bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes
Authors: Onizuka Satoru , Yamazaki Yasuharu , Park Sung-Joon , Sugimoto Takayuki , Sone Yumiko , Sjöqvist Sebastian , Usui Michihiko , Takeda Akira , Nakai Kenta , Nakashima Keisuke , Iwata Takanori 
Published: June 2020

Abstract
Background
Multipotent mesenchymal stromal cells (MSCs) can be isolated from numerous tissues and are attractive candidates for therapeutic clinical applications due to their immunomodulatory and pro-regenerative capacity. Although the minimum criteria for defining MSCs have been defined, their characteristics are known to vary depending on their tissue of origin.

Results
We isolated and characterized human MSCs from three different bones (ilium (I-MSCs), maxilla (Mx-MSCs) and mandible (Md-MSCs)) and proceeded with next generation RNA-sequencing. Furthermore, to investigate the gene expression profiles among other cell types, we obtained RNA-seq data of human embryonic stem cells (ESCs) and several types of MSCs (periodontal ligament-derived MSCs, bone marrow-derived MSCs, and ESCs-derived MSCs) from the Sequence Reads Archive and analyzed the transcriptome profile. We found that MSCs derived from tissues of the maxillofacial region, such as the jaw bone and periodontal ligament, were HOX-negative, while those derived from other tissues were HOX-positive. We also identified that MSX1, LHX8, and BARX1, an essential regulator of craniofacial development, were strongly expressed in maxillofacial tissue-derived MSCs. Although MSCs may be divided into two distinct groups, the cells originated from over the neck or not, on the basis of differences in gene expression profile, the expression patterns of all CD antigen genes were similar among different type of MSCs, except for ESCs.

Conclusions
Our findings suggest that MSCs from different anatomical locations, despite meeting general characterization criteria, have remarkable differences in gene expression and positional memory. Although stromal cells from different anatomical sources are generally categorized as MSCs, their differentiation potential and biological functions vary. We suggested that MSCs may retain an original tissue memory about the developmental process, including gene expression profiles. This could have an important impact when choosing an appropriate cell source for regenerative therapy using MSCs.
Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum
Authors: George Smitha , Palli Subba Reddy 
Published: June 2020

AbstractBackgroundHormones are chemical communication signaling molecules released into the body fluids to stimulate target cells of multicellular organisms. We recently showed that histone deacetylase 1 (HDAC1) plays an important role in juvenile hormone (JH) suppression of metamorphosis in the red flour beetle,Tribolium castaneum. Here, we investigated the function of another class I HDAC member, HDAC3, and show that it is required for the normal development ofT. castaneum.ResultsRNA interference-mediated knockdown of theHDAC3gene affected development resulting in abnormally folded wings in pupae and adults. JH analog, hydroprene, suppressed the expression ofHDAC3inT. castaneumlarvae. The knockdown ofHDAC3during the final instar larval stage resulted in an increase in the expression of genes coding for proteins involved in JH action. Sequencing of RNA isolated from larvae injected with dsRNA targetingmalE(E. coligene, control) orHDAC3followed by differential gene expression analysis identified 148 and 741 differentially expressed genes based on theP-value< 0.01 and four-fold difference, and the P-value< 0.05 and two-fold difference, respectively. Several genes, including those coding for myosin-I heavy chain (Myosin 22), Shaven, and nuclear receptor corepressor 1 were identified as differentially expressed genes inHDAC3knockdown larvae. An increase in histone H3 acetylation, specifically H3K9, H3K18, and H3K27, was detected inHDAC3knockdown insects.ConclusionOverall, these data suggest that HDAC3 affects the acetylation levels of histones and influences the expression of genes coding for proteins involved in the regulation of growth, development, and metamorphosis.
A TaqMan-based multiplex real-time PCR assay for the rapid detection of tigecycline resistance genes from bacteria, faeces and environmental samples
Authors: Li Yiming , Shen Zhangqi , Ding Shuangyang , Wang Shaolin 
Published: June 2020

Abstract
Background
Tigecycline is a last-resort antibiotic used to treat severe infections caused by extensively drug-resistant bacteria. Recently, novel tigecycline resistance genes tet(X3) and tet(X4) have been reported, which pose a great challenge to human health and food security. The current study aimed to establish a TaqMan-based real-time PCR assay for the rapid detection of the tigecycline-resistant genes tet(X3) and tet(X4).

