bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Authors: Salomaki Eric D. , Terpis Kristina X. , Rueckert Sonja , Kotyk Michael , Varadínová Zuzana Kotyková , Čepička Ivan , Lane Christopher E. , Kolisko Martin 
Published: April 2021

Abstract
Background
Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria.

Results
Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines.

Conclusions
Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.
MiR-126, IL-7, CXCR1/2 receptors, inflammation and circulating endothelial progenitor cells: The study on targets for treatment pathways in a model of subclinical cardiovascular disease (type 1 diabetes mellitus)
Authors: Coulson David J. , Bakhashab Sherin , Latief Jevi Septyani , Weaver Jolanta U. 
Published: April 2021

Abstract
Background
Type 1 diabetes (T1DM) is associated with premature cardiovascular disease (CVD) and a pro-inflammatory state whilst the proangiogenic miR-126-3p/-5p may play a role in CVD. Animal studies established miR-126 to be pro-angiogenic. We hypothesised miR-126-3p/-5p are reduced in T1DM whilst pro-inflammatory cytokines are increased.

Methods
29 well controlled, T1DM patients without CVD and 20 healthy controls (HCs) were studied. MiR-126-3p/-5p were assayed in plasma and peripheral blood mononuclear cells (PBMCs) whilst Chemokine C-X-C Receptor 1/2 (CXCR1/2) mRNA in PBMCs by real-time quantitative PCR. Cytokines were assayed by the Mesoscale Discovery. Ingenuity Pathway Analysis (IPA) was used to predict target genes, cellular functions and pathological states regulated by miR-126-3p/-5p. IPA generated both direct and indirect causations between different targets and analysed whether these effects would be inhibitory or stimulatory based on the published evidence.

Results
T1DM patients had a relatively good diabetic control (HbA1c = 7.4 ± 0.7% or 57.3 ± 7.6 mmol/mol). Homeostatic cytokine IL-7, pro-inflammatory cytokines IL-8 and TNF-α, and vascular endothelial growth factor-C (VEGF-C) were increased in T1DM, versus HCs; p = 0.008, p = 0.003, p = 0.041 and p = 0.013 respectively. MiR-126-5p was significantly upregulated in PBMCs in T1DM versus HCs; p = 0.01, but not in plasma. MiR-126-3p was unchanged. CXCR1/2 were elevated in T1DM versus HCs; p = 0.009 and p < 0.001 respectively. MiR-126-5p was positively correlated with CXCR1/2, and with HbA1c whilst negatively correlated with circulating endothelial progenitor cells (CD34+CD133+CD45dim) and fibronectin adhesion assay in a combined group of T1DM patients and HCs; p = 0.028 p = 0.049 p = 0.035 p = 0.047 and p = 0.004 respectively. IPA predicted miR-126-5p to be anti-inflammatory through the inhibition of chemokine C–C motif ligand 27, chymotrypsin-like elastase 2A and IL-7, whilst miR-126-3p had no direct anti-inflammatory effect. Simultaneously IPA predicted IL-7 as the most upstream cytokine target.

Conclusions
T1DM without apparent CVD or diabetic complications is an inflammatory state characterised not only by raised pro-inflammatory cytokines but also by increased receptor CXCR1/2 and miR-126-5p. MiR-126-5p upregulation may represent a compensatory response. Pro-miR-126-5p therapies or anti-IL-7 therapies may be a new option to reduce both inflammation and CVD risk in T1DM. Further research is required in a large prospective study in patients with T1DM.
Susceptibility to chronic immobilization stress‐induced depressive-like behaviour in middle‐aged female mice and accompanying changes in dopamine D1 and GABAA receptors in related brain regions
Authors: Cao Guofen , Meng Gaili , Zhu Li , Zhu Jie , Dong Nan , Zhou Xiaolan , Zhang Sumei , Zhang Yongai 
Published: April 2021

Abstract
Background
Middle-aged females, especially perimenopausal females, are vulnerable to depression, but the potential mechanism remains unclear. Dopaminergic and GABAergic system dysfunction is involved in the pathophysiology of depression. In the current study, we used 2-month-old and 11-month-old C57BL/6 mice as young and middle-aged mice, respectively. Chronic immobilization stress (CIS) was used to induce depressive-like behaviour, and the sucrose preference test (SPT), tail suspension test (TST) and forced swim test (FST) were used to assess these behaviours. We then measured the mRNA levels of dopamine receptor D1 (DRD1) and the GABAA receptors GABRA1, GABRB2 and GABRG2 in the nucleus accumbens (NAc) and prefrontal cortex (PFC).

