bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive value of quantitative 18F-FDG-PET radiomics analysis in patients with head and neck squamous cell carcinoma
Authors: Martens Roland M. , Koopman Thomas , Noij Daniel P. , Pfaehler Elisabeth , Übelhör Caroline , Sharma Sughandi , Vergeer Marije R. , Leemans C. René , Hoekstra Otto S. , Yaqub Maqsood , Zwezerijnen Gerben J. , Heymans Martijn W. , Peeters Carel F. W. , de Bree Remco , de Graaf Pim , Castelijns Jonas A. , Boellaard Ronald 
Published: September 2020

Abstract

Background
Radiomics is aimed at image-based tumor phenotyping, enabling application within clinical-decision-support-systems to improve diagnostic accuracy and allow for personalized treatment. The purpose was to identify predictive 18-fluor-fluoro-2-deoxyglucose (18F-FDG) positron-emission tomography (PET) radiomic features to predict recurrence, distant metastasis, and overall survival in patients with head and neck squamous cell carcinoma treated with chemoradiotherapy.

Methods
Between 2012 and 2018, 103 retrospectively (training cohort) and 71 consecutively included patients (validation cohort) underwent 18F-FDG-PET/CT imaging. The 434 extracted radiomic features were subjected, after redundancy filtering, to a projection resulting in outcome-independent meta-features (factors). Correlations between clinical, first-order 18F-FDG-PET parameters (e.g., SUVmean), and factors were assessed. Factors were combined with 18F-FDG-PET and clinical parameters in a multivariable survival regression and validated. A clinically applicable risk-stratification was constructed for patients’ outcome.

Results
Based on 124 retained radiomic features from 103 patients, 8 factors were constructed. Recurrence prediction was significantly most accurate by combining HPV-status, SUVmean, SUVpeak, factor 3 (histogram gradient and long-run-low-grey-level-emphasis), factor 4 (volume-difference, coarseness, and grey-level-non-uniformity), and factor 6 (histogram variation coefficient) (CI = 0.645). Distant metastasis prediction was most accurate assessing metabolic-active tumor volume (MATV)(CI = 0.627). Overall survival prediction was most accurate using HPV-status, SUVmean, SUVmax, factor 1 (least-axis-length, non-uniformity, high-dependence-of-high grey-levels), and factor 5 (aspherity, major-axis-length, inversed-compactness and, inversed-flatness) (CI = 0.764).

Conclusions
Combining HPV-status, first-order 18F-FDG-PET parameters, and complementary radiomic factors was most accurate for time-to-event prediction. Predictive phenotype-specific tumor characteristics and interactions might be captured and retained using radiomic factors, which allows for personalized risk stratification and optimizing personalized cancer care.

Trial registration
Trial NL3946 (NTR4111), local ethics commission reference: Prediction 2013.191 and 2016.498. Registered 7 August 2013, https://www.trialregister.nl/trial/3946
Ultrasonographic assessment of parasternal intercostal muscles during mechanical ventilation
Authors: Formenti Paolo , Umbrello Michele , Dres Martin , Chiumello Davide 
Published: September 2020

AbstractAlthough mechanical ventilation is a lifesaving treatment, abundant evidence indicates that its prolonged use (1 week or more) promotes respiratory muscle weakness due to both contractile dysfunction and atrophy. Along with the diaphragm, the intercostal muscles are one of the most important groups of respiratory muscles. In recent years, muscular ultrasound has become a useful bedside tool for the clinician to identify patients with respiratory muscle dysfunction related to critical illness and/or invasive mechanical ventilation. Images obtained over the course of illness can document changes in muscle dimension and can be used to estimate changes in function. Recent evidence suggests the clinical usefulness of ultrasound imaging in the assessment of intercostal muscle function. In this narrative review, we summarize the current literature on ultrasound imaging of the parasternal intercostal muscles as used to assess the extent of muscle activation and muscle weakness and its potential impact during discontinuation of mechanical ventilation. In addition, we proposed a practical flowchart based on recent evidence and experience of our group that can be applied during the weaning phase. This approach integrates multiple predictive parameters of weaning success with respiratory muscle ultrasound.
Bacterial and viral co-infections in patients with severe SARS-CoV-2 pneumonia admitted to a French ICU
Authors: Contou Damien , Claudinon Aurore , Pajot Olivier , Micaëlo Maïté , Longuet Flandre Pascale , Dubert Marie , Cally Radj , Logre Elsa , Fraissé Megan , Mentec Hervé , Plantefève Gaëtan 
Published: September 2020

