bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peripheral blood transcriptomic sub-phenotypes of pediatric acute respiratory distress syndrome
Authors: Yehya Nadir , Varisco Brian M. , Thomas Neal J. , Wong Hector R. , Christie Jason D. , Feng Rui 
Published: December 2020

Abstract
Background
Acute respiratory distress syndrome (ARDS) is heterogeneous and may be amenable to sub-phenotyping to improve enrichment for trials. We aimed to identify subtypes of pediatric ARDS based on whole blood transcriptomics.

Methods
This was a prospective observational study of children with ARDS at the Children’s Hospital of Philadelphia (CHOP) between January 2018 and June 2019. We collected blood within 24 h of ARDS onset, generated expression profiles, and performed k-means clustering to identify sub-phenotypes. We tested the association between sub-phenotypes and PICU mortality and ventilator-free days at 28 days using multivariable logistic and competing risk regression, respectively.

Results
We enrolled 106 subjects, of whom 96 had usable samples. We identified three sub-phenotypes, dubbed CHOP ARDS Transcriptomic Subtypes (CATS) 1, 2, and 3. CATS-1 subjects (n = 31) demonstrated persistent hypoxemia, had ten subjects (32%) with immunocompromising conditions, and 32% mortality. CATS-2 subjects (n = 29) had more immunocompromising diagnoses (48%), rapidly resolving hypoxemia, and 24% mortality. CATS-3 subjects (n = 36) had the fewest comorbidities and also had rapidly resolving hypoxemia and 8% mortality. The CATS-3 subtype was associated with lower mortality (OR 0.18, 95% CI 0.04–0.86) and higher probability of extubation (subdistribution HR 2.39, 95% CI 1.32–4.32), relative to CATS-1 after adjustment for confounders.

Conclusions
We identified three sub-phenotypes of pediatric ARDS using whole blood transcriptomics. The sub-phenotypes had divergent clinical characteristics and prognoses. Further studies should validate these findings and investigate mechanisms underlying differences between sub-phenotypes.
Postoperative hypotension in patients discharged to the intensive care unit after non-cardiac surgery is associated with adverse clinical outcomes
Authors: Smischney Nathan J. , Shaw Andrew D. , Stapelfeldt Wolf H. , Boero Isabel J. , Chen Qinyu , Stevens Mitali , Khanna Ashish K. 
Published: December 2020

AbstractBackgroundThe postoperative period is critical for a patient’s recovery, and postoperative hypotension, specifically, is associated with adverse clinical outcomes and significant harm to the patient. However, little is known about the association between postoperative hypotension in patients in the intensive care unit (ICU) after non-cardiac surgery, and morbidity and mortality, specifically among patients who did not experience intraoperative hypotension. The goal of this study was to assess the impact of postoperative hypotension at various absolute hemodynamic thresholds (≤ 75, ≤ 65 and ≤ 55 mmHg), in the absence of intraoperative hypotension (≤ 65 mmHg), on outcomes among patients in the ICU following non-cardiac surgery.MethodsThis multi-center retrospective cohort study included specific patient procedures from Optum® healthcare database for patients without intraoperative hypotension (MAP ≤ 65 mmHg) discharged to the ICU for ≥ 48 h after non-cardiac surgery with valid mean arterial pressure (MAP) readings. A total of 3185 procedures were included in the final cohort, and the association between postoperative hypotension and the primary outcome, 30-day major adverse cardiac or cerebrovascular events, was assessed. Secondary outcomes examined included all-cause 30- and 90-day mortality, 30-day acute myocardial infarction, 30-day acute ischemic stroke, 7-day acute kidney injury stage II/III and 7-day continuous renal replacement therapy/dialysis.ResultsPostoperative hypotension in the ICU was associated with an increased risk of 30-day major adverse cardiac or cerebrovascular events at MAP ≤ 65 mmHg (hazard ratio [HR] 1.52; 98.4% confidence interval [CI] 1.17–1.96) and ≤ 55 mmHg (HR 2.02, 98.4% CI 1.50–2.72). Mean arterial pressures of ≤ 65 mmHg and ≤ 55 mmHg were also associated with higher 30-day mortality (MAP ≤ 65 mmHg, [HR 1.56, 98.4% CI 1.22–2.00]; MAP ≤ 55 mmHg, [HR 1.97, 98.4% CI 1.48–2.60]) and 90-day mortality (MAP ≤ 65 mmHg, [HR 1.49, 98.4% CI 1.20–1.87]; MAP ≤ 55 mmHg, [HR 1.78, 98.4% CI 1.38–2.31]). Furthermore, we found an association between postoperative hypotension with MAP ≤ 55 mmHg and acute kidney injury stage II/III (HR 1.68, 98.4% CI 1.02–2.77). No associations were seen between postoperative hypotension and 30-day readmissions, 30-day acute myocardial infarction, 30-day acute ischemic stroke and 7-day continuous renal replacement therapy/dialysis for any MAP threshold.ConclusionsPostoperative hypotension in critical care patients with MAP ≤ 65 mmHg is associated with adverse events even without experiencing intraoperative hypotension.
Role of extracorporeal membrane oxygenation in children with sepsis: a systematic review and meta-analysis
Authors: Ramanathan Kollengode , Yeo Nicholas , Alexander Peta , Raman Lakshmi , Barbaro Ryan , Tan Chuen Seng , Schlapbach Luregn J. , MacLaren Graeme 
Published: December 2020

