bluuebunny/crossref_metadata_2025_split huggingface dataset:
CBX4-dependent regulation of HDAC3 nuclear translocation reduces Bmp2-induced osteoblastic differentiation and calcification in adamantinomatous craniopharyngioma
Authors: Yan Xiaorong , Kang Dezhi , Lin Yuanxiang , Qi Songtao , Jiang Changzhen 
Published: January 2022

Abstract
Background
Calcification of adamantinomatous craniopharyngioma (ACP) often causes problems with tumor resection, leading to a high incidence of deadly complications and tumor recurrence. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) are 2 key enzymes that regulate histone acetylation and play important roles in tumor development. However, the roles of HAT and HDAC in the calcification and osteoblastic differentiation of ACP are not known.

Methods
In this study, primary cells were isolated from ACP tissues, and calcification was induced with bone morphogenetic protein 2 (Bmp2). HDAC3 expression was assessed in 12 tissue samples by Western blotting and immunohistochemistry. ACP calcification was assessed by Alizarin red staining. A luciferase reporter assay was performed to examine the interaction between miR-181b and the 3’-untranslated region of the polycomb chromobox 4 (CBX4) gene.

Results
Our results showed that the expression of HDAC3 was increased in the calcified ACP samples, but inhibition of HDAC3 promoted ACP cell calcification and osteoblastic differentiation. Mechanistically, HDAC3 nuclear translocation was suppressed by Bmp2, leading to Runx2 protein expression and Osterix, osteocalcin (OCN), osteopontin (OPN), and alkaline phosphatase (ALP) mRNA expression. In addition, this process was suppressed by CBX4, which stabilized the nuclear localization of HDAC3. miR-181b, the expression of which was increased in Bmp2-induced ACP cells, directly targeted and decreased CBX4 expression and inhibited the nuclear localization of HDAC3.

Conclusions
Our results demonstrate that Bmp2 increases miR-181b levels to directly target and inhibit CBX4 expression, leading to a reduction in the CBX4-dependent regulation of HDAC3 nuclear translocation, which results in Runx2 activation/osteoblastic differentiation and calcium deposition in ACP. Further studies targeting these cascades may contribute to therapeutic interventions used for recurrent ACP.
Small extracellular vesicles: from mediating cancer cell metastasis to therapeutic value in pancreatic cancer
Authors: Zhang Wenjie , Xing Juan , Liu Tian , Zhang Jie , Dai Zhujiang , Zhang Huan , Wang Daorong , Tang Dong 
Published: January 2022

AbstractPancreatic cancer is a highly malignant tumor and, is extremely difficult to diagnose and treat. Metastasis is one of the critical steps in the development of cancer and uses cell to cell communication to mediate changes in the microenvironment. Small extracellular vesicles (sEVs)-carry proteins, nucleic acids and other bioactive substances, and are important medium for communication between cells. There are two primary steps in sVEs-mediated metastasis: communication between pancreatic cancer cells and their surrounding microenvironment; and the communication between primary tumor cells and distant organ cells in distant organs that promotes angiogenesis, reshaping extracellular matrix, forming immunosuppressive environment and other ways to form appropriate pre-metastasis niche. Here, we explore the mechanism of localization and metastasis of pancreatic cancer and use sEVs as early biomarkers for the detection and treatment of pancreatic cancer.
Graphical Abstract
Scavenger receptors in host defense: from functional aspects to mode of action
Authors: Taban Qamar , Mumtaz Peerzada Tajamul , Masoodi Khalid Z. , Haq Ehtishamul , Ahmad Syed Mudasir 
Published: January 2022

AbstractScavenger receptors belong to a superfamily of proteins that are structurally heterogeneous and encompass the miscellaneous group of transmembrane proteins and soluble secretory extracellular domain. They are functionally diverse as they are involved in various disorders and biological pathways and their major function in innate immunity and homeostasis. Numerous scavenger receptors have been discovered so far and are apportioned in various classes (A-L). Scavenger receptors are documented as pattern recognition receptors and known to act in coordination with other co-receptors such as Toll-like receptors in generating the immune responses against a repertoire of ligands such as microbial pathogens, non-self, intracellular and modified self-molecules through various diverse mechanisms like adhesion, endocytosis and phagocytosis etc. Unlike, most of the scavenger receptors discussed below have both membrane and soluble forms that participate in scavenging; the role of a potential scavenging receptor Angiotensin-Converting Enzyme-2 has also been discussed whereby only its soluble form might participate in preventing the pathogen entry and replication, unlike its membrane-bound form. This review majorly gives an insight on the functional aspect of scavenger receptors in host defence and describes their mode of action extensively in various immune pathways involved with each receptor type.
Mendelian randomization study updates the effect of 25-hydroxyvitamin D levels on the risk of multiple sclerosis
Authors: Wang Renxi 
Published: January 2022