Abstract
Background
Data on the prevalence of bacterial and viral co-infections among patients admitted to the ICU for acute respiratory failure related to SARS-CoV-2 pneumonia are lacking. We aimed to assess the rate of bacterial and viral co-infections, as well as to report the most common micro-organisms involved in patients admitted to the ICU for severe SARS-CoV-2 pneumonia.

Patients and methods
In this monocenter retrospective study, we reviewed all the respiratory microbiological investigations performed within the first 48 h of ICU admission of COVID-19 patients (RT-PCR positive for SARS-CoV-2) admitted for acute respiratory failure.

Results
From March 13th to April 16th 2020, a total of 92 adult patients (median age: 61 years, 1st–3rd quartiles [55–70]; males: n = 73/92, 79%; baseline SOFA: 4 [3–7] and SAPS II: 31 [21–40]; invasive mechanical ventilation: n = 83/92, 90%; ICU mortality: n = 45/92, 49%) were admitted to our 40-bed ICU for acute respiratory failure due to SARS-CoV-2 pneumonia. Among them, 26 (28%) were considered as co-infected with a pathogenic bacterium at ICU admission with no co-infection related to atypical bacteria or viruses. The distribution of the 32 bacteria isolated from culture and/or respiratory PCRs was as follows: methicillin-sensitive Staphylococcus aureus (n = 10/32, 31%), Haemophilus influenzae (n = 7/32, 22%), Streptococcus pneumoniae (n = 6/32, 19%), Enterobacteriaceae (n = 5/32, 16%), Pseudomonas aeruginosa (n = 2/32, 6%), Moraxella catarrhalis (n = 1/32, 3%) and Acinetobacter baumannii (n = 1/32, 3%). Among the 24 pathogenic bacteria isolated from culture, 2 (8%) and 5 (21%) were resistant to 3rd generation cephalosporin and to amoxicillin–clavulanate combination, respectively.

Conclusions
We report on a 28% rate of bacterial co-infection at ICU admission of patients with severe SARSCoV-2 pneumonia, mostly related to Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae and Enterobacteriaceae. In French patients with confirmed severe SARSCoV-2 pneumonia requiring ICU admission, our results encourage the systematic administration of an empiric antibiotic monotherapy with a 3rd generation cephalosporin, with a prompt de-escalation as soon as possible. Further larger studies are needed to assess the real prevalence and the predictors of co-infection together with its prognostic impact on critically ill patients with severe SARS-CoV-2 pneumonia.
Point prevalence survey of antimicrobial use in three hospitals in North-Eastern Tanzania
Authors: Horumpende Pius G. , Mshana Stephen E. , Mouw Elise F. , Mmbaga Blandina T. , Chilongola Jaffu O. , de Mast Quirijn 
Published: September 2020

Abstract
Background
Antimicrobial resistance (AMR) is one of the most urgent global health threats with low-resource countries being disproportionately affected. Targeted interventions require insight in antibiotic prescription practices. A point prevalence survey (PPS) is a well-known tool to get insight in antibiotic dispensing practices in hospitals and identify areas for improvement. Here, we describe the results of a PPS performed in a tertiary, regional and district hospital in Kilimanjaro region in Tanzania.