Results
No false-positive result was found, and the results of the TaqMan-based real-time PCR assay showed 100% concordance with the results of the sequencing analyses. This proposed method can detect the two genes at the level of 1 × 102 copies/μL, and the whole process is completed within an hour, allowing rapid screening of tet(X3) and tet(X4) genes in cultured bacteria, faeces, and soil samples.

Conclusion
Taken together, the TaqMan-based real-time PCR method established in this study is rapid, sensitive, specific, and is capable of detecting the two genes not only in bacteria, but also in environmental samples.
Size-dependent activity of silver nanoparticles on the morphological switch and biofilm formation of opportunistic pathogenic yeasts
Authors: Szerencsés Bettina , Igaz Nóra , Tóbiás Ákos , Prucsi Zsombor , Rónavári Andrea , Bélteky Péter , Madarász Dániel , Papp Csaba , Makra Ildikó , Vágvölgyi Csaba , Kónya Zoltán , Pfeiffer Ilona , Kiricsi Mónika 
Published: June 2020

Abstract
Background
Dimorphism and biofilm formation are important virulence factors of some opportunistic human pathogenic yeasts. Such species commensally colonize skin or mucosal surfaces generally in yeast form, but under particular circumstances, convert into virulent hyphae and disseminate internal organs or cause mucocutaneous infections. The yeast-to-hypha shape-conversion promotes the development of a biofilm, a thick extracellular matrix with sessile cells within. The biofilm is capable to prevent the penetration of antifungal drugs, rendering the surviving biofilm-resident cells intrinsic sources of recurrent infections. The aim of this study was to evaluate the ability of silver nanoparticles (AgNPs) to attenuate the morphological switch and biofilm formation of several opportunistic pathogenic yeasts and to determine whether this feature depends on the nanoparticle size.

Results
AgNPs in three different sizes were prepared by chemical reduction approach and characterized by transmission electron microscopy, ultraviolet–visible spectroscopy and dynamic light scattering. The antifungal activity was evaluated by the microdilution method, the inhibitory capacity on biofilm formation and the biofilm degradation ability of differently sized AgNPs was assessed by viability assay. The morphological state of opportunistic pathogenic yeast cells in monoculture and in co-culture with human keratinocytes in the presence of AgNPs was examined by flow cytometry and scanning electron microscopy. All the three AgNPs inhibited the growth of the examined opportunistic pathogenic yeasts, nevertheless, AgNPs with the smallest diameter exhibited the most prominent toxic activities. AgNPs attenuated the biofilm formation in a nanoparticle size-dependent manner; however, their biofilm destruction capacity was negligible. AgNPs with the smallest size exerted the most significant effect on suppressing the morphological change of pathogens in monoculture as well as in a co-culture with keratinocytes.

Conclusions
Our results confirm that AgNPs are capable to hinder yeast-to-hypha morphological conversion and biofilm formation of opportunistic pathogens and this biological effect of AgNPs is size-dependent.
Genome-wide identification and characterization of SnRK family genes in Brassica napus
Authors: Zhu Weizhuo , Wu Dezhi , Jiang Lixi , Ye Lingzhen 
Published: June 2020

AbstractBackgroundSucrose non-fermenting 1 related protein kinases (SnRK)play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information ofSnRKgenes was available inBrassica napus, one of important oil crops. Recently, the released sequences of the reference genome ofB.napusprovide a good chance to perform genome-wide identification and characterization ofBnSnRKgene family in the rapeseed.ResultsTotally 114SnRKgenes distributed on 19 chromosomes were identified in the genome ofB.napusand classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, theBnSnRKsequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed andArabidopsiswere also analyzed to provide insights into the evolutionary characteristics ofBnSnRKfamily genes. Cis-element analysis revealed thatBnSnRKsmay response to diverse environmental stresses. Moreover, the expression patterns ofBnSnRKsin various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity ofBnSnRKfamily genes in different genotypes of the rapeseed.ConclusionWe examined genomic structures, evolution features, expression patterns and SNP distribution of 114BnSnRKs. The results provide valuable information for functional characterization ofBnSnRKgenes in future studies.
Analysis of emergency department visits for all reasons by adults with depression in the United States
Authors: Hill Tyler , Jiang Yun , Friese Christopher R. , Darbes Lynae A. , Blazes Christopher K. , Zhang Xingyu 
Published: June 2020

Abstract
Background
We aimed to characterize Emergency Department (ED) utilization and outcomes of patients with depression seeking emergency care for all reasons.