Abstract
Background
Observational studies and previous Mendelian randomization (MR) studies have shown that genetically low 25-hydroxyvitamin D (25OHD) levels are associated with a high susceptibility to multiple sclerosis (MS). The present MR study aims to update the causal estimates for the effects of 25OHD levels on MS risk.

Methods
To date, the largest genome-wide association study (GWAS) for serum 25OHD (n = 401,460) and MS (14,498 MS cases and 24,091 controls) was used to assess the effect of serum 25OHD levels on MS. All participants were of European ancestry. The MR-egger_intercept test and Cochran’s Q statistic were used to determine the pleiotropy and the heterogeneity, respectively. MR-egger, weighted median, inverse variance weighted (multiplicative random effects), simple mode, and weighted mode methods were used to evaluate the causal association of serum 25OHD levels with MS. Finally, the effect of a single 25OHD SNP (single nucleotide polymorphism) on MS was used to test the SNP bias.

Results
One hundred and fifteen newly identified serum 25OHD genetic variants were extracted from a large-scale serum 25OHD GWAS dataset. The 20 most effective and independent 25OHD genetic instrumental variables were extracted from the MS GWAS summary statistics. Pleiotropy analysis suggested no significant pleiotropic variant among the 20 selected 25OHD genetic instrument variants in MS GWAS datasets. As serum levels of 25OHD based on genetic changes increased, the risk of MS decreased using MR-egger (Beta = − 0.940, p = 0.001; OR = 0.391), weighted median (Beta = − 0.835, p = 0.000; OR = 0.434), IVW (Beta = − 0.781, p = 0.000; OR = 0.458), simple mode (Beta = − 1.484, p = 0.016; OR = 0.227), and weighted mode (Beta = − 0.913, p = 0.000; OR = 0.401). Our results were robust, with no obvious bias based on investigating the single 25OHD SNP on MS.

Conclusions
Our analysis suggested a causal association between genetically increased serum 25OHD levels and reduced MS in the European population.
GM-CSF impairs erythropoiesis by disrupting erythroblastic island formation via macrophages
Authors: Cao Weijie , Fan Wenjuan , Wang Fang , Zhang Yinyin , Wu Guanghua , Shi Xiaojing , Shi Jian xiang , Gao Fengcai , Yan Meimei , Guo Rong , Li Yingmei , Li Wei , Du Chunyan , Jiang Zhongxing 
Published: January 2022

AbstractAnemia is a significant complication of chronic inflammation and may be related to dysregulated activities among erythroblastic island (EBI) macrophages. GM-CSF was reported to be upregulated and attracted as a therapeutic target in many inflammatory diseases. Among EBIs, we found that the GM-CSF receptor is preferentially and highly expressed among EBI macrophages but not among erythroblasts. GM-CSF treatment significantly decreases human EBI formation in vitro by decreasing the adhesion molecule expression of CD163. RNA-sequence analysis suggests that GM-CSF treatment impairs the supporting function of human EBI macrophages during erythropoiesis. GM-CSF treatment also polarizes human EBI macrophages from M2-like type to M1-like type. In addition, GM-CSF decreases mouse bone marrow (BM) erythroblasts as well as EBI macrophages, leading to a reduction in EBI numbers. In defining the molecular mechanism at work, we found that GM-CSF treatment significantly decreases the adhesion molecule expression of CD163 and Vcam1 in vivo. Importantly, GM-CSF treatment also decreases the phagocytosis rate of EBI macrophages in mouse BM as well as decreases the expression of the engulfment-related molecules Mertk, Axl, and Timd4. In addition, GM-CSF treatment polarizes mouse BM EBI macrophages from M2-like type to M1-like type. Thus, we document that GM-CSF impairs EBI formation in mice and humans. Our findings support that targeting GM-CSF or reprogramming EBI macrophages might be a novel strategy to treat anemia resulting from inflammatory diseases.
Comparison of assessment scores for fatigue between multidimensional fatigue inventory (MFI-K) and modified chalder fatigue scale (mKCFQ)
Authors: Lim Eun-Jin , Son Chang-Gue 
Published: January 2022

Abstract
Background
Because of the absence of biological parameters for fatigue, appropriate instruments for assessing the degree of fatigue are important in the diagnosis and management of people complaining of fatigue-like symptoms. This study statistically analyzed the fatigue scores from two typical questionnaire-based instruments: the Korean version of the Multidimensional Fatigue Inventory (MFI-K) and the modified Chalder Fatigue Scale (mKCFQ).