Methods
A PPS was performed in the Kilimanjaro Christian Medical Centre (KCMC; tertiary hospital), Mawenzi (regional) and St. Joseph (district) hospital in November and December 2016. Antibiotic use in all patients admitted more than 24 h and those undergoing surgery was recorded. All clinical wards were included except the pediatrics. Data from a single ward were collected on the same day.

Results
A total of 399 patients were included in the PPS: 232 patients from KCMC, 94 from Mawenzi hospital and 73 patients from St. Joseph hospital. Overall prevalence of antibiotic use was 44.0%: 38% in KCMC, 59% in Mawenzi and 63% in St. Joseph. Ceftriaxone (n = 94, 29.8%), metronidazole (n = 79, 23.9%) and other antibiotics belonging to the penicillin class (n = 89, 28.3%) were most commonly prescribed. Antibiotics prescribed for surgical prophylaxis were continued for more than 3 days in 57% of cases.

Conclusion
Our study shows a rate of broad-spectrum antibiotic use in Tanzanian hospitals and prolonged surgical antibiotic prophylaxis being a common practice. PPS is an important tool to improve future antibiotic use in Tanzania hospitals.
Parental self-medication with antibiotics for children promotes antibiotic over-prescribing in clinical settings in China
Authors: Xu Jiayao , Wang Xiaomin , Sun Kai Sing , Lin Leesa , Zhou Xudong 
Published: September 2020

Abstract
Background
Self-medication with antibiotics (SMA) is one of the most dangerous inappropriate antibiotic use behaviors. This study aims to investigate the impact of parental SMA for children before a consultation on their doctor’s subsequent antibiotic prescribing behavior, including intravenous (IV) antibiotic use in the clinical setting of China.

Methods
A cross-sectional survey was conducted between June 2017 and April 2018 in three provinces of China. A total of 9526 parents with children aged 0–13 years were investigated. Data from 1275 parents who had self-medicated their children and then visited a doctor in the past month were extracted and analyzed.

Results
One-third (410) of the studied children had parental SMA before the consultation and 83.9% of them were subsequently prescribed antibiotics by doctors. Children with parental SMA were more likely to be prescribed antibiotics (aOR = 7.79, 95% CI [5.74–10.58]), including IV antibiotics (aOR = 3.05, 95% CI [2.27–4.11]), and both oral and IV antibiotics (aOR = 3.42, 95% CI [2.42–4.84]), than children without parental SMA. Parents with SMA behaviors were more likely to request antibiotics (aOR = 4.05, 95% CI [2.59–6.31]) including IV antibiotics (aOR = 2.58, 95% CI [1.40–4.76]), and be fulfilled by doctors (aOR = 3.22, 95% CI [1.20–8.63]).

Conclusions
Tailored health education for parents is required in both community and clinical settings to discourage parental SMA for children. The doctors should not prescribe unnecessary antibiotics to reinforce parents’ SMA behaviors. We recommend expanding the current IV antibiotics ban in outpatient settings of China to cover outpatient pediatrics.
Bioinformatics analysis reveals novel hub gene pathways associated with IgA nephropathy
Authors: Jiang Xue , Xu Zhijie , Du Yuanyuan , Chen Hongyu 
Published: September 2020

Abstract

Background
Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulopathy worldwide. However, the molecular events underlying IgAN remain to be fully elucidated. This study aimed to identify novel biomarkers of IgAN through bioinformatics analysis and elucidate the possible molecular mechanism.

Methods
Based on the microarray datasets GSE93798 and GSE37460 downloaded from the Gene Expression Omnibus database, the differentially expressed genes (DEGs) between IgAN samples and normal controls were identified. Using the DEGs, we further performed a series of functional enrichment analyses. Protein–protein interaction (PPI) networks of the DEGs were constructed using the STRING online search tool and were visualized using Cytoscape. Next, hub genes were identified and the most important module among the DEGs, Biological Networks Gene Ontology tool (BiNGO), was used to elucidate the molecular mechanism of IgAN.