Methods
Using 2014–2016 ED data from the National Hospital Ambulatory Medical Care Survey, we investigated demographics, ED resource utilization, clinical characteristics, and disposition of patients with depression versus those without depression.

Results
Approximately 10,626,184 (11.4%) out of 92,899,685 annual ED visits were by patients with depression. ED patients with depression were mostly non-Hispanic White (74.0%) and were less likely to be male than patients without depression (aOR: 0.62; [95%] CI: 0.57–0.68). ED patients with depression were more likely to be admitted to the hospital (aOR: 1.50; CI: 1.38–1.63) than patients without depression. Among ED patients with depression, males were more likely than females to be seeking emergency care for psychiatric reasons (OR: 2.45; 95% CI: 2.10–2.87)) and to present with overdose/poisoning (OR: 1.46; CI: 1.03–2.05).

Conclusions
We described the unique demographic, socioeconomic, and clinical characteristics of ED patients with depression, using the most comprehensive, nationally representative study to date. We revealed notable gender disparities in rates and reasons for admissions. The higher hospital and ICU admission rates of ED patients with depression suggests this population requires a higher level of emergency care, for reasons that remain poorly understood.
Clinical features of aseptic meningitis with varicella zoster virus infection diagnosed by next-generation sequencing: case reports
Authors: Chen Lanlan , Xu Yao , Liu Chunfeng , Huang Hong , Zhong Xingxing , Ma Cancan , Zhao Haina , Chen Yingzhu 
Published: June 2020

Abstract
Background
The aseptic meningitis caused by varicella zoster virus (VZV) reactivation was less described in the literature, most of which were detected by means of polymerase chain reaction. The authors presented 4 adult immunocompetent patients with acute aseptic meningitis with VZV infection diagnosed by next-generation sequencing (NGS).

Case presentation
Four patients were admitted to the hospital with headache and fever between March 2018 and August 2019. The median ages were 37 years (range 22–52 years). The median symptoms onset to clinic time was 3.5 days (range 3–6 days). Two patients had signs of meningeal irritation. Rash occurred after the meningitis symptoms in 1 patient (time from meningitis symptoms to rash, 2 days). No other sign or symptom was reported. The brain Magnetic resonance imaging and electroencephalography were normal in all patients. Cerebrospinal fluid (CSF) samples were obtained at a median of 4 days (range 3–7 days) from the meningitis symptoms onset. Opening pressure of lumbar puncture after admission were high in these cases (median 256 mm H2O; range 165–400 mm H2O). White blood cell counts and protein levels were significantly elevated in CSF samples (median 317 × 10^6/L, range 147–478 × 10^6/L; median 1.41 g/L, range 0.57–1.79 g/L). The cytology of CSF demonstrated a lymphocytic pleocytosis, and most multinuclear cells. The culture of CSF was negative for all 4 cases, while T-cell spot test was positive for 2 cases, who were administrated with anti-tuberculosis treatment for suspicious tuberculous meningitis. NGS of CSF (the Vision Medical Research Institute) detected specific sequences of VZV in the 4 cases within 72 h after admission. The inappropriate treatment were stopped while acyclovir were continued intravenously for 10–14 days. All patients recovered completely.