Results
We found that immobility time in the FST was significantly increased in the middle-aged mice compared with the middle-aged control mice and the young mice. In addition, the preference for sucrose water was reduced in the middle-aged mice compared with the middle-aged control mice. However, CIS did not induce obvious changes in the performance of the young mice in our behavioural tests. Moreover, the middle-aged mice exhibited equal immobility times as the young mice in the absence of stress. Decreases in the mRNA levels of DRD1, GABRA1, and GABRB2 but not GABRG2 were found in the NAc and PFC in the middle-aged mice in the absence of stress. Further decreases in the mRNA levels of DRD1 in the NAc and GABRG2 in the NAc and PFC were found in the middle-aged mice subjected to CIS.

Conclusions
Our results suggested that ageing could not directly induce depression in the absence of stress. However, ageing could induce susceptibility to depression in middle-aged mice in the presence of stress. CIS-induced decreases in DRD1 and GABRG2 levels might be involved in the increase in susceptibility to depression in this context.
Biomarkers mining for spinal cord injury based on integrated multi-transcriptome expression profile data
Authors: Gong Chongcheng , Liu Lin , Shen Yang 
Published: April 2021

AbstractBackgroundThis study was aimed to discover more biomarkers associated with spinal cord injury (SCI) by constructing a competing endogenous RNA (ceRNA) network.MethodsThe transcriptome expression profile data related to SCI (GSE45006 GSE20907) were downloaded from GEO database. The differentially expressed RNAs (DERs), including lncRNAs, miRNAs, and mRNAs, between SCI and control groups were selected, which were then performed function enrichment analyses. Following that, a SCI-related ceRNA regulatory network was constructed. PCA analysis was performed on the genes constituting the ceRNA regulatory network directly related to SCI.ResultsIn GSE45006 and GSE20907 datasets, there were respectively 3336 and 1453 DERs. Venn analysis showed that there were 429 DERs which had consistent differential expression direction. RGD1564534-miR-29b-5p relation pair and 103 miRNA-target regulatory pairs were integrated to construct the ceRNA regulatory network. Then a SCI-related ceRNA regulatory network including 8 mRNAs ofIFNGR1,STAT2,CYBB,NFATC1,FCGR2B,HMOX1,TLR4, andHK2, a lncRNA of RGD1564534, and a miRNA of miR-29b-5p was constructed. Additionally, two pathways, osteoclast differentiation, and HIF-1 signaling pathway, were involved in this network. PCA indicated the samples before and after injury can be significantly distinguished based on the genes in the ceRNA network.ConclusionA total of 8 SCI-related mRNAs have been identified in the ceRNA network, includingIFNGR1,STAT2,CYBB,NFATC1,FCGR2B,HMOX1,TLR4, andHK2.Moreover, RGD1564534 may serve as ceRNA by competitively binding to miR-29b-5p to regulate the expression of 8 SCI-related mRNAs. Therefore, these genes may serve as key biomarkers of SCI.
Characteristics associated with clinical response to Comano thermal spring water balneotherapy in pediatric patients with atopic dermatitis
Authors: Geat Davide , Giovannini Mattia , Barlocco Ezio Gabriele , Pertile Riccardo , Farina Stefania , Pace Manuela , Filippeschi Cesare , Girolomoni Giampiero , Cristofolini Mario , Baldo Ermanno 
Published: April 2021