AbstractBackgroundThe benefits of extracorporeal membrane oxygenation (ECMO) in children with sepsis remain controversial. Current guidelines on management of septic shock in children recommend consideration of ECMO as salvage therapy. We sought to review peer-reviewed publications on effectiveness of ECMO in children with sepsis.MethodsStudies reporting on mortality in children with sepsis supported with ECMO, published in PubMed, Scopus and Embase from 1972 till February 2020, were included in the review. This study was done in adherence to Preferred Reporting Items for Systematic Review and Meta-Analysis statement after registering the review protocol with PROSPERO. Study eligibility was independently assessed by two authors and disagreements resolved by a third author. Publications were reviewed for quality using Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. Random-effects meta-analyses (DerSimonian and Laird) were conducted, and 95% confidence intervals were computed using the Clopper-Pearson method. Outliers were identified by the Baujat plot and leave-one-out analysis if there was considerable heterogeneity. The primary outcome measure was survival to discharge. Secondary outcome measures included hospital length of stay, subgroup analysis of neonatal and paediatric groups, types and duration of ECMO and complications .ResultsOf the 2054 articles screened, we identified 23 original articles for systematic review and meta-analysis. Cumulative estimate of survival (13 studies, 2559 patients) in the cohort was 59% (95%CI: 51–67%). Patients had a median length of hospital stay of 28.8 days, median intensive care unit stay of 13.5 days, and median ECMO duration of 129 h. Children needing venoarterial ECMO (9 studies, 208 patients) showed overall pooled survival of 65% (95%CI: 50–80%). Neonates (< 4 weeks of age) with sepsis needing ECMO (7 studies, 85 neonates) had pooled survival of 73% (95%CI: 56- 87%). Gram positive organisms were the most common pathogens (47%) in septic children supported with ECMO.ConclusionSurvival rates of children with sepsis needing ECMO was 59%. Neonates had higher survival rates (73%); gram positive organisms accounted for most common infections in children needing ECMO. Despite limitations, pooled survival data from this review indicates consideration of ECMO in refractory septic shock for all pediatric age groups.
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Authors: He Shuai , Wang Lin-He , Liu Yang , Li Yi-Qi , Chen Hai-Tian , Xu Jing-Hong , Peng Wan , Lin Guo-Wang , Wei Pan-Pan , Li Bo , Xia Xiaojun , Wang Dan , Bei Jin-Xin , He Xiaoshun , Guo Zhiyong 
Published: December 2020