Conclusions
VZV is an infectious agent that causes aseptic meningitis in immunocompetent adults and could not be accompanied by skin manifestations. The NGS of CSF is a rapid detection for the identification and differentiation of meningitis in patients, which is of great importance for providing the rapid and accurate diagnosis and the targeted antimicrobial therapy for central nervous system infection.
Towards accurate exclusion of neonatal bacterial meningitis: a feasibility study of a novel 16S rDNA PCR assay
Authors: Abelian Arthur , Mund Thomas , Curran Martin D. , Savill Stuart A. , Mitra Nipa , Charan Carol , Ogilvy-Stuart Amanda L. , Pelham Hugh R. B. , Dear Paul H. 
Published: June 2020

AbstractBackgroundPCRctic is an innovative assay based on 16S rDNA PCR technology that has been designed to detect a single intact bacterium in a specimen of cerebro-spinal fluid (CSF). The assay’s potential for accurate, fast and inexpensive discrimination of bacteria-free CSF makes it an ideal adjunct for confident exclusion of bacterial meningitis in newborn babies where the negative predictive value of bacterial culture is poor. This study aimed to stress-test and optimize PCRctic in the “field conditions” to attain a clinically useful level of specificity.MethodsThe specificity of PCRctic was evaluated in CSF obtained from newborn babies investigated for meningitis on a tertiary neonatal unit. Following an interim analysis, the method of skin antisepsis was changed to increase bactericidal effect, and snap-top tubes (Eppendorf™) replaced standard universal containers for collection of CSF to reduce environmental contamination.ResultsThe assay’s specificity was 90.5% in CSF collected into the snap-top tubes – up from 60% in CSF in the universal containers. The method of skin antisepsis had no effect on the specificity. All CSF cultures were negative and no clinical cases of neonatal bacterial meningitis occurred during the study.ConclusionsA simple and inexpensive optimization of CSF collection resulted in a high specificity output. The low prevalence of neonatal bacterial meningitis means that a large multi-centre study will be required to validate the assay’s sensitivity and its negative predictive value.
COVID-19 with acute cholecystitis: a case report
Authors: Ying Mingliang , Lu Bin , Pan Jiangfeng , Lu Guanghong , Zhou Shaobin , Wang Dingjun , Li Lu , Shen Junkang , Shu Jiner ,   From the COVID-19 Investigating and Research Team
Published: June 2020

Abstract
Background
The 2019 novel coronavirus (COVID-19) presents a major threat to public health and has rapidly spread worldwide since the outbreak in Wuhan, Hubei Province, China in 2019. To date, there have been few reports of the varying degrees of illness caused by the COVID-19.

Case presentation
A case of 68-year-old female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that was finally diagnosed as acute cholecystitis. Ultrasound-guided percutaneous transhepatic gallbladder drainage (PTGD) was performed, and the real-time fluorescence polymerase chain reaction (RT-PCR) COVID-19 nucleic acid assay of the bile was found to be negative. PTGD, antibacterial and anti-virus combined with interferon inhalation treatment were successful.

Conclusion
The time course of chest CT findings is typical for COVID-19 pneumonia. PTGD is useful for acute cholecystitis in COVID-19 patients. Acute cholecystitis is likely to be caused by COVID-19 .
HIV patients retention and attrition in care and their determinants in Ethiopia: a systematic review and meta-analysis
Authors: Abebe Moges Nurilign , Olubukola Adesina , Micheal Okunlola , Berhane Yemane 
Published: June 2020

Abstract
Background
There is paucity of evidence on the magnitude of HIV patients’ retention and attrition in Ethiopia. Hence, the aim of this study was to determine the pooled magnitude of HIV patient clinical retention and attrition and to identify factors associated with retention and attrition in Ethiopia.

Methods
Systematic review and meta-analysis were done among studies conducted in Ethiopia using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Both published and unpublished studies conducted from January 1, 2005 to June 6th, 2019 were included. Major databases and search engines such as Google Scholar, PUBMED, African Journals Online (AJOL) and unpublished sources were searched to retrieve relevant articles. Data were assessed for quality, heterogeneity and publication bias. Analysis was conducted using STATA version 14 software.

Result
From a total of 45 studies 546,250 study participants were included in this review. The pooled magnitude of retention in care among HIV patients was 70.65% (95% CI, 68.19, 73.11). The overall magnitude of loss to follow up 15.17% (95% CI, 11.86, 18.47), transfer out 11.17% (95% CI, 7.12, 15.21) and death rate were 6.75% (95% CI, 6.22, 7.27). Major determinants of attrition were being unmarried patient (OR 1.52, 95% CI: 1.15–2.01), non-disclosed HIV status (OR 6.36, 95% CI: 3.58–11.29), poor drug adherence (OR 6.60, 95% CI: 1.41–30.97), poor functional status (OR 2.11, 95% CI: 1.33–3.34), being underweight (OR 2.21, 95% CI: 1.45–3.39) and advanced clinical stage (OR 1.85, 95% CI: 1.36–2.51). Whereas absence of opportunistic infections (OR 0.52, 95% CI: 0.30–0.9), normal hemoglobin status (OR 0.29, 95% CI: 0.20–0.42) and non-substance use (OR 95% CI: 0.41, 0.17–0.98) were facilitators of HIV patient retention in clinical care.