AbstractBackgroundSeveral studies have investigated the efficacy of balneotherapy in atopic dermatitis (AD), including a pediatric open randomized clinical trial conducted at the Comano thermal spring water center, which showed a significant reduction in AD severity and an improvement of the quality of life. However, so far many studies on balneotherapy in pediatric AD have included relatively small populations without identifying patients’ characteristics associated with their response. The aim of the present study was to identify any features associated with the clinical response to the Comano thermal spring water balneotherapy in a large cohort of pediatric AD patients.MethodsAn observational study was conducted on 867 children aged ≤16 years (females 50.5%, mean patient’s age 5.9 years, standard deviation ±3.6 years) with mild to severe AD who underwent balneotherapy at the Comano thermal spring water center (Comano, Trentino, Italy) from April to October 2014. Patients were stratified according to their disease severity, which was evaluated using five SCORing Atopic Dermatitis (SCORAD) categories before and immediately after a thermal spring water balneotherapy course. Potential characteristics associated with the patients’ clinical response to Comano thermal spring water balneotherapy were investigated.ResultsA statistically significant improvement in AD severity was observed after Comano thermal spring water balneotherapy (p < 0.0001). A significantly higher percentage of patients achieving improvement in AD severity was reported among children ≤4 years old (p < 0.0001) with early-onset AD (p < 0.0001), severe AD (p < 0.0001) or coexistent reported food allergies (p < 0.01). The therapy was well tolerated, and no relevant adverse effects were reported during the treatment course.ConclusionsComano thermal spring water balneotherapy is a safe complementary treatment for pediatric patients with AD, as it was able to reduce the disease severity, especially in children ≤4 years old, with early onset AD, severe AD or concomitant food allergies.
Assessing patients’ characteristics and treatment patterns among children with atopic dermatitis
Authors: Geat Davide , Giovannini Mattia , Barlocco Gabriele , Pertile Riccardo , Pace Manuela , Mori Francesca , Novembre Elio , Girolomoni Giampiero , Cristofolini Mario , Baldo Ermanno 
Published: April 2021

AbstractBackgroundAtopic dermatitis (AD) is the most common immune-mediated skin disease in childhood. Several treatment options for pediatric AD, both topical and systemic, are currently available. We carried out a single-center observational study with the aim of describing characteristics and treatment patterns in pediatric AD patients.MethodsThe study included 867 patients aged ≤16 years (females 50.5%, mean patient’s age 5.9 years, standard deviation ±3.6 years) with a previous doctor-confirmed diagnosis of AD who underwent balneotherapy at the Comano Thermal Spring Water Center (Comano, Trentino, Italy) from April to October 2014.ResultsAmong the patients included in the study, 41.2% had mild (SCORing Atopic Dermatitis, SCORAD 0-15), 43.6% moderate (SCORAD 16–40) and 15.2% severe AD (SCORAD > 40). A higher occurrence of reported food allergy was observed among children with more severe AD(p < 0.0001), while no association was found between AD severity and reported inhalant allergy or passive smoking (p = 0.15 and 0.92, respectively). Emollients (55.1%) and topical corticosteroids (TCS; 45.7%) were the main treatment options used in the previous month. The use of oral steroids and topical calcineurin inhibitors (TCI) was considerably less common (6.3 and 4.5%, respectively), while no patients were on systemic agents other than steroids. Among patients with severe AD, 9.8% had not used TCS, TCI or any systemic treatments. Moreover, 20.0% of the patients in the study population had followed elimination diets, although only 27.2% of them had a reported food allergy.ConclusionsA significant difference in the prevalence of reported food allergy emerged across the different AD severity categories. Furthermore, although further data are necessary to confirm our findings, undertreatment in children with AD appeared to be very common, at least among those attending the Comano Thermal Spring Water Center. Moreover, many patients followed elimination diets in the absence of reported food allergy.
Bifurcation analysis in a diffusive phytoplankton–zooplankton model with harvesting
Authors: Wang Yong 
Published: April 2021

AbstractA diffusive phytoplankton–zooplankton model with nonlinear harvesting is considered in this paper. Firstly, using the harvesting as the parameter, we get the existence and stability of the positive steady state, and also investigate the existence of spatially homogeneous and inhomogeneous periodic solutions. Then, by applying the normal form theory and center manifold theorem, we give the stability and direction of Hopf bifurcation from the positive steady state. In addition, we also prove the existence of the Bogdanov–Takens bifurcation. These results reveal that the harvesting and diffusion really affect the spatiotemporal complexity of the system. Finally, numerical simulations are also given to support our theoretical analysis.
Linear stability of blowup solution of incompressible Keller–Segel–Navier–Stokes system
Authors: Yan Yan , Li Hengyan 
Published: April 2021