Results
In total, 148 DEGs were identified, comprising 53 upregulated genes and 95 downregulated genes. Gene Ontology (GO) analysis indicated that the DEGs for IgAN were mainly enriched in extracellular exosome, region and space, fibroblast growth factor stimulus, inflammatory response, and innate immunity. Module analysis showed that genes in the top 1 significant module of the PPI network were mainly associated with innate immune response, integrin-mediated signaling pathway and inflammatory response. The top 10 hub genes were constructed in the PPI network, which could well distinguish the IgAN and control group in monocyte and tissue samples. We finally identified the integrin subunit beta 2 (ITGB2) and Fc fragment of IgE receptor Ig (FCER1G) genes that may play important roles in the development of IgAN.

Conclusions
We identified key genes along with the pathways that were most closely related to IgAN initiation and progression. Our results provide a more detailed molecular mechanism for the development of IgAN and novel candidate gene targets of IgAN.
Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs
Authors: Shen Junshi , Li Zhipeng , Yu Zhongtang , Zhu Weiyun 
Published: September 2020

AbstractBackgroundDiet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR.ResultsNo interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL.ConclusionsSubstitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.
Generalized logistic distribution and its regression model
Authors: Aljarrah Mohammad A. , Famoye Felix , Lee Carl 
Published: September 2020

AbstractA new generalized asymmetric logistic distribution is defined. In some cases, existing three parameter distributions provide poor fit to heavy tailed data sets. The proposed new distribution consists of only three parameters and is shown to fit a much wider range of heavy left and right tailed data when compared with various existing distributions. The new generalized distribution has logistic, maximum and minimum Gumbel distributions as sub-models. Some properties of the new distribution including mode, skewness, kurtosis, hazard function, and moments are studied. We propose the method of maximum likelihood to estimate the parameters and assess the finite sample size performance of the method. A generalized logistic regression model, based on the new distribution, is presented. Logistic-log-logistic regression, Weibull-extreme value regression and log-Fréchet regression are special cases of the generalized logistic regression model. The model is applied to fit failure time of a new insulation technique and the survival of a heart transplant study.
Rheumatoid arthritis
Authors: Tanaka Yoshiya 
Published: September 2020

AbstractRheumatoid arthritis is an autoimmune inflammatory disease primarily characterized by synovitis which is accompanied by extra-articular organ involvement, such as interstitial pneumonia, in addition to clinical symptoms including pain, swelling, stiffness of multiple joints, fever, and malaise. Joint destruction progresses soon after the onset, and once the affected joints are deformed, the development of irreversible physical dysfunction is noted. Thus, proper diagnosis and treatment are required from the early stages of the disease. Although palliative therapy with glucocorticoids and anti-inflammatory drugs had been used, disease-modifying antirheumatic drugs (DMARDs) are currently used to suppress immune abnormalities and to control disease activity. DMARDs are classified into different groups, such as conventional synthetic DMARD, targeted synthetic DMARD, and biologic DMARD. The appropriate use of these drugs has allowed remission to be the therapeutic goal in all patients. By maintaining remission, these drugs have also been shown to prevent the progression of joint destruction and physical dysfunction over a long period. The advent of molecular-targeted therapies has allowed for the use of treatments based on pathological mechanisms, and such therapeutic strategies have also been applied to the treatment of various autoimmune inflammatory diseases. In the future, safer and more effective treatments, therapeutic strategies aimed at drug holidays or cure, and the introduction of precision medicine are expected.
Effects of alkali solution on the dissolution kinetics and optimization processes of iron from Akwuke ore
Authors: Ani Kingsley Amechi , Chukelu Chidubem Chukwuebuka 
Published: September 2020

Abstract
Background
The dissolution process kinetics and optimization of iron from Akwuke ore were investigated in this study. The effects of process parameters such as agitation rate and ore particle size on the dissolution process were also examined. The Akwuke ore was characterized employing the XRD, FT-IR, SEM, and UV-spectroscopy.

