via CCL5/CCR5 pathway.
Adipose-derived stromal cells increase the formation of collagens through paracrine and juxtacrine mechanisms in a fibroblast co-culture model utilizing macromolecular crowding
Authors: Søndergaard Rebekka Harary , Højgaard Lisbeth Drozd , Reese-Petersen Alexander Lynge , Hoeeg Cecilie , Mathiasen Anders Bruun , Haack-Sørensen Mandana , Follin Bjarke , Genovese Federica , Kastrup Jens , Juhl Morten , Ekblond Annette 
Published: June 2022

Abstract
Background
Adipose-derived stromal cells (ASCs) possess a multitude of regenerative capabilities, which include immunomodulation, angiogenesis, and stimulation of extracellular matrix (ECM) remodeling. However, the underlying mechanisms leading to ECM remodeling remain largely elusive and highlight the need for functional in vitro models for mode of action studies. Therefore, the purpose of this study was to develop an in vitro co-culture model to investigate the capabilities of ASCs to modulate fibroblasts and ECM.

Methods
An ECM in vitro model with ASCs and normal human dermal fibroblasts (NHDFs) was established utilizing macromolecular crowding, ascorbic acid, and TGF-β stimulation. Paracrine and juxtacrine co-cultures were created using transwell inserts and cell cultures with direct cell–cell contacts. The cultures were screened using RT2 PCR Profiler Arrays; the protein levels of myofibroblast differentiation marker alpha smooth muscle actin (αSMA) and ECM remodeling enzymes were analyzed using western blot on cell lysates; the formation of collagen type I, III, VI, and fibronectin was investigated using ELISA on culture supernatants; and the deposition of collagens was analyzed using immunocytochemistry.

Results
TGF-β stimulation of NHDF monocultures increased the expression of 18 transcripts relevant for ECM formation and remodeling, the protein levels of αSMA and matrix metalloproteinase-2 (MMP-2), the formation of collagen type I, III, VI, and fibronectin, and the deposition of collagen type I and VI and decreased the protein levels of MMP-14. Inclusion of ASCs in the ECM co-culture model increased the formation of collagen type I and III through paracrine mechanisms and the formation of collagen type VI through juxtacrine mechanisms.

Conclusions
The co-culture model provides effective stimulation of NHDF monocultures by TGF-β for enhanced formation and deposition of ECM. In the model, ASCs induce changes in ECM by increasing formation of collagen type I, III and VI. The obtained results could guide further investigations of ASCs’ capabilities and underlying mechanisms related to ECM formation and remodeling.
Fbxw11 impairs the repopulation capacity of hematopoietic stem/progenitor cells
Authors: Wang Lina , Piao Yongjun , Zhang Dongyue , Feng Wenli , Wang Chenchen , Cui Xiaoxi , Ren Qian , Zhu Xiaofan , Zheng Guoguang 
Published: June 2022

Abstract
Background
The ubiquitin–proteasome system plays important roles in maintaining the self-renewal and differentiation of stem and progenitor cells through highly ordered degradation of cellular proteins. Fbxw11, an E3 ligase, participates in many important biological processes by targeting a broad range of proteins. However, its roles in hematopoietic stem/progenitor cells (HSPCs) have not been established.

Methods
In this study, the effects of Fbxw11 on HSPCs were studied in vitro and in vivo by an overexpression strategy. Real-time PCR was performed to detect the expression of Fbxw11 in hematopoietic subpopulations. Colony-forming assays were performed to evaluate the in vitro function of Fbxw11 on HSPCs. Hoechst 33342 and Ki67 staining was performed to determine the cell-cycle distribution of HSPCs. Competitive transplantation experiments were used to evaluate the effect of Fbxw11 on the reconstitution potential of HSPCs. Single-cell RNA sequencing (scRNA-seq) was employed to reveal the transcriptomic alterations in HSPCs.

Results
The expression of Fbxw11 was higher in Lin−c-Kit+Sca-1+ (LSK) cells and myeloid progenitors than in lymphoid progenitors. Fbxw11 played negative roles in colony-forming and quiescence maintenance of HSPCs in vitro. Furthermore, serial competitive transplantation experiments revealed that Fbxw11 impaired the repopulation capacity of HSPCs. The proportion of granulocytes (Gr-1+CD11b+) in the differentiated mature cells was significantly higher than that in the control group, T cells and B cells were lower. Moreover, scRNA-seq revealed seven cell clusters in HSPCs. In addition, Fbxw11 downregulated the expression of Cebpa, Myc and Arid5b, which are significant regulators of HSPC activity, in most cell clusters.

Conclusion
Our data demonstrate that Fbxw11 plays a negative role in the maintenance of HSPCs in vitro and repopulation capacity in vivo. Our data also provide valuable transcriptome references for HSPCs in homeostasis.
Nk3R blockade has sex-divergent effects on memory in mice
Authors: Florido Antonio , Moreno Estefanía , Canela Enric I. , Andero Raül 
Published: June 2022

Abstract
Background
Memory consolidation is a process required for the formation of long-term memories. The G-protein-coupled receptor (GPCR) neurokinin-3-receptor (Nk3R) and its interactions with sex hormones seem important for the modulation of fear memory consolidation: Nk3R antagonism in male mice impairs fear memory, but enhances it in females. However, the involvement of the Nk3R as a modulator of other memories in both sexes remains unexplored.