AbstractIn this paper, we consider the linear stability of blowup solution for incompressible Keller–Segel–Navier–Stokes system in whole space$\mathbb{R}^{3}$R3. More precisely, we show that, if the initial data of the three dimensional Keller–Segel–Navier–Stokes system is close to the smooth initial function$(0,0,\textbf{u}_{s}(0,x) )^{T}$(0,0,us(0,x))T, then there exists a blowup solution of the three dimensional linear Keller–Segel–Navier–Stokes system satisfying the decomposition$$ \bigl(n(t,x),c(t,x),\textbf{u}(t,x) \bigr)^{T}= \bigl(0,0, \textbf{u}_{s}(t,x) \bigr)^{T}+\mathcal{O}(\varepsilon ), \quad \forall (t,x)\in \bigl(0,T^{*}\bigr) \times \mathbb{R}^{3}, $$(n(t,x),c(t,x),u(t,x))T=(0,0,us(t,x))T+O(ε),∀(t,x)∈(0,T∗)×R3,in Sobolev space$H^{s}(\mathbb{R}^{3})$Hs(R3)with$s=\frac{3}{2}-5a$s=32−5aand constant$0< a\ll 1$0<a≪1, where$T^{*}$T∗is the maximal existence time, and$\textbf{u}_{s}(t,x)$us(t,x)given in (Yan 2018) is the explicit blowup solution admitted smooth initial data for three dimensional incompressible Navier–Stokes equations.
Home range characteristics and diel patterns in space use of mutton snapper, Lutjanus analis, in St. Thomas, US Virgin Islands
Authors: Heidmann Sarah L. , Jossart Jonathan , Kimble Melissa , Nemeth Richard S. 
Published: April 2021

Abstract
Background
The movement ecology of mutton snapper Lutjanus analis is poorly understood despite their ecological and economic importance in the Caribbean. Passive acoustic telemetry was used to determine home ranges of six adult L. analis, including diel patterns, in Brewers Bay, St. Thomas, US Virgin Islands. Understanding long-term space use, including site fidelity and habitat usage, is necessary to implement effective and appropriate management actions for a species with extensive space and resource needs.

Results
Individual L. analis were tracked over an average period of 316 days (range 125–509 days) and showed high site fidelity to relatively small home ranges (mean ± SD: 0.103 ± 0.028 km2, range 0.019–0.190 km2) and core use areas with low overlap among individuals. Most home ranges had a habitat composition dominated by seagrass and to a lesser degree, coral reef and/or pavement. Nighttime activity spaces were distinct from but contained within daytime areas.

Conclusions
Mutton snapper showed strong site fidelity to home ranges in Brewers Bay. Two individuals that were absent from the array for more than a few hours were detected at separate arrays at spawning aggregation sites. This study expands upon knowledge of mutton snapper home range characteristics, highlights the importance of maintaining adjacent high-quality habitat types in any spatial management plan, and encourages the adoption of other types of management strategies, particularly for transient-aggregating species.
Intra-patient comparison of physiologic 68Ga-PSMA-11 and 18F-DCFPyL PET/CT uptake in ganglia in prostate cancer patients: a pictorial essay
Authors: Osman Medhat M. , Iravani Amir , Hofman Michael S. , Hicks Rodney J. 
Published: April 2021

Abstract
Background
Recent studies reported metabolic uptake in at least one of the evaluated ganglia in 98.5% of patients undergoing 68Ga -PSMA-11 and in 96.9% of patients undergoing 18F-DCFPyL PET/CT examination. We have observed different patterns of ganglion visualization with 18F-DCFPyL compared to 68Ga-PSMA-11. This includes more frequent visualization of cervical and sacral ganglia, which may be attributable to better imaging characteristics with 18F PET imaging.

Case presentation
This pictorial essay is to illustrate and compare, in the same patient, various representative cases of 68Ga-PSMA-11 and 18F-DCFPyL PET/CT uptake in ganglia at different anatomic locations, with different patterns and distribution of metabolic activity.