Methods
Seventy participants (males n  = 40, females n  = 30, median age 48 years old, range of 25–67) were grouped into three groups (‘mild’  = 20, ‘moderate’  = 42, and ‘severe’  = 8) according to self-reported fatigue levels using a 7-point Likert scale. The similarities and differences between two instrument-derived scores were analyzed using correlations (r) and multidimensional scaling (MDS).

Results
The total scores of the two assessments were significantly correlated (r  = 75%, p  < 0.001), as were the subscores (‘Total Physical fatigue’: r  = 76%, p  < 0.001, ‘Total Mental fatigue’: r  = 56%, p  < 0.001). Relative overestimation of the MFI-K (45.8 ± 11.3) compared to the mKCFQ (36.1 ± 16.2) was observed, which was especially prominent in the ‘mild’ group. The scores of the three groups were more easily distinguished by the mKCFQ than by the MFI-K. In terms of the five dimension scores, we found a higher correlation of the two assessments for ‘general fatigue’ (r  = 79%, p  < 0.001) and ‘physical fatigue’ (r  = 66%, p  < 0.001) than for the reductions in ‘motivation’ (r  = 41%, p  < 0.01) and ‘activity’ (r  = 26%, p  > 0.05).

Conclusions
Our results may indicate the usefulness of the two instruments, especially for the physical symptoms of fatigue (‘general’ and ‘physical’ fatigue). Furthermore, the MFI-K may be useful for conditions of moderate-to-severe fatigue, such as chronic fatigue syndrome, but the mKCFQ may be useful for all spectra of fatigue, including in subhealthy people.
The effect of age on CD4+ T-cell recovery in HIV-suppressed adult participants: a sub-study from AIDS Clinical Trial Group (ACTG) A5321 and the Bone Loss and Immune Reconstitution (BLIR) study
Authors: Chen Jingxian , Titanji Kehmia , Sheth Anandi N. , Gandhi Rajesh , McMahon Deborah , Ofotokun Ighovwerha , Weitzmann M. Neale , De Paris Kristina , Dumond Julie B. 
Published: January 2022

AbstractOlder age could be a risk factor for suboptimal CD4+ T-cell recovery in HIV-infected patients despite successful viral suppression. However, evaluation of this effect could be confounded by age-related immune processes such as decreased thymus output, increased immune activation and exhaustion. Here, we established a semi-mechanistic population model simultaneously describing naïve and memory CD4+ T-cell trajectories in 122 participants. Covariate analysis accounting for immune activation showed that older age was significantly associated with faster apparent elimination rate of the naïve T-cells. In addition, female sex predicted slower apparent elimination rate of memory T-cells. Simulations showed that the median maximal CD4+ T-cell count on ART treatment was 593 cells/μL (IQR 442-794) in patients aged 50 years or above and 738 cells/μL (IQR 548-1002) in patients aged 18-35 years. The differences in the percentage of subjects achieving sufficient immune reconstitution (CD4+ T-cell count> 500 cells/μL) between the two age groups were 15, 21 and 26% at year 1, 4 years and steady state, respectively, suggesting that advanced age may have a greater impact on long-term CD4+ T-cell recovery.
Molecular detection, phylogenetic analysis and genetic diversity of recently isolated foot-and-mouth disease virus serotype A African topotype, Genotype IV
Authors: Hassan Ayah M. , Zaher Mostafa R. , Hassanien Rabab T. , Abd-El-Moniem Mervat I. , Habashi Ahmed R. , Ibraheem Essam M. , Shahein Momtaz A. , El Zowalaty Mohamed E. , Hagag Naglaa M. 
Published: January 2022

Abstract
Background
Surveillance for circulating emerging diseases of economic importance has a major role in the rapid response to major pathogen outbreaks. Foot-and-mouth disease virus (FMDV) is one of the significant endemic viruses in Egypt. FMDV is periodically investigated for monitoring evolution and emergence of new variants. The genetic characterization of foot-and-mouth disease (FMD) virus serotype A responsible for recent outbreaks of FMD in Egypt was determined.