Conclusion
The level of retention to the care among HIV patients was low in Ethiopia. Socio-economic, clinical, nutritional and behavioral, intervention is necessary to achieve adequate patient retention in clinical care.
Utility of FDG PET/CT for assessment of lung nodules identified during low dose computed tomography screening
Authors: Hadique Sarah , Jain Pranav , Hadi Yousaf , Baig Aneeqah , Parker John E. 
Published: June 2020

Abstract
Background
Many clinical guidelines recommend FDG PET/CT for the evaluation of pulmonary nodules ≥8 mm detected during low dose computed tomography (LDCT) lung cancer screening. However, its added value in this setting requires confirmation. We evaluated the clinical utility of FDG PET/CT, including incidental findings, during the evaluation of lung nodules detected on LDCT screening.

Methods
A retrospective cohort study was performed among 75 patients who completed FDG PET/CT between January 2010 and December 2017, after lung nodules > 8 mm had been detected on LDCT lung cancer screening. We report demographic variables, characteristics of the initial nodules on LDCT and FDG PET/CT, incidental findings on FDG PET/CT, as well as further work up performed and the influence of FDG PET/CT findings on management.

Results
Nodules were reported to be benign on FDG PET/CT in 38/75 (50.6%) patients. Physicians chose either radiological follow-up or no further work up in all 38. FDG PET/CT was indeterminate or suggested malignancy in 37 (49.3%) patients. Biopsy was performed in 32 (86%) of these patients. Incidental findings on FDG PET/CT were reported in 37/75 (49%) patients. Further work-up of incidental findings was performed in 21/75 (28%) of patients.

Conclusions
In this study, for majority of individuals with lung nodules identified during LDCT lung cancer screening, FDG PET/CT results were able to guide physicians in choosing between routine follow up or invasive biopsies. Conversely, 28% of these patients required additional investigations to address incidental findings.
Prevalence of renal dysfunction among HIV infected patients receiving Tenofovir at Mulago: a cross-sectional study
Authors: Nyende Louis , Kalyesubula Robert , Sekasanvu Emmanuel , Byakika-Kibwika Pauline 
Published: June 2020

Abstract
Background
There is an increasing burden of non-communicable disease globally. Tenofovir disoproxil fumarate (TDF) is the most commonly prescribed antiretroviral drug globally. Studies show that patients receiving TDF are more prone to renal dysfunction at some point in time during treatment. Evaluation of kidney function is not routinely done in most HIV public clinics. Identification of renal dysfunction is key in resource constrained settings because managing patients with end stage renal disease is costly.

Method
This was a cross-sectional study conducted at an outpatient clinic in 2018 involving patients on TDF for at least 6 months who were 18 years or older. Patients with documented kidney disease and pregnancy were excluded. Estimated glomerular filtration rate (eGFR) was calculated using the CKD-Epi formula. Renal dysfunction was defined as any of the following; either eGFR< 60 mL/min/1.73m2,or proteinuria of ≥2+ on urine dipstick, glycosuria with normal blood glucose. Electrolyte abnormalities were also documented.

Results
We enrolled 278 participants. One hundred sixty nine (60.8%) were females, majority 234(84.2%) were < 50 years old, 205 (73.74%) were in WHO stage 1, most participants 271(97.5%) in addition to TDF were receiving lamivudine/efavirenz. The median age was 37(IQR 29–45) years; median duration on ART was 36 (IQR 24–60) months. The prevalence of renal dysfunction was 2.52% (7/278). Most noted electrolyte abnormality was hypocalcaemia (15.44%).

Conclusions
The prevalence of renal dysfunction was low though some participants had hypocalcaemia. Screening for kidney disease should be done in symptomatic HIV infected patients on TDF.