Results
The results from the rate constants indicated that the diffusion through the boundary layer process with R2 > 0.96 was the rate-determining mechanism. The maximum iron dissolution rate of 83.2% was obtained at 45-μm particle size while 81.2% and 72.6% iron dissolution rates were obtained at 490 and 390 rpm agitation rates, respectively. Silicon oxide, aluminum oxide, and iron oxide were present in Akwuke ore as indicated from the XRD analysis. The RSM predicted optimum value of the iron dissolution rate from the numerical optimization was experimentally validated to confirm the satisfactory performance of the quadratic model.

Conclusion
This study concludes and presents the potential extraction of iron from Akwuke ore, which will be of immense benefit in hydrometallurgical process.
Follistatin-like 1 as a Novel Adipomyokine Related to Insulin Resistance and Physical Activity
Authors: Xu Xiaohui , Zhang Tingran , Mokou Mani , Li Ling , Li Peng , Song Jinlin , Liu Hua , Zhu Zhiming , Liu Dongfang , Yang Mengliu , Yang Gangyi 
Published: September 2020

Abstract

Background and Aims
Follistatin-like protein-1 (FSTL-1) is considered to be an adipokine or myokine that could be a potential regulator of metabolism. Our purpose is to investigate the relationship between circulating FSTL-1 levels and insulin resistance (IR) in type 2 diabetes mellitus (T2DM) and to identify the regulatory factors.

Methods
FSTL-1 expression in C57BL/6J and db/db mice was examined by quantitative reverse transcriptase–polymerase chain reaction (qRT-PCR) and Western blots. Serum FSTL-1 levels were measured by enzyme-linked immunosorbent assay in 298 T2DM patients and 202 healthy controls. Changes in the circulating FSTL-1 level were observed during the oral glucose tolerance test, EHC (euglycemic-hyperinsulinemic clamp), lipid infusion, acute exercise, and cold-exposure test.

Results
We found that FSTL-1 protein expression in the adipose tissue of db/db mice was significantly higher than that of wild-type mice. Importantly, circulating FSTL-1 levels in T2DM and overweight/obese participants were higher than those in healthy and lean individuals, and was related to HOMA-IR, adiponectin, and obesity- and metabolism-related parameters. In the intervention study, 45 minutes of physical activity was found to significantly increase the circulating FSTL-1 concentration in young, healthy participants. Further, FSTL-1 protein expression in adipose tissue rose dramatically in response to physical activity in mice. Hyperinsulinemia during EHC and acute elevated FFA induced by lipid infusion resulted in a significant decrease in the circulating FSTL-1 levels. However, no change was found in the circulating FSTL-1 levels in response to the oral glucose challenge or cold-exposure test.

Conclusions
FSTL-1 may be an adipomyokine associated with insulin resistance and physical activity, and circulating FSTL-1 levels are increased in patients with T2DM.
Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis
Authors: Newbury Dianne F. , Simpson Nuala H. , Thompson Paul A. , Bishop Dorothy V. M. 
Published: September 2020

Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. We predicted that the impact of an additional sex chromosome on neurodevelopment would depend on common autosomal variants involved in synaptic functions. Methods: We analysed data from 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Two comparison groups were formed from 370 children from a twin study. Three indicators of phenotype were: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Preselected regions of two genes, CNTNAP2 and NRXN1, were tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. Results: There was wide phenotypic variation in the SCT group, as well as overall impairment on all three phenotypic measures. There was no association of phenotype with CNTNAP2 or NRXN1 variants in either the SCT group or the comparison groups. Supplementary analyses found no indication of any impact of trisomy type on the results, and exploratory analyses of individual SNPs confirmed the lack of association. Conclusions: We cannot rule out that a double hit may be implicated in the phenotypic variability in children with SCTs, but our analysis does not find any support for the idea that common variants in CNTNAP2 or NRXN1 are associated with the severity of language and neurodevelopmental impairments that often accompany an extra X or Y chromosome. Stage 1 report: http://dx.doi.org/10.12688/wellcomeopenres.13828.2