Methods
Samples were collected from different locations and virus isolation was performed using BHK-21 cells. Viral RNA was extracted and samples were screened for FMDV using real-time RT-PCR. DNA sequence analysis was performed and computational and bioinformatics analyses were used to determine the substitution rates and phylogenetic relationship.

Results
Sequence and phylogenetic analyses of full-length 1D region of FMDV samples collected from different governorates in 2020 showed close similarity to Egyptian FMDV strains from serotype A-African topotype-G-IV with genetic variation of 6.5%. Recently isolated FMDV strains showed high genetic variations from locally used vaccine strains in the major antigenic sites of VP1 region.

Conclusions
Although, efforts made by the veterinary authorities to implement an effective mass vaccination plan, the recently detected FMDV strains in this study could not be subtyped using the FMDV primers routinely used for molecular serotyping. These dissimilarities raise the alarm for reconsideration of the FMDV isolates used in vaccine manufacture. Clearly close monitoring of FMD in Egypt is urgently required to define the risks of future outbreaks and to ensure appropriate control measures against FMD major outbreaks.
Charting the evidence for climate change impacts on the global spread of malaria and dengue and adaptive responses: a scoping review of reviews
Authors: Kulkarni Manisha A. , Duguay Claudia , Ost Katarina 
Published: January 2022

Abstract
Background
Climate change is expected to alter the global footprint of many infectious diseases, particularly vector-borne diseases such as malaria and dengue. Knowledge of the range and geographical context of expected climate change impacts on disease transmission and spread, combined with knowledge of effective adaptation strategies and responses, can help to identify gaps and best practices to mitigate future health impacts. To investigate the types of evidence for impacts of climate change on two major mosquito-borne diseases of global health importance, malaria and dengue, and to identify the range of relevant policy responses and adaptation strategies that have been devised, we performed a scoping review of published review literature. Three electronic databases (PubMed, Scopus and Epistemonikos) were systematically searched for relevant published reviews. Inclusion criteria were: reviews with a systematic search, from 2007 to 2020, in English or French, that addressed climate change impacts and/or adaptation strategies related to malaria and/or dengue. Data extracted included: characteristics of the article, type of review, disease(s) of focus, geographic focus, and nature of the evidence. The evidence was summarized to identify and compare regional evidence for climate change impacts and adaptation measures.

Results
A total of 32 reviews met the inclusion criteria. Evidence for the impacts of climate change (including climate variability) on dengue was greatest in the Southeast Asian region, while evidence for the impacts of climate change on malaria was greatest in the African region, particularly in highland areas. Few reviews explicitly addressed the implementation of adaptation strategies to address climate change-driven disease transmission, however suggested strategies included enhanced surveillance, early warning systems, predictive models and enhanced vector control.

Conclusions
There is strong evidence for the impacts of climate change, including climate variability, on the transmission and future spread of malaria and dengue, two of the most globally important vector-borne diseases. Further efforts are needed to develop multi-sectoral climate change adaptation strategies to enhance the capacity and resilience of health systems and communities, especially in regions with predicted climatic suitability for future emergence and re-emergence of malaria and dengue. This scoping review may serve as a useful precursor to inform future systematic reviews of the primary literature.
Outcomes from the medication assisted treatment pilot program for adults with opioid use disorders in rural Colorado
Authors: Amura Claudia R. , Sorrell Tanya R. , Weber Mary , Alvarez Andrea , Beste Nancy , Hollins Ursula , Cook Paul F. 
Published: January 2022

Abstract
Background
As Colorado ranked among the top nationally in non-medical use of opioids, a pilot medication for opioid use disorder (MOUD) program was developed to increase the number of NPs and PAs providing MOUD in order to bring this evidence- based treatment to 2 counties showing disproportionally high opioid overdose deaths. Over the first 18 months, the MOUD Pilot Program led to 15 new health care providers receiving MOUD waiver training and 1005 patients receiving MOUD from the 3 participating organizations. Here we evaluate patient centered clinical and functional outcomes of the pilot MOUD program implemented in 2 rural counties severely affected by the opioid crisis.