AbstractBackgroundAs core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing.ResultsWe perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novelCOCH+fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors, and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues.ConclusionsThe adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.
Mentalization for Offending Adult Males (MOAM): study protocol for a randomized controlled trial to evaluate mentalization-based treatment for antisocial personality disorder in male offenders on community probation
Authors: Fonagy Peter , Yakeley Jessica , Gardner Tessa , Simes Elizabeth , McMurran Mary , Moran Paul , Crawford Mike , Frater Alison , Barrett Barbara , Cameron Angus , Wason James , Pilling Stephen , Butler Stephen , Bateman Anthony 
Published: December 2020

Abstract
Background
Antisocial personality disorder (ASPD), although associated with very significant health and social burden, is an under-researched mental disorder for which clinically effective and cost-effective treatment methods are urgently needed. No intervention has been established for prevention or as the treatment of choice for this disorder. Mentalization-based treatment (MBT) is a psychotherapeutic treatment that has shown some promising preliminary results for reducing personality disorder symptomatology by specifically targeting the ability to recognize and understand the mental states of oneself and others, an ability that is compromised in people with ASPD. This paper describes the protocol of a multi-site RCT designed to test the effectiveness and cost-effectiveness of MBT for reducing aggression and alleviating the wider symptoms of ASPD in male offenders subject to probation supervision who fulfil diagnostic criteria for ASPD.

Methods
Three hundred and two participants recruited from a pool of offenders subject to statutory supervision by the National Probation Service at 13 sites across the UK will be randomized on a 1:1 basis to 12 months of probation plus MBT or standard probation as usual, with follow-up to 24 months post-randomization. The primary outcome is frequency of aggressive antisocial behaviour as assessed by the Overt Aggression Scale – Modified. Secondary outcomes include violence, offending rates, alcohol use, drug use, mental health status, quality of life, and total service use costs. Data will be gathered from police and criminal justice databases, NHS record linkage, and interviews and self-report measures administered to participants. Primary analysis will be on an intent-to-treat basis; per-protocol analysis will be undertaken as secondary analysis. The primary outcome will be analysed using hierarchical mixed-effects linear regression. Secondary outcomes will be analysed using mixed-effects linear regression, mixed-effects logistic regression, and mixed-effects Poisson models for secondary outcomes depending on whether the outcome is continuous, binary, or count data. A cost-effectiveness and cost-utility analysis will be undertaken.

Discussion
This definitive, national, multi-site trial is of sufficient size to evaluate MBT to inform policymakers, service commissioners, clinicians, and service users about its potential to treat offenders with ASPD and the likely impact on the population at risk.

Trial registration
ISRCTN 32309003. Registered on 8 April 2016.
Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1
Authors: Ren Jun , Lee Hyang-Mi , Thai Thi Duc , Na Dokyun 
Published: December 2020

Abstract
Background
Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism.

Results
We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5 × 103 CFU/μg (124%). The introduced gene increased the production of carotenoid by 26%. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70% as well. The production of carotenoid was decreased by 40% when the psy gene was translationally repressed by anti-psy sRNA.

Conclusions
Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.
Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species
Authors: Chen Chong , Cui Chao-Yue , Yu Jun-Jun , He Qian , Wu Xiao-Ting , He Yu-Zhang , Cui Ze-Hua , Li Cang , Jia Qiu-Lin , Shen Xiang-Guang , Sun Ruan-Yang , Wang Xi-Ran , Wang Min-Ge , Tang Tian , Zhang Yan , Liao Xiao-Ping , Kreiswirth Barry N. , Zhou Shi-Dan , Huang Bin , Du Hong , Sun Jian , Chen Liang , Liu Ya-Hong 
Published: December 2020

Abstract
Background
The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infections caused by multidrug-resistant Gram-negative and Gram-positive pathogens. Although tet(X) has been found in various bacterial species, less is known about phylogeographic distribution and phenotypic variance of different genetic variants.