Conclusion
Reading physicians should be aware of the frequently encountered and occasionally different physiologic uptake of 68Ga-PSMA-11 and 18F DCFPyL in different ganglia.
Pain management in inflammatory bowel disease: feasibility of an online therapist-supported CBT-based self-management intervention
Authors: Sweeney Louise , Moss-Morris Rona , Czuber-Dochan Wladyslawa , Norton Christine 
Published: April 2021

AbstractBackgroundChronic pain is a poorly managed symptom of inflammatory bowel disease (IBD). Cognitive behavioural therapy (CBT) has an evidence base in functional gastrointestinal conditions and chronic pain. This study aimed to test the feasibility and acceptability of a 9-week online facilitator-supported CBT intervention, tailored for people with chronic IBD-related pain.DesignA single-arm pre-post design with nested qualitative interviews was used. Twenty individuals with IBD and chronic pain were recruited through an online IBD charity and had consented to research in a previous survey or responded to an online charity advert. Individuals who indicated a pain-interference score of ≥ 4/10 (Brief Pain Inventory) and met inclusion criteria were invited to take part. Outcomes included recruitment and retention rates, pain interference and severity, quality of life (QoL) and psychosocial measures.ResultsOf 145 individuals contacted, 55 (37.9%) responded. Two individuals were recruited from the study advertisement. Twenty out of 57 (35.1%) met screening and eligibility criteria. Eighty-five percent of the sample engaged with intervention sessions and 55% completed at least 5/9 sessions. Eighty percent of recruited participants completed the post-intervention questionnaire at week 9. The mean score for overall acceptability was 43.4 (0–70). Qualitative feedback demonstrated the value of thought monitoring and facilitator support. Scores improved for QoL and pain self-efficacy and reduced for depression, anxiety, pain catastrophising and avoidance resting behaviour.ConclusionsOnline CBT for chronic IBD-related pain appears feasible and acceptable. The study suggests positive effects for improving QoL and reducing psychological distress; however, online and face-to-face recruitment methods are recommended and establishing efficacy through larger randomised controlled trials is required.
Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury
Authors: Tang Yun , Yang Xiaobo , Shu Huaqing , Yu Yuan , Pan Shangwen , Xu Jiqian , Shang You 
Published: April 2021

Abstract
Background
Sepsis and septic shock are life-threatening diseases with high mortality rate in intensive care unit (ICU). Acute kidney injury (AKI) is a common complication of sepsis, and its occurrence is a poor prognostic sign to septic patients. We analyzed co-differentially expressed genes (co-DEGs) to explore relationships between septic shock and AKI and reveal potential biomarkers and therapeutic targets of septic-shock-associated AKI (SSAKI).

Methods
Two gene expression datasets (GSE30718 and GSE57065) were downloaded from the Gene Expression Omnibus (GEO). The GSE57065 dataset included 28 septic shock patients and 25 healthy volunteers and blood samples were collected within 0.5, 24 and 48 h after shock. Specimens of GSE30718 were collected from 26 patients with AKI and 11 control patents. AKI-DEGs and septic-shock-DEGs were identified using the two datasets. Subsequently, Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed to elucidate molecular mechanisms of DEGs. We also evaluated co-DEGs and corresponding predicted miRNAs involved in septic shock and AKI.

Results
We identified 62 DEGs in AKI specimens and 888, 870, and 717 DEGs in septic shock blood samples within 0.5, 24 and 48 h, respectively. The hub genes of EGF and OLFM4 may be involved in AKI and QPCT, CKAP4, PRKCQ, PLAC8, PRC1, BCL9L, ATP11B, KLHL2, LDLRAP1, NDUFAF1, IFIT2, CSF1R, HGF, NRN1, GZMB, and STAT4 may be associated with septic shock. Besides, co-DEGs of VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 coupled with corresponding predicted miRNAs, especially miR-29b-3p, miR-152-3p, and miR-223-3p may be regarded as promising targets for the diagnosis and treatment of SSAKI in the future.

Conclusions
Septic shock and AKI are related and VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 genes are significantly associated with novel biomarkers involved in the occurrence and development of SSAKI.