Methods
Under state-funded law (Colorado Senate Bill 17–074), three rural agencies submitted de-identified patient-level data at baseline (N = 1005) and after 6 months of treatment (N = 190, 25%) between December 2017 and January 2020. The Addiction Severity Index, PhQ9 and GAD-7 with McNemar-Bowker, and Wilcoxon Signed Rank tests analysis were used to measure patient outcomes across after participation in the program. .

Results
Patients in treatment reported using less heroin (52.1% vs 20.4%), opioids (22.3% vs 11.0%), and alcohol (28.6% vs 13.1%, all P < 0.01). Patients reported improved health (53.4% vs. 68.2%, P = 0.04), less frequency of disability (8.69 vs. 6.51, P = 0.02), symptoms (29.8% vs 21.3%), pain (67.5% to 53.6), worry (45.3% vs 62.3%), anxiety (49.7% vs 23.2%), depression (54.1% vs 23.3%, all P < 0.02) after treatment.

Conclusions
This study shows decreased substance use, improved physical and mental health, and reduced symptoms after 6 months of MOUD. Although more research on retention and long-term effects is needed, data shows improved health outcomes after 6 months of MOUD. Lessons learned from implementing this pilot program informed program expansion into other rural areas in need to address some of Colorado’ major public health crises.
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data
Authors: Gundogdu Pelin , Loucera Carlos , Alamo-Alvarez Inmaculada , Dopazo Joaquin , Nepomuceno Isabel 
Published: January 2022

Abstract
Background
Single-cell RNA sequencing (scRNA-seq) data provide valuable insights into cellular heterogeneity which is significantly improving the current knowledge on biology and human disease. One of the main applications of scRNA-seq data analysis is the identification of new cell types and cell states. Deep neural networks (DNNs) are among the best methods to address this problem. However, this performance comes with the trade-off for a lack of interpretability in the results. In this work we propose an intelligible pathway-driven neural network to correctly solve cell-type related problems at single-cell resolution while providing a biologically meaningful representation of the data.

Results
In this study, we explored the deep neural networks constrained by several types of prior biological information, e.g. signaling pathway information, as a way to reduce the dimensionality of the scRNA-seq data. We have tested the proposed biologically-based architectures on thousands of cells of human and mouse origin across a collection of public datasets in order to check the performance of the model. Specifically, we tested the architecture across different validation scenarios that try to mimic how unknown cell types are clustered by the DNN and how it correctly annotates cell types by querying a database in a retrieval problem. Moreover, our approach demonstrated to be comparable to other less interpretable DNN approaches constrained by using protein-protein interactions gene regulation data. Finally, we show how the latent structure learned by the network could be used to visualize and to interpret the composition of human single cell datasets.

Conclusions
Here we demonstrate how the integration of pathways, which convey fundamental information on functional relationships between genes, with DNNs, that provide an excellent classification framework, results in an excellent alternative to learn a biologically meaningful representation of scRNA-seq data. In addition, the introduction of prior biological knowledge in the DNN reduces the size of the network architecture. Comparative results demonstrate a superior performance of this approach with respect to other similar approaches. As an additional advantage, the use of pathways within the DNN structure enables easy interpretability of the results by connecting features to cell functionalities by means of the pathway nodes, as demonstrated with an example with human melanoma tumor cells.
Cavβ surface charged residues contribute to the regulation of neuronal calcium channels
Authors: Tran-Van-Minh Alexandra , De Waard Michel , Weiss Norbert 
Published: January 2022

AbstractVoltage-gated calcium channels are essential regulators of brain function where they support depolarization-induced calcium entry into neurons. They consist of a pore-forming subunit (Cavα1) that requires co-assembly with ancillary subunits to ensure proper functioning of the channel. Among these ancillary subunits, the Cavβ plays an essential role in regulating surface expression and gating of the channels. This regulation requires the direct binding of Cavβ onto Cavα1 and is mediated by the alpha interacting domain (AID) within the Cavα1 subunit and the α binding pocket (ABP) within the Cavβ subunit. However, additional interactions between Cavα1 and Cavβ have been proposed. In this study, we analyzed the importance of Cavβ3 surface charged residues in the regulation of Cav2.1 channels. Using alanine-scanning mutagenesis combined with electrophysiological recordings we identified several amino acids within the Cavβ3 subunit that contribute to the gating of the channel. These findings add to the notion that additional contacts besides the main AID/ABP interaction may occur to fine-tune the expression and properties of the channel.