Methods
Herein, we conducted a multiregional whole-genome sequencing study of tet(X)-positive Acinetobacter isolates from human, animal, and their surrounding environmental sources in China. The molecular and enzymatic features of tet(X) variants were characterized by clonal expression, microbial degradation, reverse transcription, and gene transfer experiments, while the tet(X) genetic diversity and molecular evolution were explored by comparative genomic and Bayesian evolutionary analyses.

Results
We identified 193 tet(X)-positive isolates from 3846 samples, with the prevalence ranging from 2.3 to 25.3% in nine provinces in China. The tet(X) was broadly distributed in 12 Acinetobacter species, including six novel species firstly described here. Besides tet(X3) (n = 188) and tet(X4) (n = 5), two tet(X5) variants, tet(X5.2) (n = 36) and tet(X5.3) (n = 4), were also found together with tet(X3) or tet(X4) but without additive effects on tetracyclines. These tet(X)-positive Acinetobacter spp. isolates exhibited 100% resistance rates to tigecycline and tetracycline, as well as high minimum inhibitory concentrations to eravacycline (2–8 μg/mL) and omadacycline (8–16 μg/mL). Genetic analysis revealed that different tet(X) variants shared an analogous ISCR2-mediated transposon structure. The molecular evolutionary analysis indicated that Tet(X) variants likely shared the same common ancestor with the chromosomal monooxygenases that are found in environmental Flavobacteriaceae bacteria, but sequence divergence suggested separation ~ 9900 years ago (7887 BC), presumably associated with the mobilization of tet(X)-like genes through horizontal transfer.

Conclusions
Four tet(X) variants were identified in this study, and they were widely distributed in multiple Acinetobacter spp. strains from various ecological niches across China. Our research also highlighted the crucial role of ISCR2 in mobilizing tet(X)-like genes between different Acinetobacter species and explored the evolutionary history of Tet(X)-like monooxygenases. Further studies are needed to evaluate the clinical impact of these mobile tigecycline resistance genes.
Seroprevalence and associated risk factors of Toxoplasma gondii infection in patients undergoing hemodialysis and healthy group
Authors: Soltani Shahrzad , Kahvaz Mehdi Sagha , Soltani Sheyda , Maghsoudi Fatemeh , Foroutan Masoud 
Published: December 2020

AbstractObjectivesIn this study, the seroprevalence of anti-Toxoplasma gondii(T. gondii) specific antibodies in patients undergoing hemodialysis compared to the control group were evaluated. In this case–control study, 200 hemodialysis patients (HDP) and 100 healthy controls were participated. The specific antibodies (IgG/IgM) in both groups were tested using enzyme-linked immunosorbent assay (ELISA) method. A structured questionnaire containing some demographic information was completed for each person in case and control groups.ResultsThe overall seroprevalence ofT. gondiiinfection was 49.5% (99/200) and 23.0% (23/100) in the case and control groups, respectively. There was a significant association between seroprevalence ofT. gondiiinfection and contact with cats (P < 0.001), consumption of raw/undercooked meat (P = 0.01), and source of drinking water (P = 0.001) in the hemodialysis patients. Also, in the control subjects, there were a significant association between consumption of raw/undercooked meat (P = 0.04) and source of drinking water (P = 0.001) withT. gondiiinfection. The findings showed a high seroprevalence ofT. gondiiinfection in HDP compared with healthy controls; thus, we recommend the regular screening programs forT. gondiiinfection in this susceptible group.
Alpha connectivity and inhibitory control in adults with autism spectrum disorder
Authors: Yuk Veronica , Dunkley Benjamin T. , Anagnostou Evdokia , Taylor Margot J. 
Published: December 2020

Abstract
Background
Individuals with autism spectrum disorder (ASD) often report difficulties with inhibition in everyday life. During inhibition tasks, adults with ASD show reduced activation of and connectivity between brain areas implicated in inhibition, suggesting impairments in inhibitory control at the neural level. Our study further investigated these differences by using magnetoencephalography (MEG) to examine the frequency band(s) in which functional connectivity underlying response inhibition occurs, as brain functions are frequency specific, and whether connectivity in certain frequency bands differs between adults with and without ASD.