Methods
We use the novel object recognition paradigm to test the effect of a systemic blockade of Nk3R during memory consolidation. Further, we assess the expression of estrogen receptor α, estrogen receptor β, and androgen receptor and heterodimerization with Nk3R in the medial prefrontal cortex (mPFC) and dorsal hippocampus (DH) of mice.

Results
Nk3R systemic antagonism elicited decreased memory consolidation in males while it enhanced it in females during proestrus. Nk3R analysis in the different subregions of the mPFC and the DH showed a higher expression in males than females. Moreover, females presented upregulation of the androgen receptor in the CA1 and the estrogen receptor beta in the cingulate cortex, CA1, and dentate gyrus. Overall, males presented an upregulation of the estrogen receptor alpha. We also explored the heterodimerization of GCPR membrane sex hormone receptors with the Nk3R. We found a higher percentage of Nk3R-membrane G-protein estrogen receptors heterodimers in the prelimbic cortex of the mPFC in females, suggesting an interaction of estradiol with Nk3R in memory consolidation. However, males presented a higher percentage of Nk3R-membrane G-protein androgen receptors heterodimers compared to females, pointing to an interaction of testosterone with Nk3R in memory consolidation.

Conclusion
These data propose novel ideas on functional interactions between Nk3R, sex hormones, estrogen receptors, and androgen receptors in memory consolidation.
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature
Authors: Binkheder Samar , Wu Heng-Yi , Quinney Sara K. , Zhang Shijun , Zitu Md. Muntasir , Chiang Chien‐Wei , Wang Lei , Jones Josette , Li Lang 
Published: June 2022

Abstract
Background
Adverse events induced by drug-drug interactions are a major concern in the United States. Current research is moving toward using electronic health record (EHR) data, including for adverse drug events discovery. One of the first steps in EHR-based studies is to define a phenotype for establishing a cohort of patients. However, phenotype definitions are not readily available for all phenotypes. One of the first steps of developing automated text mining tools is building a corpus. Therefore, this study aimed to develop annotation guidelines and a gold standard corpus to facilitate building future automated approaches for mining phenotype definitions contained in the literature. Furthermore, our aim is to improve the understanding of how these published phenotype definitions are presented in the literature and how we annotate them for future text mining tasks.

Results
Two annotators manually annotated the corpus on a sentence-level for the presence of evidence for phenotype definitions. Three major categories (inclusion, intermediate, and exclusion) with a total of ten dimensions were proposed characterizing major contextual patterns and cues for presenting phenotype definitions in published literature. The developed annotation guidelines were used to annotate the corpus that contained 3971 sentences: 1923 out of 3971 (48.4%) for the inclusion category, 1851 out of 3971 (46.6%) for the intermediate category, and 2273 out of 3971 (57.2%) for exclusion category. The highest number of annotated sentences was 1449 out of 3971 (36.5%) for the “Biomedical & Procedure” dimension. The lowest number of annotated sentences was 49 out of 3971 (1.2%) for “The use of NLP”. The overall percent inter-annotator agreement was 97.8%. Percent and Kappa statistics also showed high inter-annotator agreement across all dimensions.

Conclusions
The corpus and annotation guidelines can serve as a foundational informatics approach for annotating and mining phenotype definitions in literature, and can be used later for text mining applications.
Inclusion of a dual signal sequence enhances the immunogenicity of a novel viral vectored vaccine against the capsular group B meningococcus
Authors: Sheerin Dylan , Dold Christina , Silva-Reyes Laura , Linder Aline , Pollard Andrew J. , Rollier Christine S. 
Published: June 2022

AbstractBackgroundDisease caused by the capsular group B meningococcus (MenB) is the leading cause of infectious death in UK infants. A novel adenovirus-based vaccine encoding the MenB factor H binding protein (fHbp) with an N-terminal dual signal sequence induces high titres of protective antibody after a single dose in mice. A panel of N-terminal signal sequence variants were created to assess the contribution of components of this sequence to transgene expression kinetics of the encoded antigen from mammalian cells and the resultant effect on immunogenicity of fHbp.ResultsThe full-length signal sequence (FL SS) resulted in superior early antigen expression compared with the panel of variants, as measured by flow cytometry and confocal imaging, and supported higher bactericidal antibody levels against the expressed antigen in mouse sera < 6 weeks post-immunisation than the licensed four component MenB vaccine. The FL SS also significantly increased antigen-specific T cell responses against other adenovirus-encoded bacterial antigens in mice.ConclusionsThese findings demonstrate that the FL SS enhances immunogenicity of the encoded antigen, supporting its inclusion in other viral vectored bacterial antigen transgenes.