Methods
We analysed MEG data from 40 adults with ASD (27 males; 26.94 ± 6.08 years old) and 39 control adults (27 males; 27.29 ± 5.94 years old) who performed a Go/No-go task. The task involved two blocks with different proportions of No-go trials: Inhibition (25% No-go) and Vigilance (75% No-go). We compared whole-brain connectivity in the two groups during correct No-go trials in the Inhibition vs. Vigilance blocks between 0 and 400 ms.

Results
Despite comparable performance on the Go/No-go task, adults with ASD showed reduced connectivity compared to controls in the alpha band (8–14 Hz) in a network with a main hub in the right inferior frontal gyrus. Decreased connectivity in this network predicted more self-reported difficulties on a measure of inhibition in everyday life.

Limitations
Measures of everyday inhibitory control were not available for all participants, so this relationship between reduced network connectivity and inhibitory control abilities may not be necessarily representative of all adults with ASD or the larger ASD population. Further research with independent samples of adults with ASD, including those with a wider range of cognitive abilities, would be valuable.

Conclusions
Our findings demonstrate reduced functional brain connectivity during response inhibition in adults with ASD. As alpha-band synchrony has been linked to top-down control mechanisms, we propose that the lack of alpha synchrony observed in our ASD group may reflect difficulties in suppressing task-irrelevant information, interfering with inhibition in real-life situations.
Recurrent obstructive uropathy secondary to pyometrocolpos in an 8-month-old infant: a case report
Authors: Kiritta Richard , Balyorugulu Georgina , Ahmed Maimuna , Christopher Frank , Miltenburg Andrea Solnes , Kihunrwa Albert 
Published: December 2020

Abstract
Background
Pyometrocolpos is accumulation of infected fluid in the uterus and vagina. It is rare in children, mostly seen after menarche as a result of obstructive congenital genital malformation that impairs free drainage of the uterine secretions. In a child, it may present as an acute illness that necessitates urgent and appropriate management and treatment of the underlying cause, which can be a challenge in a resource-limited setting.

Case presentation
We report a case of pyometrocolpos in an 8-month-old African infant who presented with fever, vomiting, decreased urine output, and abdominal distension of 12 days’ duration. An abdominal examination revealed a subumbilical midline incision scar and a midline lower abdominal mass. She appeared to have presented at the emergency department with similar complaints 2 months earlier and had been diagnosed with pyometra, which was managed by emergency laparotomy for pus drainage, and she was kept on antibiotics. Recovery was established after 10 days of admission, and the patient was discharged to home. Her symptoms reappeared 2 months after the first presentation. Her blood work showed significant leukocytosis with neutrophilia, and abdominal ultrasound depicted bilateral hydronephrosis with hydroureters and a fluid-filled uterus. Examination under anesthesia in the operating theater revealed normal-looking female genitalia with a cribriform hymen, beneath which lied a transverse vaginal septum. Foul-smelling pus was aspirated through the septum, and septectomy was performed to allow 350 ml of pus to drain. A pus sample was sent for culture and sensitivity, and Escherichia coli sensitive to ceftriaxone and gentamicin was isolated.

Conclusion
Pyometrocolpos is rare in childhood but should be suspected in a girl presenting with a midline lower abdominal mass accompanied with urinary obstructive symptoms associated with fever and gastrointestinal symptoms. Escherichia coli seems to be the most probable offending organism, but pus culture is crucial for antibiotic stewardship in proper management of the infection. Definitive treatment should focus on correcting the obstructive anatomical congenital deformity that caused the obstruction in order to avoid recurrence.